Code

Simple RDKitConverter#2775

Code

Merged

IAlibay merged 107 commits intoMDAnalysis:developMDAnalysis/mdanalysis:developfrom cbouy:rdkit-convertercbouy/mdanalysis:rdkit-converterCopy head branch name to clipboardAug 21, 2020

+1,229-47

Commits

Commits on Jun 19, 2020

• simple converter

  

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Commits on Jun 22, 2020

• add PDB residue info and guessers

  

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Commits on Jun 24, 2020

• fix 2 letter atom names and fix bond order

  

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• test mol2 topology and pdb info

  

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Commits on Jun 25, 2020

• autopep8

  

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• fix code review

  

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• store other attributes in each atom

  

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• more tests on topology + pep8

  

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Commits on Jun 26, 2020

• fix other props type

  

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• bond order and charges

  

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• fix indentation and bonds with atoms outside of atomgroup

  

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  6d6a65b

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• fix test

  

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Commits on Jun 29, 2020

• fix test minimal build

  

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• add icodes to MonomerInfo

  

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• better attributes conversion

  

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• test mda to rdkit MonomerInfo conversion

  

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• Merge branch 'rdkit-converter' into rdkit-sanitize

  

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• test mda to rdkit MonomerInfo conversion

  

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• docs

  

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  f57e9e6

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• fix minimal deps test

  

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Commits on Jun 30, 2020

• fix for minimal deps tests 🙏

  

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• use util functions

  

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• Merge branch 'develop' into rdkit-converter

  

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  5493fd1

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• move min deps test up

  

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• capitalize elements by default

  

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Commits on Jul 1, 2020

• store index in MDA object

  

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• fetch singular from _TOPOLOGY_ATTRS

  

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Commits on Jul 2, 2020

• updated changelog

  

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Commits on Jul 3, 2020

• use ag intersection for bonds instead of try except

  

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• more tests + pep8

  

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  b0c39eb

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• Merge branch 'develop' into rdkit-converter

  

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Commits on Jul 6, 2020

• fix test for numpy 1.13.3

  

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• Merge branch 'rdkit-converter' of https://github.com/cbouy/mdanalysis into rdkit-converter

  

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Commits on Jul 7, 2020

• docs + pep8

  

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  0fd38b0

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• fix too long atom names in PDB output

  

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  25ee227

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• table of supported attributes for the converter

  

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• changelog convention

  

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• catch no bonds

  

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• use match in pytest.raises and pytest.warns

  

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Commits on Jul 8, 2020

• remove bondtype attribute

  

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• fix bond attributes

  

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  9c0a42e

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• Merge branch 'rdkit-sanitize' into rdkit-converter

  

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  66d644d

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• simplified the code for infering

  

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Commits on Jul 9, 2020

• include negative charges

  

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Commits on Jul 10, 2020

• skip failing test for now

  

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• new test

  

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• update doc

  

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Commits on Jul 13, 2020

• standardize groups

  

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• fix tests

  

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• add previously failing tests

  

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• Merge branch 'develop' into rdkit-converter

  

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Commits on Jul 14, 2020

• simpler pattern standardization

  

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  d1f06f3

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• more tests on inferring and patterns

  

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• test atom properties and reaction mapping

  

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  6e9c221

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• fix docs

  

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  b02fef6

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• Merge branch 'rdkit-converter' of https://github.com/cbouy/mdanalysis into rdkit-converter

  

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Commits on Jul 15, 2020

• fix minimal build tests

  

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• pep8

  

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• bfactors as TempFactor

  

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• Update CHANGELOG

  

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Commits on Jul 16, 2020

• pep8

  

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• Merge branch 'rdkit-converter' of https://github.com/cbouy/mdanalysis into rdkit-converter

  

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• pep8

  

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• no hydrogen warning

  

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Commits on Jul 17, 2020

• quickfix for polycyclic conjugated systems

  

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• Merge branch 'develop' into rdkit-converter

  

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Commits on Jul 20, 2020

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

  

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Commits on Jul 21, 2020

• general solution

  

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• back to old method for conjugated systems

  

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  ae73aff

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• Merge branch 'rdkit-converter' of https://github.com/cbouy/mdanalysis into rdkit-converter

  

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Commits on Jul 22, 2020

• Merge branch 'develop' into rdkit-converter

  

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• added "RDKit" in changelog

  

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• fix when first atom is charged

  

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  1398f8c

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• working general solution to conjugated systems

  

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  e71a686

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• pep8

  

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  925bd7f

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• Merge branch 'rdkit-converter' of https://github.com/cbouy/mdanalysis into rdkit-converter

  

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• for loop instead of while

  

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Commits on Jul 23, 2020

• bugfix for conjugated system with N at one edge

  

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Commits on Jul 27, 2020

• fix typos

  

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• fix test for min deps

  

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• use indirect parametrization

  

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Commits on Jul 29, 2020

• add coordinates + tests + fix index property

  

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• cache the molecule and only update conformers when iterating trajectory

  

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Commits on Jul 30, 2020

• update docs

  

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• add kwargs to the cache key

  

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Commits on Jul 31, 2020

• use fstrings

  

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Commits on Aug 7, 2020

• Merge branch 'develop' into rdkit-converter

  orbeckst

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Commits on Aug 10, 2020

• Merge branch 'develop' into rdkit-converter

  

  Cédric Bouysset

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• cache kwarg + fix cache tests

  

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  cec1f68

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• Merge branch 'rdkit-converter' of https://github.com/cbouy/mdanalysis into rdkit-converter

  

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Commits on Aug 14, 2020

• fix code review + improve docs

  

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• improve doc

  

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  cdb60b2

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• add test nan in coordinates

  

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• warn nan coordinates

  

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• end of code review

  

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• corrections to smarts patterns for reactions

  

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• sort atoms by NUE + more standardization tests

  

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• pdb atom names formating

  

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• test RDKit->MDA->RDKit->MDA equal

  

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• tackle conjugated systems ending with O-

  

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• docs + pep8

  

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• tests

  

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• add max_iter kwarg

  

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• Merge branch 'develop' into rdkit-converter

  

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• reorder docstring standardize_patterns

  

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• Merge branch 'rdkit-converter' of https://github.com/cbouy/mdanalysis into rdkit-converter

  

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• fix doc build

  

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