Merge pull request #196 from andrewtarzia/main

Implement unreacted graph and example.

.github/workflows/tests.yml

@@ -16,6 +16,7 @@ jobs:
           cache: "pip"
       - run: "pip install '.[dev]'"
       - run: ruff check .
+
   mypy:
     runs-on: ubuntu-22.04
     steps:
@@ -26,6 +27,7 @@ jobs:
           cache: "pip"
       - run: "pip install -e '.[dev]'"
       - run: mypy src examples
+
   ruff-format:
     runs-on: ubuntu-22.04
     steps:
@@ -36,6 +38,7 @@ jobs:
           cache: "pip"
       - run: "pip install -e '.[dev]'"
       - run: ruff format --check .
+
   pytest:
     # https://ericmjl.github.io/blog/2021/12/30/better-conda-environments-on-github-actions/
     runs-on: ubuntu-22.04
@@ -56,10 +59,12 @@ jobs:
         run: |
           conda activate pytest
           conda install -c conda-forge openff-toolkit openmm openmmtools dgl rdkit==2024.3.4 espaloma_charge
+          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]'
       - run: pytest
+
   example-tests:
     # https://ericmjl.github.io/blog/2021/12/30/better-conda-environments-on-github-actions/
     runs-on: ubuntu-22.04
@@ -86,6 +91,7 @@ jobs:
           python -m pip install -e '.[dev]'
       - name: Run script
         run: python examples/testable_example.py
+
   doctest:
     runs-on: ubuntu-22.04
     defaults:

docs/environment.yml

@@ -10,3 +10,6 @@ dependencies:
   - pip
   - rdkit==2024.3.4
   - espaloma_charge
+  - mdanalysis
+  - openbabel
+

docs/source/_templates/module.rst

@@ -2,6 +2,20 @@
 
 .. automodule:: {{ fullname }}
 
+   {% block modules %}
+   {% if modules %}
+   .. rubric:: Modules
+
+   .. autosummary::
+      :toctree:
+      :template: module.rst
+      :recursive:
+   {% for item in modules %}
+      {{ item }}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}
+
    {% block attributes %}
    {% if attributes %}
    .. rubric:: Module attributes
@@ -53,16 +67,4 @@
    {% endif %}
    {% endblock %}
 
-{% block modules %}
-{% if modules %}
-.. rubric:: Modules
 
-.. autosummary::
-   :toctree:
-   :template: module.rst
-   :recursive:
-{% for item in modules %}
-   {{ item }}
-{%- endfor %}
-{% endif %}
-{% endblock %}

docs/source/cage_analysis.rst

@@ -35,6 +35,7 @@ you would do a better optimisation with one of our
 
     import pathlib
     import os
+    import numpy as np
 
     path = pathlib.Path('cage_output')
     os.makedirs(path, exist_ok=True)
@@ -186,6 +187,12 @@ automatic analyses.
             sum(tsa.get_halfbite_angles(as_building_block))
         )
 
+.. testcode:: analysing-cage
+    :hide:
+
+    assert np.isclose(np.mean(ligand_dict['torsion']), 0.9038734003286987)
+    assert np.isclose(np.mean(ligand_dict['binder_angle']), 150.0120482677146)
+
 The printing the average of the collated values for all ligands looks
 like:
 
@@ -214,6 +221,12 @@ molecule.
     centroids = analyser.get_building_block_centroids(apdcage)
     # Out: {0: array([8.92788038, 0.41529785, 0.49671345]), ...}
 
+.. testcode:: analysing-cage
+    :hide:
+
+    assert np.allclose(
+        centroids[0], np.array([9.15025292, 0.20886534, 0.45632129])
+    )
 
 We can get measures of pore size and cage geometry.
 
@@ -241,6 +254,11 @@ We can get measures of pore size and cage geometry.
     avg_n_pd_bond_length = np.mean(analyser.calculate_bonds(apdcage)[("N", "Pd")])
     n_pd_n_angles = analyser.calculate_angles(apdcage)[("N", "Pd", "N")]
 
+.. testcode:: analysing-cage
+    :hide:
+
+    assert analyser.get_min_centroid_distance(apdcage) == 6.612215150137052
+
 Giving:
 
 .. code-block::

docs/source/molecular.rst

@@ -1,29 +1,67 @@
 Molecular
 =========
 
+Atoms, Functional Groups and Molecules
+--------------------------------------
+
 .. toctree::
   :maxdepth: 1
 
