Merge pull request #189 from andrewtarzia/optwriter_sequence

Adds a new sequence optimiser that writes to file each step to avoid rerun, fixes the docs and makes all code examples tests, which are passing now. Had to set a numpy version requirement because the order of installation could be an issue

.github/workflows/tests.yml

@@ -55,7 +55,7 @@ jobs:
       - name: Build environment
         run: |
           conda activate pytest
-          conda install -c conda-forge openff-toolkit openmm openmmtools dgl
+          conda install -c conda-forge openff-toolkit openmm openmmtools dgl rdkit==2024.3.4
           python -m pip install --upgrade pip
           python -m pip install --upgrade setuptools
           python -m pip install -e '.[dev]'
@@ -79,7 +79,7 @@ jobs:
       - name: Build environment
         run: |
           conda activate pytest
-          conda install -c conda-forge openff-toolkit openmm openmmtools dgl
+          conda install -c conda-forge openff-toolkit openmm openmmtools dgl rdkit==2024.3.4
           conda install -c conda-forge mdanalysis openbabel
           python -m pip install --upgrade pip
           python -m pip install --upgrade setuptools
@@ -104,7 +104,8 @@ jobs:
       - name: Build environment
         run: |
           conda activate pytest
-          conda install -c conda-forge openff-toolkit openmm openmmtools dgl
+          conda install -c conda-forge openff-toolkit openmm openmmtools dgl rdkit==2024.3.4
+          conda install -c conda-forge mdanalysis openbabel
           python -m pip install --upgrade pip
           python -m pip install --upgrade setuptools
           python -m pip install -e '.[dev]'

README.rst

@@ -33,7 +33,9 @@ Some optional dependencies are only available through conda:
 .. code-block:: bash
 
   # for OpenMM and espaloma charge
-  mamba install openff-toolkit openmm openmmtools dgl
+  # note the temporary issue with rdkit versions and conda will overwrite pip
+  # installed software
+  mamba install openff-toolkit openmm openmmtools dgl rdkit==2024.3.4
   # for xtb
   mamba install xtb
   # for openbabel

docs/source/cage_analysis.rst

@@ -31,10 +31,21 @@ This example structure is not great, but it does the job here. Imagine
 you would do a better optimisation with one of our
 `Optimizer <optimizers.html>`_ classes!
 
-.. code-block:: python
+.. testsetup:: analysing-cage
+
+    import pathlib
+    import os
+
+    path = pathlib.Path('cage_output')
+    os.makedirs(path, exist_ok=True)
+
+
+.. testcode:: analysing-cage
 
     import stk
     import stko
+    import numpy as np
+    from collections import defaultdict
 
     pd = stk.BuildingBlock(
         smiles="[Pd+2]",
@@ -141,13 +152,12 @@ functional group has three atoms, centered on a binder, which we can then
 pass to the ``stko.molecule_analysis.DitopicThreeSiteAnalyser`` for
 automatic analyses.
 
-.. code-block:: python
+.. testcode:: analysing-cage
 
     ligands = stko.molecule_analysis.DecomposeMOC().decompose(
         molecule=apdcage,
         metal_atom_nos=(46,),
     )
-    print(f"there are {len(ligands)} ligands")
 
     tsa = stko.molecule_analysis.DitopicThreeSiteAnalyser()
     ligand_dict = defaultdict(list)
@@ -197,7 +207,7 @@ We can get the centroid and atom ids of distinct building blocks.
 This simply extracts the parts of building blocks still present in the
 molecule.
 
-.. code-block:: python
+.. testcode:: analysing-cage
 
 
     analyser = stko.molecule_analysis.ConstructedAnalyser()
@@ -207,37 +217,29 @@ molecule.
 
 We can get measures of pore size and cage geometry.
 
