Mercurial > repos > marpiech > norwich_tools

annotate test-data/rdock/1sj0_rdock.prm @ 0:bc03dbb6eb37 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit 781926e52355f7805db8d9a4ccafeff397b19aa4-dirty
author marpiech
date Mon, 29 Aug 2016 03:38:13 -0400
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
bc03dbb6eb37 planemo upload commit 781926e52355f7805db8d9a4ccafeff397b19aa4-dirty
marpiech
parents:
diff changeset
1 RBT_PARAMETER_FILE_V1.00
bc03dbb6eb37 planemo upload commit 781926e52355f7805db8d9a4ccafeff397b19aa4-dirty
marpiech
parents:
diff changeset
2 TITLE 1sj0_ASTEX
bc03dbb6eb37 planemo upload commit 781926e52355f7805db8d9a4ccafeff397b19aa4-dirty
marpiech
parents:
diff changeset
3
bc03dbb6eb37 planemo upload commit 781926e52355f7805db8d9a4ccafeff397b19aa4-dirty
marpiech
parents:
diff changeset
4 RECEPTOR_FILE 1sj0_rdock.mol2
bc03dbb6eb37 planemo upload commit 781926e52355f7805db8d9a4ccafeff397b19aa4-dirty
marpiech
parents:
diff changeset
5 RECEPTOR_FLEX 3.0
bc03dbb6eb37 planemo upload commit 781926e52355f7805db8d9a4ccafeff397b19aa4-dirty
marpiech
parents:
diff changeset
6
bc03dbb6eb37 planemo upload commit 781926e52355f7805db8d9a4ccafeff397b19aa4-dirty
marpiech
parents:
diff changeset
7 ##################################################################
bc03dbb6eb37 planemo upload commit 781926e52355f7805db8d9a4ccafeff397b19aa4-dirty
marpiech
parents:
diff changeset
8 ### CAVITY DEFINITION: REFERENCE LIGAND METHOD
bc03dbb6eb37 planemo upload commit 781926e52355f7805db8d9a4ccafeff397b19aa4-dirty
marpiech
parents:
diff changeset
9 ##################################################################
bc03dbb6eb37 planemo upload commit 781926e52355f7805db8d9a4ccafeff397b19aa4-dirty
marpiech
parents:
diff changeset
10 SECTION MAPPER
bc03dbb6eb37 planemo upload commit 781926e52355f7805db8d9a4ccafeff397b19aa4-dirty
marpiech
parents:
diff changeset
11 SITE_MAPPER RbtLigandSiteMapper
bc03dbb6eb37 planemo upload commit 781926e52355f7805db8d9a4ccafeff397b19aa4-dirty
marpiech
parents:
diff changeset
12 REF_MOL 1sj0_ligand.sd
bc03dbb6eb37 planemo upload commit 781926e52355f7805db8d9a4ccafeff397b19aa4-dirty
marpiech
parents:
diff changeset
13 RADIUS 6.0
bc03dbb6eb37 planemo upload commit 781926e52355f7805db8d9a4ccafeff397b19aa4-dirty
marpiech
parents:
diff changeset
14 SMALL_SPHERE 1.0
bc03dbb6eb37 planemo upload commit 781926e52355f7805db8d9a4ccafeff397b19aa4-dirty
marpiech
parents:
diff changeset
15 MIN_VOLUME 100
bc03dbb6eb37 planemo upload commit 781926e52355f7805db8d9a4ccafeff397b19aa4-dirty
marpiech
parents:
diff changeset
16 MAX_CAVITIES 1
bc03dbb6eb37 planemo upload commit 781926e52355f7805db8d9a4ccafeff397b19aa4-dirty
marpiech
parents:
diff changeset
17 VOL_INCR 0.0
bc03dbb6eb37 planemo upload commit 781926e52355f7805db8d9a4ccafeff397b19aa4-dirty
marpiech
parents:
diff changeset
18 GRIDSTEP 0.5
bc03dbb6eb37 planemo upload commit 781926e52355f7805db8d9a4ccafeff397b19aa4-dirty
marpiech
parents:
diff changeset
19 END_SECTION
bc03dbb6eb37 planemo upload commit 781926e52355f7805db8d9a4ccafeff397b19aa4-dirty
marpiech
parents:
diff changeset
20
bc03dbb6eb37 planemo upload commit 781926e52355f7805db8d9a4ccafeff397b19aa4-dirty
marpiech
parents:
diff changeset
21 ################################################################
bc03dbb6eb37 planemo upload commit 781926e52355f7805db8d9a4ccafeff397b19aa4-dirty
marpiech
parents:
diff changeset
22 # CAVITY DEFINITION: TWO SPHERES METHOD
bc03dbb6eb37 planemo upload commit 781926e52355f7805db8d9a4ccafeff397b19aa4-dirty
marpiech
parents:
diff changeset
23 ################################################################
bc03dbb6eb37 planemo upload commit 781926e52355f7805db8d9a4ccafeff397b19aa4-dirty
marpiech
parents:
diff changeset
24 #SECTION MAPPER
bc03dbb6eb37 planemo upload commit 781926e52355f7805db8d9a4ccafeff397b19aa4-dirty
marpiech
parents:
diff changeset
25 # SITE_MAPPER RbtSphereSiteMapper
