From b79cb57026325fda452e976859f48c6c9df72049 Mon Sep 17 00:00:00 2001 From: Robert McGibbon Date: Sat, 26 Oct 2013 15:16:27 -0700 Subject: [PATCH] Change everything to LGPL --- LICENSE | 1130 ++++++-------- MDTraj/__init__.py | 34 +- MDTraj/arc.py | 35 +- MDTraj/binpos/binpos.pyx | 29 +- MDTraj/compatibility.py | 41 +- MDTraj/dcd/dcd.pyx | 35 +- MDTraj/dcd/dcdlib.pxd | 8 +- MDTraj/geometry/__init__.py | 27 +- MDTraj/geometry/alignment.py | 22 + MDTraj/geometry/angle.py | 27 +- MDTraj/geometry/dihedral.py | 33 +- MDTraj/geometry/distance.py | 27 +- MDTraj/geometry/hbond.py | 27 +- MDTraj/geometry/internal.py | 27 +- MDTraj/geometry/rg.py | 27 +- MDTraj/geometry/sasa.py | 27 +- MDTraj/geometry/src/_geometry.pyx | 24 +- MDTraj/geometry/src/geometry.c | 42 +- MDTraj/geometry/src/sasa.c | 83 +- MDTraj/geometry/test/test_alignment.py | 31 +- MDTraj/geometry/test/test_distance.py | 24 +- MDTraj/geometry/test/test_geometry.py | 37 +- MDTraj/geometry/test/test_hbonds.py | 25 +- MDTraj/geometry/test/test_sasa.py | 27 +- MDTraj/hdf5.py | 31 +- MDTraj/io.py | 32 +- MDTraj/mdcrd.py | 29 +- MDTraj/netcdf.py | 31 +- MDTraj/pdb/element.py | 47 +- MDTraj/pdb/pdbfile.py | 89 +- MDTraj/pdb/pdbstructure.py | 1865 +++++++++++------------ MDTraj/pdb/test_pdb.py | 29 +- MDTraj/reporters/basereporter.py | 29 +- MDTraj/reporters/dcdreporter.py | 29 +- MDTraj/reporters/hdf5reporter.py | 31 +- MDTraj/reporters/netcdfreporter.py | 29 +- MDTraj/rmsd.py | 31 +- MDTraj/rmsd/_rmsd.pyx | 29 +- MDTraj/rmsd/include/util.h | 10 +- MDTraj/rmsd/src/theobald_rmsd.c | 61 +- MDTraj/testing/__init__.py | 29 +- MDTraj/testing/docstrings.py | 29 +- MDTraj/testing/nosetester.py | 26 +- MDTraj/testing/testing.py | 29 +- MDTraj/tests/__init__.py | 15 - MDTraj/tests/test_arc.py | 29 +- MDTraj/tests/test_binpos.py | 31 +- MDTraj/tests/test_compatibility.py | 26 +- MDTraj/tests/test_dcd.py | 33 +- MDTraj/tests/test_hdf5.py | 22 + MDTraj/tests/test_io.py | 29 +- MDTraj/tests/test_mdconvert.py | 29 +- MDTraj/tests/test_mdcrd.py | 29 +- MDTraj/tests/test_netcdf.py | 33 +- MDTraj/tests/test_reporter.py | 35 +- MDTraj/tests/test_rmsd.py | 29 +- MDTraj/tests/test_topology.py | 22 + MDTraj/tests/test_trajectory.py | 46 +- MDTraj/tests/test_trr.py | 26 +- MDTraj/tests/test_xml.py | 22 + MDTraj/tests/test_xtc.py | 29 +- MDTraj/topology.py | 42 +- MDTraj/trajectory.py | 62 +- MDTraj/utils/arrays.py | 29 +- MDTraj/utils/delay_import.py | 22 + MDTraj/utils/ffi.py | 24 +- MDTraj/utils/test.py | 22 + MDTraj/utils/unit.py | 22 + MDTraj/utils/unitcell.py | 21 +- MDTraj/xtc/trr.pyx | 41 +- MDTraj/xtc/trrlib.pxd | 4 +- MDTraj/xtc/xtc.pyx | 41 +- README.md | 19 + scripts/mdconvert.py | 23 +- scripts/mdinspect.py | 23 +- tools/LICENSE_HEADER | 16 - tools/add_license.sh | 7 - tools/ci/after_sucess.sh | 2 +- tools/ci/speedpack/build.sh | 23 + tools/ci/speedpack/push-wheels-to-s3.py | 2 +- tools/examples_rst.py | 23 +- tools/hash_funcs.py | 21 + 82 files changed, 2938 insertions(+), 2400 deletions(-) delete mode 100644 tools/LICENSE_HEADER delete mode 100644 tools/add_license.sh diff --git a/LICENSE b/LICENSE index 94a9ed024..4362b4915 100644 --- a/LICENSE +++ b/LICENSE @@ -1,674 +1,502 @@ - GNU GENERAL PUBLIC LICENSE - Version 3, 29 June 2007 + GNU LESSER GENERAL PUBLIC LICENSE + Version 2.1, February 1999 - Copyright (C) 2007 Free Software Foundation, Inc. + Copyright (C) 1991, 1999 Free Software Foundation, Inc. + 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed. +[This is the first released version of the Lesser GPL. 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See the GNU General Public License for more details. +# This library is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU Lesser General Public License for more details. # -# You should have received a copy of the GNU General Public License along with -# mdtraj. If not, see http://www.gnu.org/licenses/. +# You should have received a copy of the GNU Lesser General Public +# License along with Foobar. If not, see . +############################################################################## + + """The mdtraj package contains tools for loading and saving molecular dynamics trajectories in a variety of formats, including Gromacs XTC & TRR, CHARMM/NAMD DCD, AMBER BINPOS, PDB, and HDF5. @@ -43,7 +51,7 @@ def test(label='full', verbose=2): Identifies the tests to run. The fast tests take about 10 seconds, and the full test suite takes about two minutes (as of this writing). verbose : int, optional - Verbosity value for test outputs, in the range 1-10. Default is 2. + Verbosity value for test outputs, in the range 1-10. Default is 2. """ import mdtraj from mdtraj.testing.nosetester import MDTrajTester @@ -51,4 +59,4 @@ def test(label='full', verbose=2): return tester.test(label=label, verbose=verbose, extra_argv=('--exe',)) # prevent nose from discovering this function, or otherwise when its run # the test suite in an infinite loop -test.__test__ = False +test.__test__ = False diff --git a/MDTraj/arc.py b/MDTraj/arc.py index a8de07ef7..77aa566a5 100644 --- a/MDTraj/arc.py +++ b/MDTraj/arc.py @@ -1,18 +1,25 @@ -# Copyright 2013-present mdtraj developers +############################################################################## +# MDTraj: A Python Library for Loading, Saving, and Manipulating +# Molecular Dynamics Trajectories. +# Copyright 2012-2013 Stanford University and the Authors # -# This file is part of mdtraj +# Authors: Lee-Ping Wang +# Contributors: Robert McGibbon # -# mdtraj is free software: you can redistribute it and/or modify it under the -# terms of the GNU General Public License as published by the Free Software -# Foundation, either version 3 of the License, or (at your option) any later -# version. +# MDTraj is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as +# published by the Free Software Foundation, either version 2.1 +# of the License, or (at your option) any later version. # -# mdtraj is distributed in the hope that it will be useful, but WITHOUT ANY -# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR -# A PARTICULAR PURPOSE. See the GNU General Public License for more details. +# This library is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU Lesser General Public License for more details. # -# You should have received a copy of the GNU General Public License along with -# mdtraj. If not, see http://www.gnu.org/licenses/. +# You should have received a copy of the GNU Lesser General Public +# License along with Foobar. If not, see . +############################################################################## + ############################################################################## # Imports @@ -160,7 +167,7 @@ def _read(self): line = self._fh.readline() if line == '': raise _EOF() - + self._n_atoms = int(line.split()[0]) self._line_counter += 1 @@ -181,9 +188,9 @@ def write(self, xyz): Parameters ---------- xyz : np.ndarray, shape=(n_frames, n_atoms, 3) - The cartesian coordinates of the atoms to write. + The cartesian coordinates of the atoms to write. """ - + raise RuntimeError('write() is not available for .arc files') diff --git a/MDTraj/binpos/binpos.pyx b/MDTraj/binpos/binpos.pyx index a907ddfbc..f3910870b 100644 --- a/MDTraj/binpos/binpos.pyx +++ b/MDTraj/binpos/binpos.pyx @@ -1,19 +1,26 @@ # cython: c_string_type=str, c_string_encoding=ascii -# Copyright 2012 mdtraj developers +############################################################################## +# MDTraj: A Python Library for Loading, Saving, and Manipulating +# Molecular Dynamics Trajectories. +# Copyright 2012-2013 Stanford University and the Authors # -# This file is part of mdtraj +# Authors: Robert McGibbon +# Contributors: # -# mdtraj is free software: you can redistribute it and/or modify it under the -# terms of the GNU General Public License as published by the Free Software -# Foundation, either version 3 of the License, or (at your option) any later -# version. +# MDTraj is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as +# published by the Free Software Foundation, either version 2.1 +# of the License, or (at your option) any later version. # -# mdtraj is distributed in the hope that it will be useful, but WITHOUT ANY -# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR -# A PARTICULAR PURPOSE. See the GNU General Public License for more details. +# This library is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU Lesser General Public License for more details. # -# You should have received a copy of the GNU General Public License along with -# mdtraj. If not, see http://www.gnu.org/licenses/. +# You should have received a copy of the GNU Lesser General Public +# License along with Foobar. If not, see . +############################################################################## + ############################################################################### # Imports diff --git a/MDTraj/compatibility.py b/MDTraj/compatibility.py index 44a23359a..e9f3dcb27 100644 --- a/MDTraj/compatibility.py +++ b/MDTraj/compatibility.py @@ -1,18 +1,25 @@ -# Copyright 2012-present mdtraj developers +############################################################################## +# MDTraj: A Python Library for Loading, Saving, and Manipulating +# Molecular Dynamics Trajectories. +# Copyright 2012-2013 Stanford University and the Authors # -# This file is part of mdtraj +# Authors: Robert McGibbon, Kyle A. Beauchamp +# Contributors: # -# mdtraj is free software: you can redistribute it and/or modify it under the -# terms of the GNU General Public License as published by the Free Software -# Foundation, either version 3 of the License, or (at your option) any later -# version. +# MDTraj is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as +# published by the Free Software Foundation, either version 2.1 +# of the License, or (at your option) any later version. # -# mdtraj is distributed in the hope that it will be useful, but WITHOUT ANY -# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR -# A PARTICULAR PURPOSE. See the GNU General Public License for more details. +# This library is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU Lesser General Public License for more details. # -# You should have received a copy of the GNU General Public License along with -# mdtraj. If not, see http://www.gnu.org/licenses/. +# You should have received a copy of the GNU Lesser General Public +# License along with Foobar. If not, see . +############################################################################## + """Compatibility loader for MSMBuilder2 "LH5" trajectory format. To load .lh5 trajectory files produced by MSMBuilder2, you can import this @@ -45,6 +52,7 @@ from __future__ import print_function, division import numpy as np +from mdtraj import Trajectory, Topology import mdtraj.pdb.element import mdtraj.trajectory from mdtraj.utils import import_ @@ -92,7 +100,7 @@ def load_legacy_hdf(filename, stride=1, frame=None, chunk=50000, trajectory : md.Trajectory The resulting trajectory, as an md.Trajectory object. """ - from mdtraj import Trajectory + def _convert_from_lossy_integers(X, precision=1000): """Implementation of the lossy compression used in Gromacs XTC using the pytables library. Convert 16 bit integers into 32 bit floats.""" @@ -201,7 +209,7 @@ def _convert_to_lossy_integers(X, precision): data_dict["ChainID"] = top.chainID.values data_dict["ResidueID"] = top.resSeq.values + 1 data_dict["XYZList"] = _convert_to_lossy_integers(traj.xyz, DEFAULT_PRECISION) - + atom_dict = {} atom_dict["AtomID"] = tables.Int64Atom() atom_dict["AtomNames"] = tables.StringAtom(itemsize=4) @@ -209,7 +217,7 @@ def _convert_to_lossy_integers(X, precision): atom_dict["ChainID"] = tables.StringAtom(itemsize=1) atom_dict["ResidueID"] = tables.Int64Atom() atom_dict["XYZList"] = tables.Int16Atom() - + file_handle = tables.File(filename, 'w') for key, val in iteritems(data_dict): @@ -217,10 +225,9 @@ def _convert_to_lossy_integers(X, precision): node[:] = val[:] file_handle.close() - + def _topology_from_arrays(AtomID, AtomNames, ChainID, ResidueID, ResidueNames): - from mdtraj import Topology topology = Topology() # assert that the ChainID is just an array of empty strings, which appears @@ -254,4 +261,4 @@ def _topology_from_arrays(AtomID, AtomNames, ChainID, ResidueID, ResidueNames): # register this reader with mdtraj! -#mdtraj.trajectory._LoaderRegistry['.lh5'] = load_legacy_hdf +mdtraj.trajectory._LoaderRegistry['.lh5'] = load_legacy_hdf diff --git a/MDTraj/dcd/dcd.pyx b/MDTraj/dcd/dcd.pyx index f00338b29..d5db83241 100644 --- a/MDTraj/dcd/dcd.pyx +++ b/MDTraj/dcd/dcd.pyx @@ -1,19 +1,26 @@ # cython: c_string_type=str, c_string_encoding=ascii -# Copyright 2013 mdtraj developers +############################################################################## +# MDTraj: A Python Library for Loading, Saving, and Manipulating +# Molecular Dynamics Trajectories. +# Copyright 2012-2013 Stanford University and the Authors # -# This file is part of mdtraj +# Authors: Robert McGibbon +# Contributors: # -# mdtraj is free software: you can redistribute it and/or modify it under the -# terms of the GNU General Public License as published by the Free Software -# Foundation, either version 3 of the License, or (at your option) any later -# version. +# MDTraj is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as +# published by the Free Software Foundation, either version 2.1 +# of the License, or (at your option) any later version. # -# mdtraj is distributed in the hope that it will be useful, but WITHOUT ANY -# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR -# A PARTICULAR PURPOSE. See the GNU General Public License for more details. +# This library is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU Lesser General Public License for more details. # -# You should have received a copy of the GNU General Public License along with -# mdtraj. If not, see http://www.gnu.org/licenses/. +# You should have received a copy of the GNU Lesser General Public +# License along with Foobar. If not, see . +############################################################################## + ############################################################################## # Imports @@ -60,7 +67,7 @@ cdef ERROR_MESSAGES = { cdef class DCDTrajectoryFile: """DCDTrajectoryFile(filename, mode='r', force_overwrite=True) - + Interface for reading and writing to a CHARMM/NAMD DCD file. This is a file-like object, that both reading or writing depending on the `mode` flag. It implements the context manager protocol, @@ -189,7 +196,7 @@ cdef class DCDTrajectoryFile: def read(self, n_frames=None, stride=None, atom_indices=None): """read(n_frames=None, stride=None, atom_indices=None) - + Read the data from a DCD file Parameters @@ -306,7 +313,7 @@ cdef class DCDTrajectoryFile: def write(self, xyz, cell_lengths=None, cell_angles=None): """write(xyz, cell_lengths=None, cell_angles=None) - + Write one or more frames of data to the DCD file Parameters diff --git a/MDTraj/dcd/dcdlib.pxd b/MDTraj/dcd/dcdlib.pxd index b48c48470..239b1896d 100644 --- a/MDTraj/dcd/dcdlib.pxd +++ b/MDTraj/dcd/dcdlib.pxd @@ -1,16 +1,16 @@ cdef extern from "include/dcdplugin.h": ctypedef struct dcdhandle: pass - + dcdhandle* open_dcd_read(char *path, char *filetype, int *natoms, int* nsets) int read_next_timestep(dcdhandle *v, int natoms, molfile_timestep_t *ts) void close_file_read(dcdhandle *v) - + dcdhandle* open_dcd_write(char *path, char *filetype, int natoms) int write_timestep(dcdhandle *v, molfile_timestep_t *ts) void close_file_write(dcdhandle *v) - - + + cdef extern from "include/molfile_plugin.h": ctypedef struct molfile_timestep_t: float *coords # coordinates of all atoms, arranged xyzxyzxyz diff --git a/MDTraj/geometry/__init__.py b/MDTraj/geometry/__init__.py index 74064f0eb..aed908814 100644 --- a/MDTraj/geometry/__init__.py +++ b/MDTraj/geometry/__init__.py @@ -1,20 +1,25 @@ -# This file is part of MDTraj. +############################################################################## +# MDTraj: A Python Library for Loading, Saving, and Manipulating +# Molecular Dynamics Trajectories. +# Copyright 2012-2013 Stanford University and the Authors # -# Copyright 2013 Stanford University +# Authors: Robert McGibbon +# Contributors: Kyle A. Beauchamp # -# MDTraj is free software; you can redistribute it and/or modify -# it under the terms of the GNU General Public License as published by -# the Free Software Foundation; either version 2 of the License, or -# (at your option) any later version. +# MDTraj is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as +# published by the Free Software Foundation, either version 2.1 +# of the License, or (at your option) any later version. # -# This program is distributed in the hope that it will be useful, +# This library is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -# GNU General Public License for more details. +# GNU Lesser General Public License for more details. # -# You should have received a copy of the GNU General Public License -# along with this program; if not, write to the Free Software -# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +# You should have received a copy of the GNU Lesser General Public +# License along with Foobar. If not, see . +############################################################################## + from __future__ import print_function, division __all__ = ['compute_distances', 'compute_angles', 'compute_dihedrals'] diff --git a/MDTraj/geometry/alignment.py b/MDTraj/geometry/alignment.py index bf154ef5b..bc204db19 100644 --- a/MDTraj/geometry/alignment.py +++ b/MDTraj/geometry/alignment.py @@ -1,3 +1,25 @@ +############################################################################## +# MDTraj: A Python Library for Loading, Saving, and Manipulating +# Molecular Dynamics Trajectories. +# Copyright 2012-2013 Stanford University and the Authors +# +# Authors: Kyle A. Beachamp +# Contributors: Robert McGibbon +# +# MDTraj is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as +# published by the Free Software Foundation, either version 2.1 +# of the License, or (at your option) any later version. +# +# This library is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with Foobar. If not, see . +############################################################################## + """ Here, we have implemented RMSD calculation using both Kabsch algorithm and via the quaterion-based characteristic polynomial. Both are implemented diff --git a/MDTraj/geometry/angle.py b/MDTraj/geometry/angle.py index 52e9850a4..f0781f818 100644 --- a/MDTraj/geometry/angle.py +++ b/MDTraj/geometry/angle.py @@ -1,20 +1,25 @@ -# This file is part of MDTraj. +############################################################################## +# MDTraj: A Python Library for Loading, Saving, and Manipulating +# Molecular Dynamics Trajectories. +# Copyright 2012-2013 Stanford University and the Authors # -# Copyright 2013 Stanford University +# Authors: Robert McGibbon +# Contributors: Kyle A Beauchamp # -# MDTraj is free software; you can redistribute it and/or modify -# it under the terms of the GNU General Public License as published by -# the Free Software Foundation; either version 2 of the License, or -# (at your option) any later version. +# MDTraj is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as +# published by the Free Software Foundation, either version 2.1 +# of the License, or (at your option) any later version. # -# This program is distributed in the hope that it will be useful, +# This library is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -# GNU General Public License for more details. +# GNU Lesser General Public License for more details. # -# You should have received a copy of the GNU General Public License -# along with this program; if not, write to the Free Software -# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +# You should have received a copy of the GNU Lesser General Public +# License along with Foobar. If not, see . +############################################################################## + ############################################################################## # Imports diff --git a/MDTraj/geometry/dihedral.py b/MDTraj/geometry/dihedral.py index 9cea0e15c..f5b596c67 100644 --- a/MDTraj/geometry/dihedral.py +++ b/MDTraj/geometry/dihedral.py @@ -1,20 +1,25 @@ -# This file is part of MDTraj. +############################################################################## +# MDTraj: A Python Library for Loading, Saving, and Manipulating +# Molecular Dynamics Trajectories. +# Copyright 2012-2013 Stanford University and the Authors # -# Copyright 2013 Stanford University +# Authors: Robert McGibbon +# Contributors: Kyle A Beauchamp # -# MDTraj is free software; you can redistribute it and/or modify -# it under the terms of the GNU General Public License as published by -# the Free Software Foundation; either version 2 of the License, or -# (at your option) any later version. +# MDTraj is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as +# published by the Free Software Foundation, either version 2.1 +# of the License, or (at your option) any later version. # -# This program is distributed in the hope that it will be useful, +# This library is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -# GNU General Public License for more details. +# GNU Lesser General Public License for more details. # -# You should have received a copy of the GNU General Public License -# along with this program; if not, write to the Free Software -# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +# You should have received a copy of the GNU Lesser General Public +# License along with Foobar. If not, see . +############################################################################## + ############################################################################## # Imports @@ -68,7 +73,7 @@ def _dihedral(xyz, indices, out=None): p1 = (b1 * c1).sum(-1) p1 *= (b2 * b2).sum(-1) ** 0.5 p2 = (c1 * c2).sum(-1) - + return np.arctan2(p1, p2, out) @@ -90,7 +95,7 @@ def compute_dihedrals(trajectory, indices, opt=True): Returns ------- dihedrals : np.ndarray, shape=(n_frames, n_dihedrals), dtype=float - The output array gives, in each frame from the trajectory, each of the + The output array gives, in each frame from the trajectory, each of the `n_dihedrals` torsion angles. The angles are measured in **radians**. """ @@ -132,7 +137,7 @@ def _construct_atom_dict(topology, chain_id=0): def atom_sequence_finder(trajectory, atom_names, residue_offsets=None, chain_id=0): """Find sequences of atom indices correponding to desired atoms. - + This method can be used to find sets of atoms corresponding to specific dihedral angles (like phi or psi). It looks for the given pattern of atoms in each residue of a given chain. See the example for details. diff --git a/MDTraj/geometry/distance.py b/MDTraj/geometry/distance.py index c6a1c72b3..c5ea5eb04 100644 --- a/MDTraj/geometry/distance.py +++ b/MDTraj/geometry/distance.py @@ -1,20 +1,25 @@ -# This file is part of MDTraj. +############################################################################## +# MDTraj: A Python Library for Loading, Saving, and Manipulating +# Molecular Dynamics Trajectories. +# Copyright 2012-2013 Stanford University and the Authors # -# Copyright 2013 Stanford University +# Authors: Robert McGibbon +# Contributors: Kyle A Beauchamp # -# MDTraj is free software; you can redistribute it and/or modify -# it under the terms of the GNU General Public License as published by -# the Free Software Foundation; either version 2 of the License, or -# (at your option) any later version. +# MDTraj is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as +# published by the Free Software Foundation, either version 2.1 +# of the License, or (at your option) any later version. # -# This program is distributed in the hope that it will be useful, +# This library is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -# GNU General Public License for more details. +# GNU Lesser General Public License for more details. # -# You should have received a copy of the GNU General Public License -# along with this program; if not, write to the Free Software -# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +# You should have received a copy of the GNU Lesser General Public +# License along with Foobar. If not, see . +############################################################################## + ############################################################################## # Imports diff --git a/MDTraj/geometry/hbond.py b/MDTraj/geometry/hbond.py index 1e1a0c52b..fbe8748b1 100644 --- a/MDTraj/geometry/hbond.py +++ b/MDTraj/geometry/hbond.py @@ -1,20 +1,25 @@ -# This file is part of MDTraj. +############################################################################## +# MDTraj: A Python Library for Loading, Saving, and Manipulating +# Molecular Dynamics Trajectories. +# Copyright 2012-2013 Stanford University and the Authors # -# Copyright 2013 Stanford University +# Authors: Robert McGibbon +# Contributors: # -# MDTraj is free software; you can redistribute it and/or modify -# it under the terms of the GNU General Public License as published by -# the Free Software Foundation; either version 2 of the License, or -# (at your option) any later version. +# MDTraj is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as +# published by the Free Software Foundation, either version 2.1 +# of the License, or (at your option) any later version. # -# This program is distributed in the hope that it will be useful, +# This library is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -# GNU General Public License for more details. +# GNU Lesser General Public License for more details. # -# You should have received a copy of the GNU General Public License -# along with this program; if not, write to the Free Software -# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +# You should have received a copy of the GNU Lesser General Public +# License along with Foobar. If not, see . +############################################################################## + ############################################################################## # Imports diff --git a/MDTraj/geometry/internal.py b/MDTraj/geometry/internal.py index bc8068217..bfeaca4d1 100644 --- a/MDTraj/geometry/internal.py +++ b/MDTraj/geometry/internal.py @@ -1,20 +1,25 @@ -# This file is part of MDTraj. +############################################################################## +# MDTraj: A Python Library for Loading, Saving, and Manipulating +# Molecular Dynamics Trajectories. +# Copyright 2012-2013 Stanford University and the Authors # -# Copyright 2011 Stanford University +# Authors: Robert McGibbon +# Contributors: Kyle A. Beauchamp # -# MDTraj is free software; you can redistribute it and/or modify -# it under the terms of the GNU General Public License as published by -# the Free Software Foundation; either version 2 of the License, or -# (at your option) any later version. +# MDTraj is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as +# published by the Free Software Foundation, either version 2.1 +# of the License, or (at your option) any later version. # -# This program is distributed in the hope that it will be useful, +# This library is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -# GNU General Public License for more details. +# GNU Lesser General Public License for more details. # -# You should have received a copy of the GNU General Public License -# along with this program; if not, write to the Free Software -# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +# You should have received a copy of the GNU Lesser General Public +# License along with Foobar. If not, see . +############################################################################## + """Methods to calculate internal coordinates from the cartesian coordinates This code is new and should be considered __unstable__ diff --git a/MDTraj/geometry/rg.py b/MDTraj/geometry/rg.py index fc3bcd0d3..f53bdbb99 100644 --- a/MDTraj/geometry/rg.py +++ b/MDTraj/geometry/rg.py @@ -1,20 +1,25 @@ -# This file is part of MDTraj. +############################################################################## +# MDTraj: A Python Library for Loading, Saving, and Manipulating +# Molecular Dynamics Trajectories. +# Copyright 2012-2013 Stanford University and the Authors # -# Copyright 2013 Stanford University +# Authors: Kyle A Beauchamp +# Contributors: Robert McGibbon # -# MDTraj is free software; you can redistribute it and/or modify -# it under the terms of the GNU General Public License as published by -# the Free Software Foundation; either version 2 of the License, or -# (at your option) any later version. +# MDTraj is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as +# published by the Free Software Foundation, either version 2.1 +# of the License, or (at your option) any later version. # -# This program is distributed in the hope that it will be useful, +# This library is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -# GNU General Public License for more details. +# GNU Lesser General Public License for more details. # -# You should have received a copy of the GNU General Public License -# along with this program; if not, write to the Free Software -# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +# You should have received a copy of the GNU Lesser General Public +# License along with Foobar. If not, see . +############################################################################## + """Pure python code to calculate the radius of gyration of frames in a trajectory """ diff --git a/MDTraj/geometry/sasa.py b/MDTraj/geometry/sasa.py index 3009a6157..9451d19c7 100644 --- a/MDTraj/geometry/sasa.py +++ b/MDTraj/geometry/sasa.py @@ -1,20 +1,25 @@ -# This file is part of MDTraj. +############################################################################## +# MDTraj: A Python Library for Loading, Saving, and Manipulating +# Molecular Dynamics Trajectories. +# Copyright 2012-2013 Stanford University and the Authors # -# Copyright 2013 Stanford University +# Authors: Robert McGibbon +# Contributors: # -# MDTraj is free software; you can redistribute it and/or modify -# it under the terms of the GNU General Public License as published by -# the Free Software Foundation; either version 2 of the License, or -# (at your option) any later version. +# MDTraj is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as +# published by the Free Software Foundation, either version 2.1 +# of the License, or (at your option) any later version. # -# This program is distributed in the hope that it will be useful, +# This library is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -# GNU General Public License for more details. +# GNU Lesser General Public License for more details. # -# You should have received a copy of the GNU General Public License -# along with this program; if not, write to the Free Software -# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +# You should have received a copy of the GNU Lesser General Public +# License along with Foobar. If not, see . +############################################################################## + ############################################################################## # Imports diff --git a/MDTraj/geometry/src/_geometry.pyx b/MDTraj/geometry/src/_geometry.pyx index a4d838ae5..486a4d1a0 100644 --- a/MDTraj/geometry/src/_geometry.pyx +++ b/MDTraj/geometry/src/_geometry.pyx @@ -1,5 +1,25 @@ -#cython: boundscheck=False -#cython: wraparound=False +############################################################################## +# MDTraj: A Python Library for Loading, Saving, and Manipulating +# Molecular Dynamics Trajectories. +# Copyright 2012-2013 Stanford University and the Authors +# +# Authors: Robert McGibbon +# Contributors: +# +# MDTraj is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as +# published by the Free Software Foundation, either version 2.1 +# of the License, or (at your option) any later version. +# +# This library is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with Foobar. If not, see . +############################################################################## + import cython import numpy as np cimport numpy as np diff --git a/MDTraj/geometry/src/geometry.c b/MDTraj/geometry/src/geometry.c index 854f0f9c1..983da5d41 100644 --- a/MDTraj/geometry/src/geometry.c +++ b/MDTraj/geometry/src/geometry.c @@ -1,21 +1,25 @@ -/* This file is part of MDTraj - * - * Copyright 2013 Stanford University - * - * MDTraj is free software; you can redistribute it and/or modify - * it under the terms of the GNU General Public License as published by - * the Free Software Foundation; either version 2 of the License, or - * (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License - * along with this program; if not, write to the Free Software - * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA - */ +/* +MDTraj: A Python Library for Loading, Saving, and Manipulating + Molecular Dynamics Trajectories. +Copyright 2012-2013 Stanford University and the Authors + +Authors: Robert McGibbon +Contributors: + +MDTraj is free software: you can redistribute it and/or modify +it under the terms of the GNU Lesser General Public License as +published by the Free Software Foundation, either version 2.1 +of the License, or (at your option) any later version. + +This library is distributed in the hope that it will be useful, +but WITHOUT ANY WARRANTY; without even the implied warranty of +MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +GNU Lesser General Public License for more details. + +You should have received a copy of the GNU Lesser General Public +License along with Foobar. If not, see . +/* + #include #include @@ -211,7 +215,7 @@ int dist_mic(const float* xyz, const int* pairs, const float* box_matrix, // Calculate the inverse of the box matrix, and also store it in the same // format. inverse33(box_matrix, hinv+0, hinv+1, hinv+2); - + for (j = 0; j < n_pairs; j++) { // Load the two vectors whos distance we want to compute r1 = load_float3(xyz + 3*pairs[2*j + 0]); diff --git a/MDTraj/geometry/src/sasa.c b/MDTraj/geometry/src/sasa.c index 2ac6925b7..aa4a1c817 100644 --- a/MDTraj/geometry/src/sasa.c +++ b/MDTraj/geometry/src/sasa.c @@ -1,21 +1,24 @@ -/* This file is part of MDTraj - * - * Copyright 2013 Stanford University - * - * MDTraj is free software; you can redistribute it and/or modify - * it under the terms of the GNU General Public License as published by - * the Free Software Foundation; either version 2 of the License, or - * (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License - * along with this program; if not, write to the Free Software - * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA - */ +/* +MDTraj: A Python Library for Loading, Saving, and Manipulating + Molecular Dynamics Trajectories. +Copyright 2012-2013 Stanford University and the Authors + +Authors: Robert McGibbon +Contributors: + +MDTraj is free software: you can redistribute it and/or modify +it under the terms of the GNU Lesser General Public License as +published by the Free Software Foundation, either version 2.1 +of the License, or (at your option) any later version. + +This library is distributed in the hope that it will be useful, +but WITHOUT ANY WARRANTY; without even the implied warranty of +MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +GNU Lesser General Public License for more details. + +You should have received a copy of the GNU Lesser General Public +License along with Foobar. If not, see . +/* #include #include @@ -38,7 +41,7 @@ static void asa_frame(const float* frame, const int n_atoms, const float* atom_r int* neighbor_indices, float* centered_sphere_points, float* areas) { // Calculate the accessible surface area of each atom in a single snapshot - // + // // Parameters // ---------- // frame : 2d array, shape=[n_atoms, 3] @@ -51,7 +54,7 @@ static void asa_frame(const float* frame, const int n_atoms, const float* atom_r // a bunch of uniformly distributed points on a sphere // n_sphere_points : int // the number of sphere points - + // centered_sphere_points : WORK BUFFER 2d array, shape=[n_sphere_points, 3] // empty memory that intermediate calculations can be stored in // neighbor_indices : WORK BUFFER 2d array, shape=[n_atoms] @@ -59,17 +62,17 @@ static void asa_frame(const float* frame, const int n_atoms, const float* atom_r // NOTE: the point of these work buffers is that if we want to call // this function repreatedly, its more efficient not to keep re-mallocing // these work buffers, but instead just reuse them. - + // areas : 1d array, shape=[n_atoms] // the output buffer to place the results in -- the surface area of each // atom - + int i, j, k, k_prime; __m128 r, r_i, r_j, r_ij, atom_radius_i, atom_radius_j, radius_cutoff; __m128 radius_cutoff2, sp, r_jk, r2; int n_neighbor_indices, is_accessible, k_closest_neighbor; float constant = 4.0 * M_PI / n_sphere_points; - + for (i = 0; i < n_atoms; i++) { atom_radius_i = _mm_set1_ps(atom_radii[i]); r_i = load_float3(frame+i*3); @@ -80,7 +83,7 @@ static void asa_frame(const float* frame, const int n_atoms, const float* atom_r if (i == j) { continue; } - + r_j = load_float3(frame+j*3); r_ij = _mm_sub_ps(r_i, r_j); atom_radius_j = _mm_set1_ps(atom_radii[j]); @@ -100,19 +103,19 @@ static void asa_frame(const float* frame, const int n_atoms, const float* atom_r exit(1); } } - + // Center the sphere points on atom i for (j = 0; j < n_sphere_points; j++) { sp = _mm_add_ps(r_i, _mm_mul_ps(atom_radius_i, load_float3(sphere_points + 3*j))); store_float3(centered_sphere_points + 3*j, sp); } - + // Check if each of these points is accessible k_closest_neighbor = 0; for (j = 0; j < n_sphere_points; j++) { is_accessible = 1; r_j = load_float3(centered_sphere_points + 3*j); - + // iterate through the sphere points by cycling through them // in a circle, starting with k_closest_neighbor and then wrapping // around @@ -127,7 +130,7 @@ static void asa_frame(const float* frame, const int n_atoms, const float* atom_r break; } } - + if (is_accessible) { areas[i]++; } @@ -141,7 +144,7 @@ static void generate_sphere_points(float* sphere_points, int n_points) { // Compute the coordinates of points on a sphere using the // Golden Section Spiral algorithm. - // + // // Parameters // ---------- // sphere_points : array, shape=(n_points, 3) @@ -150,18 +153,18 @@ static void generate_sphere_points(float* sphere_points, int n_points) // and sphere_points[3*i+2] are the x,y,z coordinates of the ith point // n_pts : int // Number of points to generate on the sphere - // + // // """ int i; float y, r, phi; float inc = M_PI * (3.0 - sqrt(5)); float offset = 2.0 / n_points; - + for (i = 0; i < n_points; i++) { y = i * offset - 1.0 + (offset / 2.0); r = sqrt(1.0 - y*y); phi = i * inc; - + sphere_points[3*i] = cos(phi) * r; sphere_points[3*i+1] = y; sphere_points[3*i+2] = sin(phi) * r; @@ -174,7 +177,7 @@ int sasa(const int n_frames, const int n_atoms, const float* xyzlist, { // Calculate the accessible surface area of each atom in each frame of // a trajectory - // + // // Parameters // ---------- // xyzlist : 3d array, shape=[n_frames, n_atoms, 3] @@ -191,17 +194,17 @@ int sasa(const int n_frames, const int n_atoms, const float* xyzlist, // array_of_areas : 2d array, shape=[n_frames, n_atoms] // the output buffer to place the results in -- the surface area of each // frame (each atom within that frame) - + int i; - + //work buffers that will be thread-local int* wb1; float* wb2; - + //generate the sphere points float* sphere_points = (float*) malloc(n_sphere_points*3*sizeof(float)); generate_sphere_points(sphere_points, n_sphere_points); - + #ifdef _OPENMP #pragma omp parallel private(wb1, wb2) { #endif @@ -214,7 +217,7 @@ int sasa(const int n_frames, const int n_atoms, const float* xyzlist, #pragma omp for #endif for (i = 0; i < n_frames; i++) { - asa_frame(xyzlist + i*n_atoms*3, n_atoms, atom_radii, sphere_points, + asa_frame(xyzlist + i*n_atoms*3, n_atoms, atom_radii, sphere_points, n_sphere_points, wb1, wb2, array_of_areas + i*n_atoms); } @@ -222,8 +225,8 @@ int sasa(const int n_frames, const int n_atoms, const float* xyzlist, free(wb2); #ifdef _OPENMP } // close omp parallel private -#endif - +#endif + free(sphere_points); return 1; } diff --git a/MDTraj/geometry/test/test_alignment.py b/MDTraj/geometry/test/test_alignment.py index d89992f57..4e881733b 100644 --- a/MDTraj/geometry/test/test_alignment.py +++ b/MDTraj/geometry/test/test_alignment.py @@ -1,18 +1,25 @@ -# Copyright 2012 mdtraj developers +############################################################################## +# MDTraj: A Python Library for Loading, Saving, and Manipulating +# Molecular Dynamics Trajectories. +# Copyright 2012-2013 Stanford University and the Authors # -# This file is part of mdtraj +# Authors: Kyle A. Beauchamp +# Contributors: Robert McGibbon # -# mdtraj is free software: you can redistribute it and/or modify it under the -# terms of the GNU General Public License as published by the Free Software -# Foundation, either version 3 of the License, or (at your option) any later -# version. +# MDTraj is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as +# published by the Free Software Foundation, either version 2.1 +# of the License, or (at your option) any later version. # -# mdtraj is distributed in the hope that it will be useful, but WITHOUT ANY -# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR -# A PARTICULAR PURPOSE. See the GNU General Public License for more details. +# This library is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU Lesser General Public License for more details. # -# You should have received a copy of the GNU General Public License along with -# mdtraj. If not, see http://www.gnu.org/licenses/. +# You should have received a copy of the GNU Lesser General Public +# License along with Foobar. If not, see . +############################################################################## + from mdtraj.testing import get_fn, eq, DocStringFormatTester from mdtraj.geometry import alignment @@ -39,5 +46,5 @@ def test_rmsd_nonzero(): def test_transform(): T = alignment.compute_transformation(xyz2, xyz1) xyz2_prime = T.transform(xyz2) - + eq(xyz1, xyz2_prime) diff --git a/MDTraj/geometry/test/test_distance.py b/MDTraj/geometry/test/test_distance.py index 4ae0b9fd1..ea83c1cf5 100644 --- a/MDTraj/geometry/test/test_distance.py +++ b/MDTraj/geometry/test/test_distance.py @@ -1,3 +1,25 @@ +############################################################################## +# MDTraj: A Python Library for Loading, Saving, and Manipulating +# Molecular Dynamics Trajectories. +# Copyright 2012-2013 Stanford University and the Authors +# +# Authors: Robert McGibbon +# Contributors: +# +# MDTraj is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as +# published by the Free Software Foundation, either version 2.1 +# of the License, or (at your option) any later version. +# +# This library is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with Foobar. If not, see . +############################################################################## + import time import itertools import numpy as np @@ -81,4 +103,4 @@ def test_5(): box = np.eye(3,3).reshape(1,3,3) result = _displacement_mic(xyz, np.array([[0,1]]), box) eq(result, np.array([[[0, 0, 0.2]]])) - \ No newline at end of file + diff --git a/MDTraj/geometry/test/test_geometry.py b/MDTraj/geometry/test/test_geometry.py index 3e3c3140e..8b0d0e16e 100644 --- a/MDTraj/geometry/test/test_geometry.py +++ b/MDTraj/geometry/test/test_geometry.py @@ -1,18 +1,25 @@ -# Copyright 2012 mdtraj developers +############################################################################## +# MDTraj: A Python Library for Loading, Saving, and Manipulating +# Molecular Dynamics Trajectories. +# Copyright 2012-2013 Stanford University and the Authors # -# This file is part of mdtraj +# Authors: Robert McGibbon +# Contributors: # -# mdtraj is free software: you can redistribute it and/or modify it under the -# terms of the GNU General Public License as published by the Free Software -# Foundation, either version 3 of the License, or (at your option) any later -# version. +# MDTraj is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as +# published by the Free Software Foundation, either version 2.1 +# of the License, or (at your option) any later version. # -# mdtraj is distributed in the hope that it will be useful, but WITHOUT ANY -# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR -# A PARTICULAR PURPOSE. See the GNU General Public License for more details. +# This library is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU Lesser General Public License for more details. # -# You should have received a copy of the GNU General Public License along with -# mdtraj. If not, see http://www.gnu.org/licenses/. +# You should have received a copy of the GNU Lesser General Public +# License along with Foobar. If not, see . +############################################################################## + from __future__ import print_function import itertools @@ -115,7 +122,7 @@ def test_dihedral_0(): psi0 = np.array([134.52554, 144.880173]) * np.pi / 180. # Pymol eq(psi[0,0:2], psi0, decimal=4) eq(int(rid[0]), 0) - + rid, chi = mdtraj.geometry.dihedral.compute_chi(traj) chi0 = np.array([-43.37841, -18.14592]) * np.pi / 180. # Pymol eq(chi[0,0:2], chi0, decimal=4) @@ -150,7 +157,7 @@ def test_angle_1(): # taylor series expansions -- are parameterized slightly differently on # different libraries/platforms. setting the random number seed helps to # ensure that this doesn't break stochastically too often. - + n_atoms = 5 np.random.seed(24) xyz = np.random.randn(50, n_atoms, 3) @@ -174,7 +181,7 @@ def test_dihedral_performance(): t2 = time.time() r2 = md.geometry.compute_dihedrals(t, indices, opt=True) t3 = time.time() - + print('\ndihedral performance:') print('numpy: %f s' % (t2 - t1)) print('opt sse: %f s' % (t3 - t2)) @@ -191,7 +198,7 @@ def test_angle_performance(): t2 = time.time() r2 = md.geometry.compute_angles(t, indices, opt=True) t3 = time.time() - + print('\nangle performance:') print('numpy: %f s' % (t2 - t1)) print('opt sse: %f s' % (t3 - t2)) diff --git a/MDTraj/geometry/test/test_hbonds.py b/MDTraj/geometry/test/test_hbonds.py index 1729e8d05..5a766da86 100644 --- a/MDTraj/geometry/test/test_hbonds.py +++ b/MDTraj/geometry/test/test_hbonds.py @@ -1,6 +1,25 @@ -############################################################################### -# Imports -############################################################################### +############################################################################## +# MDTraj: A Python Library for Loading, Saving, and Manipulating +# Molecular Dynamics Trajectories. +# Copyright 2012-2013 Stanford University and the Authors +# +# Authors: Robert McGibbon +# Contributors: +# +# MDTraj is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as +# published by the Free Software Foundation, either version 2.1 +# of the License, or (at your option) any later version. +# +# This library is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with Foobar. If not, see . +############################################################################## + import os import shutil diff --git a/MDTraj/geometry/test/test_sasa.py b/MDTraj/geometry/test/test_sasa.py index 7dcd0d16d..89917e992 100644 --- a/MDTraj/geometry/test/test_sasa.py +++ b/MDTraj/geometry/test/test_sasa.py @@ -1,20 +1,25 @@ -# This file is part of MDTraj. +############################################################################## +# MDTraj: A Python Library for Loading, Saving, and Manipulating +# Molecular Dynamics Trajectories. +# Copyright 2012-2013 Stanford University and the Authors # -# Copyright 2013 Stanford University +# Authors: Robert McGibbon +# Contributors: # -# MDTraj is free software; you can redistribute it and/or modify -# it under the terms of the GNU General Public License as published by -# the Free Software Foundation; either version 2 of the License, or -# (at your option) any later version. +# MDTraj is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as +# published by the Free Software Foundation, either version 2.1 +# of the License, or (at your option) any later version. # -# This program is distributed in the hope that it will be useful, +# This library is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -# GNU General Public License for more details. +# GNU Lesser General Public License for more details. # -# You should have received a copy of the GNU General Public License -# along with this program; if not, write to the Free Software -# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +# You should have received a copy of the GNU Lesser General Public +# License along with Foobar. If not, see . +############################################################################## + ############################################################################## # Imports diff --git a/MDTraj/hdf5.py b/MDTraj/hdf5.py index 404696803..f00a07d73 100644 --- a/MDTraj/hdf5.py +++ b/MDTraj/hdf5.py @@ -1,18 +1,25 @@ -# Copyright 2013 mdtraj developers +############################################################################## +# MDTraj: A Python Library for Loading, Saving, and Manipulating +# Molecular Dynamics Trajectories. +# Copyright 2012-2013 Stanford University and the Authors # -# This file is part of mdtraj +# Authors: Robert McGibbon +# Contributors: # -# mdtraj is free software: you can redistribute it and/or modify it under the -# terms of the GNU General Public License as published by the Free Software -# Foundation, either version 3 of the License, or (at your option) any later -# version. +# MDTraj is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as +# published by the Free Software Foundation, either version 2.1 +# of the License, or (at your option) any later version. # -# mdtraj is distributed in the hope that it will be useful, but WITHOUT ANY -# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR -# A PARTICULAR PURPOSE. See the GNU General Public License for more details. +# This library is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU Lesser General Public License for more details. # -# You should have received a copy of the GNU General Public License along with -# mdtraj. If not, see http://www.gnu.org/licenses/. +# You should have received a copy of the GNU Lesser General Public +# License along with Foobar. If not, see . +############################################################################## + """ This module implements the MDTraj HDF5 format described in https://github.com/rmcgibbo/mdtraj/issues/36 @@ -280,7 +287,7 @@ def topology(self, topology_object): 'chains': [], 'bonds': [] } - + # we want to be able to handle the simtk.openmm Topology object # here too, for the purpose of having a reporter # it doesnt use decorators on the chains/residues/atoms/bonds diff --git a/MDTraj/io.py b/MDTraj/io.py index f7fc889f3..2a9995720 100644 --- a/MDTraj/io.py +++ b/MDTraj/io.py @@ -1,18 +1,26 @@ -# Copyright 2012 mdtraj developers +############################################################################## +# MDTraj: A Python Library for Loading, Saving, and Manipulating +# Molecular Dynamics Trajectories. +# Copyright 2012-2013 Stanford University and the Authors # -# This file is part of mdtraj +# Authors: Robert McGibbon +# Contributors: # -# mdtraj is free software: you can redistribute it and/or modify it under the -# terms of the GNU General Public License as published by the Free Software -# Foundation, either version 3 of the License, or (at your option) any later -# version. +# MDTraj is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as +# published by the Free Software Foundation, either version 2.1 +# of the License, or (at your option) any later version. # -# mdtraj is distributed in the hope that it will be useful, but WITHOUT ANY -# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR -# A PARTICULAR PURPOSE. See the GNU General Public License for