Merge pull request #22 from andrewtarzia/scram_dev2

Added (WIP) multiple new features for structure exploration, plus some cleaning up.
andrewtarzia · Jan 18, 2025 · ae64708 · ae64708
2 parents a8f9f4f + 44802a7
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diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
@@ -37,24 +37,20 @@ jobs:
       - 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
 
     defaults:
       run:
         shell: bash -l {0}
 
     steps:
-      - uses: actions/checkout@v2
-      - uses: conda-incubator/setup-miniconda@v2
+      - uses: actions/checkout@v4
+      - uses: conda-incubator/setup-miniconda@v3
 
         with:
-          auto-update-conda: true
-          miniforge-variant: Mambaforge
-          channels: conda-forge,defaults
+          miniforge-version: latest
           python-version: 3.11
           activate-environment: pytest
-          use-mamba: true
 
       - name: Build environment
         run: |
@@ -68,24 +64,20 @@ jobs:
         run: pytest
 
   build-test:
-    # https://ericmjl.github.io/blog/2021/12/30/better-conda-environments-on-github-actions/
     runs-on: ubuntu-22.04
 
     defaults:
       run:
         shell: bash -l {0}
 
     steps:
-      - uses: actions/checkout@v2
-      - uses: conda-incubator/setup-miniconda@v2
+      - uses: actions/checkout@v4
+      - uses: conda-incubator/setup-miniconda@v3
 
         with:
-          auto-update-conda: true
-          miniforge-variant: Mambaforge
-          channels: conda-forge,defaults
+          miniforge-version: latest
           python-version: 3.11
           activate-environment: buildtest
-          use-mamba: true
 
       - name: Build environment
         run: |

diff --git a/README.rst b/README.rst
@@ -8,7 +8,7 @@
 Overview
 ========
 
-:mod:`cgexplore` or ``cgx`` is a general toolkit built on
+``cgexplore`` or ``cgx`` is a general toolkit built on
 `stk <https://stk.readthedocs.io/en/stable/>`_ for constructing,
 optimising and exploring molecular coarse-grained models.
 
@@ -20,7 +20,7 @@ optimising and exploring molecular coarse-grained models.
 Installation
 ============
 
-:mod:`cgexplore` can be installed with pip:
+``cgexplore`` can be installed with pip:
 
 .. code-block:: bash
 
@@ -33,18 +33,18 @@ With dependancies `openmm <https://openmm.org/>`_ and `openmmtools <https://open
   mamba install openmm openmmtools
 
 
-Then, update directory structure in `env_set.py` if using example code.
+Then, update directory structure in ``env_set.py`` if using example code.
 
 
-The library implements some analysis that uses `Shape 2.1`. Follow the
+The library implements some analysis that uses ``Shape 2.1``. Follow the
 instructions to download and installed at
 `Shape <https://www.iqtc.ub.edu/uncategorised/program-for-the-stereochemical-analysis-of-molecular-fragments-by-means-of-continous-shape-measures-and-associated-tools/>`_
 
 
 Developer Setup
 ---------------
 
-To develop with :mod:`cgexplore`, you can clone the repo and use
+To develop with ``cgexplore``, you can clone the repo and use
 `just <https://github.com/casey/just>`_ to setup the dev environment:
 
 .. code-block:: bash
@@ -57,7 +57,7 @@ Usage
 
 **To reproduce data in DOI:
 `10.1039/D3SC03991A <https://doi.org/10.1039/D3SC03991A>`_**:
-Download the source code from `first_paper_example - presubmission`
+Download the source code from ``first_paper_example - presubmission``
 release from ``Releases``.I do not guarantee that running the example code
 on the current version will work. However, with each pull request a test is run
 as a GitHub Action connected to this
@@ -68,26 +68,26 @@ convention has changed and force field xml files should provide the
 appropriate information for mapping angles to models.
 
 
-* The directory `cgexplore` contains the actual source code for the package.
-* The directory `first_paper_example` contains the code for `10.1039/D3SC03991A <https://doi.org/10.1039/D3SC03991A>`_.
-  * `generate_XX.py` generates cage structures for different topology sets
-  * `env_set.py` sets a specific environment for file outputs
-  * `plot_XX.py` produces images and figures, and performs analysis
+* The directory ``cgexplore`` contains the actual source code for the package.
+* The directory ``first_paper_example`` contains the code for `10.1039/D3SC03991A <https://doi.org/10.1039/D3SC03991A>`_.
+  * ``generate_XX.py`` generates cage structures for different topology sets
+  * ``env_set.py`` sets a specific environment for file outputs
+  * ``plot_XX.py`` produces images and figures, and performs analysis
 
 .. important::
   **Warning**: If you have a CUDA-capable GPU and attempt to use CUDA in the
-  first example, you may get `NaN` errors due to the torsion restriction for
+  first example, you may get ``NaN`` errors due to the torsion restriction for
   angles at 180 degrees, which cause problematic forces. This will be handled
   in future versions of the code. And logically, I would suggest removing the
-  torsion restriction for those angles. The `platform` can be handled through
-  this argument in `build_building_blocks` and `build_populations`, which I
-  currently set to `None`, meaning `OpenMM` will decide for itself.
+  torsion restriction for those angles. The ``platform`` can be handled through
+  this argument in ``build_building_blocks`` and ``build_populations``, which I
+  currently set to ``None``, meaning ``OpenMM`` will decide for itself.
 
