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annotate tools/rdock/data/sf/RbtPMFIdxSF.prm @ 5:a2f9c8a46a4b draft default tip

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planemo upload commit b9501ecca66b6a66c8cb87b945ad5f95181d7790-dirty
author marpiech
date Thu, 06 Oct 2016 07:09:26 -0400
parents 75f2b4087722
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1 RBT_PARAMETER_FILE_V1.00
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2 TITLE Protein-ligand PMF (indexed version)
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3 VERSION $Id: //depot/dev/client3/rdock/2013.1/data/sf/RbtPMFIdxSF.prm#2 $
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4 ################################################################################
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5 #
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6 # Revision history:
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7 #
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8 # References:
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9 #
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10 ################################################################################
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11 # Constant scoring function
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12 # Represents loss of translation, rotational entropy of ligand
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13 SECTION CONST
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14 SCORING_FUNCTION RbtConstSF
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15 WEIGHT +5.4 # Free-energy weighting
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16 END_SECTION
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17
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18 ################################################################################
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19 # Rotational scoring function
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20 # Represents loss of torsional entropy of ligand
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21 SECTION ROT
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22 SCORING_FUNCTION RbtRotSF
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23 WEIGHT +1.0 # Free-energy weighting
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24 END_SECTION
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25
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26 ################################################################################
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27 # Setup PMF atom types
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28 SECTION SETUP_PMF
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29 SCORING_FUNCTION RbtSetupPMFSF
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30 END_SECTION
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32 ################################################################################
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33 # Intermolecular PMF
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34 SECTION PMF
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35 SCORING_FUNCTION RbtPMFIdxSF
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36 SLOPE -3.0 # slope of the repulsive short-range linear term
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37 CC_CUTOFF 6.0 # count only shorter C_receptor - C_ligand interactions
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38 WEIGHT 1.0
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39 GRIDSTEP 1.0 # indexed grid distance (need not be dense)
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40 BORDER 1.0 #
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41 PMFDIR data/pmf # ${RBT_ROOT/}data/pmf where the .pmfs are
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42 END_SECTION
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43 ###############################################################################
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44 # OVERALL_CUTOFF 9.0 # value of overall cutoff (similar to C cutoff but for all types)
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