   PositionedAtom <_autosummary/stko.PositionedAtom>
-  dummy atom (Du) <_autosummary/stko.Du>
-  MDAnalysis <_autosummary/stko.MDAnalysis>
-  ZMatrix <_autosummary/stko.ZMatrix>
-  MoleculeSplitter <_autosummary/stko.MoleculeSplitter>
-  MoleculeTransformer <_autosummary/stko.MoleculeTransformer>
-  Network <_autosummary/stko.Network>
+  Dummy atom (Du) <_autosummary/stko.Du>
   UnitCell <_autosummary/stko.UnitCell>
-  TopologyExtractor <_autosummary/stko.TopologyExtractor>
-  TopologyInfo <_autosummary/stko.TopologyInfo>
   Torsion <_autosummary/stko.Torsion>
   TorsionInfo <_autosummary/stko.TorsionInfo>
   ThreeSiteFG <_autosummary/stko.functional_groups.ThreeSiteFG>
   ThreeSiteFactory <_autosummary/stko.functional_groups.ThreeSiteFactory>
+
+
+Molecular Analysis
+------------------
+
+.. toctree::
+  :maxdepth: 1
+
+  MoleculeSplitter <_autosummary/stko.MoleculeSplitter>
+  MoleculeTransformer <_autosummary/stko.MoleculeTransformer>
   DecomposeMOC <_autosummary/stko.molecule_analysis.DecomposeMOC>
   DitopicThreeSiteAnalyser <_autosummary/stko.molecule_analysis.DitopicThreeSiteAnalyser>
   ConstructedAnalyser <_autosummary/stko.molecule_analysis.ConstructedAnalyser>
+
+
+Subgroup Analysis
+-----------------
+
+.. toctree::
+  :maxdepth: 1
+
+  Subgroup <_autosummary/stko.molecule_analysis.Subgroup>
+  SubgroupAnalyser <_autosummary/stko.molecule_analysis.SubgroupAnalyser>
   AlkyneAngle <_autosummary/stko.molecule_analysis.AlkyneAngle>
   X5Planarity <_autosummary/stko.molecule_analysis.X5Planarity>
   C5N1Planarity <_autosummary/stko.molecule_analysis.C5N1Planarity>
   C6Planarity <_autosummary/stko.molecule_analysis.C6Planarity>
-  Subgroup <_autosummary/stko.molecule_analysis.Subgroup>
-  SubgroupAnalyser <_autosummary/stko.molecule_analysis.SubgroupAnalyser>
+
+
+Manipulating Topology Graphs
+----------------------------
+
+.. toctree::
+  :maxdepth: 1
+
+  TopologyExtractor <_autosummary/stko.TopologyExtractor>
+  TopologyInfo <_autosummary/stko.TopologyInfo>
+  UnreactedToplogyGraph <_autosummary/stko.topology_functions.UnreactedTopologyGraph>
+  NamedIntermediate <_autosummary/stko.topology_functions.NamedIntermediate>
+  IntermediatePool <_autosummary/stko.topology_functions.IntermediatePool>
+
+
+Conversion
+----------
+
+.. toctree::
+  :maxdepth: 1
+
+  MDAnalysis <_autosummary/stko.MDAnalysis>
+  ZMatrix <_autosummary/stko.ZMatrix>
+  Network <_autosummary/stko.Network>

examples/intermediates_example.py

@@ -0,0 +1,52 @@
+import logging
+from pathlib import Path
+
+import stk
+
+import stko
+
+
+def main() -> None:
+    """Run the example."""
+    # Two building blocks you want to react to form a topology graph.
+    bb1 = stk.BuildingBlock(
+        smiles="NCCN", functional_groups=(stk.PrimaryAminoFactory(),)
+    )
+    bb2 = stk.BuildingBlock(
+        smiles="O=CC(C=O)C=O", functional_groups=(stk.AldehydeFactory(),)
+    )
+
+    examples_output = Path("out_intermediates")
+    examples_output.mkdir(parents=True, exist_ok=True)
+
+    # Produce a `TopologyGraph` without doing any reactions.
+    cage_graphs = stko.topology_functions.UnreactedTopologyGraph(
+        stk.cage.FourPlusSix((bb1, bb2))
+    )
+    logging.info(
+        "there are %s possible reactions",
+        len(cage_graphs.get_available_reactions()),
+    )
+
+    # With up to N reactions performed.
+    intermediate_pool = cage_graphs.get_named_intermediates(n=4)
+    logging.info(
+        "there are %s structures with n=%s", len(intermediate_pool), 4
+    )
+    for named_intermediate in intermediate_pool.intermediates:
+        named_intermediate.molecule.write(
+            examples_output / f"{named_intermediate.intermediate_name}.mol"
+        )
+
+    # Now iterate over all possible reactions with varying amounts of
+    # completeness and get their smiles.
+    all_possible_smiles = cage_graphs.get_reacted_smiles()
+    logging.info("there are %s unique smiles", len(all_possible_smiles))
+
+
+if __name__ == "__main__":
+    logging.basicConfig(
+        level=logging.INFO,
+        format="%(asctime)s | %(levelname)s | %(message)s",
+    )
+    main()

