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Simple RDKitConverter #2775

Merged
merged 107 commits into from
Aug 21, 2020
Merged

Simple RDKitConverter #2775

merged 107 commits into from
Aug 21, 2020

Commits on Jun 19, 2020

  1. simple converter

    Cédric Bouysset committed Jun 19, 2020
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Commits on Jun 22, 2020

  1. add PDB residue info and guessers

    Cédric Bouysset committed Jun 22, 2020
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Commits on Jun 24, 2020

  1. fix 2 letter atom names and fix bond order

    Cédric Bouysset committed Jun 24, 2020
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  2. test mol2 topology and pdb info

    Cédric Bouysset committed Jun 24, 2020
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Commits on Jun 25, 2020

  1. autopep8

    Cédric Bouysset committed Jun 25, 2020
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  2. fix code review

    Cédric Bouysset committed Jun 25, 2020
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  3. store other attributes in each atom

    Cédric Bouysset committed Jun 25, 2020
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  4. more tests on topology + pep8

    Cédric Bouysset committed Jun 25, 2020
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Commits on Jun 26, 2020

  1. fix other props type

    Cédric Bouysset committed Jun 26, 2020
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  2. bond order and charges

    Cédric Bouysset committed Jun 26, 2020
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  3. fix indentation and bonds with atoms outside of atomgroup

    Cédric Bouysset committed Jun 26, 2020
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  4. fix test

    Cédric Bouysset committed Jun 26, 2020
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Commits on Jun 29, 2020

  1. fix test minimal build

    Cédric Bouysset committed Jun 29, 2020
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  2. add icodes to MonomerInfo

    Cédric Bouysset committed Jun 29, 2020
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  3. better attributes conversion

    Cédric Bouysset committed Jun 29, 2020
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  4. test mda to rdkit MonomerInfo conversion

    Cédric Bouysset committed Jun 29, 2020
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  5. Merge branch 'rdkit-converter' into rdkit-sanitize

    Cédric Bouysset committed Jun 29, 2020
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  6. test mda to rdkit MonomerInfo conversion

    Cédric Bouysset committed Jun 29, 2020
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  7. docs

    Cédric Bouysset committed Jun 29, 2020
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  8. fix minimal deps test

    Cédric Bouysset committed Jun 29, 2020
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Commits on Jun 30, 2020

  1. fix for minimal deps tests 🙏

    Cédric Bouysset committed Jun 30, 2020
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  2. use util functions

    Cédric Bouysset committed Jun 30, 2020
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  3. Merge branch 'develop' into rdkit-converter

    Cédric Bouysset committed Jun 30, 2020
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  4. move min deps test up

    Cédric Bouysset committed Jun 30, 2020
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  5. capitalize elements by default

    Cédric Bouysset committed Jun 30, 2020
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Commits on Jul 1, 2020

  1. store index in MDA object

    Cédric Bouysset committed Jul 1, 2020
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  2. fetch singular from _TOPOLOGY_ATTRS

    Cédric Bouysset committed Jul 1, 2020
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Commits on Jul 2, 2020

  1. updated changelog

    Cédric Bouysset committed Jul 2, 2020
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Commits on Jul 3, 2020

  1. use ag intersection for bonds instead of try except

    Cédric Bouysset committed Jul 3, 2020
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  2. more tests + pep8

    Cédric Bouysset committed Jul 3, 2020
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  3. Merge branch 'develop' into rdkit-converter

    Cédric Bouysset committed Jul 3, 2020
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Commits on Jul 6, 2020

  1. fix test for numpy 1.13.3

    Cédric Bouysset committed Jul 6, 2020
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  2. Merge branch 'rdkit-converter' of https://github.com/cbouy/mdanalysis … 

    …into rdkit-converter
    Cédric Bouysset committed Jul 6, 2020
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Commits on Jul 7, 2020

  1. docs + pep8

    Cédric Bouysset committed Jul 7, 2020
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  2. fix too long atom names in PDB output