-.. code-block:: python
+.. testcode:: analysing-cage
 
     analyser = stko.molecule_analysis.GeometryAnalyser()
-    print(
-        f"approximate pore size: {analyser.get_min_centroid_distance(apdcage)}"
-    )
-    print(f"avg cage size: {analyser.get_avg_centroid_distance(apdcage)}")
+    pore_size = analyser.get_min_centroid_distance(apdcage)
+    avg_cage_size = analyser.get_avg_centroid_distance(apdcage)
     m_distances = list(
         analyser.get_metal_distances(
             apdcage,
             metal_atom_nos=(46,),
         ).values()
     )
-    print(f"avg. metal distance: {np.mean(m_distances)}")
+    avg_m_distances = np.mean(m_distances)
     m_angles = list(
         analyser.get_metal_centroid_metal_angle(
             apdcage,
             metal_atom_nos=(46,),
         ).values()
     )
-    print(f"avg. metal-centroid-angles: {np.mean(m_angles)}")
+    avg_m_angles = np.mean(m_angles)
 
     # And some geometrical measures.
-    print(
-        f"avg. N-Pd bond length:"
-        f' {np.mean(analyser.calculate_bonds(apdcage)[("N", "Pd")])}'
-    )
-    print(
-        f"N-Pd-N angles: "
-        f'{analyser.calculate_angles(apdcage)[("N", "Pd", "N")]}'
-    )
+    avg_n_pd_bond_length = np.mean(analyser.calculate_bonds(apdcage)[("N", "Pd")])
+    n_pd_n_angles = analyser.calculate_angles(apdcage)[("N", "Pd", "N")]
 
 Giving:
 
@@ -249,3 +251,9 @@ Giving:
   avg. metal-centroid-angles: 107.491677523429
   avg. N-Pd bond length: 2.0559406288465105
   N-Pd-N angles: [175.92946759351747, 89.4607655701432, 92.55953467090808, ...]
+
+.. testcleanup:: analysing-cage
+
+    import shutil
+
+    shutil.rmtree('cage_output')