bc03dbb6eb37 planemo upload commit 781926e52355f7805db8d9a4ccafeff397b19aa4-dirty
marpiech
parents:
diff changeset
26 ##HETATM 2815 O HOH 756 37.266 -20.992 -4.910 0.90 24.86 1CSE2940
bc03dbb6eb37 planemo upload commit 781926e52355f7805db8d9a4ccafeff397b19aa4-dirty
marpiech
parents:
diff changeset
27 # CENTER (7.185,8.250,22.649)
bc03dbb6eb37 planemo upload commit 781926e52355f7805db8d9a4ccafeff397b19aa4-dirty
marpiech
parents:
diff changeset
28 # RADIUS 15.0
bc03dbb6eb37 planemo upload commit 781926e52355f7805db8d9a4ccafeff397b19aa4-dirty
marpiech
parents:
diff changeset
29 # SMALL_SPHERE 1.5
bc03dbb6eb37 planemo upload commit 781926e52355f7805db8d9a4ccafeff397b19aa4-dirty
marpiech
parents:
diff changeset
30 # LARGE_SPHERE 6.0
bc03dbb6eb37 planemo upload commit 781926e52355f7805db8d9a4ccafeff397b19aa4-dirty
marpiech
parents:
diff changeset
31 # MAX_CAVITIES 1
bc03dbb6eb37 planemo upload commit 781926e52355f7805db8d9a4ccafeff397b19aa4-dirty
marpiech
parents:
diff changeset
32 #END_SECTION
bc03dbb6eb37 planemo upload commit 781926e52355f7805db8d9a4ccafeff397b19aa4-dirty
marpiech
parents:
diff changeset
33
bc03dbb6eb37 planemo upload commit 781926e52355f7805db8d9a4ccafeff397b19aa4-dirty
marpiech
parents:
diff changeset
34 #################################
bc03dbb6eb37 planemo upload commit 781926e52355f7805db8d9a4ccafeff397b19aa4-dirty
marpiech
parents:
diff changeset
35 #CAVITY RESTRAINT PENALTY
bc03dbb6eb37 planemo upload commit 781926e52355f7805db8d9a4ccafeff397b19aa4-dirty
marpiech
parents:
diff changeset
36 #################################
bc03dbb6eb37 planemo upload commit 781926e52355f7805db8d9a4ccafeff397b19aa4-dirty
marpiech
parents:
diff changeset
37 SECTION CAVITY
bc03dbb6eb37 planemo upload commit 781926e52355f7805db8d9a4ccafeff397b19aa4-dirty
marpiech
parents:
diff changeset
38 SCORING_FUNCTION RbtCavityGridSF
bc03dbb6eb37 planemo upload commit 781926e52355f7805db8d9a4ccafeff397b19aa4-dirty
marpiech
parents:
diff changeset
39 WEIGHT 1.0
bc03dbb6eb37 planemo upload commit 781926e52355f7805db8d9a4ccafeff397b19aa4-dirty
marpiech
parents:
diff changeset
40 END_SECTION
bc03dbb6eb37 planemo upload commit 781926e52355f7805db8d9a4ccafeff397b19aa4-dirty
marpiech
parents:
diff changeset
41
bc03dbb6eb37 planemo upload commit 781926e52355f7805db8d9a4ccafeff397b19aa4-dirty
marpiech
parents:
diff changeset
42 #################################
bc03dbb6eb37 planemo upload commit 781926e52355f7805db8d9a4ccafeff397b19aa4-dirty
marpiech
parents:
diff changeset
43 ## PHARMACOPHORIC RESTRAINTS
bc03dbb6eb37 planemo upload commit 781926e52355f7805db8d9a4ccafeff397b19aa4-dirty
marpiech
parents:
diff changeset
44 #################################
bc03dbb6eb37 planemo upload commit 781926e52355f7805db8d9a4ccafeff397b19aa4-dirty
marpiech
parents:
diff changeset
45 #SECTION PHARMA
bc03dbb6eb37 planemo upload commit 781926e52355f7805db8d9a4ccafeff397b19aa4-dirty
marpiech
parents:
diff changeset
46 # SCORING_FUNCTION RbtPharmaSF
bc03dbb6eb37 planemo upload commit 781926e52355f7805db8d9a4ccafeff397b19aa4-dirty
marpiech
parents:
diff changeset
47 # WEIGHT 1.0
bc03dbb6eb37 planemo upload commit 781926e52355f7805db8d9a4ccafeff397b19aa4-dirty
marpiech
parents:
diff changeset
48 # CONSTRAINTS_FILE pharma_cdk2.const
bc03dbb6eb37 planemo upload commit 781926e52355f7805db8d9a4ccafeff397b19aa4-dirty
marpiech
parents:
diff changeset
49 # OPTIONAL_FILE optional.const
bc03dbb6eb37 planemo upload commit 781926e52355f7805db8d9a4ccafeff397b19aa4-dirty
marpiech
parents:
diff changeset
50 # NOPT 3
bc03dbb6eb37 planemo upload commit 781926e52355f7805db8d9a4ccafeff397b19aa4-dirty
marpiech
parents:
diff changeset
51 # WRITE_ERRORS TRUE
bc03dbb6eb37 planemo upload commit 781926e52355f7805db8d9a4ccafeff397b19aa4-dirty
marpiech
parents:
diff changeset
52 #END_SECTION
bc03dbb6eb37 planemo upload commit 781926e52355f7805db8d9a4ccafeff397b19aa4-dirty
marpiech
parents:
diff changeset
53