    Cédric Bouysset committed Jul 7, 2020
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  3. table of supported attributes for the converter

    Cédric Bouysset committed Jul 7, 2020
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  4. changelog convention

    Cédric Bouysset committed Jul 7, 2020
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  5. catch no bonds

    Cédric Bouysset committed Jul 7, 2020
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  6. use match in pytest.raises and pytest.warns

    Cédric Bouysset committed Jul 7, 2020
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Commits on Jul 8, 2020

  1. remove bondtype attribute

    Cédric Bouysset committed Jul 8, 2020
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  2. fix bond attributes

    Cédric Bouysset committed Jul 8, 2020
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  3. Merge branch 'rdkit-sanitize' into rdkit-converter

    Cédric Bouysset committed Jul 8, 2020
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  4. simplified the code for infering

    Cédric Bouysset committed Jul 8, 2020
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Commits on Jul 9, 2020

  1. include negative charges

    Cédric Bouysset committed Jul 9, 2020
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Commits on Jul 10, 2020

  1. skip failing test for now

    Cédric Bouysset committed Jul 10, 2020
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  2. new test

    Cédric Bouysset committed Jul 10, 2020
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  3. update doc

    Cédric Bouysset committed Jul 10, 2020
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Commits on Jul 13, 2020

  1. standardize groups

    Cédric Bouysset committed Jul 13, 2020
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  2. fix tests

    Cédric Bouysset committed Jul 13, 2020
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  3. add previously failing tests

    Cédric Bouysset committed Jul 13, 2020
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  4. Merge branch 'develop' into rdkit-converter

    Cédric Bouysset committed Jul 13, 2020
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Commits on Jul 14, 2020

  1. simpler pattern standardization

    Cédric Bouysset committed Jul 14, 2020
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  2. more tests on inferring and patterns

    Cédric Bouysset committed Jul 14, 2020
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  3. test atom properties and reaction mapping

    Cédric Bouysset committed Jul 14, 2020
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  4. fix docs

    Cédric Bouysset committed Jul 14, 2020
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  5. Merge branch 'rdkit-converter' of https://github.com/cbouy/mdanalysis … 

    …into rdkit-converter
    Cédric Bouysset committed Jul 14, 2020
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Commits on Jul 15, 2020

  1. fix minimal build tests

    Cédric Bouysset committed Jul 15, 2020
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  2. pep8

    Cédric Bouysset committed Jul 15, 2020
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  3. bfactors as TempFactor

    Cédric Bouysset committed Jul 15, 2020
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  4. Update CHANGELOG

    Cédric Bouysset committed Jul 15, 2020
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Commits on Jul 16, 2020

  1. pep8

    Cédric Bouysset committed Jul 16, 2020
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  2. Merge branch 'rdkit-converter' of https://github.com/cbouy/mdanalysis … 

    …into rdkit-converter
    Cédric Bouysset committed Jul 16, 2020
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  3. pep8

    Cédric Bouysset committed Jul 16, 2020
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  4. no hydrogen warning

    Cédric Bouysset committed Jul 16, 2020
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Commits on Jul 17, 2020

  1. quickfix for polycyclic conjugated systems

    Cédric Bouysset committed Jul 17, 2020
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  2. Merge branch 'develop' into rdkit-converter

    Cédric Bouysset committed Jul 17, 2020
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Commits on Jul 20, 2020

  1. save any atom property instead of just the ones tagged with "_MDAnaly… 

    …sis"
    Cédric Bouysset committed Jul 20, 2020
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Commits on Jul 21, 2020

  1. general solution

    Cédric Bouysset committed Jul 21, 2020
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  2. back to old method for conjugated systems

    Cédric Bouysset committed Jul 21, 2020
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  3. Merge branch 'rdkit-converter' of https://github.com/cbouy/mdanalysis … 

    …into rdkit-converter
    Cédric Bouysset committed Jul 21, 2020
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Commits on Jul 22, 2020