more details. +# This library is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU Lesser General Public License for more details. # -# You should have received a copy of the GNU General Public License along with -# mdtraj. If not, see http://www.gnu.org/licenses/. +# You should have received a copy of the GNU Lesser General Public +# License along with Foobar. If not, see . +############################################################################## + + # Portions of this code were copied from the Numpy source # those portions are owned by the numpy developers, and released @@ -211,7 +219,7 @@ def loadh(file, name=Ellipsis, deferred=True): If file does not exist KeyError If the request name does not exist - + See Also -------- numpy.load : Load an array(s) or pickled objects from .npy, .npz, or pickled files. diff --git a/MDTraj/mdcrd.py b/MDTraj/mdcrd.py index e03f4fdea..fbc95a586 100644 --- a/MDTraj/mdcrd.py +++ b/MDTraj/mdcrd.py @@ -1,18 +1,25 @@ -# Copyright 2013-present mdtraj developers +############################################################################## +# MDTraj: A Python Library for Loading, Saving, and Manipulating +# Molecular Dynamics Trajectories. +# Copyright 2012-2013 Stanford University and the Authors # -# This file is part of mdtraj +# Authors: Robert McGibbon +# Contributors: # -# mdtraj is free software: you can redistribute it and/or modify it under the -# terms of the GNU General Public License as published by the Free Software -# Foundation, either version 3 of the License, or (at your option) any later -# version. +# MDTraj is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as +# published by the Free Software Foundation, either version 2.1 +# of the License, or (at your option) any later version. # -# mdtraj is distributed in the hope that it will be useful, but WITHOUT ANY -# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR -# A PARTICULAR PURPOSE. See the GNU General Public License for more details. +# This library is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU Lesser General Public License for more details. # -# You should have received a copy of the GNU General Public License along with -# mdtraj. If not, see http://www.gnu.org/licenses/. +# You should have received a copy of the GNU Lesser General Public +# License along with Foobar. If not, see . +############################################################################## + ############################################################################## # Imports diff --git a/MDTraj/netcdf.py b/MDTraj/netcdf.py index 96a735e33..ab24b5a12 100644 --- a/MDTraj/netcdf.py +++ b/MDTraj/netcdf.py @@ -1,18 +1,25 @@ -# Copyright 2013 mdtraj developers +############################################################################## +# MDTraj: A Python Library for Loading, Saving, and Manipulating +# Molecular Dynamics Trajectories. +# Copyright 2012-2013 Stanford University and the Authors # -# This file is part of mdtraj +# Authors: Robert McGibbon +# Contributors: # -# mdtraj is free software: you can redistribute it and/or modify it under the -# terms of the GNU General Public License as published by the Free Software -# Foundation, either version 3 of the License, or (at your option) any later -# version. +# MDTraj is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as +# published by the Free Software Foundation, either version 2.1 +# of the License, or (at your option) any later version. # -# mdtraj is distributed in the hope that it will be useful, but WITHOUT ANY -# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR -# A PARTICULAR PURPOSE. See the GNU General Public License for more details. +# This library is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU Lesser General Public License for more details. # -# You should have received a copy of the GNU General Public License along with -# mdtraj. If not, see http://www.gnu.org/licenses/. +# You should have received a copy of the GNU Lesser General Public +# License along with Foobar. If not, see . +############################################################################## + """ This module provides the ability to read and write AMBER NetCDF trajectories. @@ -70,7 +77,7 @@ def __init__(self, filename, mode='r', force_overwrite=True): " 'r' indicates read, 'w' indicates write, and 'a' indicates" " append. 'a' and 'w' can be appended with 's', which turns " " off buffering")) - + if mode in ['w', 'ws'] and not force_overwrite and os.path.exists(filename): raise IOError('"%s" already exists') diff --git a/MDTraj/pdb/element.py b/MDTraj/pdb/element.py index ab4c0ce51..d2e29b4a4 100644 --- a/MDTraj/pdb/element.py +++ b/MDTraj/pdb/element.py @@ -1,18 +1,25 @@ -# Copyright 2012 mdtraj developers +############################################################################## +# MDTraj: A Python Library for Loading, Saving, and Manipulating +# Molecular Dynamics Trajectories. +# Copyright 2012-2013 Stanford University and the Authors # -# This file is part of mdtraj +# Authors: Christopher M. Bruns +# Contributors: Robert McGibbon, Jason Swails # -# mdtraj is free software: you can redistribute it and/or modify it under the -# terms of the GNU General Public License as published by the Free Software -# Foundation, either version 3 of the License, or (at your option) any later -# version. +# MDTraj is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as +# published by the Free Software Foundation, either version 2.1 +# of the License, or (at your option) any later version. # -# mdtraj is distributed in the hope that it will be useful, but WITHOUT ANY -# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR -# A PARTICULAR PURPOSE. See the GNU General Public License for more details. +# This library is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU Lesser General Public License for more details. # -# You should have received a copy of the GNU General Public License along with -# mdtraj. If not, see http://www.gnu.org/licenses/. +# You should have received a copy of the GNU Lesser General Public +# License along with Foobar. If not, see . +############################################################################## + """ element.py: Used for managing elements. @@ -45,8 +52,6 @@ USE OR OTHER DEALINGS IN THE SOFTWARE. """ from __future__ import print_function, division -__author__ = "Christopher M. Bruns" -__version__ = "1.0" class Element: @@ -57,6 +62,7 @@ class Element: look up the Element with a particular chemical symbol.""" _elements_by_symbol = {} + _elements_by_atomic_number = {} def __init__(self, number, name, symbol, mass): ## The atomic number of the element @@ -71,6 +77,16 @@ def __init__(self, number, name, symbol, mass): s = symbol.strip().upper() assert s not in Element._elements_by_symbol Element._elements_by_symbol[s] = self + if number in Element._elements_by_atomic_number: + other_element = Element._elements_by_atomic_number[number] + if mass < other_element.mass: + # If two "elements" share the same atomic number, they're + # probably hydrogen and deuterium, and we want to choose + # the lighter one to put in the table by atomic_number, + # since it's the "canonical" element. + Element._elements_by_atomic_number[number] = self + else: + Element._elements_by_atomic_number[number] = self @staticmethod def getBySymbol(symbol): @@ -201,3 +217,8 @@ def get_by_symbol(symbol): ununquadium = Element(114, "ununquadium", "Uuq", 289) ununpentium = Element(115, "ununpentium", "Uup", 288) ununhexium = Element(116, "ununhexium", "Uuh", 292) + +# Aliases to recognize common alternative spellings. Both the '==' and 'is' +# relational operators will work with any chosen name +sulphur = sulfur +aluminium = aluminum diff --git a/MDTraj/pdb/pdbfile.py b/MDTraj/pdb/pdbfile.py index bacd69a04..43d7600e9 100644 --- a/MDTraj/pdb/pdbfile.py +++ b/MDTraj/pdb/pdbfile.py @@ -1,54 +1,49 @@ -# Copyright 2012 mdtraj developers +############################################################################## +# MDTraj: A Python Library for Loading, Saving, and Manipulating +# Molecular Dynamics Trajectories. +# Copyright 2012-2013 Stanford University and the Authors # -# This file is part of mdtraj +# Authors: Peter Eastman, Robert McGibbon +# Contributors: # -# mdtraj is free software: you can redistribute it and/or modify it under the -# terms of the GNU General Public License as published by the Free Software -# Foundation, either version 3 of the License, or (at your option) any later -# version. +# MDTraj is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as +# published by the Free Software Foundation, either version 2.1 +# of the License, or (at your option) any later version. # -# mdtraj is distributed in the hope that it will be useful, but WITHOUT ANY -# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR -# A PARTICULAR PURPOSE. See the GNU General Public License for more details. +# This library is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU Lesser General Public License for more details. # -# You should have received a copy of the GNU General Public License along with -# mdtraj. If not, see http://www.gnu.org/licenses/. - -""" -pdbfile.py: Used for loading PDB files. - -This is part of the OpenMM molecular simulation toolkit originating from -Simbios, the NIH National Center for Physics-Based Simulation of -Biological Structures at Stanford, funded under the NIH Roadmap for -Medical Research, grant U54 GM072970. See https://simtk.org. - -Portions copyright (c) 2012 Stanford University and the Authors. -Authors: Peter Eastman -Contributors: - -Permission is hereby granted, free of charge, to any person obtaining a -copy of this software and associated documentation files (the "Software"), -to deal in the Software without restriction, including without limitation -the rights to use, copy, modify, merge, publish, distribute, sublicense, -and/or sell copies of the Software, and to permit persons to whom the -Software is furnished to do so, subject to the following conditions: - -The above copyright notice and this permission notice shall be included in -all copies or substantial portions of the Software. - -THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR -IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, -FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL -THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, -DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR -OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE -USE OR OTHER DEALINGS IN THE SOFTWARE. -""" -from __future__ import print_function, division - -__author__ = "Peter Eastman" -__version__ = "1.0" +# You should have received a copy of the GNU Lesser General Public +# License along with Foobar. If not, see . +# Portions copyright (c) 2012 Stanford University and the Authors. +# +# Portions of this code originate from the OpenMM molecular simulation +# toolkit. Those portions are Copyright 2008-2012 Stanford University +# and Peter Eastman, and distributed under the following license: +# +# Permission is hereby granted, free of charge, to any person obtaining a +# copy of this software and associated documentation files (the "Software"), +# to deal in the Software without restriction, including without limitation +# the rights to use, copy, modify, merge, publish, distribute, sublicense, +# and/or sell copies of the Software, and to permit persons to whom the +# Software is furnished to do so, subject to the following conditions: +# +# The above copyright notice and this permission notice shall be included in +# all copies or substantial portions of the Software. +# +# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL +# THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, +# DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR +# OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE +# USE OR OTHER DEALINGS IN THE SOFTWARE. +############################################################################## +from __future__ import print_function, division import os import numpy as np import xml.etree.ElementTree as etree @@ -414,7 +409,7 @@ def _guess_element(self, atom_name, residue): except KeyError: try: symbol = atom_name[0:2].strip().rstrip("AB0123456789").lstrip("0123456789") - element = elem.get_by_symbol(symbol) + element = elem.get_by_symbol(symbol) except KeyError: element = None diff --git a/MDTraj/pdb/pdbstructure.py b/MDTraj/pdb/pdbstructure.py index 403d4d5c6..cdc099e23 100644 --- a/MDTraj/pdb/pdbstructure.py +++ b/MDTraj/pdb/pdbstructure.py @@ -1,935 +1,930 @@ -# Copyright 2012 mdtraj developers -# -# This file is part of mdtraj -# -# mdtraj is free software: you can redistribute it and/or modify it under the -# terms of the GNU General Public License as published by the Free Software -# Foundation, either version 3 of the License, or (at your option) any later -# version. -# -# mdtraj is distributed in the hope that it will be useful, but WITHOUT ANY -# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR -# A PARTICULAR PURPOSE. See the GNU General Public License for more details. -# -# You should have received a copy of the GNU General Public License along with -# mdtraj. If not, see http://www.gnu.org/licenses/. -""" -pdbstructure.py: Used for managing PDB formated files. - -This is part of the OpenMM molecular simulation toolkit originating from -Simbios, the NIH National Center for Physics-Based Simulation of -Biological Structures at Stanford, funded under the NIH Roadmap for -Medical Research, grant U54 GM072970. See https://simtk.org. - -Portions copyright (c) 2012 Stanford University and the Authors. -Authors: Christopher M. Bruns -Contributors: Peter Eastman - -Permission is hereby granted, free of charge, to any person obtaining a -copy of this software and associated documentation files (the "Software"), -to deal in the Software without restriction, including without limitation -the rights to use, copy, modify, merge, publish, distribute, sublicense, -and/or sell copies of the Software, and to permit persons to whom the -Software is furnished to do so, subject to the following conditions: - -The above copyright notice and this permission notice shall be included in -all copies or substantial portions of the Software. - -THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR -IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, -FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL -THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, -DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR -OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE -USE OR OTHER DEALINGS IN THE SOFTWARE. -""" -from __future__ import print_function, division - -__author__ = "Christopher M. Bruns" -__version__ = "1.0" - -import sys -import warnings -import numpy as np -from . import element - - -class PdbStructure(object): - """ - PdbStructure object holds a parsed Protein Data Bank format file. - - Examples: - - Load a pdb structure from a file: - > pdb = PdbStructure(open("1ARJ.pdb")) - - Fetch the first atom of the structure: - > print(pdb.iter_atoms().next()) - ATOM 1 O5' G N 17 13.768 -8.431 11.865 1.00 0.00 O - - Loop over all of the atoms of the structure - > for atom in pdb.iter_atoms(): - > print(atom) - ATOM 1 O5' G N 17 13.768 -8.431 11.865 1.00 0.00 O - ... - - Get a list of all atoms in the structure: - > atoms = list(pdb.iter_atoms()) - - also: - residues = list(pdb.iter_residues()) - positions = list(pdb.iter_positions()) - chains = list(pdb.iter_chains()) - models = list(pdb.iter_models()) - - Fetch atomic coordinates of first atom: - > print(pdb.iter_positions().next()) - [13.768, -8.431, 11.865] - - or - - > print(pdb.iter_atoms().next().position) - [13.768, -8.431, 11.865] - - Strip the length units from an atomic position: - > pos = pdb.iter_positions().next() - > print(pos) - [13.768, -8.431, 11.865] - > print(pos) - [13.768, -8.431, 11.865] - > print(pos) - [1.3768, -0.8431, 1.1865] - - - The hierarchical structure of the parsed PDB structure is as follows: - PdbStructure - Model - Chain - Residue - Atom - Location - - Model - A PDB structure consists of one or more Models. Each model corresponds to one version of - an NMR structure, or to one frame of a molecular dynamics trajectory. - - Chain - A Model contains one or more Chains. Each chain corresponds to one molecule, although multiple - water molecules are frequently included in the same chain. - - Residue - A Chain contains one or more Residues. One Residue corresponds to one of the repeating - unit that constitutes a polymer such as protein or DNA. For non-polymeric molecules, one Residue - represents one molecule. - - Atom - A Residue contains one or more Atoms. Atoms are chemical atoms. - - Location - An atom can sometimes have more that one position, due to static disorder in X-ray - crystal structures. To see all of the atom positions, use the atom.iter_positions() method, - or pass the parameter "include_alt_loc=True" to one of the other iter_positions() methods. - - > for pos in pdb.iter_positions(include_alt_loc=True): - > ... - - Will loop over all atom positions, including multiple alternate locations for atoms that have - multiple positions. The default value of include_alt_loc is False for the iter_positions() - methods. - """ - - - def __init__(self, input_stream, load_all_models=True): - """Create a PDB model from a PDB file stream. - - Parameters: - - self (PdbStructure) The new object that is created. - - input_stream (stream) An input file stream, probably created with - open(). - - load_all_models (bool) Whether to load every model of an NMR - structure or trajectory, or just load the first model, to save memory. - """ - # initialize models - self.load_all_models = load_all_models - self.models = [] - self._current_model = None - self.default_model = None - self.models_by_number = {} - self._unit_cell_lengths = None - self._unit_cell_angles = None - # read file - self._load(input_stream) - - def _load(self, input_stream): - state = None - - # Read one line at a time - for pdb_line in input_stream: - # Look for atoms - if (pdb_line.find("ATOM ") == 0) or (pdb_line.find("HETATM") == 0): - if state == 'NEW_MODEL': - new_number = self._current_model.number + 1 - self._add_model(Model(new_number)) - state = None - self._add_atom(Atom(pdb_line)) - # Notice MODEL punctuation, for the next level of detail - # in the structure->model->chain->residue->atom->position hierarchy - elif (pdb_line.find("MODEL") == 0): - #model_number = int(pdb_line[10:14]) - if self._current_model is None: - new_number = 0 - else: - new_number = self._current_model.number + 1 - self._add_model(Model(new_number)) - state = None - - elif (pdb_line.find("ENDMDL") == 0): - self._current_model._finalize() - if self.load_all_models: - state = 'NEW_MODEL' - else: - break - - elif (pdb_line.find("END") == 0): - self._current_model._finalize() - if self.load_all_models: - state = 'NEW_MODEL' - else: - break - - elif (pdb_line.find("TER") == 0 and pdb_line.split()[0] == "TER"): - self._current_model._current_chain._add_ter_record() - - elif (pdb_line.find("CRYST1") == 0): - self._unit_cell_lengths = (float(pdb_line[6:15]), float(pdb_line[15:24]), float(pdb_line[24:33])) - self._unit_cell_angles = (float(pdb_line[33:40]), float(pdb_line[40:47]), float(pdb_line[47:54])) - - elif (pdb_line.find("CONECT") == 0): - atoms = [int(pdb_line[7:12])] - for pos in (12,17,22,27): - try: - atoms.append(int(pdb_line[pos:pos+5])) - except: - pass - - self._current_model.connects.append(atoms) - self._finalize() - - def write(self, output_stream=sys.stdout): - """Write out structure in PDB format""" - for model in self.models: - if len(model.chains) == 0: - continue - if len(self.models) > 1: - print("MODEL %4d" % model.number, file=output_stream) - model.write(output_stream) - if len(self.models) > 1: - print("ENDMDL", file=output_stream) - print("END", file=output_stream) - - def _add_model(self, model): - if self.default_model == None: - self.default_model = model - self.models.append(model) - self._current_model = model - if model.number not in self.models_by_number: - self.models_by_number[model.number] = model - - def get_model(self, model_number): - return self.models_by_number[model_number] - - def model_numbers(self): - return list(self.models_by_number.keys()) - - def __contains__(self, model_number): - return self.models_by_number.__contains__(model_number) - - def __getitem__(self, model_number): - return self.models_by_number[model_number] - - def __iter__(self): - for model in self.models: - yield model - - def iter_models(self, use_all_models=False): - if use_all_models: - for model in self: - yield model - elif len(self.models) > 0: - yield self.models[0] - - def iter_chains(self, use_all_models=False): - for model in self.iter_models(use_all_models): - for chain in model.iter_chains(): - yield chain - - def iter_residues(self, use_all_models=False): - for model in self.iter_models(use_all_models): - for res in model.iter_residues(): - yield res - - def iter_atoms(self, use_all_models=False): - for model in self.iter_models(use_all_models): - for atom in model.iter_atoms(): - yield atom - - def iter_positions(self, use_all_models=False, include_alt_loc=False): - """ - Iterate over atomic positions. - - Parameters - - use_all_models (bool=False) Get positions from all models or just the first one. - - include_alt_loc (bool=False) Get all positions for each atom, or just the first one. - """ - for model in self.iter_models(use_all_models): - for loc in model.iter_positions(include_alt_loc): - yield loc - - def __len__(self): - return len(self.models) - - def _add_atom(self, atom): - """ - """ - if self._current_model == None: - self._add_model(Model(0)) - atom.model_number = self._current_model.number - # Atom might be alternate position for existing atom - self._current_model._add_atom(atom) - - def _finalize(self): - """Establish first and last residues, atoms, etc.""" - for model in self.models: - model._finalize() - - def get_unit_cell_lengths(self): - """Get the lengths of the crystallographic unit cell (may be None).""" - return self._unit_cell_lengths - - def get_unit_cell_angles(self): - """Get the angles of the crystallographic unit cell (may be None).""" - return self._unit_cell_angles - -class Model(object): - """Model holds one model of a PDB structure. - - NMR structures usually have multiple models. This represents one - of them. - """ - def __init__(self, model_number=1): - self.number = model_number - self.chains = [] - self._current_chain = None - self.chains_by_id = {} - self.connects = [] - - def _add_atom(self, atom): - """ - """ - if len(self.chains) == 0: - self._add_chain(Chain(atom.chain_id)) - # Create a new chain if the chain id has changed - if self._current_chain.chain_id != atom.chain_id: - self._add_chain(Chain(atom.chain_id)) - # Create a new chain after TER record, even if ID is the same - elif self._current_chain.has_ter_record: - self._add_chain(Chain(atom.chain_id)) - self._current_chain._add_atom(atom) - - def _add_chain(self, chain): - self.chains.append(chain) - self._current_chain = chain - if not chain.chain_id in self.chains_by_id: - self.chains_by_id[chain.chain_id] = chain - - def get_chain(self, chain_id): - return self.chains_by_id[chain_id] - - def chain_ids(self): - return list(self.chains_by_id.keys()) - - def __contains__(self, chain_id): - return self.chains_by_id.__contains__(chain_id) - - def __getitem__(self, chain_id): - return self.chains_by_id[chain_id] - - def __iter__(self): - return iter(self.chains) - - def iter_chains(self): - for chain in self: - yield chain - - def iter_residues(self): - for chain in self: - for res in chain.iter_residues(): - yield res - - def iter_atoms(self): - for chain in self: - for atom in chain.iter_atoms(): - yield atom - - def iter_positions(self, include_alt_loc=False): - for chain in self: - for loc in chain.iter_positions(include_alt_loc): - yield loc - - def __len__(self): - return len(self.chains) - - def write(self, output_stream=sys.stdout): - # Start atom serial numbers at 1 - sn = Model.AtomSerialNumber(1) - for chain in self.chains: - chain.write(sn, output_stream) - - def _finalize(self): - for chain in self.chains: - chain._finalize() - - - class AtomSerialNumber(object): - """pdb.Model inner class for pass-by-reference incrementable serial number""" - def __init__(self, val): - self.val = val - - def increment(self): - self.val += 1 - - -class Chain(object): - def __init__(self, chain_id=' '): - self.chain_id = chain_id - self.residues = [] - self.has_ter_record = False - self._current_residue = None - self.residues_by_num_icode = {} - self.residues_by_number = {} - - def _add_atom(self, atom): - """ - """ - # Create a residue if none have been created - if len(self.residues) == 0: - self._add_residue(Residue(atom.residue_name_with_spaces, atom.residue_number, atom.insertion_code, atom.alternate_location_indicator)) - # Create a residue if the residue information has changed - elif self._current_residue.number != atom.residue_number: - self._add_residue(Residue(atom.residue_name_with_spaces, atom.residue_number, atom.insertion_code, atom.alternate_location_indicator)) - elif self._current_residue.insertion_code != atom.insertion_code: - self._add_residue(Residue(atom.residue_name_with_spaces, atom.residue_number, atom.insertion_code, atom.alternate_location_indicator)) - elif self._current_residue.name_with_spaces == atom.residue_name_with_spaces: - # This is a normal case: number, name, and iCode have not changed - pass - elif atom.alternate_location_indicator != ' ': - # OK - this is a point mutation, Residue._add_atom will know what to do - pass - else: # Residue name does not match - # Only residue name does not match - warnings.warn("WARNING: two consecutive residues with same number (%s, %s)" % (atom, self._current_residue.atoms[-1])) - self._add_residue(Residue(atom.residue_name_with_spaces, atom.residue_number, atom.insertion_code, atom.alternate_location_indicator)) - self._current_residue._add_atom(atom) - - def _add_residue(self, residue): - if len(self.residues) == 0: - residue.is_first_in_chain = True - self.residues.append(residue) - self._current_residue = residue - key = str(residue.number) + residue.insertion_code - # only store the first residue with a particular key - if key not in self.residues_by_num_icode: - self.residues_by_num_icode[key] = residue - if residue.number not in self.residues_by_number: - self.residues_by_number[residue.number] = residue - - def write(self, next_serial_number, output_stream=sys.stdout): - for residue in self.residues: - residue.write(next_serial_number, output_stream) - if self.has_ter_record: - r = self.residues[-1] - print("TER %5d %3s %1s%4d%1s" % (next_serial_number.val, r.name_with_spaces, self.chain_id, r.number, r.insertion_code), file=output_stream) - next_serial_number.increment() - - def _add_ter_record(self): - self.has_ter_record = True - self._finalize() - - def get_residue(self, residue_number, insertion_code=' '): - return self.residues_by_num_icode[str(residue_number) + insertion_code] - - def __contains__(self, residue_number): - return self.residues_by_number.