README.md

K-Near Neighbour Analysis (NN) of ECFP or GOBBI RDKit fingerprints

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This is a script to perform near neighbour analysis of compound sets. Can be used to calculate intra- or inter- similarity for compounds. Intra-similarity is automatically performed if no second file provided. Can take multiple files using * wildcard.

Main dependencies: 'RDKit'

NN_analysis.py [options]

Options:

-h, --help show this help message and exit

--i1=FILE First inputfile

--i2=FILE Second inputfile (optional)

-o FILE, --out=FILE Outputfile (optional)

--d1=DELIM1, --delim1=DELIM1 Delimiter for first file (default: ' ')

--d2=DELIM2, --delim2=DELIM2 Delimiter for second file (default: ' ')

--delimcol1=DELIMCOL1 Delimiter column of smiles in first file (default:0)

--delimcol2=DELIMCOL2 Delimiter column of smiles in second file (default:0)

-b BITS, --bits=BITS No. bits in morgan fingerprint (default:2048)

-r RADIUS, --radius=RADIUS Radius of morgan fingerprint (default:2)

-t TOPN, --topn=TOPN Top n neighbors (default:1)

-n NCORES, --ncores=NCORES No. cores (default:1)

--pf1 Parallel process list of first files, not lines per file

--pf2 Parallel process list of second files, not lines per file

--gobbi Use Gobbi 2D pharmacophore FPs

--mw=MW Max. Mw filter