annotate test-data/1sj0_rdock.prm @ 0:63f3f7b17aa4 draft default tip

planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/rdock/ commit d3da4ff3bfb86ce0686a87c4987e94486854d839

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