RDKitReader and RDKitParser#2707

Merged

richardjgowers merged 43 commits intoMDAnalysis:developfrom

cbouy:develop

Jun 19, 2020

Commits on Jun 1, 2020

barebones topology from RDKitParser
Cédric Bouysset
committed

Commits on Jun 2, 2020

test for PDB and MOL2 + fix atomtypes and residues
Cédric Bouysset
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Commits on Jun 3, 2020

fix test on bond orders
Cédric Bouysset
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add SMILES parser test
Cédric Bouysset
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reorganize code + create name if not present
Cédric Bouysset
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added Segids attribute
Cédric Bouysset
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added rdkit to appveyor and travis
Cédric Bouysset
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Commits on Jun 4, 2020

added SDF file for rdkit tests
Cédric Bouysset
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forgot hydrogens and 3D on SDFile
Cédric Bouysset
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SDF test
Cédric Bouysset
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added formal charges + attrs specific to PDB files
Cédric Bouysset
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fix charges to partial instead of formal
Cédric Bouysset
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Commits on Jun 5, 2020

Merge branch 'develop' into develop
Cédric Bouysset
authored
added warning if multiple partial charges
Cédric Bouysset
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updated parser doc
Cédric Bouysset
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universe.from_smiles + tests on MOL2 charges
Cédric Bouysset
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Commits on Jun 8, 2020

universe from smiles generate coordinates and tests + doc
Cédric Bouysset
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renamed n_frames to numConfs to be in line with RDKit
Cédric Bouysset
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bond order testing from rdkit
Cédric Bouysset
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added aromaticity attr
Cédric Bouysset
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Commits on Jun 9, 2020

coordinates reader
Cédric Bouysset
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added tests on coordinates
Cédric Bouysset
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aromatic atomselection + test
Cédric Bouysset
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Commits on Jun 10, 2020

fix minimal dependency
Cédric Bouysset
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Commits on Jun 11, 2020

updated docs
Cédric Bouysset
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Commits on Jun 12, 2020

updated doc
Cédric Bouysset
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fix PEP8 and init array
Cédric Bouysset
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test combine aromatic selection
Cédric Bouysset
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test compare with mol2reader
Cédric Bouysset
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added kwargs for EmbedMultipleConfs
Cédric Bouysset
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Commits on Jun 15, 2020

example for EmbedMultipleConfs kwargs
Cédric Bouysset
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warning and tests on coordinates
Cédric Bouysset
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Merge branch 'develop' into develop
Cédric Bouysset
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drop python 2 support
Cédric Bouysset
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Merge branch 'develop' of https://github.com/cbouy/mdanalysis into develop
Cédric Bouysset
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modified tests
Cédric Bouysset
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fix using fixtures in parametrize
Cédric Bouysset
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Commits on Jun 16, 2020

actual fix for coordinate tests
Cédric Bouysset
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Commits on Jun 18, 2020

fix the docs and style guide
Cédric Bouysset
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Commits on Jun 19, 2020

update docs and changelog for 2.0.0
Cédric Bouysset
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Merge branch 'develop' into develop
Cédric Bouysset
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Update selection.py
richardjgowers
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Update selection.py
richardjgowers
authored