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
-
one query on a small database
$ acpc -q query.mol2 -db database.mol2
-
same but storing the top 10 molecules
$ acpc -q query.mol2 -db database.mol2 -top 10 -o ten_best.mol2
-
one query on a large database
$ acpc_big -q query.mol2 -db database.mol2
-
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).