  1. Merge branch 'develop' into rdkit-converter

    Cédric Bouysset committed Jul 22, 2020
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  2. added "RDKit" in changelog

    Cédric Bouysset committed Jul 22, 2020
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  3. fix when first atom is charged

    Cédric Bouysset committed Jul 22, 2020
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  4. working general solution to conjugated systems

    Cédric Bouysset committed Jul 22, 2020
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  5. pep8

    Cédric Bouysset committed Jul 22, 2020
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  6. Merge branch 'rdkit-converter' of https://github.com/cbouy/mdanalysis … 

    …into rdkit-converter
    Cédric Bouysset committed Jul 22, 2020
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  7. for loop instead of while

    Cédric Bouysset committed Jul 22, 2020
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Commits on Jul 23, 2020

  1. bugfix for conjugated system with N at one edge

    Cédric Bouysset committed Jul 23, 2020
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Commits on Jul 27, 2020

  1. fix typos

    Cédric Bouysset committed Jul 27, 2020
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  2. fix test for min deps

    Cédric Bouysset committed Jul 27, 2020
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  3. use indirect parametrization

    Cédric Bouysset committed Jul 27, 2020
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Commits on Jul 29, 2020

  1. add coordinates + tests + fix index property

    Cédric Bouysset committed Jul 29, 2020
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  2. cache the molecule and only update conformers when iterating trajectory

    Cédric Bouysset committed Jul 29, 2020
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Commits on Jul 30, 2020

  1. update docs

    Cédric Bouysset committed Jul 30, 2020
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  2. add kwargs to the cache key

    Cédric Bouysset committed Jul 30, 2020
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Commits on Jul 31, 2020

  1. use fstrings

    Cédric Bouysset committed Jul 31, 2020
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Commits on Aug 7, 2020

  1. Merge branch 'develop' into rdkit-converter

    @orbeckst
    orbeckst committed Aug 7, 2020
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Commits on Aug 10, 2020

  1. Merge branch 'develop' into rdkit-converter

    Cédric Bouysset committed Aug 10, 2020
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  2. cache kwarg + fix cache tests

    Cédric Bouysset committed Aug 10, 2020
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  3. Merge branch 'rdkit-converter' of https://github.com/cbouy/mdanalysis … 

    …into rdkit-converter
    Cédric Bouysset committed Aug 10, 2020
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Commits on Aug 14, 2020

  1. fix code review + improve docs

    Cédric Bouysset committed Aug 14, 2020
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  2. improve doc

    Cédric Bouysset committed Aug 14, 2020
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  3. add test nan in coordinates

    Cédric Bouysset committed Aug 14, 2020
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  4. warn nan coordinates

    Cédric Bouysset committed Aug 14, 2020
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  5. end of code review

    Cédric Bouysset committed Aug 14, 2020
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  6. corrections to smarts patterns for reactions

    Cédric Bouysset committed Aug 14, 2020
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  7. sort atoms by NUE + more standardization tests

    Cédric Bouysset committed Aug 14, 2020
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  8. pdb atom names formating

    Cédric Bouysset committed Aug 14, 2020
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  9. test RDKit->MDA->RDKit->MDA equal

    Cédric Bouysset committed Aug 14, 2020
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  10. tackle conjugated systems ending with O-

    Cédric Bouysset committed Aug 14, 2020
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  11. docs + pep8

    Cédric Bouysset committed Aug 14, 2020
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  12. tests

    Cédric Bouysset committed Aug 14, 2020
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  13. add max_iter kwarg

    Cédric Bouysset committed Aug 14, 2020
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  14. Merge branch 'develop' into rdkit-converter

    Cédric Bouysset committed Aug 14, 2020
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  15. reorder docstring standardize_patterns

    Cédric Bouysset committed Aug 14, 2020
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  16. Merge branch 'rdkit-converter' of https://github.com/cbouy/mdanalysis … 

    …into rdkit-converter
    Cédric Bouysset committed Aug 14, 2020
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  17. fix doc build

    Cédric Bouysset committed Aug 14, 2020
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