https://github.com/unixjunkie/acp4
AutoCorrelation of Pharmacophore Features
https://github.com/unixjunkie/acp4
autocorrelation binding-site ligand ocaml-program pharmacophore virtual-screening
Last synced: 2 months ago
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AutoCorrelation of Pharmacophore Features
- Host: GitHub
- URL: https://github.com/unixjunkie/acp4
- Owner: UnixJunkie
- License: gpl-3.0
- Created: 2022-11-08T06:56:42.000Z (over 3 years ago)
- Default Branch: master
- Last Pushed: 2025-02-25T16:01:28.000Z (about 1 year ago)
- Last Synced: 2025-11-23T20:03:02.840Z (5 months ago)
- Topics: autocorrelation, binding-site, ligand, ocaml-program, pharmacophore, virtual-screening
- Language: OCaml
- Homepage:
- Size: 623 KB
- Stars: 3
- Watchers: 2
- Forks: 3
- Open Issues: 1
-
Metadata Files:
- Readme: README.md
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README
# ACP4: AutoCorrelation of Pharmacophore Features
```
acp4 program usage:
./acp4
[-i ]: input file to encode
[-q ]: query molecule
[--queries ]: query molecules
[-db ]: database to screen
-o : output file (encoded db or query scores)
[-np ]: nprocs (default=1)
[-s ]: BST chunk size (default=100000)
[-c ]: 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 ]: 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 ]: file containing a list of serialized BST filenames
[-td ]: 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 : binding-site ligand input file
-p : receptor protein input file
[-d ]: distance cutoff (default=5.00)
-o : 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
```