examples/out_intermediates/idx0_3x3FG+2x2FG.mol

@@ -0,0 +1,103 @@
+
+     RDKit          3D
+
+  0  0  0  0  0  0  0  0  0  0999 V3000
+M  V30 BEGIN CTAB
+M  V30 COUNTS 45 44 0 0 0
+M  V30 BEGIN ATOM
+M  V30 1 C -1.2134 -0.7006 7.6921 0
+M  V30 2 C 0.0024 0.0195 8.1532 0
+M  V30 3 C 1.2289 -0.7128 7.6921 0
+M  V30 4 C -0.0155 1.4134 7.6921 0
+M  V30 5 O -0.9554 1.8112 7.0270 0
+M  V30 6 H -1.4106 -0.8660 6.6467 0
+M  V30 7 H 0.0228 0.0328 9.2640 0
+M  V30 8 H 1.3779 -0.8508 6.6158 0
+M  V30 9 H 0.7696 2.1271 7.9093 0
+M  V30 10 C -6.6851 -3.8596 -1.2430 0
+M  V30 11 C -6.6459 -3.8550 -2.7289 0
+M  V30 12 C -6.6921 -2.4414 -3.2314 0
+M  V30 13 O -7.5962 -2.0548 -3.9611 0
+M  V30 14 C -5.4646 -4.5773 -3.2177 0
+M  V30 15 O -4.6918 -5.0716 -2.4160 0
+M  V30 16 H -5.9270 -3.3704 -0.6555 0
+M  V30 17 H -7.5451 -4.3758 -3.1221 0
+M  V30 18 H -5.8930 -1.7560 -2.9293 0
+M  V30 19 H -5.2299 -4.7022 -4.2675 0
+M  V30 20 C 6.6851 -3.8596 -1.2430 0
+M  V30 21 C 6.6615 -3.8280 -2.7289 0
+M  V30 22 C 5.4604 -4.5748 -3.2314 0
+M  V30 23 O 5.5776 -5.5511 -3.9611 0
+M  V30 24 C 6.6963 -2.4438 -3.2177 0
+M  V30 25 O 6.7381 -1.5274 -2.4160 0
+M  V30 26 H 5.8824 -3.4478 -0.6555 0
+M  V30 27 H 7.5621 -4.3463 -3.1221 0
+M  V30 28 H 4.4673 -4.2255 -2.9293 0
+M  V30 29 H 6.6872 -2.1781 -4.2675 0
+M  V30 30 N -3.2178 -1.8578 4.4191 0
+M  V30 31 C -4.6051 -2.2313 4.4421 0
+M  V30 32 C -4.9290 -3.2079 3.3152 0
+M  V30 33 N -4.6808 -2.7024 2.0300 0
+M  V30 34 H -5.2477 -1.3300 4.3651 0
+M  V30 35 H -4.7784 -2.7831 5.3911 0
+M  V30 36 H -4.2388 -4.0831 3.4884 0
+M  V30 37 H -5.9702 -3.5517 3.4212 0
+M  V30 38 N 3.2255 -1.8639 4.4191 0
+M  V30 39 C 4.2425 -2.8787 4.4421 0
+M  V30 40 C 5.2503 -2.6710 3.3153 0
+M  V30 41 N 4.6885 -2.7085 2.0300 0
+M  V30 42 H 3.7830 -3.8858 4.3649 0
+M  V30 43 H 4.8069 -2.7532 5.3911 0
+M  V30 44 H 5.6634 -1.6358 3.4886 0
+M  V30 45 H 6.0684 -3.4011 3.4212 0
+M  V30 END ATOM
+M  V30 BEGIN BOND
+M  V30 1 1 1 2
+M  V30 2 1 2 3
+M  V30 3 1 2 4
+M  V30 4 2 4 5
+M  V30 5 1 1 6
+M  V30 6 1 2 7
+M  V30 7 1 3 8
+M  V30 8 1 4 9
+M  V30 9 1 10 11
+M  V30 10 1 11 12
+M  V30 11 2 12 13
+M  V30 12 1 11 14
+M  V30 13 2 14 15
+M  V30 14 1 10 16
+M  V30 15 1 11 17
+M  V30 16 1 12 18
+M  V30 17 1 14 19
+M  V30 18 1 20 21
+M  V30 19 1 21 22
+M  V30 20 2 22 23
+M  V30 21 1 21 24
+M  V30 22 2 24 25
+M  V30 23 1 20 26
+M  V30 24 1 21 27
+M  V30 25 1 22 28
+M  V30 26 1 24 29
+M  V30 27 1 30 31
+M  V30 28 1 31 32
+M  V30 29 1 32 33
+M  V30 30 1 31 34
+M  V30 31 1 31 35
+M  V30 32 1 32 36
+M  V30 33 1 32 37
+M  V30 34 1 38 39
+M  V30 35 1 39 40
+M  V30 36 1 40 41
+M  V30 37 1 39 42
+M  V30 38 1 39 43
+M  V30 39 1 40 44
+M  V30 40 1 40 45
+M  V30 41 2 1 30
+M  V30 42 2 10 33
+M  V30 43 2 3 38
+M  V30 44 2 20 41
+M  V30 END BOND
+M  V30 END CTAB
+M  END
+
+$$$$