#
#     Copyright (C) 1999-2004  Liz Potterton, Peter Briggs
#
#     This code is distributed under the terms and conditions of the
#     CCP4 Program Suite Licence Agreement as a CCP4 Library.
#     A copy of the CCP4 licence can be obtained by writing to the
#     CCP4 Secretary, Daresbury Laboratory, Warrington WA4 4AD, UK.
#     
#     Extended by Nicholas Furnham 2007 for RAPPER     
#
#===========================================================================
#
# rapper.script
#
#===========================================================================


#set up command line 

set cmd "[BinPath rapper]"

set rapperdatadir [FileJoin [GetEnvPath CCP4] share rapper]
set paramsfile [FileJoin [GetEnvPath CCP4] share rapper params.xml]
set dirout [GetCurrentProjectDir]

if { $BUILD_TYPE == "MODEL_LOOP_BENCHMARK" } {
   append cmd " $paramsfile model-loops-benchmark --pdb "
}
if { $BUILD_TYPE == "MODEL_LOOP" } {
   append cmd " $paramsfile model-loops --pdb "
}
if [ regexp MODEL_CATRACE|MODEL_BADFIT $BUILD_TYPE ] {
   append cmd " $paramsfile ca-trace --pdb "
}
append cmd "  \"$XYZIN\""
append cmd " --rapper-dir \"$rapperdatadir\""

if { $BUILD_TYPE == "MODEL_LOOP" } {
   append cmd " --seq $SEQ "
}

if { $MAP_TYPE == "WITH" } {
   append cmd " --map "
   append cmd "  \"$MAPIN\""
}

if {[ regexp PART $CATRACE_TYPE ] && ![regexp MODEL_BADFIT $BUILD_TYPE]} {
   append cmd " --start"
   append cmd "  \"$RES_START\""
   append cmd " --stop"
   append cmd "  \"$RES_STOP\""
   append cmd " --chain-id"
   append cmd "  \"$CHAIN_ID\""
}

append cmd " --models"
append cmd "  \"$MODEL_NUM\""

if { $MAP_TYPE == "WITH"  } {
   append cmd " --cryst-d-high"
   append cmd "  \"$RESOLUTION\""
   append cmd " --edm-fit true"
   append cmd " --chi-squared-electron-density-scoring true "
   ## other args
   if $EDM_FILTERS {
      append cmd " --use-edm-filters true "
   }
   if $RES_OPT {
   append cmd " --restraints-are-pass-optional true "
   }  
}

append cmd " --use-CCP4i-file-name true"
append cmd " --ccp4i-file-name"
## need to have the name minus root path and .pdb extension
set root [ SetOutputFileRoot ]
append cmd "  \"$root\""

append cmd " --runs-dir"
append cmd " \"$dirout\""

##main chain args
if { $MC_RES || [ regexp BENCHMARK $BUILD_TYPE] }  {
   append cmd " --enforce-mainchain-restraints true"
   append cmd " --mainchain-restraint-threshold"
   append cmd "  \"$MC_RAD\""
}

##side chain args
if $SC_BUILD {
  append cmd " --sidechain-mode smart"
  append cmd " --sidechain-radius-reduction 0.5"

  if { $SC_RES || [ regexp BENCHMARK $BUILD_TYPE] } {
      append cmd " --enforce-sidechain-centroid-restraints true"
      append cmd " --sidechain-centroid-restraint-threshold"
      append cmd "  \"$SC_RAD\""
  }
  if [ regexp RICHARDSON $ROTOMER_LIB ] {
	append cmd " --sidechain-library RAPPER-DIR/data/richardson.lib "
  } elseif [ regexp SCL1 $ROTOMER_LIB ] {
	append cmd " --sidechain-library RAPPER-DIR/data/scl-B30-occ1.0-rmsd1.0-chi60.pdb "	
  } elseif [ regexp SCL2 $ROTOMER_LIB ] {
       append cmd " --sidechain-library RAPPER-DIR/data/scl-B30-occ1.0-rmsd0.5-chi60.pdb "	
  } elseif [ regexp SCL2 $ROTOMER_LIB ] {
       append cmd " --sidechain-library RAPPER-DIR/data/scl-B30-occ1.0-rmsd0.2-chi60.pdb "	
  }	
  
