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phi-grib / flame_installer_windows

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RDKit molecular descriptors are reduced to 114 from 200 in self-contained installation. #2

Open josecarlosgomezt opened 4 years ago

josecarlosgomezt commented 4 years ago

When using self-contained flame, RDKit computes only 114 descriptors instead of 200. There is no error message, I realized of this when using a model created in a regular flame version.

It seems to be that rdkit can not access to FragmentDescriptors.csv anymore due to path integrity loss after exporting the environment.

To fix this, unzip the attached file into:

_flame_installer_windows\setup_self_contained\flameenv\Lib\site-packages\rdkit\Chem\

to replace non-working files before compiling the installer.

fix.zip

manuelpastor commented 3 years ago

Alternative:

  1. copy FragmentDescriptors.csv, from the folder Library\share\RDKit\Data to Lib\site-package\rdkit\Chem
  2. edit Fragments.py in Lib\site-package\rdkit\Chem 
    # defaultPatternFileName = os.path.join(RDConfig.RDDataDir, 'FragmentDescriptors.csv')
defaultPatternFileName = os.path.join(os.path.dirname(os.path.realpath(__file__)), 'FragmentDescriptors.csv')