docs/source/cage_optimisation.rst

@@ -183,8 +183,182 @@ to get the structure below in a few minutes!
         smiles="C1=C(C=C(C=C1C=O)C=O)C=O",
         functional_groups=[stk.AldehydeFactory()],
     )
-    cage = stk.BuildingBlock.init_from_file(
-        'source/_static/openmm_opt_file.mol'
+    cage = stk.ConstructedMolecule(
+        topology_graph=stk.cage.FourPlusSix((bb1, bb2)),
+    )
+    cage = cage.with_position_matrix(
+        np.array(
+            (
+                (-1.9792, -2.3384, 5.2933),
+                (-3.2185, -2.0128, 4.7072),
+                (-3.3418, -0.8081, 3.9884),
+                (-2.2459, 0.0633, 3.8438),
+                (-1.0129, -0.2787, 4.4340),
+                (-0.8691, -1.4797, 5.1587),
+                (0.4539, -1.8374, 5.7277),
+                (-2.4066, 1.2933, 3.0336),
+                (-4.3549, -2.9589, 4.8174),
+                (-1.8487, -3.2699, 5.8281),
+                (-4.2896, -0.5827, 3.5176),
+                (-0.1724, 0.3871, 4.2901),
+                (1.2798, -1.1664, 5.5382),
+                (-3.3696, 1.4629, 2.5733),
+                (-4.1898, -3.8917, 5.3382),
+                (-4.7803, -5.2041, -0.1516),
+                (-4.3247, -6.0542, 0.8753),
+                (-3.3559, -7.0307, 0.5802),
+                (-2.8384, -7.1630, -0.7222),
+                (-3.3237, -6.3243, -1.7450),
+                (-4.2922, -5.3406, -1.4672),
+                (-4.7621, -4.4130, -2.5213),
+                (-1.7453, -8.1184, -1.0084),
+                (-4.8125, -5.9199, 2.2663),
+                (-5.5032, -4.4377, 0.0956),
+                (-2.9651, -7.6718, 1.3590),
+                (-2.9383, -6.3968, -2.7529),
+                (-5.1288, -3.4502, -2.1965),
+                (-1.1578, -7.9386, -1.8973),
+                (-4.3149, -6.4955, 3.0355),
+                (2.3470, -5.6245, 2.4744),
+                (3.0253, -4.3910, 2.4097),
+                (3.4773, -3.9184, 1.1616),
+                (3.2342, -4.6532, -0.0146),
+                (2.5581, -5.8863, 0.0689),
+                (2.1190, -6.3844, 1.3104),
+                (1.3921, -7.6722, 1.4108),
+                (3.6201, -4.1242, -1.3411),
+                (3.2214, -3.5604, 3.6207),
+                (1.9818, -5.9636, 3.4353),
+                (3.9801, -2.9641, 1.0784),
+                (2.3476, -6.4622, -0.8217),
+                (0.8728, -7.8922, 2.3343),
+                (3.0634, -4.4889, -2.1917),
+                (3.5944, -2.5529, 3.4935),
+                (0.0003, 0.1776, -1.6595),
+                (-1.4006, 0.2907, -1.7411),
+                (-2.1049, -0.5319, -2.6414),
+                (-1.4225, -1.4575, -3.4556),
+                (-0.0176, -1.5471, -3.3710),
+                (0.7007, -0.7336, -2.4734),
+                (2.1741, -0.8221, -2.3473),
+                (-2.1595, -2.3694, -4.3603),
+                (-2.1436, 1.2339, -0.8736),
+                (0.5263, 0.7923, -0.9400),
+                (-3.1838, -0.4868, -2.7014),
+                (0.5309, -2.2582, -3.9736),
+                (2.6371, -0.3127, -1.5126),
+                (-1.6213, -3.2046, -4.7884),
+                (-3.2228, 1.1631, -0.8483),
+                (-8.7475, -5.4098, 3.2440),
+                (-9.0659, -3.9533, 3.6377),
+                (-7.8037, -3.0695, 3.5465),
+                (-6.6610, -3.6323, 4.4095),
+                (-6.3139, -5.0978, 3.9792),
+                (-7.5791, -5.9787, 4.0854),
+                (-5.8477, -5.1698, 2.5758),
+                (-5.5362, -2.6767, 4.3083),
+                (-8.4781, -5.4466, 2.1851),
+                (-9.6340, -6.0334, 3.3680),
+                (-9.4577, -3.9245, 4.6560),
+                (-9.8412, -3.5549, 2.9807),
+                (-8.0337, -2.0536, 3.8688),
+                (-7.4661, -3.0074, 2.5101),
+                (-6.9999, -3.6461, 5.4468),
+                (-5.5532, -5.4945, 4.6537),
+                (-7.3453, -6.9888, 3.7459),
+                (-7.8813, -6.0535, 5.1302),
+                (4.3501, -5.0254, 7.2779),
+                (3.1457, -5.1703, 8.2306),
+                (1.8378, -4.7139, 7.5481),
+                (1.9504, -3.2750, 7.0131),
+                (3.1487, -3.1507, 6.0102),
+                (4.4541, -3.5888, 6.7112),
+                (2.9636, -4.0200, 4.8266),
+                (0.6242, -2.9236, 6.4531),
+                (4.2421, -5.7299, 6.4492),
+                (5.2718, -5.2881, 7.7993),
+                (3.3146, -4.5744, 9.1291),
+                (3.0491, -6.2107, 8.5468),
+                (1.0084, -4.7732, 8.2535),
+                (1.5972, -5.3812, 6.7182),
+                (2.1399, -2.6169, 7.8624),
+                (3.2503, -2.1082, 5.7047),
+                (5.2801, -3.5366, 6.0004),
+                (4.6810, -2.8918, 7.5183),
+                (-1.0278, 5.1099, -0.3060),
+                (-0.3333, 5.3337, 1.0526),
+                (-0.2367, 4.0142, 1.8498),
+                (-1.6218, 3.3715, 2.0394),
+                (-2.3076, 3.1120, 0.6526),
+                (-2.4117, 4.4416, -0.1254),
+                (-1.5287, 2.1705, -0.1833),
+                (-1.4305, 2.1619, 2.8727),
+                (-0.3987, 4.4713, -0.9318),
+                (-1.1389, 6.0602, -0.8304),
+                (-0.8928, 6.0690, 1.6334),
+                (0.6670, 5.7401, 0.8924),
+                (0.2126, 4.1982, 2.8262),
+                (0.4129, 3.3090, 1.3278),
+                (-2.2390, 4.0725, 2.6039),
+                (-3.3151, 2.7281, 0.8187),
+                (-2.8578, 4.2533, -1.1031),
+                (-3.0784, 5.1198, 0.4077),
+                (2.3815, -11.0436, -0.9318),
+                (1.2844, -11.1927, -2.0094),
+                (0.2185, -10.0819, -1.8754),
+                (-0.3832, -10.0826, -0.4473),
+                (0.7226, -9.8624, 0.6209),
+                (1.7792, -10.9799, 0.4942),
+                (1.4225, -8.5662, 0.4443),
+                (-1.5084, -9.1419, -0.2118),
+                (2.9494, -10.1287, -1.1196),
+                (3.0863, -11.8738, -0.9990),
+                (0.8065, -12.1694, -1.9127),
+                (1.7363, -11.1510, -3.0023),
+                (-0.5726, -10.2374, -2.6099),
+                (0.6820, -9.1150, -2.0791),
+                (-0.7920, -11.0790, -0.2724),
+                (0.2645, -9.9205, 1.6110),
+                (2.5743, -10.8053, 1.2204),
+                (1.3215, -11.9378, 0.7429),
+                (-5.7675, -1.3419, -6.3528),
+                (-6.9145, -2.0492, -5.5981),
+                (-6.3712, -2.8433, -4.3903),
+                (-5.2902, -3.8534, -4.8500),
+                (-4.1141, -3.1344, -5.5638),
+                (-4.6593, -2.3401, -6.7712),
+                (-3.4263, -2.1784, -4.6643),
+                (-4.7907, -4.7707, -3.7910),
+                (-5.3308, -0.5745, -5.7086),
+                (-6.1603, -0.8326, -7.2342),
+                (-7.4381, -2.7264, -6.2754),
+                (-7.6407, -1.3096, -5.2559),
+                (-7.1839, -3.3766, -3.8957),
+                (-5.9431, -2.1431, -3.6717),
+                (-5.7571, -4.4978, -5.5969),
+                (-3.4162, -3.8928, -5.9258),
+                (-3.8390, -1.8005, -7.2469),
+                (-5.0564, -3.0368, -7.5099),
+                (4.7797, -1.7686, -5.5998),
+                (5.3604, -3.1692, -5.3070),
+                (4.7690, -3.7441, -4.0020),
+                (5.0246, -2.7739, -2.8224),
+                (4.4044, -1.3765, -3.0936),
+                (4.9868, -0.8052, -4.4052),
+                (2.9293, -1.4185, -3.2470),
+                (4.6293, -3.2878, -1.4857),
+                (3.7098, -1.8569, -5.8039),
+                (5.2419, -1.3522, -6.4964),
+                (6.4470, -3.1069, -5.2207),
+                (5.1393, -3.8409, -6.1385),
+                (5.2166, -4.7142, -3.7828),
+                (3.6966, -3.8914, -4.1361),
+                (6.1042, -2.6245, -2.7671),
+                (4.6823, -0.7125, -2.2719),
+                (4.5102, 0.1523, -4.6210),
+                (6.0517, -0.6121, -4.2723),
+            )
+        )
     )
 
