Add InChI sanity check (#45)

Sanity module:
- Add InChI chemistry check requiring that a valid molecule can be converted to a standard InChI key and back. This test detects some chemical issues that the RDKit sanitization test does not flag.

Energy ratio module:
- Improve warning messages.

Config:
- Add InChI check to all default configurations.

.gitignore

@@ -4,6 +4,7 @@ temp
 ignore*
 notebooks*
 .test*
+.vscode
 
 # Byte-compiled / optimized / DLL files
 __pycache__/

docs/source/checks.rst

@@ -177,6 +177,12 @@ with in a receptor's binding pocket without any steric clash.
 | Ligand and receptor clash                   |                                        |
 +---------------------------------------------+----------------------------------------+
 
+.. _sanitisation: https://www.rdkit.org/docs/RDKit_Book.html#molecular-sanitization
+
+In addition to these geometric considerations, molecules should always pass RDKit's chemical `sanitisation`_ checks, as well as be interconvertible with InChI strings.
+
+
+
 More details on tests and docking method comparison
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 

docs/source/index.rst

@@ -134,24 +134,26 @@ Docking methods comparison
 ====================================
 
 .. _preprint: https://arxiv.org/abs/2308.05777
+.. _paper: https://doi.org/10.1039/D3SC04185A
 
-For more detailed information about the tests and for a study using PoseBusters to compare docking methods, refer to our `preprint`_:
+For more detailed information about the tests and for a study using PoseBusters to compare docking methods, refer to our `paper`_:
 
 .. code-block:: bibtex
 
-   @online{buttenschoen2023posebusters,
+   @article{buttenschoen2023posebusters,
       title = {{{PoseBusters}}: {{AI-based}} Docking Methods Fail to Generate Physically Valid Poses or Generalise to Novel Sequences},
       shorttitle = {{{PoseBusters}}},
       author = {Buttenschoen, Martin and Morris, Garrett M. and Deane, Charlotte M.},
-      date = {2023-08-10},
-      eprint = {2308.05777},
-      eprinttype = {arxiv}
+      year = "2023",
+      publisher = "The Royal Society of Chemistry",
+      doi = "10.1039/D3SC04185A",
+      url = "http://dx.doi.org/10.1039/D3SC04185A",
    }
 
 Sample checks
 ====================================
 
-For more information on the checks, see :ref:`checks`.
+For more examples and information on the checks, see :ref:`checks`.
 
 +---------------------------------------------+----------------------------------------+
 | Steric clash                                                                         |
@@ -184,7 +186,7 @@ For more information on the checks, see :ref:`checks`.
 +---------------------------------------------+----------------------------------------+
 
 
-For more information on the checks, see :ref:`checks`.
+For more examples and information on the checks, see :ref:`checks`.
 
 Contents
 ====================================

posebusters/__init__.py

@@ -7,12 +7,20 @@
 from posebusters.modules.intermolecular_distance import check_intermolecular_distance
 from posebusters.modules.loading import check_loading
 from posebusters.modules.rmsd import check_rmsd
-from posebusters.modules.sanity import check_chemistry
+from posebusters.modules.sanity import (
+    check_all_atoms_connected,
+    check_chemistry,
+    check_chemistry_using_inchi,
+    check_chemistry_using_rdkit,
+)
 from posebusters.modules.volume_overlap import check_volume_overlap
 from posebusters.posebusters import PoseBusters
 
 __all__ = [
     "PoseBusters",
+    "check_all_atoms_connected",
+    "check_chemistry_using_inchi",
+    "check_chemistry_using_rdkit",
     "check_chemistry",
     "check_energy_ratio",
     "check_flatness",
@@ -24,4 +32,4 @@
     "check_volume_overlap",
 ]
 
-__version__ = "0.2.16"
+__version__ = "0.3.1"