__contains__(residue_number) - - def __getitem__(self, residue_number): - """Returns the FIRST residue in this chain with a particular residue number""" - return self.residues_by_number[residue_number] - - def __iter__(self): - for res in self.residues: - yield res - - def iter_residues(self): - for res in self: - yield res - - def iter_atoms(self): - for res in self: - for atom in res: - yield atom; - - def iter_positions(self, include_alt_loc=False): - for res in self: - for loc in res.iter_positions(include_alt_loc): - yield loc - - def __len__(self): - return len(self.residues) - - def _finalize(self): - self.residues[0].is_first_in_chain = True - self.residues[-1].is_final_in_chain = True - for residue in self.residues: - residue._finalize() - - -class Residue(object): - def __init__(self, name, number, insertion_code=' ', primary_alternate_location_indicator=' '): - alt_loc = primary_alternate_location_indicator - self.primary_location_id = alt_loc - self.locations = {} - self.locations[alt_loc] = Residue.Location(alt_loc, name) - self.name_with_spaces = name - self.number = number - self.insertion_code = insertion_code - self.atoms = [] - self.atoms_by_name = {} - self.is_first_in_chain = False - self.is_final_in_chain = False - self._current_atom = None - - def _add_atom(self, atom): - """ - """ - alt_loc = atom.alternate_location_indicator - if not alt_loc in self.locations: - self.locations[alt_loc] = Residue.Location(alt_loc, atom.residue_name_with_spaces) - assert atom.residue_number == self.number - assert atom.insertion_code == self.insertion_code - - # Check whether this is an existing atom with another position - if (atom.name_with_spaces in self.atoms_by_name): - old_atom = self.atoms_by_name[atom.name_with_spaces] - # Unless this is a duplicated atom (warn about file error) - if atom.alternate_location_indicator in old_atom.locations: - pass # TJL COMMENTED OUT - #warnings.warn("WARNING: duplicate atom (%s, %s)" % (atom, old_atom._pdb_string(old_atom.serial_number, atom.alternate_location_indicator))) - else: - for alt_loc, position in atom.locations.items(): - old_atom.locations[alt_loc] = position - return # no new atom added - - # actually use new atom - self.atoms_by_name[atom.name] = atom - self.atoms_by_name[atom.name_with_spaces] = atom - self.atoms.append(atom) - self._current_atom = atom - - def write(self, next_serial_number, output_stream=sys.stdout, alt_loc = "*"): - for atom in self.atoms: - atom.write(next_serial_number, output_stream, alt_loc) - - def _finalize(self): - if len(self.atoms) > 0: - self.atoms[0].is_first_atom_in_chain = self.is_first_in_chain - self.atoms[-1].is_final_atom_in_chain = self.is_final_in_chain - for atom in self.atoms: - atom.is_first_residue_in_chain = self.is_first_in_chain - atom.is_final_residue_in_chain = self.is_final_in_chain - - def set_name_with_spaces(self, name, alt_loc=None): - # Gromacs ffamber PDB files can have 4-character residue names - # assert len(name) == 3 - if alt_loc == None: - alt_loc = self.primary_location_id - loc = self.locations[alt_loc] - loc.name_with_spaces = name - loc.name = name.strip() - def get_name_with_spaces(self, alt_loc=None): - if alt_loc == None: - alt_loc = self.primary_location_id - loc = self.locations[alt_loc] - return loc.name_with_spaces - name_with_spaces = property(get_name_with_spaces, set_name_with_spaces, doc='four-character residue name including spaces') - - def get_name(self, alt_loc=None): - if alt_loc == None: - alt_loc = self.primary_location_id - loc = self.locations[alt_loc] - return loc.name - name = property(get_name, doc='residue name') - - def get_atom(self, atom_name): - return self.atoms_by_name[atom_name] - - def __contains__(self, atom_name): - return self.atoms_by_name.__contains__(atom_name) - - def __getitem__(self, atom_name): - """Returns the FIRST atom in this residue with a particular atom name""" - return self.atoms_by_name[atom_name] - - def __iter__(self): - """ - >>> pdb_lines = [ \ - "ATOM 188 N CYS A 42 40.714 -5.292 12.123 1.00 11.29 N",\ - "ATOM 189 CA CYS A 42 39.736 -5.883 12.911 1.00 10.01 C",\ - "ATOM 190 C CYS A 42 40.339 -6.654 14.087 1.00 22.28 C",\ - "ATOM 191 O CYS A 42 41.181 -7.530 13.859 1.00 13.70 O",\ - "ATOM 192 CB CYS A 42 38.949 -6.825 12.002 1.00 9.67 C",\ - "ATOM 193 SG CYS A 42 37.557 -7.514 12.922 1.00 20.12 S"] - >>> res = Residue("CYS", 42) - >>> for l in pdb_lines: - ... res._add_atom(Atom(l)) - ... - >>> for atom in res: - ... print(atom) - ATOM 188 N CYS A 42 40.714 -5.292 12.123 1.00 11.29 N - ATOM 189 CA CYS A 42 39.736 -5.883 12.911 1.00 10.01 C - ATOM 190 C CYS A 42 40.339 -6.654 14.087 1.00 22.28 C - ATOM 191 O CYS A 42 41.181 -7.530 13.859 1.00 13.70 O - ATOM 192 CB CYS A 42 38.949 -6.825 12.002 1.00 9.67 C - ATOM 193 SG CYS A 42 37.557 -7.514 12.922 1.00 20.12 S - """ - for atom in self.iter_atoms(): - yield atom - - # Three possibilities: primary alt_loc, certain alt_loc, or all alt_locs - def iter_atoms(self, alt_loc=None): - if alt_loc == None: - locs = [self.primary_location_id] - elif alt_loc == "": - locs = [self.primary_location_id] - elif alt_loc == "*": - locs = None - else: - locs = list(alt_loc) - # If an atom has any location in alt_loc, emit the atom - for atom in self.atoms: - use_atom = False # start pessimistic - for loc2 in atom.locations.keys(): - if locs == None: # means all locations - use_atom = True - elif loc2 in locs: - use_atom = True - if use_atom: - yield atom - - def iter_positions(self, include_alt_loc=False): - """ - Returns one position per atom, even if an individual atom has multiple positions. - - >>> pdb_lines = [ \ - "ATOM 188 N CYS A 42 40.714 -5.292 12.123 1.00 11.29 N",\ - "ATOM 189 CA CYS A 42 39.736 -5.883 12.911 1.00 10.01 C",\ - "ATOM 190 C CYS A 42 40.339 -6.654 14.087 1.00 22.28 C",\ - "ATOM 191 O CYS A 42 41.181 -7.530 13.859 1.00 13.70 O",\ - "ATOM 192 CB CYS A 42 38.949 -6.825 12.002 1.00 9.67 C",\ - "ATOM 193 SG CYS A 42 37.557 -7.514 12.922 1.00 20.12 S"] - >>> res = Residue("CYS", 42) - >>> for l in pdb_lines: res._add_atom(Atom(l)) - >>> for c in res.iter_positions(): - ... print(c) - [ 40.714 -5.292 12.123] - [ 39.736 -5.883 12.911] - [ 40.339 -6.654 14.087] - [ 41.181 -7.53 13.859] - [ 38.949 -6.825 12.002] - [ 37.557 -7.514 12.922] - """ - for atom in self: - if include_alt_loc: - for loc in atom.iter_positions(): - yield loc - else: - yield atom.position - - def __len__(self): - return len(self.atoms) - - # Residues can have multiple locations, based on alt_loc indicator - class Location: - """ - Inner class of residue to allow different residue names for different alternate_locations. - """ - def __init__(self, alternate_location_indicator, residue_name_with_spaces): - self.alternate_location_indicator = alternate_location_indicator - self.residue_name_with_spaces = residue_name_with_spaces - - -class Atom(object): - """Atom represents one atom in a PDB structure. - """ - def __init__(self, pdb_line): - """Create a new pdb.Atom from an ATOM or HETATM line. - - Example line: - ATOM 2209 CB TYR A 299 6.167 22.607 20.046 1.00 8.12 C - 00000000011111111112222222222333333333344444444445555555555666666666677777777778 - 12345678901234567890123456789012345678901234567890123456789012345678901234567890 - - ATOM line format description from - http://deposit.rcsb.org/adit/docs/pdb_atom_format.html: - - COLUMNS DATA TYPE CONTENTS - -------------------------------------------------------------------------------- - 1 - 6 Record name "ATOM " - 7 - 11 Integer Atom serial number. - 13 - 16 Atom Atom name. - 17 Character Alternate location indicator. - 18 - 20 Residue name Residue name. - 22 Character Chain identifier. - 23 - 26 Integer Residue sequence number. - 27 AChar Code for insertion of residues. - 31 - 38 Real(8.3) Orthogonal coordinates for X in Angstroms. - 39 - 46 Real(8.3) Orthogonal coordinates for Y in Angstroms. - 47 - 54 Real(8.3) Orthogonal coordinates for Z in Angstroms. - 55 - 60 Real(6.2) Occupancy (Default = 1.0). - 61 - 66 Real(6.2) Temperature factor (Default = 0.0). - 73 - 76 LString(4) Segment identifier, left-justified. - 77 - 78 LString(2) Element symbol, right-justified. - 79 - 80 LString(2) Charge on the atom. - - """ - # We might modify first/final status during _finalize() methods - self.is_first_atom_in_chain = False - self.is_final_atom_in_chain = False - self.is_first_residue_in_chain = False - self.is_final_residue_in_chain = False - # Start parsing fields from pdb line - self.record_name = pdb_line[0:6].strip() - self.serial_number = int(pdb_line[6:11]) - self.name_with_spaces = pdb_line[12:16] - alternate_location_indicator = pdb_line[16] - - self.residue_name_with_spaces = pdb_line[17:20] - # In some MD codes, notably ffamber in gromacs, residue name has a fourth character in - # column 21 - possible_fourth_character = pdb_line[20:21] - if possible_fourth_character != " ": - # Fourth character should only be there if official 3 are already full - if len(self.residue_name_with_spaces.strip()) != 3: - raise ValueError('Misaligned residue name: %s' % pdb_line) - self.residue_name_with_spaces += possible_fourth_character - self.residue_name = self.residue_name_with_spaces.strip() - - self.chain_id = pdb_line[21] - self.residue_number = int(pdb_line[22:26]) - self.insertion_code = pdb_line[26] - # coordinates, occupancy, and temperature factor belong in Atom.Location object - x = float(pdb_line[30:38]) - y = float(pdb_line[38:46]) - z = float(pdb_line[46:54]) - try: - occupancy = float(pdb_line[54:60]) - except: - occupancy = 1.0 - try: - temperature_factor = float(pdb_line[60:66]) - except: - temperature_factor = 0.0 - self.locations = {} - loc = Atom.Location(alternate_location_indicator, np.array([x,y,z]), occupancy, temperature_factor, self.residue_name_with_spaces) - self.locations[alternate_location_indicator] = loc - self.default_location_id = alternate_location_indicator - # segment id, element_symbol, and formal_charge are not always present - self.segment_id = pdb_line[72:76].strip() - self.element_symbol = pdb_line[76:78].strip() - try: self.formal_charge = int(pdb_line[78:80]) - except ValueError: self.formal_charge = None - # figure out atom element - try: - # First try to find a sensible element symbol from columns 76-77 - self.element = element.get_by_symbol(self.element_symbol) - except KeyError: - # otherwise, deduce element from first two characters of atom name - # remove digits found in some hydrogen atom names - symbol = self.name_with_spaces[0:2].strip().lstrip("0123456789") - try: - # Some molecular dynamics PDB files, such as gromacs with ffamber force - # field, include 4-character hydrogen atom names beginning with "H". - # Hopefully elements like holmium (Ho) and mercury (Hg) will have fewer than four - # characters in the atom name. This problem is the fault of molecular - # dynamics code authors who feel the need to make up their own atom - # nomenclature because it is too tedious to read that provided by the PDB. - # These are the same folks who invent their own meanings for biochemical terms - # like "dipeptide". Clowntards. - if len(self.name) == 4 and self.name[0:1] == "H": - self.element = element.hydrogen - else: - self.element = element.get_by_symbol(symbol) - except KeyError: - # OK, I give up - self.element = None - - def iter_locations(self): - """ - Iterate over Atom.Location objects for this atom, including primary location. - - >>> atom = Atom("ATOM 2209 CB TYR A 299 6.167 22.607 20.046 1.00 8.12 C") - >>> for c in atom.iter_locations(): - ... print(c) - ... - [ 6.167 22.607 20.046] - """ - for alt_loc in self.locations: - yield self.locations[alt_loc] - - def iter_positions(self): - """ - Iterate over atomic positions. Returns Quantity(Vec3(), unit) objects, unlike - iter_locations, which returns Atom.Location objects. - """ - for loc in self.iter_locations(): - yield loc.position - - def iter_coordinates(self): - """ - Iterate over x, y, z values of primary atom position. - - >>> atom = Atom("ATOM 2209 CB TYR A 299 6.167 22.607 20.046 1.00 8.12 C") - >>> for c in atom.iter_coordinates(): - ... print(c) - ... - 6.167 - 22.607 - 20.046 - """ - for coord in self.position: - yield coord - - # Hide existence of multiple alternate locations to avoid scaring casual users - def get_location(self, location_id=None): - id = location_id - if (id == None): - id = self.default_location_id - return self.locations[id] - def set_location(self, new_location, location_id=None): - id = location_id - if (id == None): - id = self.default_location_id - self.locations[id] = new_location - location = property(get_location, set_location, doc='default Atom.Location object') - - def get_position(self): - return self.location.position - def set_position(self, coords): - self.location.position = coords - position = property(get_position, set_position, doc='orthogonal coordinates') - - def get_alternate_location_indicator(self): - return self.location.alternate_location_indicator - alternate_location_indicator = property(get_alternate_location_indicator) - - def get_occupancy(self): - return self.location.occupancy - occupancy = property(get_occupancy) - - def get_temperature_factor(self): - return self.location.temperature_factor - temperature_factor = property(get_temperature_factor) - - def get_x(self): return self.position[0] - x = property(get_x) - - def get_y(self): return self.position[1] - y = property(get_y) - - def get_z(self): return self.position[2] - z = property(get_z) - - def _pdb_string(self, serial_number=None, alternate_location_indicator=None): - """ - Produce a PDB line for this atom using a particular serial number and alternate location - """ - if serial_number == None: - serial_number = self.serial_number - if alternate_location_indicator == None: - alternate_location_indicator = self.alternate_location_indicator - # produce PDB line in three parts: names, numbers, and end - # Accomodate 4-character residue names that use column 21 - long_res_name = self.residue_name_with_spaces - if len(long_res_name) == 3: - long_res_name += " " - assert len(long_res_name) == 4 - names = "%-6s%5d %4s%1s%4s%1s%4d%1s " % ( - self.record_name, serial_number, \ - self.name_with_spaces, alternate_location_indicator, \ - long_res_name, self.chain_id, \ - self.residue_number, self.insertion_code) - numbers = "%8.3f%8.3f%8.3f%6.2f%6.2f " % ( - self.x, self.y, self.z, self.occupancy, self.temperature_factor) - end = "%-4s%2s" % (\ - self.segment_id, self.element_symbol) - formal_charge = " " - if (self.formal_charge != None): formal_charge = "%+2d" % self.formal_charge - return names+numbers+end+formal_charge - - def __str__(self): - return self._pdb_string(self.serial_number, self.alternate_location_indicator) - - def write(self, next_serial_number, output_stream=sys.stdout, alt_loc = "*"): - """ - alt_loc = "*" means write all alternate locations - alt_loc = None means write just the primary location - alt_loc = "AB" means write locations "A" and "B" - """ - if alt_loc == None: - locs = [self.default_location_id] - elif alt_loc == "": - locs = [self.default_location_id] - elif alt_loc == "*": - locs = self.locations.keys() - locs.sort() - else: - locs = list(alt_loc) - for loc_id in locs: - print(self._pdb_string(next_serial_number.val, loc_id), file=output_stream) - next_serial_number.increment() - - def set_name_with_spaces(self, name): - assert len(name) == 4 - self._name_with_spaces = name - self._name = name.strip() - def get_name_with_spaces(self): - return self._name_with_spaces - name_with_spaces = property(get_name_with_spaces, set_name_with_spaces, doc='four-character residue name including spaces') - - def get_name(self): - return self._name - name = property(get_name, doc='residue name') - - class Location(object): - """ - Inner class of Atom for holding alternate locations - """ - def __init__(self, alt_loc, position, occupancy, temperature_factor, residue_name): - self.alternate_location_indicator = alt_loc - self.position = position - self.occupancy = occupancy - self.temperature_factor = temperature_factor - self.residue_name = residue_name - - def __iter__(self): - """ - Examples - - >>> l = Atom.Location(' ', [1,2,3], 1.0, 20.0, "XXX") - >>> for c in l: - ... print(c) - ... - 1 - 2 - 3 - """ - for coord in self.position: - yield coord - - def __str__(self): - return str(self.position) - +############################################################################## +# MDTraj: A Python Library for Loading, Saving, and Manipulating +# Molecular Dynamics Trajectories. +# Copyright 2012-2013 Stanford University and the Authors +# +# Authors: Christopher M. Bruns +# Contributors: Peter Eastman, Robert McGibbon +# +# MDTraj is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as +# published by the Free Software Foundation, either version 2.1 +# of the License, or (at your option) any later version. +# +# This library is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with Foobar. If not, see . +# +# Portions of this code originate from the OpenMM molecular simulation toolkit, +# copyright (c) 2012 Stanford University, Christopher M. Bruns and Peter Eastman, +# and are distributed under the following terms: +# Permission is hereby granted, free of charge, to any person obtaining a +# copy of this software and associated documentation files (the "Software"), +# to deal in the Software without restriction, including without limitation +# the rights to use, copy, modify, merge, publish, distribute, sublicense, +# and/or sell copies of the Software, and to permit persons to whom the +# Software is furnished to do so, subject to the following conditions: +# +# The above copyright notice and this permission notice shall be included in +# all copies or substantial portions of the Software. +# +# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL +# THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, +# DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR +# OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE +# USE OR OTHER DEALINGS IN THE SOFTWARE. +############################################################################## + +from __future__ import print_function, division + +import sys +import warnings +import numpy as np +from . import element + + +class PdbStructure(object): + """ + PdbStructure object holds a parsed Protein Data Bank format file. + + Examples: + + Load a pdb structure from a file: + > pdb = PdbStructure(open("1ARJ.pdb")) + + Fetch the first atom of the structure: + > print(pdb.iter_atoms().next()) + ATOM 1 O5' G N 17 13.768 -8.431 11.865 1.00 0.00 O + + Loop over all of the atoms of the structure + > for atom in pdb.iter_atoms(): + > print(atom) + ATOM 1 O5' G N 17 13.768 -8.431 11.865 1.00 0.00 O + ... + + Get a list of all atoms in the structure: + > atoms = list(pdb.iter_atoms()) + + also: + residues = list(pdb.iter_residues()) + positions = list(pdb.iter_positions()) + chains = list(pdb.iter_chains()) + models = list(pdb.iter_models()) + + Fetch atomic coordinates of first atom: + > print(pdb.iter_positions().next()) + [13.768, -8.431, 11.865] + + or + + > print(pdb.iter_atoms().next().position) + [13.768, -8.431, 11.865] + + Strip the length units from an atomic position: + > pos = pdb.iter_positions().next() + > print(pos) + [13.768, -8.431, 11.865] + > print(pos) + [13.768, -8.431, 11.865] + > print(pos) + [1.3768, -0.8431, 1.1865] + + + The hierarchical structure of the parsed PDB structure is as follows: + PdbStructure + Model + Chain + Residue + Atom + Location + + Model - A PDB structure consists of one or more Models. Each model corresponds to one version of + an NMR structure, or to one frame of a molecular dynamics trajectory. + + Chain - A Model contains one or more Chains. Each chain corresponds to one molecule, although multiple + water molecules are frequently included in the same chain. + + Residue - A Chain contains one or more Residues. One Residue corresponds to one of the repeating + unit that constitutes a polymer such as protein or DNA. For non-polymeric molecules, one Residue + represents one molecule. + + Atom - A Residue contains one or more Atoms. Atoms are chemical atoms. + + Location - An atom can sometimes have more that one position, due to static disorder in X-ray + crystal structures. To see all of the atom positions, use the atom.iter_positions() method, + or pass the parameter "include_alt_loc=True" to one of the other iter_positions() methods. + + > for pos in pdb.iter_positions(include_alt_loc=True): + > ... + + Will loop over all atom positions, including multiple alternate locations for atoms that have + multiple positions. The default value of include_alt_loc is False for the iter_positions() + methods. + """ + + + def __init__(self, input_stream, load_all_models=True): + """Create a PDB model from a PDB file stream. + + Parameters: + - self (PdbStructure) The new object that is created. + - input_stream (stream) An input file stream, probably created with + open(). + - load_all_models (bool) Whether to load every model of an NMR + structure or trajectory, or just load the first model, to save memory. + """ + # initialize models + self.load_all_models = load_all_models + self.models = [] + self._current_model = None + self.default_model = None + self.models_by_number = {} + self._unit_cell_lengths = None + self._unit_cell_angles = None + # read file + self._load(input_stream) + + def _load(self, input_stream): + state = None + + # Read one line at a time + for pdb_line in input_stream: + # Look for atoms + if (pdb_line.find("ATOM ") == 0) or (pdb_line.find("HETATM") == 0): + if state == 'NEW_MODEL': + new_number = self._current_model.number + 1 + self._add_model(Model(new_number)) + state = None + self._add_atom(Atom(pdb_line)) + # Notice MODEL punctuation, for the next level of detail + # in the structure->model->chain->residue->atom->position hierarchy + elif (pdb_line.find("MODEL") == 0): + #model_number = int(pdb_line[10:14]) + if self._current_model is None: + new_number = 0 + else: + new_number = self._current_model.number + 1 + self._add_model(Model(new_number)) + state = None + + elif (pdb_line.find("ENDMDL") == 0): + self._current_model._finalize() + if self.load_all_models: + state = 'NEW_MODEL' + else: + break + + elif (pdb_line.find("END") == 0): + self._current_model._finalize() + if self.load_all_models: + state = 'NEW_MODEL' + else: + break + + elif (pdb_line.find("TER") == 0 and pdb_line.split()[0] == "TER"): + self._current_model._current_chain._add_ter_record() + + elif (pdb_line.find("CRYST1") == 0): + self._unit_cell_lengths = (float(pdb_line[6:15]), float(pdb_line[15:24]), float(pdb_line[24:33])) + self._unit_cell_angles = (float(pdb_line[33:40]), float(pdb_line[40:47]), float(pdb_line[47:54])) + + elif (pdb_line.find("CONECT") == 0): + atoms = [int(pdb_line[7:12])] + for pos in (12,17,22,27): + try: + atoms.append(int(pdb_line[pos:pos+5])) + except: + pass + + self._current_model.connects.append(atoms) + self._finalize() + + def write(self, output_stream=sys.stdout): + """Write out structure in PDB format""" + for model in self.models: + if len(model.chains) == 0: + continue + if len(self.models) > 1: + print("MODEL %4d" % model.number, file=output_stream) + model.write(output_stream) + if len(self.models) > 1: + print("ENDMDL", file=output_stream) + print("END", file=output_stream) + + def _add_model(self, model): + if self.default_model == None: + self.default_model = model + self.models.append(model) + self._current_model = model + if model.number not in self.models_by_number: + self.models_by_number[model.number] = model + + def get_model(self, model_number): + return self.models_by_number[model_number] + + def model_numbers(self): + return list(self.models_by_number.keys()) + + def __contains__(self, model_number): + return self.models_by_number.