Knitwork

Refactor of FragmentKnitwork

Installation

git clone https://github.com/xchem/Knitwork
cd Knitwork
pip install --user -e .

Configuration

The configure command can be used to set variables that the package will use when running commands:

e.g.

python -m knitwork configure GRAPH_LOCATION XXXXX
python -m knitwork configure GRAPH_USERNAME XXXXX
python -m knitwork configure GRAPH_PASSWORD XXXXX

Running Fragment Knitwork

Run the following steps to generate merges from ligands in an SDF.

Fragmentation

To run the Fragment process which looks for subnodes and synthons for a given set of fragments/molecules in an SDF and groups them into pairs:

python -m knitwork fragment INPUT_SDF

This will generate pickled pandas dataframes, along with caches and other outputs in fragment_output by default:

• molecules.pkl.gz: pickled dataframe of input molecules
• molecules.sdf: SDF of input molecules
• pairs.pkl.gz: pickled dataframe of output pairs

For more options see:

python -m knitwork fragment --help

Pure Knitting

To query the graph database for "pure" merges matching fragment pairs in the fragment_output folder by default:

python -m knitwork pure-merge

This will generate pickled pandas dataframes, along with caches and other outputs in knitwork_output by default:

• pure_merges.pkl.gz: pickled dataframe of merges
• pure_merges.sdf: SDF of merges

Impure Knitting

To query the graph database for "impure" merges matching fragment pairs in the fragment_output folder by default:

python -m knitwork impure-merge

This will generate pickled pandas dataframes, along with caches and other outputs in knitwork_output by default:

• impure_merges.pkl.gz: pickled dataframe of merges
• impure_merges.sdf: SDF of merges