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https://github.com/unixjunkie/acpc
Chemoinformatics tool for ligand-based virtual screening
https://github.com/unixjunkie/acpc
chemoinformatics lbvs ligand ocaml partial-charges
Last synced: 3 months ago
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Chemoinformatics tool for ligand-based virtual screening
- Host: GitHub
- URL: https://github.com/unixjunkie/acpc
- Owner: UnixJunkie
- License: other
- Created: 2014-01-09T01:52:28.000Z (almost 11 years ago)
- Default Branch: master
- Last Pushed: 2023-01-11T03:43:14.000Z (almost 2 years ago)
- Last Synced: 2023-10-20T23:36:35.009Z (about 1 year ago)
- Topics: chemoinformatics, lbvs, ligand, ocaml, partial-charges
- Language: OCaml
- Size: 673 KB
- Stars: 18
- Watchers: 4
- Forks: 2
- Open Issues: 8
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
ACPC v1.0
=========
Don't hesitate to contact the author in case you have problems running
the software or discover a bug.
Installation
------------
To install ACPC, you first need to install and configure
the OCaml package manager (OPAM). Cf. http://opam.ocaml.org/
Once this is done, you can automatically install ACPC
with the following command:
$ opam install acpc
Recommended usage (protocol)
----------------------------
ACPC was designed to be rotation and translation invariant.
ACPC is not invariant to the conformer of a molecule,
neither to the charge model that was used to assign partial charges to it.
The following protocol has been validated:
the query molecule(s) _AND_ the database to screen must be prepared in
the same way. The same software with same parameters must be used
to assign partial charges and generate conformers for _ALL_ molecules.
The recommended charge models are:
MOE's MMFF94x or as a fallback Open Babel's Gasteiger.
Reading the related research article is highly recommended:
"A rotation-translation invariant molecular descriptor of
partial charges and its use in ligand-based virtual screening".
Citing the article is kindly asked from users of the software.
Examples
--------
1) one query on a small database
$ acpc -q query.mol2 -db database.mol2
2) same but storing the top 10 molecules
$ acpc -q query.mol2 -db database.mol2 -top 10 -o ten_best.mol2
3) one query on a large database
$ acpc_big -q query.mol2 -db database.mol2
4) separate each molecule from a mol2 file into separate files
$ acpc_mol2tool some_molecules.mol2
Get some help
-------------
$ acpc -h
-cmp {CC|Tani|Tref|Tdb} LBAC+/- comparison method (default: CC)
-htq list molecules scoring Higher Than the Query with itself
-q query.mol2 query (incompatible with -qf)
-qf f file containing a list of mol2 files (incompatible with -q)
-db db.mol2 database
-dx float X axis discretization (default: 0.005000)
-v output intermediate results
-nopp don't rm duplicate molecules
-np nprocs max CPUs to use (default: 1)
-ng no gnuplot
-nr no ROC curve (also sets -ng)
-o output.mol2 output file (also requires -top, incompatible with -qf)
-top N nb. best scoring molecules to output (also requires -o)
-help Display this list of options
--help Display this list of options
# acpc_big -h
-q query.mol2 query
-db db.mol2 database
-dx float X axis discretization (default: 0.005000)
-help Display this list of options
--help Display this list of options
WARNING
-------
Don't do two queries at the same time on the same computer or on top of NFS
with a same query molecule file (-q SOME_QUERY.mol2), this may overwrite
result files in a strange way (SOME_QUERY.ranks, SOME_QUERY.scores and
SOME_QUERY.scored-label).