__contains__(model_number) + + def __getitem__(self, model_number): + return self.models_by_number[model_number] + + def __iter__(self): + for model in self.models: + yield model + + def iter_models(self, use_all_models=False): + if use_all_models: + for model in self: + yield model + elif len(self.models) > 0: + yield self.models[0] + + def iter_chains(self, use_all_models=False): + for model in self.iter_models(use_all_models): + for chain in model.iter_chains(): + yield chain + + def iter_residues(self, use_all_models=False): + for model in self.iter_models(use_all_models): + for res in model.iter_residues(): + yield res + + def iter_atoms(self, use_all_models=False): + for model in self.iter_models(use_all_models): + for atom in model.iter_atoms(): + yield atom + + def iter_positions(self, use_all_models=False, include_alt_loc=False): + """ + Iterate over atomic positions. + + Parameters + - use_all_models (bool=False) Get positions from all models or just the first one. + - include_alt_loc (bool=False) Get all positions for each atom, or just the first one. + """ + for model in self.iter_models(use_all_models): + for loc in model.iter_positions(include_alt_loc): + yield loc + + def __len__(self): + return len(self.models) + + def _add_atom(self, atom): + """ + """ + if self._current_model == None: + self._add_model(Model(0)) + atom.model_number = self._current_model.number + # Atom might be alternate position for existing atom + self._current_model._add_atom(atom) + + def _finalize(self): + """Establish first and last residues, atoms, etc.""" + for model in self.models: + model._finalize() + + def get_unit_cell_lengths(self): + """Get the lengths of the crystallographic unit cell (may be None).""" + return self._unit_cell_lengths + + def get_unit_cell_angles(self): + """Get the angles of the crystallographic unit cell (may be None).""" + return self._unit_cell_angles + +class Model(object): + """Model holds one model of a PDB structure. + + NMR structures usually have multiple models. This represents one + of them. + """ + def __init__(self, model_number=1): + self.number = model_number + self.chains = [] + self._current_chain = None + self.chains_by_id = {} + self.connects = [] + + def _add_atom(self, atom): + """ + """ + if len(self.chains) == 0: + self._add_chain(Chain(atom.chain_id)) + # Create a new chain if the chain id has changed + if self._current_chain.chain_id != atom.chain_id: + self._add_chain(Chain(atom.chain_id)) + # Create a new chain after TER record, even if ID is the same + elif self._current_chain.has_ter_record: + self._add_chain(Chain(atom.chain_id)) + self._current_chain._add_atom(atom) + + def _add_chain(self, chain): + self.chains.append(chain) + self._current_chain = chain + if not chain.chain_id in self.chains_by_id: + self.chains_by_id[chain.chain_id] = chain + + def get_chain(self, chain_id): + return self.chains_by_id[chain_id] + + def chain_ids(self): + return list(self.chains_by_id.keys()) + + def __contains__(self, chain_id): + return self.chains_by_id.__contains__(chain_id) + + def __getitem__(self, chain_id): + return self.chains_by_id[chain_id] + + def __iter__(self): + return iter(self.chains) + + def iter_chains(self): + for chain in self: + yield chain + + def iter_residues(self): + for chain in self: + for res in chain.iter_residues(): + yield res + + def iter_atoms(self): + for chain in self: + for atom in chain.iter_atoms(): + yield atom + + def iter_positions(self, include_alt_loc=False): + for chain in self: + for loc in chain.iter_positions(include_alt_loc): + yield loc + + def __len__(self): + return len(self.chains) + + def write(self, output_stream=sys.stdout): + # Start atom serial numbers at 1 + sn = Model.AtomSerialNumber(1) + for chain in self.chains: + chain.write(sn, output_stream) + + def _finalize(self): + for chain in self.chains: + chain._finalize() + + + class AtomSerialNumber(object): + """pdb.Model inner class for pass-by-reference incrementable serial number""" + def __init__(self, val): + self.val = val + + def increment(self): + self.val += 1 + + +class Chain(object): + def __init__(self, chain_id=' '): + self.chain_id = chain_id + self.residues = [] + self.has_ter_record = False + self._current_residue = None + self.residues_by_num_icode = {} + self.residues_by_number = {} + + def _add_atom(self, atom): + """ + """ + # Create a residue if none have been created + if len(self.residues) == 0: + self._add_residue(Residue(atom.residue_name_with_spaces, atom.residue_number, atom.insertion_code, atom.alternate_location_indicator)) + # Create a residue if the residue information has changed + elif self._current_residue.number != atom.residue_number: + self._add_residue(Residue(atom.residue_name_with_spaces, atom.residue_number, atom.insertion_code, atom.alternate_location_indicator)) + elif self._current_residue.insertion_code != atom.insertion_code: + self._add_residue(Residue(atom.residue_name_with_spaces, atom.residue_number, atom.insertion_code, atom.alternate_location_indicator)) + elif self._current_residue.name_with_spaces == atom.residue_name_with_spaces: + # This is a normal case: number, name, and iCode have not changed + pass + elif atom.alternate_location_indicator != ' ': + # OK - this is a point mutation, Residue._add_atom will know what to do + pass + else: # Residue name does not match + # Only residue name does not match + warnings.warn("WARNING: two consecutive residues with same number (%s, %s)" % (atom, self._current_residue.atoms[-1])) + self._add_residue(Residue(atom.residue_name_with_spaces, atom.residue_number, atom.insertion_code, atom.alternate_location_indicator)) + self._current_residue._add_atom(atom) + + def _add_residue(self, residue): + if len(self.residues) == 0: + residue.is_first_in_chain = True + self.residues.append(residue) + self._current_residue = residue + key = str(residue.number) + residue.insertion_code + # only store the first residue with a particular key + if key not in self.residues_by_num_icode: + self.residues_by_num_icode[key] = residue + if residue.number not in self.residues_by_number: + self.residues_by_number[residue.number] = residue + + def write(self, next_serial_number, output_stream=sys.stdout): + for residue in self.residues: + residue.write(next_serial_number, output_stream) + if self.has_ter_record: + r = self.residues[-1] + print("TER %5d %3s %1s%4d%1s" % (next_serial_number.val, r.name_with_spaces, self.chain_id, r.number, r.insertion_code), file=output_stream) + next_serial_number.increment() + + def _add_ter_record(self): + self.has_ter_record = True + self._finalize() + + def get_residue(self, residue_number, insertion_code=' '): + return self.residues_by_num_icode[str(residue_number) + insertion_code] + + def __contains__(self, residue_number): + return self.residues_by_number.__contains__(residue_number) + + def __getitem__(self, residue_number): + """Returns the FIRST residue in this chain with a particular residue number""" + return self.residues_by_number[residue_number] + + def __iter__(self): + for res in self.residues: + yield res + + def iter_residues(self): + for res in self: + yield res + + def iter_atoms(self): + for res in self: + for atom in res: + yield atom; + + def iter_positions(self, include_alt_loc=False): + for res in self: + for loc in res.iter_positions(include_alt_loc): + yield loc + + def __len__(self): + return len(self.residues) + + def _finalize(self): + self.residues[0].is_first_in_chain = True + self.residues[-1].is_final_in_chain = True + for residue in self.residues: + residue._finalize() + + +class Residue(object): + def __init__(self, name, number, insertion_code=' ', primary_alternate_location_indicator=' '): + alt_loc = primary_alternate_location_indicator + self.primary_location_id = alt_loc + self.locations = {} + self.locations[alt_loc] = Residue.Location(alt_loc, name) + self.name_with_spaces = name + self.number = number + self.insertion_code = insertion_code + self.atoms = [] + self.atoms_by_name = {} + self.is_first_in_chain = False + self.is_final_in_chain = False + self._current_atom = None + + def _add_atom(self, atom): + """ + """ + alt_loc = atom.alternate_location_indicator + if not alt_loc in self.locations: + self.locations[alt_loc] = Residue.Location(alt_loc, atom.residue_name_with_spaces) + assert atom.residue_number == self.number + assert atom.insertion_code == self.insertion_code + + # Check whether this is an existing atom with another position + if (atom.name_with_spaces in self.atoms_by_name): + old_atom = self.atoms_by_name[atom.name_with_spaces] + # Unless this is a duplicated atom (warn about file error) + if atom.alternate_location_indicator in old_atom.locations: + pass # TJL COMMENTED OUT + #warnings.warn("WARNING: duplicate atom (%s, %s)" % (atom, old_atom._pdb_string(old_atom.serial_number, atom.alternate_location_indicator))) + else: + for alt_loc, position in atom.locations.items(): + old_atom.locations[alt_loc] = position + return # no new atom added + + # actually use new atom + self.atoms_by_name[atom.name] = atom + self.atoms_by_name[atom.name_with_spaces] = atom + self.atoms.append(atom) + self._current_atom = atom + + def write(self, next_serial_number, output_stream=sys.stdout, alt_loc = "*"): + for atom in self.atoms: + atom.write(next_serial_number, output_stream, alt_loc) + + def _finalize(self): + if len(self.atoms) > 0: + self.atoms[0].is_first_atom_in_chain = self.is_first_in_chain + self.atoms[-1].is_final_atom_in_chain = self.is_final_in_chain + for atom in self.atoms: + atom.is_first_residue_in_chain = self.is_first_in_chain + atom.is_final_residue_in_chain = self.is_final_in_chain + + def set_name_with_spaces(self, name, alt_loc=None): + # Gromacs ffamber PDB files can have 4-character residue names + # assert len(name) == 3 + if alt_loc == None: + alt_loc = self.primary_location_id + loc = self.locations[alt_loc] + loc.name_with_spaces = name + loc.name = name.strip() + def get_name_with_spaces(self, alt_loc=None): + if alt_loc == None: + alt_loc = self.primary_location_id + loc = self.locations[alt_loc] + return loc.name_with_spaces + name_with_spaces = property(get_name_with_spaces, set_name_with_spaces, doc='four-character residue name including spaces') + + def get_name(self, alt_loc=None): + if alt_loc == None: + alt_loc = self.primary_location_id + loc = self.locations[alt_loc] + return loc.name + name = property(get_name, doc='residue name') + + def get_atom(self, atom_name): + return self.atoms_by_name[atom_name] + + def __contains__(self, atom_name): + return self.atoms_by_name.__contains__(atom_name) + + def __getitem__(self, atom_name): + """Returns the FIRST atom in this residue with a particular atom name""" + return self.atoms_by_name[atom_name] + + def __iter__(self): + """ + >>> pdb_lines = [ \ + "ATOM 188 N CYS A 42 40.714 -5.292 12.123 1.00 11.29 N",\ + "ATOM 189 CA CYS A 42 39.736 -5.883 12.911 1.00 10.01 C",\ + "ATOM 190 C CYS A 42 40.339 -6.654 14.087 1.00 22.28 C",\ + "ATOM 191 O CYS A 42 41.181 -7.530 13.859 1.00 13.70 O",\ + "ATOM 192 CB CYS A 42 38.949 -6.825 12.002 1.00 9.67 C",\ + "ATOM 193 SG CYS A 42 37.557 -7.514 12.922 1.00 20.12 S"] + >>> res = Residue("CYS", 42) + >>> for l in pdb_lines: + ... res._add_atom(Atom(l)) + ... + >>> for atom in res: + ... print(atom) + ATOM 188 N CYS A 42 40.714 -5.292 12.123 1.00 11.29 N + ATOM 189 CA CYS A 42 39.736 -5.883 12.911 1.00 10.01 C + ATOM 190 C CYS A 42 40.339 -6.654 14.087 1.00 22.28 C + ATOM 191 O CYS A 42 41.181 -7.530 13.859 1.00 13.70 O + ATOM 192 CB CYS A 42 38.949 -6.825 12.002 1.00 9.67 C + ATOM 193 SG CYS A 42 37.557 -7.514 12.922 1.00 20.12 S + """ + for atom in self.iter_atoms(): + yield atom + + # Three possibilities: primary alt_loc, certain alt_loc, or all alt_locs + def iter_atoms(self, alt_loc=None): + if alt_loc == None: + locs = [self.primary_location_id] + elif alt_loc == "": + locs = [self.primary_location_id] + elif alt_loc == "*": + locs = None + else: + locs = list(alt_loc) + # If an atom has any location in alt_loc, emit the atom + for atom in self.atoms: + use_atom = False # start pessimistic + for loc2 in atom.locations.keys(): + if locs == None: # means all locations + use_atom = True + elif loc2 in locs: + use_atom = True + if use_atom: + yield atom + + def iter_positions(self, include_alt_loc=False): + """ + Returns one position per atom, even if an individual atom has multiple positions. + + >>> pdb_lines = [ \ + "ATOM 188 N CYS A 42 40.714 -5.292 12.123 1.00 11.29 N",\ + "ATOM 189 CA CYS A 42 39.736 -5.883 12.911 1.00 10.01 C",\ + "ATOM 190 C CYS A 42 40.339 -6.654 14.087 1.00 22.28 C",\ + "ATOM 191 O CYS A 42 41.181 -7.530 13.859 1.00 13.70 O",\ + "ATOM 192 CB CYS A 42 38.949 -6.825 12.002 1.00 9.67 C",\ + "ATOM 193 SG CYS A 42 37.557 -7.514 12.922 1.00 20.12 S"] + >>> res = Residue("CYS", 42) + >>> for l in pdb_lines: res._add_atom(Atom(l)) + >>> for c in res.iter_positions(): + ... print(c) + [ 40.714 -5.292 12.123] + [ 39.736 -5.883 12.911] + [ 40.339 -6.654 14.087] + [ 41.181 -7.53 13.859] + [ 38.949 -6.825 12.002] + [ 37.557 -7.514 12.922] + """ + for atom in self: + if include_alt_loc: + for loc in atom.iter_positions(): + yield loc + else: + yield atom.position + + def __len__(self): + return len(self.atoms) + + # Residues can have multiple locations, based on alt_loc indicator + class Location: + """ + Inner class of residue to allow different residue names for different alternate_locations. + """ + def __init__(self, alternate_location_indicator, residue_name_with_spaces): + self.alternate_location_indicator = alternate_location_indicator + self.residue_name_with_spaces = residue_name_with_spaces + + +class Atom(object): + """Atom represents one atom in a PDB structure. + """ + def __init__(self, pdb_line): + """Create a new pdb.Atom from an ATOM or HETATM line. + + Example line: + ATOM 2209 CB TYR A 299 6.167 22.607 20.046 1.00 8.12 C + 00000000011111111112222222222333333333344444444445555555555666666666677777777778 + 12345678901234567890123456789012345678901234567890123456789012345678901234567890 + + ATOM line format description from + http://deposit.rcsb.org/adit/docs/pdb_atom_format.html: + + COLUMNS DATA TYPE CONTENTS + -------------------------------------------------------------------------------- + 1 - 6 Record name "ATOM " + 7 - 11 Integer Atom serial number. + 13 - 16 Atom Atom name. + 17 Character Alternate location indicator. + 18 - 20 Residue name Residue name. + 22 Character Chain identifier. + 23 - 26 Integer Residue sequence number. + 27 AChar Code for insertion of residues. + 31 - 38 Real(8.3) Orthogonal coordinates for X in Angstroms. + 39 - 46 Real(8.3) Orthogonal coordinates for Y in Angstroms. + 47 - 54 Real(8.3) Orthogonal coordinates for Z in Angstroms. + 55 - 60 Real(6.2) Occupancy (Default = 1.0). + 61 - 66 Real(6.2) Temperature factor (Default = 0.0). + 73 - 76 LString(4) Segment identifier, left-justified. + 77 - 78 LString(2) Element symbol, right-justified. + 79 - 80 LString(2) Charge on the atom. + + """ + # We might modify first/final status during _finalize() methods + self.is_first_atom_in_chain = False + self.is_final_atom_in_chain = False + self.is_first_residue_in_chain = False + self.is_final_residue_in_chain = False + # Start parsing fields from pdb line + self.record_name = pdb_line[0:6].strip() + self.serial_number = int(pdb_line[6:11]) + self.name_with_spaces = pdb_line[12:16] + alternate_location_indicator = pdb_line[16] + + self.residue_name_with_spaces = pdb_line[17:20] + # In some MD codes, notably ffamber in gromacs, residue name has a fourth character in + # column 21 + possible_fourth_character = pdb_line[20:21] + if possible_fourth_character != " ": + # Fourth character should only be there if official 3 are already full + if len(self.residue_name_with_spaces.strip()) != 3: + raise ValueError('Misaligned residue name: %s' % pdb_line) + self.residue_name_with_spaces += possible_fourth_character + self.residue_name = self.residue_name_with_spaces.strip() + + self.chain_id = pdb_line[21] + self.residue_number = int(pdb_line[22:26]) + self.insertion_code = pdb_line[26] + # coordinates, occupancy, and temperature factor belong in Atom.Location object + x = float(pdb_line[30:38]) + y = float(pdb_line[38:46]) + z = float(pdb_line[46:54]) + try: + occupancy = float(pdb_line[54:60]) + except: + occupancy = 1.0 + try: + temperature_factor = float(pdb_line[60:66]) + except: + temperature_factor = 0.0 + self.locations = {} + loc = Atom.Location(alternate_location_indicator, np.array([x,y,z]), occupancy, temperature_factor, self.residue_name_with_spaces) + self.locations[alternate_location_indicator] = loc + self.default_location_id = alternate_location_indicator + # segment id, element_symbol, and formal_charge are not always present + self.segment_id = pdb_line[72:76].strip() + self.element_symbol = pdb_line[76:78].strip() + try: self.formal_charge = int(pdb_line[78:80]) + except ValueError: self.formal_charge = None + # figure out atom element + try: + # First try to find a sensible element symbol from columns 76-77 + self.element = element.get_by_symbol(self.element_symbol) + except KeyError: + # otherwise, deduce element from first two characters of atom name + # remove digits found in some hydrogen atom names + symbol = self.name_with_spaces[0:2].strip().lstrip("0123456789") + try: + # Some molecular dynamics PDB files, such as gromacs with ffamber force + # field, include 4-character hydrogen atom names beginning with "H". + # Hopefully elements like holmium (Ho) and mercury (Hg) will have fewer than four + # characters in the atom name. This problem is the fault of molecular + # dynamics code authors who feel the need to make up their own atom + # nomenclature because it is too tedious to read that provided by the PDB. + # These are the same folks who invent their own meanings for biochemical terms + # like "dipeptide". Clowntards. + if len(self.name) == 4 and self.name[0:1] == "H": + self.element = element.hydrogen + else: + self.element = element.get_by_symbol(symbol) + except KeyError: + # OK, I give up + self.element = None + + def iter_locations(self): + """ + Iterate over Atom.Location objects for this atom, including primary location. + + >>> atom = Atom("ATOM 2209 CB TYR A 299 6.167 22.607 20.046 1.00 8.12 C") + >>> for c in atom.iter_locations(): + ... print(c) + ... + [ 6.167 22.607 20.046] + """ + for alt_loc in self.locations: + yield self.locations[alt_loc] + + def iter_positions(self): + """ + Iterate over atomic positions. Returns Quantity(Vec3(), unit) objects, unlike + iter_locations, which returns Atom.Location objects. + """ + for loc in self.iter_locations(): + yield loc.position + + def iter_coordinates(self): + """ + Iterate over x, y, z values of primary atom position. + + >>> atom = Atom("ATOM 2209 CB TYR A 299 6.167 22.607 20.046 1.00 8.12 C") + >>> for c in atom.iter_coordinates(): + ... print(c) + ... + 6.167 + 22.607 + 20.046 + """ + for coord in self.position: + yield coord + + # Hide existence of multiple alternate locations to avoid scaring casual users + def get_location(self, location_id=None): + id = location_id + if (id == None): + id = self.default_location_id + return self.locations[id] + def set_location(self, new_location, location_id=None): + id = location_id + if (id == None): + id = self.default_location_id + self.locations[id] = new_location + location = property(get_location, set_location, doc='default Atom.Location object') + + def get_position(self): + return self.location.position + def set_position(self, coords): + self.location.position = coords + position = property(get_position, set_position, doc='orthogonal coordinates') + + def get_alternate_location_indicator(self): + return self.location.alternate_location_indicator + alternate_location_indicator = property(get_alternate_location_indicator) + + def get_occupancy(self): + return self.location.occupancy + occupancy = property(get_occupancy) + + def get_temperature_factor(self): + return self.location.temperature_factor + temperature_factor = property(get_temperature_factor) + + def get_x(self): return self.position[0] + x = property(get_x) + + def get_y(self): return self.position[1] + y = property(get_y) + + def get_z(self): return self.position[2] + z = property(get_z) + + def _pdb_string(self, serial_number=None, alternate_location_indicator=None): + """ + Produce a PDB line for this atom using a particular serial number and alternate location + """ + if serial_number == None: + serial_number = self.serial_number + if alternate_location_indicator == None: + alternate_location_indicator = self.alternate_location_indicator + # produce PDB line in three parts: names, numbers, and end + # Accomodate 4-character residue names that use column 21 + long_res_name = self.residue_name_with_spaces + if len(long_res_name) == 3: + long_res_name += " " + assert len(long_res_name) == 4 + names = "%-6s%5d %4s%1s%4s%1s%4d%1s " % ( + self.record_name, serial_number, \ + self.name_with_spaces, alternate_location_indicator, \ + long_res_name, self.chain_id, \ + self.residue_number, self.insertion_code) + numbers = "%8.3f%8.3f%8.3f%6.2f%6.2f " % ( + self.x, self.y, self.z, self.occupancy, self.temperature_factor) + end = "%-4s%2s" % (\ + self.segment_id, self.element_symbol) + formal_charge = " " + if (self.formal_charge != None): formal_charge = "%+2d" % self.formal_charge + return names+numbers+end+formal_charge + + def __str__(self): + return self._pdb_string(self.serial_number, self.alternate_location_indicator) + + def write(self, next_serial_number, output_stream=sys.stdout, alt_loc = "*"): + """ + alt_loc = "*" means write all alternate locations + alt_loc = None means write just the primary location + alt_loc = "AB" means write locations "A" and "B" + """ + if alt_loc == None: + locs = [self.default_location_id] + elif alt_loc == "": + locs = [self.default_location_id] + elif alt_loc == "*": + locs = self.locations.keys() + locs.sort() + else: + locs = list(alt_loc) + for loc_id in locs: + print(self._pdb_string(next_serial_number.val, loc_id), file=output_stream) + next_serial_number.increment() + + def set_name_with_spaces(self, name): + assert len(name) == 4 + self._name_with_spaces = name + self._name = name.strip() + def get_name_with_spaces(self): + return self._name_with_spaces + name_with_spaces = property(get_name_with_spaces, set_name_with_spaces, doc='four-character residue name including spaces') + + def get_name(self): + return self._name + name = property(get_name, doc='residue name') + + class Location(object): + """ + Inner class of Atom for holding alternate locations + """ + def __init__(self, alt_loc, position, occupancy, temperature_factor, residue_name): + self.alternate_location_indicator = alt_loc + self.position = position + self.occupancy = occupancy + self.temperature_factor = temperature_factor + self.residue_name = residue_name + + def __iter__(self): + """ + Examples + + >>> l = Atom.Location(' ', [1,2,3], 1.0, 20.0, "XXX") + >>> for c in l: + ... print(c) + ... + 1 + 2 + 3 + """ + for coord in self.position: + yield coord + + def __str__(self): + return str(self.position) + diff --git a/MDTraj/pdb/test_pdb.py b/MDTraj/pdb/test_pdb.py index 169e09e3d..ccdb9dae8 100644 --- a/MDTraj/pdb/test_pdb.py +++ b/MDTraj/pdb/test_pdb.py @@ -1,18 +1,25 @@ -# Copyright 2012 mdtraj developers +############################################################################## +# MDTraj: A Python Library for Loading, Saving, and Manipulating +# Molecular Dynamics Trajectories. +# Copyright 2012-2013 Stanford University and the Authors # -# This file is part of mdtraj +# Authors: Robert McGibbon +# Contributors: # -# mdtraj is free software: you can redistribute it and/or modify it under the -# terms of the GNU General Public License as published by the Free Software -# Foundation, either version 3 of the License, or (at your option) any later -# version. +# MDTraj is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as +# published by the Free Software Foundation, either version 2.1 +# of the License, or (at your option) any later version. # -# mdtraj is distributed in the hope that it will be useful, but WITHOUT ANY -# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR -# A PARTICULAR PURPOSE. See the GNU General Public License for more details. +# This library is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU Lesser General Public License for more details. # -# You should have received a copy of the GNU General Public License along with -# mdtraj. If not, see http://www.gnu.org/licenses/. +# You should have received a copy of the GNU Lesser General Public +# License along with Foobar. If not, see . +############################################################################## + from __future__ import print_function, division import numpy as np diff --git a/MDTraj/reporters/basereporter.py b/MDTraj/reporters/basereporter.py index e5a6e4050..c75cb7b88 100644 --- a/MDTraj/reporters/basereporter.py +++ b/MDTraj/reporters/basereporter.py @@ -1,18 +1,25 @@ -# Copyright 2013 mdtraj developers +############################################################################## +# MDTraj: A Python Library for Loading, Saving, and Manipulating +# Molecular Dynamics Trajectories. +# Copyright 2012-2013 Stanford University and the Authors # -# This file is part of mdtraj +# Authors: Robert McGibbon +# Contributors: # -# mdtraj is free software: you can redistribute it and/or modify it under the -# terms of the GNU General Public License as published by the Free Software -# Foundation, either version 3 of the License, or (at your option) any later -# version. +# MDTraj is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as +# published by the Free Software Foundation, either version 2.1 +# of the License, or (at your option) any later version. # -# mdtraj is distributed in the hope that it will be useful, but WITHOUT ANY -# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR -# A PARTICULAR PURPOSE. See the GNU General Public License for more details. +# This library is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU Lesser General Public License for more details. # -# You should have received a copy of the GNU General Public License along with -# mdtraj. If not, see http://www.gnu.org/licenses/. +# You should have received a copy of the GNU Lesser General Public +# License along with Foobar. If not, see . +############################################################################## + ############################################################################## # Imports diff --git a/MDTraj/reporters/dcdreporter.py b/MDTraj/reporters/dcdreporter.py index bb93068ca..5a214e603 100644 --- a/MDTraj/reporters/dcdreporter.py +++ b/MDTraj/reporters/dcdreporter.py @@ -1,18 +1,25 @@ -# Copyright 2013 mdtraj developers +############################################################################## +# MDTraj: A Python Library for Loading, Saving, and Manipulating +# Molecular Dynamics Trajectories. +# Copyright 2012-2013 Stanford University and the Authors # -# This file is part of mdtraj +# Authors: Robert McGibbon +# Contributors: # -# mdtraj is free software: you can redistribute it and/or modify it under the -# terms of the GNU General Public License as published by the Free Software -# Foundation, either version 3 of the License, or (at your option) any later -# version. +# MDTraj is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as +# published by the Free Software Foundation, either version 2.1 +# of the License, or (at your option) any later version. # -# mdtraj is distributed in the hope that it will be useful, but WITHOUT ANY -# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR -# A PARTICULAR PURPOSE. See the GNU General Public License for more details. +# This library is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU Lesser General Public License for more details. # -# You should have received a copy of the GNU General Public License along with -# mdtraj. If not, see http://www.gnu.org/licenses/. +# You should have received a copy of the GNU Lesser General Public +# License along with Foobar. If not, see . +############################################################################## + """OpenMM Reporter for saving the state of a molecular dynamics simulation through time in the AMBER NetCDF format """ diff --git a/MDTraj/reporters/hdf5reporter.py b/MDTraj/reporters/hdf5reporter.py index 78728580a..01311a496 100644 --- a/MDTraj/reporters/hdf5reporter.py +++ b/MDTraj/reporters/hdf5reporter.py @@ -1,18 +1,25 @@ -# Copyright 2013 mdtraj developers +############################################################################## +# MDTraj: A Python Library for Loading, Saving, and Manipulating +# Molecular Dynamics Trajectories. +# Copyright 2012-2013 Stanford University and the Authors # -# This file is part of mdtraj +# Authors: Robert McGibbon +# Contributors: # -# mdtraj is free software: you can redistribute it and/or modify it under the -# terms of the GNU General Public License as published by the Free Software -# Foundation, either version 3 of the License, or (at your option) any later -# version. +# MDTraj is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as +# published by the Free Software Foundation, either version 2.1 +# of the License, or (at your option) any later version. # -# mdtraj is distributed in the hope that it will be useful, but WITHOUT ANY -# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR -# A PARTICULAR PURPOSE. See the GNU General Public License for more details. +# This library is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU Lesser General Public License for more details. # -# You should have received a copy of the GNU General Public License along with -# mdtraj. If not, see http://www.gnu.org/licenses/. +# You should have received a copy of the GNU Lesser General Public +# License along with Foobar. If not, see . +############################################################################## + """OpenMM Reporter for saving the positions of a molecular dynamics simulation in the HDF5 format. """ @@ -81,7 +88,7 @@ class HDF5Reporter(_BaseReporter): """ @property def backend(self): - return HDF5TrajectoryFile + return HDF5TrajectoryFile def __init__(self, file, reportInterval, coordinates=True, time=True, cell=True, potentialEnergy=True, kineticEnergy=True, diff --git a/MDTraj/reporters/netcdfreporter.py b/MDTraj/reporters/netcdfreporter.py index efe23c337..2f4985339 100644 --- a/MDTraj/reporters/netcdfreporter.py +++ b/MDTraj/reporters/netcdfreporter.py @@ -1,18 +1,25 @@ -# Copyright 2013 mdtraj developers +############################################################################## +# MDTraj: A Python Library for Loading, Saving, and Manipulating +# Molecular Dynamics Trajectories. +# Copyright 2012-2013 Stanford University and the Authors # -# This file is part of mdtraj +# Authors: Robert McGibbon +# Contributors: # -# mdtraj is free software: you can redistribute it and/or modify it under the -# terms of the GNU General Public License as published by the Free Software -# Foundation, either version 3 of the License, or (at your option) any later -# version. +# MDTraj is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as +# published by the Free Software Foundation, either version 2.1 +# of the License, or (at your option) any later version. # -# mdtraj is distributed in the hope that it will be useful, but WITHOUT ANY -# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR -# A PARTICULAR PURPOSE. See the GNU General Public License for more details. +# This library is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU Lesser General Public License for more details. # -# You should have received a copy of the GNU General Public License along with -# mdtraj. If not, see http://www.gnu.org/licenses/. +# You should have received a copy of the GNU Lesser General Public +# License along with Foobar. If not, see . +############################################################################## + """OpenMM Reporter for saving the state of a molecular dynamics simulation through time in the AMBER NetCDF format """ diff --git a/MDTraj/rmsd.py b/MDTraj/rmsd.py index 28fb9182e..b8205b01f 100644 --- a/MDTraj/rmsd.py +++ b/MDTraj/rmsd.py @@ -1,21 +1,24 @@ -# Copyright 2012-present mdtraj developers +############################################################################## +# MDTraj: A Python Library for Loading, Saving, and Manipulating +# Molecular Dynamics Trajectories. +# Copyright 2012-2013 Stanford University and the Authors # -# This file is part of mdtraj +# Authors: Imran S. Haque +# Contributors: Robert McGibbon # -# mdtraj is free software: you can redistribute it and/or modify it under the -# terms of the GNU General Public License as published by the Free Software -# Foundation, either version 3 of the License, or (at your option) any later -# version. +# MDTraj is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as +# published by the Free Software Foundation, either version 2.1 +# of the License, or (at your option) any later version. # -# mdtraj is distributed in the hope that it will be useful, but WITHOUT ANY -# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR -# A PARTICULAR PURPOSE. See the GNU General Public License for more details. +# This library is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU Lesser General Public License for more details. # -# You should have received a copy of the GNU General Public License along with -# mdtraj. If not, see http://www.gnu.org/licenses/. - -# This code was written by Imran S. Haque, with some contributes by -# Robert McGibbon +# You should have received a copy of the GNU Lesser General Public +# License along with Foobar. If not, see . +############################################################################## ############################################################################## diff --git a/MDTraj/rmsd/_rmsd.pyx b/MDTraj/rmsd/_rmsd.pyx index 23107b219..cb6373587 100644 --- a/MDTraj/rmsd/_rmsd.pyx +++ b/MDTraj/rmsd/_rmsd.pyx @@ -1,18 +1,25 @@ -# Copyright 2012-present mdtraj developers +############################################################################## +# MDTraj: A Python Library for Loading, Saving, and Manipulating +# Molecular Dynamics Trajectories. +# Copyright 2012-2013 Stanford University and the Authors # -# This file is part of mdtraj +# Authors: Robert McGibbon +# Contributors: # -# mdtraj is free software: you can redistribute it and/or modify it under the -# terms of the GNU General Public License as published by the Free Software -# Foundation, either version 3 of the License, or (at your option) any later -# version. +# MDTraj is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as +# published by the Free Software Foundation, either version 2.1 +# of the License, or (at your option) any later version. # -# mdtraj is distributed in the hope that it will be useful, but WITHOUT ANY -# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR -# A PARTICULAR PURPOSE. See the GNU General Public License for more details. +# This library is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU Lesser General Public License for more details. # -# You should have received a copy of the GNU General Public License along with -# mdtraj. If not, see http://www.gnu.org/licenses/. +# You should have received a copy of the GNU Lesser General Public +# License along with Foobar. If not, see . +############################################################################## + # This code was written by Kyle Beauchamp with some contributes by # Robert McGibbon diff --git a/MDTraj/rmsd/include/util.h b/MDTraj/rmsd/include/util.h index 30ad1a6a8..58794a259 100644 --- a/MDTraj/rmsd/include/util.h +++ b/MDTraj/rmsd/include/util.h @@ -1,6 +1,6 @@ #ifndef __UTIL_H__ #define __UTIL_H__ -/* +/* Utility functions for IRMSD matrix multiply routines. Common intrinsic subroutines shared among files. @@ -20,7 +20,7 @@ static INLINE void aos_deinterleaved_load(const float* S, __m128* x, __m128* y, t1 = _mm_load_ps(S+8); *z = *x; t2 = *y; - + t2 = _mm_shuffle_ps_yzyz(t2,t1); *z = _mm_shuffle_ps_yzxw(*z,t2); *x = _mm_shuffle_ps_xwyz(*x,t2); @@ -42,7 +42,7 @@ static INLINE void aos_deinterleaved_load(const float* S, __m128* x, __m128* y, xmm13 = zx0 zx1 zx2 zx3 xmm14 = zy0 zy1 zy2 zy3 xmm15 = zz0 zz1 zz2 zz3 - + haddps xmm07 xmm08 xmm07 = xx0+1 xx2+3 xy0+1 xy2+3 haddps xmm09 xmm10 @@ -53,14 +53,14 @@ static INLINE void aos_deinterleaved_load(const float* S, __m128* x, __m128* y, xmm13 = zx0+1 zx2+3 zy0+1 zy2+3 haddps xmm15 xmm14 xmm15 = zz0+1 zz2+3 zy0+1 zy2+3 - + haddps xmm07 xmm09 xmm07 = xx0123 xy0123 xz0123 yx0123 haddps xmm11 xmm13 xmm11 = yy0123 yz0123 zx0123 zy0123 haddps xmm15 xmm09 xmm15 = zz0123 zy0123 xz0123 yx0123 -*/ +*/ #define REDUCTION_EPILOGUE(xx, xy, xz, yx, yy, yz, zx, zy, zz, t0, t1, t2) \ xx = _mm_hadd_ps(xx,xy); /* xx = xx01 xx23 xy01 xy23 */\ xz = _mm_hadd_ps(xz,yx); /* xz = xz01 xz23 yx01 yx23 */\ diff --git a/MDTraj/rmsd/src/theobald_rmsd.c b/MDTraj/rmsd/src/theobald_rmsd.c index 0d64b9627..1f9a1ccb8 100644 --- a/MDTraj/rmsd/src/theobald_rmsd.c +++ b/MDTraj/rmsd/src/theobald_rmsd.c @@ -1,33 +1,36 @@ -// Copyright 2011 Stanford University +///////////////////////////////////////////////////////////////////////////// +// MDTraj: A Python Library for Loading, Saving, and Manipulating +// Molecular Dynamics Trajectories. +// Copyright 2012-2013 Stanford University and the Authors // -// IRMSD is free software; you can redistribute it and/or modify -// it under the terms of the GNU General Public License as published by -// the Free Software Foundation; either version 2 of the License, or -// (at your option) any later version. +// Authors: Imran S. Haque +// Contributors: John D. Chodera, Kyle Beauchamp, Peter Kasson, +// Kai Kohlhoff, Jonathan Zrake, Robert McGibbon // -// This program is distributed in the hope that it will be useful, +// MDTraj is free software: you can redistribute it and/or modify +// it under the terms of the GNU Lesser General Public License as +// published by the Free Software Foundation, either version 2.1 +// of the License, or (at your option) any later version. +// +// This library is distributed in the hope that it will be useful, // but WITHOUT ANY WARRANTY; without even the implied warranty of // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -// GNU General Public License for more details. +// GNU Lesser General Public License for more details. // -// You should have received a copy of the GNU General Public License -// along with this program; if not, write to the Free Software -// Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +// You should have received a copy of the GNU Lesser General Public +// License along with Foobar. If not, see . +/////////////////////////////////////////////////////////////////////////////// + +/////////////////////////////////////////////////////////////////////////////// +// Calculation of RMSD by a the quaternion-based characteristic polynomial +// (QCP) algorithm of Theobald [1]. // -//============================================================================================= -// Calculation of RMSD by a the quaternion-based characteristic polynomial (QCP) algorithm of Theobald [1]. -// -// [1] Theobald DL. Rapid calculation of RMSDs using a quaternion-based characteristic polynomial. -// Acta Cryst., A61:478, 2005. doi:10.1107/50108767305015266 -// -// Contributions from: -// John D. Chodera , Dill lab, UCSF, 2006. -// Kyle Beauchamp(kyleb AT stanford.edu) -// Peter Kasson (kasson AT stanford.edu) -// Kai Kohlhoff (kohlhoff AT stanford.edu) -// Imran Haque (ihaque AT cs.stanford.edu) -//============================================================================================= +// [1] Theobald DL. Rapid calculation of RMSDs using a quaternion-based +// characteristic polynomial. Acta Cryst., A61:478, 2005. +// doi:10.1107/50108767305015266 +/////////////////////////////////////////////////////////////////////////////// + #include "msvccompat.h" #include @@ -184,12 +187,12 @@ float DirectSolve(float lambda, float C_0, float C_1, float C_2) result=max(r1,r2); result=max(result,r3); result=max(result,r4); - + return (float) result; } float NewtonSolve(float lambda, float C_0, float C_1, float C_2) -{ +{ unsigned int i; unsigned int maxits = 500; float tolerance = 1.0e-6f; @@ -197,7 +200,7 @@ float NewtonSolve(float lambda, float C_0, float C_1, float C_2) float a,b; for (i = 0; i < maxits; i++) - { + { lambda_old = lambda; lambda2 = lambda_old * lambda_old; b = (lambda2 + C_2) * lambda_old; @@ -205,15 +208,15 @@ float NewtonSolve(float lambda, float C_0, float C_1, float C_2) lambda = lambda_old - (a * lambda_old + C_0) / (2.0f * lambda2 * lambda_old + b + a); if (fabsf(lambda - lambda_old) < fabsf(tolerance * lambda)) break; } - if (fabsf(lambda - lambda_old) >= fabsf(100*tolerance * lambda)) + if (fabsf(lambda - lambda_old) >= fabsf(100*tolerance * lambda)) { printf("RMSD Warning: No convergence after %d iterations: Lambda,Lambda0,Diff,Allowed = %f, %f, %f, %f \n",maxits,lambda, lambda_old, fabsf(lambda - lambda_old), fabsf(tolerance * lambda) ); } - + return(lambda); } -float msdFromMandG(const float M[9],const float G_x,const float G_y,const int numAtoms) +float msdFromMandG(const float M[9],const float G_x,const float G_y,const int numAtoms) { int i; const int m = 3; diff --git a/MDTraj/testing/__init__.py b/MDTraj/testing/__init__.py index 02b0f96c3..a3773e15e 100644 --- a/MDTraj/testing/__init__.py +++ b/MDTraj/testing/__init__.py @@ -1,18 +1,25 @@ -# Copyright 2012 mdtraj developers +############################################################################## +# MDTraj: A Python Library for Loading, Saving, and Manipulating +# Molecular Dynamics Trajectories. +# Copyright 2012-2013 Stanford University and the Authors # -# This file is part of mdtraj +# Authors: Robert McGibbon +# Contributors: # -# mdtraj is free software: you can redistribute it and/or modify it under the -# terms of the GNU General Public License as published by the Free Software -# Foundation, either version 3 of the License, or (at your option) any later -# version. +# MDTraj is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as +# published by the Free Software Foundation, either version 2.1 +# of the License, or (at your option) any later version. # -# mdtraj is distributed in the hope that it will be useful, but WITHOUT ANY -# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR -# A PARTICULAR PURPOSE. See the GNU General Public License for more details. +# This library is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU Lesser General Public License for more details. # -# You should have received a copy of the GNU General Public License along with -# mdtraj. If not, see http://www.gnu.org/licenses/. +# You should have received a copy of the GNU Lesser General Public +# License along with Foobar. If not, see . +############################################################################## + from __future__ import print_function, division from .testing import * diff --git a/MDTraj/testing/docstrings.py b/MDTraj/testing/docstrings.py index d642a6447..132a0e393 100644 --- a/MDTraj/testing/docstrings.py +++ b/MDTraj/testing/docstrings.py @@ -1,18 +1,25 @@ -# Copyright 2012 mdtraj developers +############################################################################## +# MDTraj: A Python Library for Loading, Saving, and Manipulating +# Molecular Dynamics Trajectories. +# Copyright 2012-2013 Stanford University and the Authors # -# This file is part of mdtraj +# Authors: Robert McGibbon +# Contributors: # -# mdtraj is free software: you can redistribute it and/or modify it under the -# terms of the GNU General Public License as published by the Free Software -# Foundation, either version 3 of the License, or (at your option) any later -# version. +# MDTraj is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as +# published by the Free Software Foundation, either version 2.1 +# of the License, or (at your option) any later version. # -# mdtraj is distributed in the hope that it will be useful, but WITHOUT ANY -# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR -# A PARTICULAR PURPOSE. See the GNU General Public License for more details. +# This library is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU Lesser General Public License for more details. # -# You should have received a copy of the GNU General Public License along with -# mdtraj. If not, see http://www.gnu.org/licenses/ +# You should have received a copy of the GNU Lesser General Public +# License along with Foobar. If not, see . +############################################################################## + ############################################################################## # Imports diff --git a/MDTraj/testing/nosetester.py b/MDTraj/testing/nosetester.py index 08c024e69..6460feb2a 100644 --- a/MDTraj/testing/nosetester.py +++ b/MDTraj/testing/nosetester.py @@ -1,3 +1,25 @@ +############################################################################## +# MDTraj: A Python Library for Loading, Saving, and Manipulating +# Molecular Dynamics Trajectories. +# Copyright 2012-2013 Stanford University and the Authors +# +# Authors: Robert McGibbon +# Contributors: +# +# MDTraj is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as +# published by the Free Software Foundation, either version 2.1 +# of the License, or (at your option) any later version. +# +# This library is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with Foobar. If not, see . +############################################################################## + from __future__ import print_function, division import os import mdtraj @@ -16,7 +38,7 @@ def _show_system_info(self): print('tables hdf5 version %s' % tables.hdf5Version) except ImportError: print('tables is not installed') - + try: import netCDF4 print('netCDF4 version %s' % netCDF4.__version__) @@ -24,4 +46,4 @@ def _show_system_info(self): except ImportError: print('netCDF4 not installed') - + diff --git a/MDTraj/testing/testing.py b/MDTraj/testing/testing.py index 1d7cb6b29..b63c36860 100644 --- a/MDTraj/testing/testing.py +++ b/MDTraj/testing/testing.py @@ -1,18 +1,25 @@ -# Copyright 2012 mdtraj developers +############################################################################## +# MDTraj: A Python Library for Loading, Saving, and Manipulating +# Molecular Dynamics Trajectories. +# Copyright 2012-2013 Stanford University and the Authors # -# This file is part of mdtraj +# Authors: Robert McGibbon +# Contributors: Kyle A Beauchamp # -# mdtraj is free software: you can redistribute it and/or modify it under the -# terms of the GNU General Public License as published by the Free Software -# Foundation, either version 3 of the License, or (at your option) any later -# version. +# MDTraj is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as +# published by the Free Software Foundation, either version 2.1 +# of the License, or (at your option) any later version. # -# mdtraj is distributed in the hope that it will be useful, but WITHOUT ANY -# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR -# A PARTICULAR PURPOSE. See the GNU General Public License for more details. +# This library is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU Lesser General Public License for more details. # -# You should have received a copy of the GNU General Public License along with -# mdtraj. If not, see http://www.gnu.org/licenses/. +# You should have received a copy of the GNU Lesser General Public +# License along with Foobar. If not, see . +############################################################################## + ############################################################################## # imports diff --git a/MDTraj/tests/__init__.py b/MDTraj/tests/__init__.py index 4c643a4b9..e69de29bb 100644 --- a/MDTraj/tests/__init__.py +++ b/MDTraj/tests/__init__.py @@ -1,15 +0,0 @@ -# Copyright 2012 mdtraj developers -# -# This file is part of mdtraj -# -# mdtraj is free software: you can redistribute it and/or modify it under the -# terms of the GNU General Public License as published by the Free Software -# Foundation, either version 3 of the License, or (at your option) any later -# version. -# -# mdtraj is distributed in the hope that it will be useful, but WITHOUT ANY -# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR -# A PARTICULAR PURPOSE. See the GNU General Public License for more details. -# -# You should have received a copy of the GNU General Public License along with -# mdtraj. If not, see http://www.gnu.org/licenses/. diff --git a/MDTraj/tests/test_arc.py b/MDTraj/tests/test_arc.py index 90f78a101..f12a61b6f 100644 --- a/MDTraj/tests/test_arc.py +++ b/MDTraj/tests/test_arc.py @@ -1,18 +1,25 @@ -# Copyright 2012 mdtraj developers +############################################################################## +# MDTraj: A Python Library for Loading, Saving, and Manipulating +# Molecular Dynamics Trajectories. +# Copyright 2012-2013 Stanford University and the Authors # -# This file is part of mdtraj +# Authors: Lee-Ping Wang +# Contributors: Robert McGibbon # -# mdtraj is free software: you can redistribute it and/or modify it under the -# terms of the GNU General Public License as published by the Free Software -# Foundation, either version 3 of the License, or (at your option) any later -# version. +# MDTraj is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as +# published by the Free Software Foundation, either version 2.1 +# of the License, or (at your option) any later version. # -# mdtraj is distributed in the hope that it will be useful, but WITHOUT ANY -# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR -# A PARTICULAR PURPOSE. See the GNU General Public License for more details. +# This library is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU Lesser General Public License for more details. # -# You should have received a copy of the GNU General Public License along with -# mdtraj. If not, see http://www.gnu.org/licenses/. +# You should have received a copy of the GNU Lesser General Public +# License along with Foobar. If not, see . +############################################################################## + import tempfile, os import numpy as np diff --git a/MDTraj/tests/test_binpos.py b/MDTraj/tests/test_binpos.py index 4905d219b..53b088aad 100644 --- a/MDTraj/tests/test_binpos.py +++ b/MDTraj/tests/test_binpos.py @@ -1,18 +1,25 @@ -# Copyright 2012 mdtraj developers +############################################################################## +# MDTraj: A Python Library for Loading, Saving, and Manipulating +# Molecular Dynamics Trajectories. +# Copyright 2012-2013 Stanford University and the Authors # -# This file is part of mdtraj +# Authors: Robert McGibbon +# Contributors: # -# mdtraj is free software: you can redistribute it and/or modify it under the -# terms of the GNU General Public License as published by the Free Software -# Foundation, either version 3 of the License, or (at your option) any later -# version. +# MDTraj is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as +# published by the Free Software Foundation, either version 2.1 +# of the License, or (at your option) any later version. # -# mdtraj is distributed in the hope that it will be useful, but WITHOUT ANY -# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR -# A PARTICULAR PURPOSE. See the GNU General Public License for more details. +# This library is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU Lesser General Public License for more details. # -# You should have received a copy of the GNU General Public License along with -# mdtraj. If not, see http://www.gnu.org/licenses/. +# You should have received a copy of the GNU Lesser General Public +# License along with Foobar. If not, see . +############################################################################## + """ Test the cython binpos module @@ -127,4 +134,4 @@ def test_write_2(): xyz2 = BINPOSTrajectoryFile(temp).read() eq(xyz, xyz2) - + diff --git a/MDTraj/tests/test_compatibility.py b/MDTraj/tests/test_compatibility.py index 63f34e073..842f70b3b 100644 --- a/MDTraj/tests/test_compatibility.py +++ b/MDTraj/tests/test_compatibility.py @@ -1,3 +1,25 @@ +############################################################################## +# MDTraj: A Python Library for Loading, Saving, and Manipulating +# Molecular Dynamics Trajectories. +# Copyright 2012-2013 Stanford University and the Authors +# +# Authors: Robert McGibbon +# Contributors: Kyle A. Beauchamp +# +# MDTraj is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as +# published by the Free Software Foundation, either version 2.1 +# of the License, or (at your option) any later version. +# +# This library is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with Foobar. If not, see . +############################################################################## + import os from mdtraj import load @@ -31,7 +53,7 @@ def test_legacy_hdf2(): yield lambda: eq(t0.xyz, t2.xyz) yield lambda: eq(t0.xyz, t3.xyz[::10]) yield lambda: t0.topology == load(nat).topology - + def test_legacy_hdf3(): t0 = load(fn, frame=0) t1 = load(fn) @@ -46,7 +68,7 @@ def test_legacy_hdf4_save_and_load(): temp = tempfile.NamedTemporaryFile(suffix=".lh5") mdtraj.compatibility.save_legacy_hdf(t0, temp.name) - + t2 = load(temp.name) yield lambda: eq(t0.xyz, t2.xyz) diff --git