}

## rebuild poor fit regions args
if [ regexp MODEL_BADFIT $BUILD_TYPE ] {
   append cmd " --edm-rebuild-poor-regions true "
   append cmd " --divide-and-conquer false "
   append cmd " --divide-and-conquer-ignore-chain-breaks true "
   append cmd " --default-mainchain-b-factor 20.0 --default-sidechain-b-factor 30.0 --models-get-native-bfactors false "
   append cmd " --error-for-no-models false --fix-mislabeled-atoms false --write-user-remarks false "
   append cmd " --edm-poor-region-threshold "
   append cmd " \"$EDM_POOR_TH\" "
   append cmd " --edm-poor-region-buffer-size "
   append cmd " \"$EDM_BUFF_SIZE\" "
}
if $CONTACT_FILTERS {
   append cmd " --use-contact-filters true "
}

if $ANCHOR_OPT {
  append cmd " --strict-anchors true "
}
if $ANCHOR_OPT2 {
  append cmd " --enforce-strict-anchor-geometry true "
}
if $MC_SIGMA_OPT {
   append cmd " --enforce-mainchain-min-sigma-restraints true"
   append cmd " --edm-mainchain-min-sigma "
   append cmd " \"$MC_SIGMA\" "
}
if $SC_SIGMA_OPT {
   append cmd " --enforce-sidechain-min-sigma-restraints true"
   append cmd " --edm-sidechain-min-sigma "
   append cmd " \"$SC_SIGMA\" "
}
if $EDM_OPT { 
   append cmd " --optional-edm-mainchain-restraints true "
}

CreateComScript rapper rapper_script

# Run RAPPER
set status [ Execute $cmd $rapper_script program_status report ]

# collate together the output files
set outfiles AddOutputFile
if [ regexp MODEL_CATRACE $BUILD_TYPE ] {
   set file1 "\$root\-trace.pdb"
   set file7 "\$root\-multitrace.pdb"
} else {
  set file1 "\$root\-loop.pdb"
  set file7 "\$root\-multiloop.pdb"
}

set file3 "\$root\-joined.pdb"
set file2 "\$root\-framework.pdb"
set file4 "\$root\-benchmark.dat"
set file5 "\$root\-models.dat"
set file6 "\$root\-native.pdb"
set file7 "\$root\-multiloop.pdb"

append outfiles " $file1 PROJECT"
append outfiles " $file2 PROJECT"

if [ regexp MODEL_LOOP|MODEL_LOOP_BENCHMARK|MODEL_BADFIT $BUILD_TYPE ] {
   append outfiles " $file3 PROJECT"
}
append outfiles " $file4 PROJECT"
append outfiles " $file5 PROJECT"
append outfiles " $file6 PROJECT"
append outfiles " $file7 PROJECT"
append outfiles " $XYZOUT PROJECT" 

# Run RAPPER to join loop back to framework and out put to defined pdb file
# Also need to sort out multimodel files join - FIX ME
set cmd2 "[BinPath rapper]"
append cmd2 " $paramsfile joinpdb "
append cmd2 " --pdb2 \"$root\-loop.pdb\" "
append cmd2 " --pdb  \"$root\-framework.pdb\" "
append cmd2 " --pdb-out \"$root\-joined.pdb\" "
append cmd2 " --rapper-dir \"$rapperdatadir\""

# Run RAPPER
if [ regexp MODEL_LOOP|MODEL_LOOP_BENCHMARK|MODEL_BADFIT $BUILD_TYPE ] {
   WriteToLog " *** Joining modelled loops back to framework structure *** \n"
   set status [Execute $cmd2 {} program_status report]

   #Copy joined file to named output file
   CopyFile "$root\-joined.pdb" $XYZOUT
} else {
  if { [ regexp PART $CATRACE_TYPE ] && $BUILD_TYPE == "MODEL_CATRACE"  } {
     WriteToLog " *** Joining modelled loops back to framework structure *** \n"
   set status [Execute $cmd2 {} program_status report]

   #Copy joined file to named output file
   CopyFile "$root\-joined.pdb" $XYZOUT
   }
  MoveFile "$root\-loop.pdb" "$root\-trace.pdb"
  MoveFile "$root\-multiloop.pdb" "$root\-multitrace.pdb"
}

eval  "$outfiles"