 
 How To Cite
 ===========
 
-If you use ``stk`` please cite
+If you use ``cgexplore`` please cite
 
   https://github.com/andrewtarzia/CGExplore
 
@@ -98,7 +98,7 @@ and
 Publications using CGExplore
 ============================
 
-* Using stk for constructing larger numbers of coarse-grained models: `Systematic exploration of accessible topologies of cage molecules via minimalistic models`__
+* Using stk for constructing larger numbers of coarse-grained models: `Systematic exploration of accessible topologies of cage molecules via minimalistic models <https://doi.org/10.1039/D3SC03991A>`_.
 
 
 Acknowledgements

diff --git a/docs/source/_autosummary/cgexplore.atomistic.extract_ditopic_ensemble.rst b/docs/source/_autosummary/cgexplore.atomistic.extract_ditopic_ensemble.rst
@@ -0,0 +1,6 @@
+cgexplore.atomistic.extract\_ditopic\_ensemble
+==============================================
+
+.. currentmodule:: cgexplore.atomistic
+
+.. autofunction:: extract_ditopic_ensemble
diff --git a/docs/source/_autosummary/cgexplore.atomistic.extract_ensemble.rst b/docs/source/_autosummary/cgexplore.atomistic.extract_ensemble.rst
diff --git a/docs/source/_autosummary/cgexplore.atomistic.get_ditopic_aligned_bb.rst b/docs/source/_autosummary/cgexplore.atomistic.get_ditopic_aligned_bb.rst
@@ -0,0 +1,6 @@
+cgexplore.atomistic.get\_ditopic\_aligned\_bb
+=============================================
+
+.. currentmodule:: cgexplore.atomistic
+
+.. autofunction:: get_ditopic_aligned_bb
diff --git a/docs/source/_autosummary/cgexplore.atomistic.rst b/docs/source/_autosummary/cgexplore.atomistic.rst
@@ -30,7 +30,8 @@ cgexplore.atomistic
       :nosignatures:
 
       cgx_optimisation_sequence
-      extract_ensemble
+      extract_ditopic_ensemble
+      get_ditopic_aligned_bb
       run_conformer_analysis
 
 

diff --git a/...lore.scram.HomolepticTopologyIterator.rst → ...tosummary/cgexplore.molecular.SixBead.rst b/...lore.scram.HomolepticTopologyIterator.rst → ...tosummary/cgexplore.molecular.SixBead.rst
@@ -1,9 +1,9 @@
-cgexplore.scram.HomolepticTopologyIterator
-==========================================
+cgexplore.molecular.SixBead
+===========================
 
-.. currentmodule:: cgexplore.scram
+.. currentmodule:: cgexplore.molecular
 
-.. autoclass:: HomolepticTopologyIterator
+.. autoclass:: SixBead
    :members:
    :inherited-members:
    :undoc-members:

diff --git a/docs/source/_autosummary/cgexplore.molecular.StericSixBead.rst b/docs/source/_autosummary/cgexplore.molecular.StericSixBead.rst
@@ -0,0 +1,25 @@
+cgexplore.molecular.StericSixBead
+=================================
+
+.. currentmodule:: cgexplore.molecular
+
+.. autoclass:: StericSixBead
+   :members:
+   :inherited-members:
+   :undoc-members:
+   :show-inheritance:
+
+
+
+
+   .. rubric:: Methods
+
+   .. autosummary::
+      :nosignatures:
+
+
+
+
+
+
+
diff --git a/docs/source/_autosummary/cgexplore.molecular.rst b/docs/source/_autosummary/cgexplore.molecular.rst
@@ -26,8 +26,10 @@ cgexplore.molecular
       LinearPrecursor
       Precursor
       PrecursorGenerator
+      SixBead
       SpindryConformer
       SquarePrecursor
+      StericSixBead
       ThreeC0Arm
       ThreeC1Arm
       ThreeC2Arm

