acp4 program usage:
./acp4
[-i <filename.ph4>]: input file to encode
[-q <filename.ph4>]: query molecule
[--queries <filename.ph4>]: query molecules
[-db <filename.ph4>]: database to screen
-o <filename.{csv|scores}>: output file (encoded db or query scores)
[-np <int>]: nprocs (default=1)
[-s <int>]: BST chunk size (default=100000)
[-c <float>]: cutoff distance (default=5.00)
[-f]: force overwriting binary cache files, if any
use -f if you are changing -dx or -c compared to previous queries
[-dx <float>]: radial discretization step (default=0.5)
[--no-plot]: turn OFF gnuplot
[--no-tap]: neither read nor write from/to binary cache files
[--confs]: if the DB has several _consecutive_ conformers
[--quick]: quick; exit right after scoring; no perf. metrics
[--index]: create a BST index for the DB being screened
[--BSTs <filename.txt>]: file containing a list of serialized BST filenames
[-td <float>]: maximum Tanimoto _distance_ to (single) query
[--BS]: load optimal defaults for binding-sites (ignores -c and -dx)
[-v]: verbose/debug mode
acp4_scissors program usage:
./scissors
-l <ligand.sdf>: binding-site ligand input file
-p <protein.ph4>: receptor protein input file
[-d <float>]: distance cutoff (default=5.00)
-o <output.ph4>: ligand-defined binding site output file
[-v]: verbose/debug mode
To extract pharmacophore points from a molecule in SDF format, use molenc_ph4.py:
usage: molenc_ph4.py [-h] [-i input.sdf] [-o output.ph4] [--bild] [--no-group]
[--permissive]
compute pharmacophore features for 3D molecules
options:
-h, --help show this help message and exit
-i input.sdf conformers input file
-o output.ph4 ph4 features output file
--bild output BILD files for visu in chimera
--no-group turn OFF grouping of HYD features
--permissive turn OFF rdkit valence check