Mercurial > repos > marpiech > norwich_docking_tools
diff galaxy-tools/test-data/rdock/1sj0_rdock.prm @ 0:4eb3f9cb2a51 draft
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| author | dzesikah |
|---|---|
| date | Fri, 26 Aug 2016 09:53:37 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/galaxy-tools/test-data/rdock/1sj0_rdock.prm Fri Aug 26 09:53:37 2016 -0400 @@ -0,0 +1,53 @@ +RBT_PARAMETER_FILE_V1.00 +TITLE 1sj0_ASTEX + +RECEPTOR_FILE 1sj0_rdock.mol2 +RECEPTOR_FLEX 3.0 + +################################################################## +### CAVITY DEFINITION: REFERENCE LIGAND METHOD +################################################################## +SECTION MAPPER + SITE_MAPPER RbtLigandSiteMapper + REF_MOL 1sj0_ligand.sd + RADIUS 6.0 + SMALL_SPHERE 1.0 + MIN_VOLUME 100 + MAX_CAVITIES 1 + VOL_INCR 0.0 + GRIDSTEP 0.5 +END_SECTION + +################################################################ +# CAVITY DEFINITION: TWO SPHERES METHOD +################################################################ +#SECTION MAPPER +# SITE_MAPPER RbtSphereSiteMapper +##HETATM 2815 O HOH 756 37.266 -20.992 -4.910 0.90 24.86 1CSE2940 +# CENTER (7.185,8.250,22.649) +# RADIUS 15.0 +# SMALL_SPHERE 1.5 +# LARGE_SPHERE 6.0 +# MAX_CAVITIES 1 +#END_SECTION + +################################# +#CAVITY RESTRAINT PENALTY +################################# +SECTION CAVITY + SCORING_FUNCTION RbtCavityGridSF + WEIGHT 1.0 +END_SECTION + +################################# +## PHARMACOPHORIC RESTRAINTS +################################# +#SECTION PHARMA +# SCORING_FUNCTION RbtPharmaSF +# WEIGHT 1.0 +# CONSTRAINTS_FILE pharma_cdk2.const +# OPTIONAL_FILE optional.const +# NOPT 3 +# WRITE_ERRORS TRUE +#END_SECTION +