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An "accurate and reliable" RDKitConverter #3044

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merged 55 commits into from
Apr 2, 2022
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f464d3c
fix carbonyl
Oct 5, 2020
d129537
fix charged mols
Oct 12, 2020
24ddb3e
remove false premature return
Oct 14, 2020
4b6afc1
minor comments
Oct 14, 2020
c9513c7
assign most likely charges to monatomic ions
Oct 14, 2020
338dad3
fix when 2 ending patterns are matched
Oct 14, 2020
029ab1f
skip when backtrack prevents changes
Oct 15, 2020
046383e
improvements for Nterm, sulfones, and nitrogen next to a charged atom
Oct 27, 2020
bd12bc1
better handling of ring conjugated systems and conjugated triple bonds
Oct 28, 2020
bd14836
revert rdkitcache branch changes
Oct 28, 2020
0e7d4e4
monatomic default charges handling
Nov 13, 2020
d9b4d95
fix multiple types of end pattern + test
Nov 17, 2020
b36eab6
fix some sulfur and nitrogen compounds
Nov 18, 2020
555eab3
add amino and nucleic acids test
Nov 18, 2020
3e4d066
add test for ions
Nov 18, 2020
ec54125
final fixes
Nov 19, 2020
3167e43
fix docs and unused import
Nov 19, 2020
7b6823b
pep8
Nov 19, 2020
f695f91
Merge branch 'develop' into fix-converter
cbouy May 11, 2021
3f4645f
pep8
cbouy May 11, 2021
20a64ae
comments
cbouy May 11, 2021
5c03ee8
fix rdkit pdb atom names formatting
cbouy May 11, 2021
44c523e
skip sanitization if fails
cbouy May 11, 2021
0ce3271
reorder rdkit atoms to match mdanalysis
cbouy May 11, 2021
7477e7f
change setting and transferring atom properties
cbouy May 12, 2021
df4feb4
fix tests + pep8
cbouy May 12, 2021
359fdf4
fix tests
cbouy May 12, 2021
e358504
add more comments and UGM presentation
cbouy May 13, 2021
8fbc852
fix links
cbouy May 13, 2021
2c3e2fa
add test for new atom reordering
cbouy May 24, 2021
9ba698d
remove unnecessary sorting when using rdkit-based guessers or selection
cbouy May 24, 2021
896e7dc
Merge branch 'MDAnalysis:develop' into fix-converter
cbouy Jan 18, 2022
923dfb1
Merge branch 'MDAnalysis:develop' into fix-converter
cbouy Feb 16, 2022
3f6ff64
add missing test
cbouy Feb 16, 2022
5872559
add bond stereo test
cbouy Feb 17, 2022
7108da8
Merge branch 'MDAnalysis:develop' into fix-converter
cbouy Mar 7, 2022
428d341
more docs and comments
cbouy Mar 7, 2022
50de418
use PDBWriter.deduce_pdb_atom_name instead of custom code
cbouy Mar 7, 2022
eec6b1d
remove unnecessary bond stereo assignment
cbouy Mar 7, 2022
393d141
remove unused bond test
cbouy Mar 11, 2022
a2886e5
add _MDAnalysis_name atom property
cbouy Mar 16, 2022
ccd4bca
Merge branch 'MDAnalysis:develop' into fix-converter
cbouy Mar 16, 2022
055692b
add bond stereo test
cbouy Mar 16, 2022
3c9d874
mention failing molecules in docs
cbouy Mar 16, 2022
1a094fa
update changelog
cbouy Mar 16, 2022
9b3b7b5
improve readability
cbouy Mar 16, 2022
b18150f
improve tests readability
cbouy Mar 16, 2022
e01fc07
fix resonance struct test
cbouy Mar 17, 2022
4e4a40b
add xfail test
cbouy Mar 17, 2022
1a08adb
Merge branch 'develop' into fix-converter
orbeckst Mar 23, 2022
05c5c1b
Merge branch 'develop' into fix-converter
cbouy Mar 30, 2022
5a48bd6
lint
cbouy Mar 30, 2022
430f3e6
docs update from code review
cbouy Mar 30, 2022
d324223
Merge branch 'fix-converter' of github.com:cbouy/mdanalysis into fix-…
cbouy Mar 30, 2022
f019d28
fix docs
cbouy Mar 30, 2022
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12 changes: 11 additions & 1 deletion package/CHANGELOG
Original file line number Diff line number Diff line change
Expand Up @@ -13,17 +13,27 @@ The rules for this file:
* release numbers follow "Semantic Versioning" http://semver.org

------------------------------------------------------------------------------
??/??/?? IAlibay, BFedder, inomag, Agorfa, aya9aladdin, shudipto-amin
??/??/?? IAlibay, BFedder, inomag, Agorfa, aya9aladdin, shudipto-amin, cbouy

* 2.2.0

Fixes
* When converting an AtomGroup to an RDKit molecule (PR #3044):
orbeckst marked this conversation as resolved.
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- the atoms are now in the same order
- the output of `atom.GetMonomerInfo().GetName()` now follows the
guidelines for PDB files while the original name is still available
through `atom.GetProp("_MDAnalysis_name")`
- using `NoImplicit=False` should no longer throw a `SanitizationError`
* Contacts can now accept static AtomGroups as well as selection texts.
(Issue #2666, PR #3565)
* Fixed DumpReader triclinic box dimensions reading. (Issue #3386, PR #3403)
* Updated the badge in README of MDAnalysisTest to point to Github CI Actions

Enhancements
* Improves the RDKitConverter's accuracy (PR #3044): AtomGroups containing
monatomic ion charges or edge cases with nitrogen, sulfur, phosphorus and
conjugated systems should now have correctly assigned bond orders and
charges.

Changes
* ITPParser no longer adds an angle for water molecules that have the SETTLE
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