diff --git a/docs/source/_autosummary/cgexplore.scram.BuildingBlockConfiguration.rst b/docs/source/_autosummary/cgexplore.scram.BuildingBlockConfiguration.rst
@@ -0,0 +1,35 @@
+cgexplore.scram.BuildingBlockConfiguration
+==========================================
+
+.. currentmodule:: cgexplore.scram
+
+.. autoclass:: BuildingBlockConfiguration
+   :members:
+   :inherited-members:
+   :undoc-members:
+   :show-inheritance:
+
+
+
+
+   .. rubric:: Methods
+
+   .. autosummary::
+      :nosignatures:
+
+      ~BuildingBlockConfiguration.get_building_block_dictionary
+      ~BuildingBlockConfiguration.get_hashable_bbidx_dict
+
+
+
+
+
+   .. rubric:: Attributes
+
+   .. autosummary::
+
+      ~BuildingBlockConfiguration.idx
+      ~BuildingBlockConfiguration.building_block_idx_map
+      ~BuildingBlockConfiguration.building_block_idx_dict
+
+
diff --git a/docs/source/_autosummary/cgexplore.scram.IHomolepticTopologyIterator.rst b/docs/source/_autosummary/cgexplore.scram.IHomolepticTopologyIterator.rst
@@ -17,9 +17,10 @@ cgexplore.scram.IHomolepticTopologyIterator
    .. autosummary::
       :nosignatures:
 
-      ~IHomolepticTopologyIterator.get_graphs
+      ~IHomolepticTopologyIterator.count_graphs
       ~IHomolepticTopologyIterator.get_num_building_blocks
       ~IHomolepticTopologyIterator.get_vertex_prototypes
+      ~IHomolepticTopologyIterator.yield_graphs
 
 
 

diff --git a/docs/source/_autosummary/cgexplore.scram.get_custom_bb_configurations.rst b/docs/source/_autosummary/cgexplore.scram.get_custom_bb_configurations.rst
@@ -0,0 +1,6 @@
+cgexplore.scram.get\_custom\_bb\_configurations
+===============================================
+
+.. currentmodule:: cgexplore.scram
+
+.. autofunction:: get_custom_bb_configurations
diff --git a/docs/source/_autosummary/cgexplore.scram.rst b/docs/source/_autosummary/cgexplore.scram.rst
@@ -16,8 +16,8 @@ cgexplore.scram
       :template: class.rst
       :nosignatures:
 
+      BuildingBlockConfiguration
       Constructed
-      HomolepticTopologyIterator
       IHomolepticTopologyIterator
       TopologyCode
       TopologyIterator
@@ -33,6 +33,7 @@ cgexplore.scram
       :toctree:
       :nosignatures:
 
+      get_custom_bb_configurations
       get_potential_bb_dicts
       graph_optimise_cage
       optimise_cage

diff --git a/first_paper_example/analysis.py b/first_paper_example/analysis.py
@@ -122,8 +122,10 @@ def analyse_cage(
             lig_shape_measures = liga_shape.calculate(l_shape_mol)
             l_shape_mol.write(shape_molfile2)
 
-        # Always want to extract target torions if present.
         g_measure = cgx.analysis.GeomMeasure(
+            # Always want to extract target torions if present, in toff, they
+            # are no in the forcefield, so cannot use
+            # `GeomMeasure.from_forcefield`.
             target_torsions=(
                 cgx.terms.TargetTorsion(
                     search_string=("b1", "a1", "c1", "a1", "b1"),
@@ -429,25 +431,6 @@ def xc_map(tstr: str) -> int:
     }[tstr]
 
 
-def stoich_map(tstr: str) -> int:
-    """Stoichiometry maps to the number of building blocks."""
-    return {
-        "2P3": 5,
-        "4P6": 10,
-        "4P62": 10,
-        "6P9": 15,
-        "8P12": 20,
-        "2P4": 6,
-        "3P6": 9,
-        "4P8": 12,
-        "4P82": 12,
-        "6P12": 18,
-        "8P16": 24,
-        "12P24": 36,
-        "6P8": 14,
-    }[tstr]
-
-
 def cltypetopo_to_colormap() -> dict[str, dict]:
     """Convert label."""
     return {
@@ -670,9 +653,9 @@ def data_to_array(json_files, output_dir: pathlib.Path) -> pd.DataFrame:
 
         if row["optimised"]:
             row["strain_energy"] = res_dict["fin_energy_kjmol"]
-            row["energy_per_bb"] = res_dict["fin_energy_kjmol"] / stoich_map(
-                t_str
-            )
+            row["energy_per_bb"] = res_dict[
+                "fin_energy_kjmol"
+            ] / cgx.topologies.stoich_map(t_str)
             for force_title in res_dict["fin_energy_decomp"]:
                 if force_title in (
                     "CMMotionRemover_kJ/mol",

diff --git a/first_paper_example/plot_cages.py b/first_paper_example/plot_cages.py
@@ -829,8 +829,7 @@ def webapp_csv(
     logging.info("running webapp_csv")
 
     github_base_url = (
-        "https://github.com/andrewtarzia/cgmodels/blob/main/"
-        "cg_model_jul2023/"
+        "https://github.com/andrewtarzia/cgmodels/blob/main/cg_model_jul2023/"
     )
     github_selfsort_url = github_base_url + "self_sort_outcomes/"