a/MDTraj/tests/test_dcd.py b/MDTraj/tests/test_dcd.py index a3dc29765..444b6a53c 100644 --- a/MDTraj/tests/test_dcd.py +++ b/MDTraj/tests/test_dcd.py @@ -1,18 +1,27 @@ -# Copyright 2012 mdtraj developers +############################################################################## +# MDTraj: A Python Library for Loading, Saving, and Manipulating +# Molecular Dynamics Trajectories. +# Copyright 2012-2013 Stanford University and the Authors # -# This file is part of mdtraj +# Authors: Robert McGibbon +# Contributors: # -# mdtraj is free software: you can redistribute it and/or modify it under the -# terms of the GNU General Public License as published by the Free Software -# Foundation, either version 3 of the License, or (at your option) any later -# version. +# MDTraj is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as +# published by the Free Software Foundation, either version 2.1 +# of the License, or (at your option) any later version. # -# mdtraj is distributed in the hope that it will be useful, but WITHOUT ANY -# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR -# A PARTICULAR PURPOSE. See the GNU General Public License for more details. +# This library is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU Lesser General Public License for more details. # -# You should have received a copy of the GNU General Public License along with -# mdtraj. If not, see http://www.gnu.org/licenses/. +# You should have received a copy of the GNU Lesser General Public +# License along with Foobar. If not, see . +############################################################################## + + + """ Test the cython dcd module @@ -225,4 +234,4 @@ def test_write_closed(): f = DCDTrajectoryFile(fn_dcd, 'w') f.close() f.write(np.random.randn(10,3,3)) - + diff --git a/MDTraj/tests/test_hdf5.py b/MDTraj/tests/test_hdf5.py index 0279d639c..16baa878d 100644 --- a/MDTraj/tests/test_hdf5.py +++ b/MDTraj/tests/test_hdf5.py @@ -1,3 +1,25 @@ +############################################################################## +# MDTraj: A Python Library for Loading, Saving, and Manipulating +# Molecular Dynamics Trajectories. +# Copyright 2012-2013 Stanford University and the Authors +# +# Authors: Robert McGibbon +# Contributors: +# +# MDTraj is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as +# published by the Free Software Foundation, either version 2.1 +# of the License, or (at your option) any later version. +# +# This library is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with Foobar. If not, see . +############################################################################## + import numpy as np import tempfile import os diff --git a/MDTraj/tests/test_io.py b/MDTraj/tests/test_io.py index 6ebe8dbf6..89f68d3fa 100644 --- a/MDTraj/tests/test_io.py +++ b/MDTraj/tests/test_io.py @@ -1,11 +1,24 @@ -''' -Created on Nov 23, 2010 -author: gbowman - -Adapted for msmbuilder.io by Robert McGibbon -September 15, 2012 -''' - +############################################################################## +# MDTraj: A Python Library for Loading, Saving, and Manipulating +# Molecular Dynamics Trajectories. +# Copyright 2012-2013 Stanford University and the Authors +# +# Authors: Gregory Bowman +# Contributors: Robert McGibbon +# +# MDTraj is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as +# published by the Free Software Foundation, either version 2.1 +# of the License, or (at your option) any later version. +# +# This library is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with Foobar. If not, see . +############################################################################## import os import os.path diff --git a/MDTraj/tests/test_mdconvert.py b/MDTraj/tests/test_mdconvert.py index 305df559f..2e864430b 100644 --- a/MDTraj/tests/test_mdconvert.py +++ b/MDTraj/tests/test_mdconvert.py @@ -1,18 +1,25 @@ -# Copyright 2013-present mdtraj developers +############################################################################## +# MDTraj: A Python Library for Loading, Saving, and Manipulating +# Molecular Dynamics Trajectories. +# Copyright 2012-2013 Stanford University and the Authors # -# This file is part of mdtraj +# Authors: Robert McGibbon +# Contributors: # -# mdtraj is free software: you can redistribute it and/or modify it under the -# terms of the GNU General Public License as published by the Free Software -# Foundation, either version 3 of the License, or (at your option) any later -# version. +# MDTraj is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as +# published by the Free Software Foundation, either version 2.1 +# of the License, or (at your option) any later version. # -# mdtraj is distributed in the hope that it will be useful, but WITHOUT ANY -# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR -# A PARTICULAR PURPOSE. See the GNU General Public License for more details. +# This library is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU Lesser General Public License for more details. # -# You should have received a copy of the GNU General Public License along with -# mdtraj. If not, see http://www.gnu.org/licenses/. +# You should have received a copy of the GNU Lesser General Public +# License along with Foobar. If not, see . +############################################################################## + """ Code to test the mdconvert script. These tests take about two minutes to run. diff --git a/MDTraj/tests/test_mdcrd.py b/MDTraj/tests/test_mdcrd.py index 73a96898f..c903ff84b 100644 --- a/MDTraj/tests/test_mdcrd.py +++ b/MDTraj/tests/test_mdcrd.py @@ -1,18 +1,25 @@ -# Copyright 2012 mdtraj developers +############################################################################## +# MDTraj: A Python Library for Loading, Saving, and Manipulating +# Molecular Dynamics Trajectories. +# Copyright 2012-2013 Stanford University and the Authors # -# This file is part of mdtraj +# Authors: Robert McGibbon +# Contributors: # -# mdtraj is free software: you can redistribute it and/or modify it under the -# terms of the GNU General Public License as published by the Free Software -# Foundation, either version 3 of the License, or (at your option) any later -# version. +# MDTraj is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as +# published by the Free Software Foundation, either version 2.1 +# of the License, or (at your option) any later version. # -# mdtraj is distributed in the hope that it will be useful, but WITHOUT ANY -# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR -# A PARTICULAR PURPOSE. See the GNU General Public License for more details. +# This library is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU Lesser General Public License for more details. # -# You should have received a copy of the GNU General Public License along with -# mdtraj. If not, see http://www.gnu.org/licenses/. +# You should have received a copy of the GNU Lesser General Public +# License along with Foobar. If not, see . +############################################################################## + import tempfile, os import numpy as np diff --git a/MDTraj/tests/test_netcdf.py b/MDTraj/tests/test_netcdf.py index 3bad20731..d2ea02136 100644 --- a/MDTraj/tests/test_netcdf.py +++ b/MDTraj/tests/test_netcdf.py @@ -1,18 +1,25 @@ -# Copyright 2012 mdtraj developers +############################################################################## +# MDTraj: A Python Library for Loading, Saving, and Manipulating +# Molecular Dynamics Trajectories. +# Copyright 2012-2013 Stanford University and the Authors # -# This file is part of mdtraj +# Authors: Robert McGibbon +# Contributors: # -# mdtraj is free software: you can redistribute it and/or modify it under the -# terms of the GNU General Public License as published by the Free Software -# Foundation, either version 3 of the License, or (at your option) any later -# version. +# MDTraj is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as +# published by the Free Software Foundation, either version 2.1 +# of the License, or (at your option) any later version. # -# mdtraj is distributed in the hope that it will be useful, but WITHOUT ANY -# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR -# A PARTICULAR PURPOSE. See the GNU General Public License for more details. +# This library is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU Lesser General Public License for more details. # -# You should have received a copy of the GNU General Public License along with -# mdtraj. If not, see http://www.gnu.org/licenses/. +# You should have received a copy of the GNU Lesser General Public +# License along with Foobar. If not, see . +############################################################################## + """ Tests for the AMBER netcdf reader/writer code @@ -165,7 +172,7 @@ def test_n_atoms(): f.write(np.random.randn(1,11,3)) with NetCDFTrajectoryFile(temp) as f: eq(f.n_atoms, 11) - + def test_do_overwrite(): with open(temp, 'w') as f: @@ -190,6 +197,6 @@ def test_trajectory_save_load(): t.save(temp) t2 = md.load(temp, top=t.topology) - + eq(t.xyz, t2.xyz) eq(t.unitcell_lengths, t2.unitcell_lengths) diff --git a/MDTraj/tests/test_reporter.py b/MDTraj/tests/test_reporter.py index 3462c112a..5e67f63ea 100644 --- a/MDTraj/tests/test_reporter.py +++ b/MDTraj/tests/test_reporter.py @@ -1,18 +1,25 @@ -# Copyright 2012 mdtraj developers +############################################################################## +# MDTraj: A Python Library for Loading, Saving, and Manipulating +# Molecular Dynamics Trajectories. +# Copyright 2012-2013 Stanford University and the Authors # -# This file is part of mdtraj +# Authors: Robert McGibbon +# Contributors: # -# mdtraj is free software: you can redistribute it and/or modify it under the -# terms of the GNU General Public License as published by the Free Software -# Foundation, either version 3 of the License, or (at your option) any later -# version. +# MDTraj is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as +# published by the Free Software Foundation, either version 2.1 +# of the License, or (at your option) any later version. # -# mdtraj is distributed in the hope that it will be useful, but WITHOUT ANY -# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR -# A PARTICULAR PURPOSE. See the GNU General Public License for more details. +# This library is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU Lesser General Public License for more details. # -# You should have received a copy of the GNU General Public License along with -# mdtraj. If not, see http://www.gnu.org/licenses/. +# You should have received a copy of the GNU Lesser General Public +# License along with Foobar. If not, see . +############################################################################## + from __future__ import print_function import os import shutil @@ -48,7 +55,7 @@ def test_reporter(): tempdir = os.path.join(dir, 'test1') os.makedirs(tempdir) - pdb = PDBFile(get_fn('native.pdb')) + pdb = PDBFile(get_fn('native.pdb')) forcefield = ForceField('amber99sbildn.xml', 'amber99_obc.xml') system = forcefield.createSystem(pdb.topology, nonbondedMethod=CutoffNonPeriodic, nonbondedCutoff=1.0*nanometers, constraints=HBonds, rigidWater=True) @@ -102,7 +109,7 @@ def test_reporter(): hdf5_traj = md.load(hdf5file) dcd_traj = md.load(dcdfile, top=get_fn('native.pdb')) netcdf_traj = md.load(ncfile, top=get_fn('native.pdb')) - + # we don't have to convert units here, because md.load already # handles that yield lambda: eq(hdf5_traj.xyz, netcdf_traj.xyz) @@ -178,7 +185,7 @@ def test_reporter_subset(): hdf5_traj = md.load(hdf5file) dcd_traj = md.load(dcdfile, top=hdf5_traj) netcdf_traj = md.load(ncfile, top=hdf5_traj) - + # we don't have to convert units here, because md.load already handles # that yield lambda: eq(hdf5_traj.xyz, netcdf_traj.xyz) diff --git a/MDTraj/tests/test_rmsd.py b/MDTraj/tests/test_rmsd.py index 82dc2ff92..58b501c58 100644 --- a/MDTraj/tests/test_rmsd.py +++ b/MDTraj/tests/test_rmsd.py @@ -1,18 +1,25 @@ -# Copyright 2013-present mdtraj developers +############################################################################## +# MDTraj: A Python Library for Loading, Saving, and Manipulating +# Molecular Dynamics Trajectories. +# Copyright 2012-2013 Stanford University and the Authors # -# This file is part of mdtraj +# Authors: Robert McGibbon +# Contributors: # -# mdtraj is free software: you can redistribute it and/or modify it under the -# terms of the GNU General Public License as published by the Free Software -# Foundation, either version 3 of the License, or (at your option) any later -# version. +# MDTraj is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as +# published by the Free Software Foundation, either version 2.1 +# of the License, or (at your option) any later version. # -# mdtraj is distributed in the hope that it will be useful, but WITHOUT ANY -# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR -# A PARTICULAR PURPOSE. See the GNU General Public License for more details. +# This library is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU Lesser General Public License for more details. # -# You should have received a copy of the GNU General Public License along with -# mdtraj. If not, see http://www.gnu.org/licenses/. +# You should have received a copy of the GNU Lesser General Public +# License along with Foobar. If not, see . +############################################################################## + import numpy as np diff --git a/MDTraj/tests/test_topology.py b/MDTraj/tests/test_topology.py index ead315f3a..6c65a06c0 100644 --- a/MDTraj/tests/test_topology.py +++ b/MDTraj/tests/test_topology.py @@ -1,3 +1,25 @@ +############################################################################## +# MDTraj: A Python Library for Loading, Saving, and Manipulating +# Molecular Dynamics Trajectories. +# Copyright 2012-2013 Stanford University and the Authors +# +# Authors: Kyle A. Beauchamp +# Contributors: Robert McGibbon +# +# MDTraj is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as +# published by the Free Software Foundation, either version 2.1 +# of the License, or (at your option) any later version. +# +# This library is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with Foobar. If not, see . +############################################################################## + import mdtraj as md from mdtraj.testing import get_fn, eq, DocStringFormatTester, skipif import numpy as np diff --git a/MDTraj/tests/test_trajectory.py b/MDTraj/tests/test_trajectory.py index cdce3a30e..8606edd8a 100644 --- a/MDTraj/tests/test_trajectory.py +++ b/MDTraj/tests/test_trajectory.py @@ -1,18 +1,25 @@ -# Copyright 2012 mdtraj developers +############################################################################## +# MDTraj: A Python Library for Loading, Saving, and Manipulating +# Molecular Dynamics Trajectories. +# Copyright 2012-2013 Stanford University and the Authors # -# This file is part of mdtraj +# Authors: Robert McGibbon +# Contributors: Kyle A Beauchamp # -# mdtraj is free software: you can redistribute it and/or modify it under the -# terms of the GNU General Public License as published by the Free Software -# Foundation, either version 3 of the License, or (at your option) any later -# version. +# MDTraj is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as +# published by the Free Software Foundation, either version 2.1 +# of the License, or (at your option) any later version. # -# mdtraj is distributed in the hope that it will be useful, but WITHOUT ANY -# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR -# A PARTICULAR PURPOSE. See the GNU General Public License for more details. +# This library is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU Lesser General Public License for more details. # -# You should have received a copy of the GNU General Public License along with -# mdtraj. If not, see http://www.gnu.org/licenses/. +# You should have received a copy of the GNU Lesser General Public +# License along with Foobar. If not, see . +############################################################################## + import tempfile, os from mdtraj.testing import get_fn, eq, DocStringFormatTester, assert_raises @@ -34,11 +41,8 @@ fd5, temp5 = tempfile.mkstemp(suffix='.h5') fd6, temp6 = tempfile.mkstemp(suffix='.pdb') fd7, temp7 = tempfile.mkstemp(suffix='.nc') -fd8, temp8 = tempfile.mkstemp(suffix='.lh5') - -for e in [fd1, fd2, fd3, fd4, fd5, fd6, fd7, fd8]: +for e in [fd1, fd2, fd3, fd4, fd5, fd6, fd7]: os.close(e) - def teardown_module(module): """remove the temporary file created by tests in this file this gets automatically called by nose""" @@ -173,14 +177,6 @@ def test_load(): yield lambda: eq(t3.n_frames, t2.n_frames) -def test_legacy_hdf_save(): - t = md.load(get_fn('traj.h5')) - t.save(temp8) - - t2 = md.load_legacy_hdf(temp8) - - eq(t.xyz, t2.xyz, decimal=3) - def test_hdf5_0(): t = md.load(get_fn('traj.h5')) t2 = md.load(get_fn('native.pdb')) @@ -200,10 +196,10 @@ def test_center(): mu = traj.xyz.mean(1) mu0 = np.zeros(mu.shape) eq(mu0, mu) - + for a in traj.top.atoms: a.element.mass = 1.0 # Set all masses equal so we can compare against unweighted result - + traj.center_coordinates(mass_weighted=True) mu2 = traj.xyz.mean(1) eq(mu0, mu2) diff --git a/MDTraj/tests/test_trr.py b/MDTraj/tests/test_trr.py index bbef9ca85..05c29ffeb 100644 --- a/MDTraj/tests/test_trr.py +++ b/MDTraj/tests/test_trr.py @@ -1,3 +1,25 @@ +############################################################################## +# MDTraj: A Python Library for Loading, Saving, and Manipulating +# Molecular Dynamics Trajectories. +# Copyright 2012-2013 Stanford University and the Authors +# +# Authors: Robert McGibbon +# Contributors: +# +# MDTraj is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as +# published by the Free Software Foundation, either version 2.1 +# of the License, or (at your option) any later version. +# +# This library is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with Foobar. If not, see . +############################################################################## + from mdtraj import trr, TRRTrajectoryFile import os, tempfile import numpy as np @@ -74,7 +96,7 @@ def test_15(): def test_read_atomindices_1(): with TRRTrajectoryFile(temp) as f: xyz, time, step, box, lambd = f.read() - + with TRRTrajectoryFile(temp) as f: xyz2, time2, step2, box2, lambd2 = f.read(atom_indices=[0,1,2]) yield lambda: eq(xyz[:, [0,1,2]], xyz2) @@ -86,7 +108,7 @@ def test_read_atomindices_1(): def test_read_atomindices_2(): with TRRTrajectoryFile(temp) as f: xyz, time, step, box, lambd = f.read() - + with TRRTrajectoryFile(temp) as f: xyz2, time2, step2, box2, lambd2 = f.read(atom_indices=slice(None, None, 2)) yield lambda: eq(xyz[:, ::2], xyz2) diff --git a/MDTraj/tests/test_xml.py b/MDTraj/tests/test_xml.py index 46fcc0849..40e26fa39 100644 --- a/MDTraj/tests/test_xml.py +++ b/MDTraj/tests/test_xml.py @@ -1,3 +1,25 @@ +############################################################################## +# MDTraj: A Python Library for Loading, Saving, and Manipulating +# Molecular Dynamics Trajectories. +# Copyright 2012-2013 Stanford University and the Authors +# +# Authors: Robert McGibbon +# Contributors: +# +# MDTraj is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as +# published by the Free Software Foundation, either version 2.1 +# of the License, or (at your option) any later version. +# +# This library is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with Foobar. If not, see . +############################################################################## + from mdtraj.testing import get_fn, eq from mdtraj.trajectory import load diff --git a/MDTraj/tests/test_xtc.py b/MDTraj/tests/test_xtc.py index 6fc35a789..1d9ef99d9 100644 --- a/MDTraj/tests/test_xtc.py +++ b/MDTraj/tests/test_xtc.py @@ -1,18 +1,25 @@ -# Copyright 2012 mdtraj developers +############################################################################## +# MDTraj: A Python Library for Loading, Saving, and Manipulating +# Molecular Dynamics Trajectories. +# Copyright 2012-2013 Stanford University and the Authors # -# This file is part of mdtraj +# Authors: Robert McGibbon +# Contributors: # -# mdtraj is free software: you can redistribute it and/or modify it under the -# terms of the GNU General Public License as published by the Free Software -# Foundation, either version 3 of the License, or (at your option) any later -# version. +# MDTraj is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as +# published by the Free Software Foundation, either version 2.1 +# of the License, or (at your option) any later version. # -# mdtraj is distributed in the hope that it will be useful, but WITHOUT ANY -# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR -# A PARTICULAR PURPOSE. See the GNU General Public License for more details. +# This library is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU Lesser General Public License for more details. # -# You should have received a copy of the GNU General Public License along with -# mdtraj. If not, see http://www.gnu.org/licenses/. +# You should have received a copy of the GNU Lesser General Public +# License along with Foobar. If not, see . +############################################################################## + """ Test the cython xtc module diff --git a/MDTraj/topology.py b/MDTraj/topology.py index 2299121e3..dc2436a00 100644 --- a/MDTraj/topology.py +++ b/MDTraj/topology.py @@ -1,27 +1,27 @@ -# Copyright 2012 the authors -# This file is part of mdtraj -# -# mdtraj is free software: you can redistribute it and/or modify it under the -# terms of the GNU General Public License as published by the Free Software -# Foundation, either version 3 of the License, or (at your option) any later -# version. +############################################################################## +# MDTraj: A Python Library for Loading, Saving, and Manipulating +# Molecular Dynamics Trajectories. +# Copyright 2012-2013 Stanford University and the Authors # -# mdtraj is distributed in the hope that it will be useful, but WITHOUT ANY -# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR -# A PARTICULAR PURPOSE. See the GNU General Public License for more details. +# Authors: Peter Eastman, Robert McGibbon +# Contributors: Kyle A. Beauchamp # -# You should have received a copy of the GNU General Public License along with -# mdtraj. If not, see http://www.gnu.org/licenses/. +# MDTraj is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as +# published by the Free Software Foundation, either version 2.1 +# of the License, or (at your option) any later version. # -# topology.py: Used for storing topological information about a system. +# This library is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU Lesser General Public License for more details. # -# This is part of the OpenMM molecular simulation toolkit originating from -# Simbios, the NIH National Center for Physics-Based Simulation of -# Biological Structures at Stanford, funded under the NIH Roadmap for -# Medical Research, grant U54 GM072970. See https://simtk.org. +# You should have received a copy of the GNU Lesser General Public +# License along with Foobar. If not, see . # -# Portions copyright (c) 2012 Stanford University and the Authors. -# Authors: Peter Eastman, Robert McGibbon +# Portions of this code originate from the OpenMM molecular simulation +# toolkit, copyright (c) 2012 Stanford University and Peter Eastman. Those +# portions are distributed under the following terms: # # Permission is hereby granted, free of charge, to any person obtaining a # copy of this software and associated documentation files (the "Software"), @@ -40,6 +40,8 @@ # DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR # OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE # USE OR OTHER DEALINGS IN THE SOFTWARE. +############################################################################## + ############################################################################## # Imports @@ -385,7 +387,7 @@ def from_dataframe(cls, atoms, bonds=None): if bonds is not None: for ai1, ai2 in bonds: out.add_bond(out.atom(ai1), out.atom(ai2)) - + out._numAtoms = out.n_atoms return out diff --git a/MDTraj/trajectory.py b/MDTraj/trajectory.py index af0c01f6c..b7e134c72 100644 --- a/MDTraj/trajectory.py +++ b/MDTraj/trajectory.py @@ -1,18 +1,25 @@ -# Copyright 2012 mdtraj developers +############################################################################## +# MDTraj: A Python Library for Loading, Saving, and Manipulating +# Molecular Dynamics Trajectories. +# Copyright 2012-2013 Stanford University and the Authors # -# This file is part of mdtraj +# Authors: Robert McGibbon +# Contributors: Kyle A. Beauchamp, TJ Lane, Joshua Adelman, Lee-Ping Wang # -# mdtraj is free software: you can redistribute it and/or modify it under the -# terms of the GNU General Public License as published by the Free Software -# Foundation, either version 3 of the License, or (at your option) any later -# version. +# MDTraj is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as +# published by the Free Software Foundation, either version 2.1 +# of the License, or (at your option) any later version. # -# mdtraj is distributed in the hope that it will be useful, but WITHOUT ANY -# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR -# A PARTICULAR PURPOSE. See the GNU General Public License for more details. +# This library is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU Lesser General Public License for more details. # -# You should have received a copy of the GNU General Public License along with -# mdtraj. If not, see http://www.gnu.org/licenses/. +# You should have received a copy of the GNU Lesser General Public +# License along with Foobar. If not, see . +############################################################################## + ############################################################################## # Imports @@ -32,13 +39,11 @@ from mdtraj.utils import unitcell, ensure_type from