Change everything to LGPL

MDTraj/__init__.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 <http://www.gnu.org/licenses/>.
+##############################################################################
+
+
 """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.
@@ -43,12 +51,12 @@ 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
     tester = MDTrajTester(mdtraj)
     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

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 <http://www.gnu.org/licenses/>.
+##############################################################################
+
 
 ##############################################################################
 # 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')
 

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 <http://www.gnu.org/licenses/>.
+##############################################################################
+
 
 ###############################################################################
 # Imports

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 <http://www.gnu.org/licenses/>.
+##############################################################################
+
 """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."""
@@ -201,26 +209,25 @@ 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)
     atom_dict["ResidueNames"] = tables.StringAtom(itemsize=4)
     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):
         node = file_handle.createCArray(where='/', name=key, atom=atom_dict[key], shape=val.shape, filters=COMPRESSION)
         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

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 <http://www.gnu.org/licenses/>.
+##############################################################################
+
 
 ##############################################################################
 # 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

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

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 <http://www.gnu.org/licenses/>.
+##############################################################################
+
 from __future__ import print_function, division
 
 __all__ = ['compute_distances', 'compute_angles', 'compute_dihedrals']

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 <http://www.gnu.org/licenses/>.
+##############################################################################
+
 """
 Here, we have implemented RMSD calculation using both Kabsch algorithm and
 via the quaterion-based characteristic polynomial.  Both are implemented