     moldoc_display_molecule = molecule.Molecule(

docs/source/index.rst

@@ -39,7 +39,9 @@ Some optional dependencies are only available through conda:
 .. code-block:: bash
 
   # for OpenMM and espaloma charge
-  mamba install openff-toolkit openmm openmmtools dgl
+  # note the temporary issue with rdkit versions and conda will overwrite pip
+  # installed software
+  mamba install openff-toolkit openmm openmmtools dgl rdkit==2024.3.4
   # for xtb
   mamba install xtb
   # for openbabel

docs/source/optimizers.rst

@@ -9,7 +9,9 @@ Optimizers
 .. toctree::
   :maxdepth: 1
 
+  NullOptimizer <_autosummary/stko.NullOptimizer>
   OptimizerSequence <_autosummary/stko.OptimizerSequence>
+  OptWriterSequence <_autosummary/stko.OptWriterSequence>
   TryCatchOptimizer <_autosummary/stko.TryCatchOptimizer>
 
   Aligner <_autosummary/stko.Aligner>
@@ -21,7 +23,6 @@ Optimizers
   MetalOptimizer <_autosummary/stko.MetalOptimizer>
   OpenBabel <_autosummary/stko.OpenBabel>
   OpenMMForceField <_autosummary/stko.OpenMMForceField>
-  OpenMMMD <_autosummary/stko.OpenMMMD>
   GulpUFFOptimizer <_autosummary/stko.GulpUFFOptimizer>
   MacroModelForceField <_autosummary/stko.MacroModelForceField>
   XTB <_autosummary/stko.XTB>
@@ -31,3 +32,4 @@ Optimizers
 
   GulpUFFMDOptimizer <_autosummary/stko.GulpUFFMDOptimizer>
   MacroModelMD <_autosummary/stko.MacroModelMD>
+  OpenMMMD <_autosummary/stko.OpenMMMD>