mdtraj.utils.six.moves import xrange from mdtraj.utils.six import PY3 -import mdtraj.compatibility - if PY3: basestring = str __all__ = ['Trajectory', 'load', 'load_pdb', 'load_xtc', 'load_trr', 'load_binpos', - 'load_dcd', 'load_netcdf', 'load_hdf5', 'load_netcdf', 'load_arc', 'load_xml', 'load_legacy_hdf'] + 'load_dcd', 'load_netcdf', 'load_hdf5', 'load_netcdf', 'load_arc', 'load_xml'] ############################################################################## # Globals @@ -173,7 +178,7 @@ def load(filename_or_filenames, discard_overlapping_frames=False, **kwargs): """ _assert_files_exist(filename_or_filenames) - + if "top" in kwargs: # If applicable, pre-loads the topology from PDB for major performance boost. kwargs["top"] = _parse_topology(kwargs["top"]) @@ -772,7 +777,6 @@ def load_netcdf(filename, top=None, stride=None, atom_indices=None): unitcell_angles=cell_angles) return trajectory -load_legacy_hdf = mdtraj.compatibility.load_legacy_hdf class Trajectory(object): """Container object for a molecular dynamics trajectory @@ -1127,7 +1131,7 @@ def join(self, other, check_topology=True, discard_overlapping_frames=False): x0 = self.xyz[-1] x1 = other.xyz[0] start_frame = 1 if np.linalg.norm(x1 - x0) < 1e-8 else 0 - else: + else: start_frame = 0 xyz = other.xyz[start_frame:] @@ -1363,7 +1367,6 @@ def save(self, filename, **kwargs): '.pdb': self.save_pdb, '.dcd': self.save_dcd, '.h5': self.save_hdf5, - ".lh5": self.save_legacy_hdf, '.binpos': self.save_binpos, '.nc': self.save_netcdf, '.crd': self.save_mdcrd, @@ -1396,17 +1399,6 @@ def save_hdf5(self, filename, force_overwrite=True): cell_lengths=self.unitcell_lengths) f.topology = self.topology - def save_legacy_hdf(self, filename): - """Saves an MDTraj Trajectory as an MSMB2 lh5 file. - - Parameters - ---------- - filename : str - String filename of HDF Trajectory file. - """ - print("Warning: Legacy (MSMBuilder2) HDF files ('.lh5') are deprecated and should be replaced with standard trajectory formats.") - mdtraj.compatibility.save_legacy_hdf(self, filename) - def save_pdb(self, filename, force_overwrite=True): """Save trajectory to RCSB PDB format @@ -1535,16 +1527,16 @@ def save_netcdf(self, filename, force_overwrite=True): def center_coordinates(self, mass_weighted=False): """Center each trajectory frame at the origin (0,0,0). - This method acts inplace on the trajectory. The centering can + This method acts inplace on the trajectory. The centering can be either uniformly weighted (mass_weighted=False) or weighted by - the mass of each atom (mass_weighted=True). + the mass of each atom (mass_weighted=True). Parameters ---------- mass_weighted : bool, optional (default = False) If True, weight atoms by mass when removing COM. - - + + """ if mass_weighted == True: masses = np.array([a.element.mass for a in self.top.atoms]) @@ -1601,9 +1593,9 @@ def _have_unitcell(self): '.h5': load_hdf5, '.crd': load_mdcrd, '.mdcrd': load_mdcrd, - '.lh5': mdtraj.compatibility.load_legacy_hdf, + #'.lh5': _load_legacy_hdf, '.binpos': load_binpos, '.ncdf': load_netcdf, '.nc': load_netcdf, - '.arc': load_arc, + '.arc': load_arc } diff --git a/MDTraj/utils/arrays.py b/MDTraj/utils/arrays.py index 1cf7d5773..1f5ef2140 100644 --- a/MDTraj/utils/arrays.py +++ b/MDTraj/utils/arrays.py @@ -1,18 +1,25 @@ -# Copyright 2013 mdtraj developers +############################################################################## +# MDTraj: A Python Library for Loading, Saving, and Manipulating +# Molecular Dynamics Trajectories. +# Copyright 2012-2013 Stanford University and the Authors # -# This file is part of mdtraj +# Authors: Robert McGibbon +# Contributors: # -# mdtraj is free software: you can redistribute it and/or modify it under the -# terms of the GNU General Public License as published by the Free Software -# Foundation, either version 3 of the License, or (at your option) any later -# version. +# MDTraj is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as +# published by the Free Software Foundation, either version 2.1 +# of the License, or (at your option) any later version. # -# mdtraj is distributed in the hope that it will be useful, but WITHOUT ANY -# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR -# A PARTICULAR PURPOSE. See the GNU General Public License for more details. +# This library is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU Lesser General Public License for more details. # -# You should have received a copy of the GNU General Public License along with -# mdtraj. If not, see http://www.gnu.org/licenses/. +# You should have received a copy of the GNU Lesser General Public +# License along with Foobar. If not, see . +############################################################################## + ############################################################################## # imports diff --git a/MDTraj/utils/delay_import.py b/MDTraj/utils/delay_import.py index 4aeec4016..df2a1e0ca 100644 --- a/MDTraj/utils/delay_import.py +++ b/MDTraj/utils/delay_import.py @@ -1,3 +1,25 @@ +############################################################################## +# MDTraj: A Python Library for Loading, Saving, and Manipulating +# Molecular Dynamics Trajectories. +# Copyright 2012-2013 Stanford University and the Authors +# +# Authors: Robert McGibbon +# Contributors: +# +# MDTraj is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as +# published by the Free Software Foundation, either version 2.1 +# of the License, or (at your option) any later version. +# +# This library is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with Foobar. If not, see . +############################################################################## + """ Code to delay the import of a moldule, and give a nice error message if the module is not installed. for dealing with dependencies. diff --git a/MDTraj/utils/ffi.py b/MDTraj/utils/ffi.py index 5872e232f..63f7d8a93 100644 --- a/MDTraj/utils/ffi.py +++ b/MDTraj/utils/ffi.py @@ -1,3 +1,25 @@ +############################################################################## +# MDTraj: A Python Library for Loading, Saving, and Manipulating +# Molecular Dynamics Trajectories. +# Copyright 2012-2013 Stanford University and the Authors +# +# Authors: Robert McGibbon +# Contributors: +# +# MDTraj is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as +# published by the Free Software Foundation, either version 2.1 +# of the License, or (at your option) any later version. +# +# This library is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with Foobar. If not, see . +############################################################################## + from __future__ import print_function, division from distutils.ccompiler import new_compiler try: @@ -34,7 +56,7 @@ def _delayed_init(self): casts = {} for code, names in iteritems(self.ctypes): - for name in names: + for name in names: casts[nptype_descr['%s%d' % (code, ffi.sizeof(name))]] = name + ' *' # casts is a dict that helps us cast numpy arrays, like # {np.float32 : 'float *', np.int32: 'int *'} diff --git a/MDTraj/utils/test.py b/MDTraj/utils/test.py index 020d9d1aa..749f78d39 100644 --- a/MDTraj/utils/test.py +++ b/MDTraj/utils/test.py @@ -1,3 +1,25 @@ +############################################################################## +# MDTraj: A Python Library for Loading, Saving, and Manipulating +# Molecular Dynamics Trajectories. +# Copyright 2012-2013 Stanford University and the Authors +# +# Authors: Robert McGibbon +# Contributors: +# +# MDTraj is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as +# published by the Free Software Foundation, either version 2.1 +# of the License, or (at your option) any later version. +# +# This library is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with Foobar. If not, see . +############################################################################## + """Tests for some of the utilities """ ############################################################################## diff --git a/MDTraj/utils/unit.py b/MDTraj/utils/unit.py index 5d6e209fa..8bea30469 100644 --- a/MDTraj/utils/unit.py +++ b/MDTraj/utils/unit.py @@ -1,3 +1,25 @@ +############################################################################## +# MDTraj: A Python Library for Loading, Saving, and Manipulating +# Molecular Dynamics Trajectories. +# Copyright 2012-2013 Stanford University and the Authors +# +# Authors: Robert McGibbon +# Contributors: +# +# MDTraj is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as +# published by the Free Software Foundation, either version 2.1 +# of the License, or (at your option) any later version. +# +# This library is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with Foobar. If not, see . +############################################################################## + """Automatic unit conversion using simtk.units behind the scenes. """ ############################################################################## diff --git a/MDTraj/utils/unitcell.py b/MDTraj/utils/unitcell.py index 23d3186ab..44d8d9ec1 100644 --- a/MDTraj/utils/unitcell.py +++ b/MDTraj/utils/unitcell.py @@ -1,7 +1,26 @@ ############################################################################## -# Imports +# MDTraj: A Python Library for Loading, Saving, and Manipulating +# Molecular Dynamics Trajectories. +# Copyright 2012-2013 Stanford University and the Authors +# +# Authors: Robert McGibbon +# Contributors: +# +# MDTraj is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as +# published by the Free Software Foundation, either version 2.1 +# of the License, or (at your option) any later version. +# +# This library is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with Foobar. If not, see . ############################################################################## + from __future__ import print_function, division import warnings import numpy as np diff --git a/MDTraj/xtc/trr.pyx b/MDTraj/xtc/trr.pyx index cbdd35307..9bd4b0420 100644 --- a/MDTraj/xtc/trr.pyx +++ b/MDTraj/xtc/trr.pyx @@ -1,19 +1,26 @@ # cython: c_string_type=str, c_string_encoding=ascii -# Copyright 2012 mdtraj developers +############################################################################## +# MDTraj: A Python Library for Loading, Saving, and Manipulating +# Molecular Dynamics Trajectories. +# Copyright 2012-2013 Stanford University and the Authors # -# This file is part of mdtraj +# Authors: Robert McGibbon +# Contributors: # -# mdtraj is free software: you can redistribute it and/or modify it under the -# terms of the GNU General Public License as published by the Free Software -# Foundation, either version 3 of the License, or (at your option) any later -# version. +# MDTraj is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as +# published by the Free Software Foundation, either version 2.1 +# of the License, or (at your option) any later version. # -# mdtraj is distributed in the hope that it will be useful, but WITHOUT ANY -# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR -# A PARTICULAR PURPOSE. See the GNU General Public License for more details. +# This library is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU Lesser General Public License for more details. # -# You should have received a copy of the GNU General Public License along with -# mdtraj. If not, see http://www.gnu.org/licenses/. +# You should have received a copy of the GNU Lesser General Public +# License along with Foobar. If not, see . +############################################################################## + # Copyright 2012 mdtraj developers # @@ -79,7 +86,7 @@ if sizeof(float) != sizeof(np.float32_t): cdef class TRRTrajectoryFile: """TRRTrajectoryFile(filename, mode='r', force_overwrite=True, **kwargs) - + Interface for reading and writing to a GROMACS TRR file. This is a file-like objec that supports both reading and writing. It also supports the context manager protocol, so you can use it @@ -88,7 +95,7 @@ cdef class TRRTrajectoryFile: The conventional units in the TRR file are nanometers and picoseconds. The format only supports saving coordinates, the time, the md step, and the unit cell parametrs (box vectors) - + Parameters ---------- filename : str @@ -191,7 +198,7 @@ cdef class TRRTrajectoryFile: def read(self, n_frames=None, stride=None, atom_indices=None): """read(n_frames=None, stride=None, atom_indices=None) - + Read data from a TRR file Parameters @@ -269,7 +276,7 @@ cdef class TRRTrajectoryFile: cdef int i = 0 cdef int status = _EXDROK cdef int n_atoms_to_read - + if atom_indices is None: n_atoms_to_read = self.n_atoms elif isinstance(atom_indices, slice): @@ -292,7 +299,7 @@ cdef class TRRTrajectoryFile: np.empty((n_frames), dtype=np.float32) cdef np.ndarray[ndim=3, dtype=np.float32_t, mode='c'] box = \ np.empty((n_frames, 3, 3), dtype=np.float32) - + # only used if atom_indices is given cdef np.ndarray[dtype=np.float32_t, ndim=2] framebuffer = np.zeros((self.n_atoms, 3), dtype=np.float32) @@ -306,7 +313,7 @@ cdef class TRRTrajectoryFile: status = trrlib.read_trr(self.fh, self.n_atoms, &step[i], &time[i], &lambd[i], &box[i,0,0], &framebuffer[0,0], NULL, NULL) xyz[i, :, :] = framebuffer[atom_indices, :] - + if status != _EXDRENDOFFILE and status != _EXDROK: raise RuntimeError('TRR read error: %s' % _EXDR_ERROR_MESSAGES.get(status, 'unknown')) i += 1 diff --git a/MDTraj/xtc/trrlib.pxd b/MDTraj/xtc/trrlib.pxd index fe0524a2e..02ba1e760 100644 --- a/MDTraj/xtc/trrlib.pxd +++ b/MDTraj/xtc/trrlib.pxd @@ -11,10 +11,10 @@ cdef extern from "include/xdrfile_trr.h": int read_trr_natoms(char *fn, int *natoms) # Read one frame of an open xtc file. If either of x, v, f, box are - # NULL the arrays will be read from the file but not used. + # NULL the arrays will be read from the file but not used. int read_trr(XDRFILE *xd, int natoms, int *step, float *t, float* lambd, float* box, float* x, float* v, float* f) - # Write a frame to xtc file + # Write a frame to xtc file int write_trr(XDRFILE *xd, int natoms, int step, float t, float lambd, float* box, float* x, float* v, float* f) diff --git a/MDTraj/xtc/xtc.pyx b/MDTraj/xtc/xtc.pyx index 864135adf..74da2ea7e 100644 --- a/MDTraj/xtc/xtc.pyx +++ b/MDTraj/xtc/xtc.pyx @@ -1,19 +1,26 @@ # cython: c_string_type=str, c_string_encoding=ascii -# Copyright 2012 mdtraj developers +############################################################################## +# MDTraj: A Python Library for Loading, Saving, and Manipulating +# Molecular Dynamics Trajectories. +# Copyright 2012-2013 Stanford University and the Authors # -# This file is part of mdtraj +# Authors: Robert McGibbon +# Contributors: # -# mdtraj is free software: you can redistribute it and/or modify it under the -# terms of the GNU General Public License as published by the Free Software -# Foundation, either version 3 of the License, or (at your option) any later -# version. +# MDTraj is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as +# published by the Free Software Foundation, either version 2.1 +# of the License, or (at your option) any later version. # -# mdtraj is distributed in the hope that it will be useful, but WITHOUT ANY -# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR -# A PARTICULAR PURPOSE. See the GNU General Public License for more details. +# This library is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU Lesser General Public License for more details. # -# You should have received a copy of the GNU General Public License along with -# mdtraj. If not, see http://www.gnu.org/licenses/. +# You should have received a copy of the GNU Lesser General Public +# License along with Foobar. If not, see . +############################################################################## + ############################################################################### # Imports @@ -63,7 +70,7 @@ if sizeof(float) != sizeof(np.float32_t): cdef class XTCTrajectoryFile: """XTCTrajectoryFile(filenamee, mode='r', force_overwrite=True, **kwargs) - + Interface for reading and writing to a GROMACS XTC file. This is a file-like objec that supports both reading and writing. It also supports the context manager ptorocol, so you can use it @@ -72,7 +79,7 @@ cdef class XTCTrajectoryFile: The conventional units in the XTC file are nanometers and picoseconds. The format only supports saving coordinates, the time, the md step, and the unit cell parametrs (box vectors) - + Parameters ---------- filename : str @@ -187,7 +194,7 @@ cdef class XTCTrajectoryFile: def read(self, n_frames=None, stride=None, atom_indices=None): """read(n_frames=None, stride=None, atom_indices=None) - + Read data from an XTC file Parameters @@ -259,7 +266,7 @@ cdef class XTCTrajectoryFile: cdef int i = 0 cdef int status = _EXDROK cdef int n_atoms_to_read - + if atom_indices is None: n_atoms_to_read = self.n_atoms elif isinstance(atom_indices, slice): @@ -295,7 +302,7 @@ cdef class XTCTrajectoryFile: status = xdrlib.read_xtc(self.fh, self.n_atoms, &step[i], &time[i], &box[i,0,0], &framebuffer[0,0], &prec[i]) xyz[i, :, :] = framebuffer[atom_indices, :] - + if status != _EXDRENDOFFILE and status != _EXDROK: raise RuntimeError('XTC read error: %s' % _EXDR_ERROR_MESSAGES.get(status, 'unknown')) i += 1 @@ -313,7 +320,7 @@ cdef class XTCTrajectoryFile: def write(self, xyz, time=None, step=None, box=None): """write(xyz, time=None, step=None, box=None) - + Write data to an XTC file Parameters diff --git a/README.md b/README.md index 35c1c7e28..eab030c0e 100644 --- a/README.md +++ b/README.md @@ -16,3 +16,22 @@ deviations using the quaternion characteristic polynomial (Theobald QCP) method speed of the original Theobald code and over 3x as fast as Theobald code modified to use GotoBLAS. For details, see the [documentation](http://rmcgibbo.github.io/mdtraj/). + +License +------- + +``` +MDtraj is free software; you can redistribute it and/or modify it under the +terms of the GNU Lesser General Public License as published by the Free +Software Foundation; either version 2.1 of the License, or (at your option) +any later version. + +This library is distributed in the hope that it will be useful, but WITHOUT ANY +WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR +A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more +details. You should have received a copy of the GNU Lesser General Public +License along with this Module; if not, see . +``` + +Various sub-portions of this library may be individually distributed under +different licenses. See those files for their specific terms. diff --git a/scripts/mdconvert.py b/scripts/mdconvert.py index 800544267..24aaa7d21 100644 --- a/scripts/mdconvert.py +++ b/scripts/mdconvert.py @@ -1,4 +1,25 @@ -#!/usr/bin/env python +############################################################################## +# MDTraj: A Python Library for Loading, Saving, and Manipulating +# Molecular Dynamics Trajectories. +# Copyright 2012-2013 Stanford University and the Authors +# +# Authors: Robert McGibbon +# Contributors: +# +# MDTraj is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as +# published by the Free Software Foundation, either version 2.1 +# of the License, or (at your option) any later version. +# +# This library is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with Foobar. If not, see . +############################################################################## + ############################################################################### # Imports diff --git a/scripts/mdinspect.py b/scripts/mdinspect.py index f796e0cb9..c9da7f951 100644 --- a/scripts/mdinspect.py +++ b/scripts/mdinspect.py @@ -1,4 +1,25 @@ -#!/usr/bin/env python +############################################################################## +# MDTraj: A Python Library for Loading, Saving, and Manipulating +# Molecular Dynamics Trajectories. +# Copyright 2012-2013 Stanford University and the Authors +# +# Authors: Robert McGibbon +# Contributors: +# +# MDTraj is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as +# published by the Free Software Foundation, either version 2.1 +# of the License, or (at your option) any later version. +# +# This library is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with Foobar. If not, see . +############################################################################## + """Sanity checking for molecular dynamics trajectories. This script is currently a work in progress. Contributions are encouraged. """ diff --git a/tools/LICENSE_HEADER b/tools/LICENSE_HEADER deleted file mode 100644 index 82b0a8302..000000000 --- a/tools/LICENSE_HEADER +++ /dev/null @@ -1,16 +0,0 @@ -# Copyright 2012-present mdtraj developers -# -# This file is part of mdtraj -# -# mdtraj is free software: you can redistribute it and/or modify it under the -# terms of the GNU General Public License as published by the Free Software -# Foundation, either version 3 of the License, or (at your option) any later -# version. -# -# mdtraj is distributed in the hope that it will be useful, but WITHOUT ANY -# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR -# A PARTICULAR PURPOSE. See the GNU General Public License for more details. -# -# You should have received a copy of the GNU General Public License along with -# mdtraj. If not, see http://www.gnu.org/licenses/. - diff --git a/tools/add_license.sh b/tools/add_license.sh deleted file mode 100644 index e849a8c1b..000000000 --- a/tools/add_license.sh +++ /dev/null @@ -1,7 +0,0 @@ -for i in `find . -name '*.py' -o -name '*.pyx'` # or whatever other pattern... -do - if ! grep -q "Copyright" $i - then - cat LICENSE_HEADER $i >$i.new && mv $i.new $i - fi -done \ No newline at end of file diff --git a/tools/ci/after_sucess.sh b/tools/ci/after_sucess.sh index 4cf472c0b..b6d59df32 100755 --- a/tools/ci/after_sucess.sh +++ b/tools/ci/after_sucess.sh @@ -1,6 +1,6 @@ PYTHON_VERSION=`python -c 'import sys; print("%d.%d" % sys.version_info[:2])'` -if [[ "$TRAVIS_PULL_REQUEST" == "true" ]]; then +if [[ "$TRAVIS_PULL_REQUEST" == "true" ]]; then echo "This is a pull request. No deployment will be done."; exit 0 fi diff --git a/tools/ci/speedpack/build.sh b/tools/ci/speedpack/build.sh index 39bcad40e..890c1b444 100644 --- a/tools/ci/speedpack/build.sh +++ b/tools/ci/speedpack/build.sh @@ -6,6 +6,29 @@ # # Runtime can be up to an hour or more. +# Copyright (c) 2011-2012, Lambda Foundry, Inc. and PyData Development Team +# All rights reserved. +# +# Copyright (c) 2008-2011 AQR Capital Management, LLC +# All rights reserved. +# +# Redistribution and use in source and binary forms, with or without +# modification, are permitted provided that the following conditions are +# met: +# +# * Redistributions of source code must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# * Redistributions in binary form must reproduce the above +# copyright notice, this list of conditions and the following +# disclaimer in the documentation and/or other materials provided +# with the distribution. +# +# * Neither the name of the copyright holder nor the names of any +# contributors may be used to endorse or promote products derived +# from this software without specific prior written permission. + + echo "Building wheels..." # print a trace for everything; RTFM diff --git a/tools/ci/speedpack/push-wheels-to-s3.py b/tools/ci/speedpack/push-wheels-to-s3.py index 77f6bf172..e2bf34d3a 100755 --- a/tools/ci/speedpack/push-wheels-to-s3.py +++ b/tools/ci/speedpack/push-wheels-to-s3.py @@ -28,7 +28,7 @@ def main(): k = Key(bucket) k.key = os.path.relpath(fn, ROOT) k.set_contents_from_filename(fn) - + # Put up an index page k = Key(bucket) k.key = os.path.relpath(os.path.join(dirpath, 'index.html'), ROOT) diff --git a/tools/examples_rst.py b/tools/examples_rst.py index 336a90d21..ae4f7e231 100755 --- a/tools/examples_rst.py +++ b/tools/examples_rst.py @@ -2,7 +2,28 @@ """ This script takes python example files, runs them, and converts them to .rst for sphinx. It was copied from statsmodels (BSD): -https://github.com/statsmodels/statsmodels/tree/master/tools + +Copyright (C) 2006, Jonathan E. Taylor +All rights reserved. + +Copyright (c) 2006-2008 Scipy Developers. +All rights reserved. + +Copyright (c) 2009-2012 Statsmodels Developers. +All rights reserved. + + +Redistribution and use in source and binary forms, with or without +modification, are permitted provided that the following conditions are met: + + a. Redistributions of source code must retain the above copyright notice, + this list of conditions and the following disclaimer. + b. Redistributions in binary form must reproduce the above copyright + notice, this list of conditions and the following disclaimer in the + documentation and/or other materials provided with the distribution. + c. Neither the name of Statsmodels nor the names of its contributors + may be used to endorse or promote products derived from this software + without specific prior written permission. """ import os diff --git a/tools/hash_funcs.py b/tools/hash_funcs.py index 601a24c80..69295988e 100644 --- a/tools/hash_funcs.py +++ b/tools/hash_funcs.py @@ -1,7 +1,28 @@ +# Copyright (C) 2006, Jonathan E. Taylor +# All rights reserved. +# +# Copyright (c) 2006-2008 Scipy Developers. +# All rights reserved. +# +# Copyright (c) 2009-2012 Statsmodels Developers. +# All rights reserved. +# +# Redistribution and use in source and binary forms, with or without +# modification, are permitted provided that the following conditions are met: +# +# a. Redistributions of source code must retain the above copyright notice, +# this list of conditions and the following disclaimer. +# b. Redistributions in binary form must reproduce the above copyright +# notice, this list of conditions and the following disclaimer in the +# documentation and/or other materials provided with the distribution. +# c. Neither the name of Statsmodels nor the names of its contributors +# may be used to endorse or promote products derived from this software +# without specific prior written permission. """ A collection of utilities to see if new ReST files need to be automatically generated from certain files in the project (examples, datasets). """ + import os import pickle