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Pandas support #15

Merged
merged 56 commits into from
Jan 3, 2017
Merged

Pandas support #15

merged 56 commits into from
Jan 3, 2017

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mwojcikowski
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@mwojcikowski mwojcikowski commented Oct 3, 2016

Initial resolution of #11. Pandas rendering in Jupyter Notebook, plus additional IO methods like read_sdf, etc.

  • series ligands in pandas (implemented on oddt.toolkit level)
  • PNG and SVG rendering in Jupyter Notebook
  • documentation
  • tests
  • docstrings

oddt.pandas functions:

  • read_sdf (all reading support chunksize for big SD/Mol2)
  • read_mol2
  • read_csv (TODO: support chunks)

oddt.pandas.ChemDataFrame methods:

  • to_sdf
  • to_mol2
  • to_csv (with molecule column to smiles) exporting
  • to_excel (replace molecule column with PNGs)
  • substructure searching [chemseries <= mol and chemseries >= mol, "lower" molecules/series is substructure]
  • similarity searching [(chemseries.calcfp() | mol.calcfp()) >= 0.7]

oddt.pandas.ChemSeries methods:

  • to_smiles
  • to_sdf
  • to_mol2

@mwojcikowski mwojcikowski merged commit 14bafe9 into master Jan 3, 2017
@mwojcikowski mwojcikowski deleted the experimental-pandas branch December 5, 2017 14:10
mwojcikowski added a commit that referenced this pull request Apr 27, 2018
…master'

Resolve "Add missing atoms using Contrained Embedding"

Closes #15

See merge request mwojcikowski/rdkit-fixer!10
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