Simple RDKitConverter (#2775)

* simple converter

* add PDB residue info and guessers

* fix 2 letter atom names and fix bond order

* test mol2 topology and pdb info

* autopep8

* fix code review

* store other attributes in each atom

* more tests on topology + pep8

* fix other props type

* bond order and charges

* fix indentation and bonds with atoms outside of atomgroup

* fix test

* fix test minimal build

* add icodes to MonomerInfo

* better attributes conversion

* test mda to rdkit MonomerInfo conversion

* test mda to rdkit MonomerInfo conversion

* docs

* fix minimal deps test

* fix for minimal deps tests 🙏

* use util functions

* move min deps test up

* capitalize elements by default

* store index in MDA object

* fetch singular from _TOPOLOGY_ATTRS

* updated changelog

* use ag intersection for bonds instead of try except

* more tests + pep8

* fix test for numpy 1.13.3

* docs + pep8

* fix too long atom names in PDB output

* table of supported attributes for the converter

* changelog convention

* catch no bonds

* use match in pytest.raises and pytest.warns

* remove bondtype attribute

* fix bond attributes

* simplified the code for infering

* include negative charges

* skip failing test for now

* new test

* update doc

* standardize groups

* fix tests

* add previously failing tests

* simpler pattern standardization

* more tests on inferring and patterns

* test atom properties and reaction mapping

* fix docs

* fix minimal build tests

* pep8

* bfactors as TempFactor

* Update CHANGELOG

* pep8

* pep8

* no hydrogen warning

* quickfix for polycyclic conjugated systems

* save any atom property instead of just the ones tagged with "_MDAnalysis"

* general solution

* back to old method for conjugated systems

* added "RDKit" in changelog

* fix when first atom is charged

* working general solution to conjugated systems

* pep8

* for loop instead of while

* bugfix for conjugated system with N at one edge

* fix typos

* fix test for min deps

* use indirect parametrization

* add coordinates + tests + fix index property

* cache the molecule and only update conformers when iterating trajectory

* update docs

* add kwargs to the cache key

* use fstrings

* cache kwarg + fix cache tests

* fix code review + improve docs

* improve doc

* add test nan in coordinates

* warn nan coordinates

* end of code review

* corrections to smarts patterns for reactions

* sort atoms by NUE + more standardization tests

* pdb atom names formating

* test RDKit->MDA->RDKit->MDA equal

* tackle conjugated systems ending with O-

* docs + pep8

* tests

* add max_iter kwarg

* reorder docstring standardize_patterns

* fix doc build

Co-authored-by: Oliver Beckstein <[email protected]>

package/CHANGELOG

@@ -79,6 +79,8 @@ Enhancements
   * Added new kwargs `select_remove` and `select_protein` to
     analysis.dihedrals.Janin analysis to give user more fine grained control
     over selections (PR #2899)
+  * Added an RDKit converter that works for any input with all hydrogens
+    explicit in the topology (Issue #2468, PR #2775)
 
 Changes
   * deprecated NumPy type aliases have been replaced with their actual types

package/doc/sphinx/source/conf.py

@@ -346,4 +346,5 @@
                        'https://gsd.readthedocs.io/en/stable/': None,
                        'https://parmed.github.io/ParmEd/html/': None,
                        'https://docs.h5py.org/en/stable': None,
+                       'https://www.rdkit.org/docs/': None,
                        }

package/doc/sphinx/source/documentation_pages/converters.rst

@@ -33,4 +33,5 @@ you will have to specify a package name (case-insensitive). ::
    :maxdepth: 1
 
    converters/ParmEdParser
+   converters/RDKitParser
 

package/doc/sphinx/source/documentation_pages/converters/RDKitParser.rst

@@ -0,0 +1,3 @@
+.. automodule:: MDAnalysis.topology.RDKitParser
+
+.. automodule:: MDAnalysis.coordinates.RDKit

package/doc/sphinx/source/documentation_pages/topology_modules.rst

@@ -43,7 +43,6 @@ topology file format in the *topology_format* keyword argument to
    topology/PDBQTParser
    topology/PQRParser
    topology/PSFParser
-   topology/RDKitParser
    topology/TOPParser
    topology/TPRParser
    topology/TXYZParser