/
modelmaker.tcl
2068 lines (1743 loc) · 57.3 KB
/
modelmaker.tcl
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package require RosettaVMD
package require MakePsf
package require ssrestraints
package require cispeptide
package require chirality
package require mdff
package require SSAnalysis
package provide modelmaker 0.1
namespace eval ::MODELMAKER {
variable defaultGapfindSel "protein"
if {[info exists env(ROSETTAEXE)]} {
variable rosettaEXE $env(ROSETTAEXE)
} else {
switch $tcl_platform(os) {
"Darwin" {
variable rosettaEXE "static.macos*release"
}
"Linux" {
variable rosettaEXE "static.linux*release"
}
default {
variable rosettaEXE "Unrecognized"
}
}
}
if {[info exists env(ROSETTADB)]} {
variable rosettadbpath $env(ROSETTADB)
} else {
variable rosettadbpath ""
}
if {[info exists env(ROSETTAPATH)]} {
variable rosettaPath $env(ROSETTAPATH)
} else {
variable rosettaPath ""
}
variable DefaultNStruct 5000
variable DefaultCluster 0
variable DefaultNPerTask 1
variable DefaultTestRun 0
variable DefaultResStart 1
variable DefaultAlignTemplate "all"
variable DefaultInsertion "no"
variable DefaultKmin 2
variable DefaultKmax 10
variable DefaultWorkDir "[pwd]/workdir"
variable DefaultMDFFWorkDir "[pwd]/mdff-workdir"
variable workdir $DefaultWorkDir
variable DefaultScore -0.3
variable DefaultRefineMode "backbone"
variable DefaultPDB2SeqSel "protein"
variable DefaultFixed "none"
variable DefaultBestN 1
variable DefaultNumSteps 10000
variable DefaultMinSteps 200
variable DefaultGScale 0.3
variable DefaultGridPDBSel "noh and (protein or nucleic)"
variable DefaultDCDFreq 100
variable DefaultTopFiles [list [file join $env(CHARMMTOPDIR) top_all36_prot.rtf] \
[file join $env(CHARMMTOPDIR) top_all36_lipid.rtf] \
[file join $env(CHARMMTOPDIR) top_all36_na.rtf] \
[file join $env(CHARMMTOPDIR) top_all36_carb.rtf] \
[file join $env(CHARMMTOPDIR) top_all36_cgenff.rtf] \
[file join $env(CHARMMTOPDIR) toppar_all36_carb_glycopeptide.str] \
[file join $env(CHARMMTOPDIR) toppar_water_ions_namd.str] ]
variable DefaultParFiles [list [file join $env(CHARMMPARDIR) par_all36_prot.prm]\
[file join $env(CHARMMPARDIR) par_all36_lipid.prm] \
[file join $env(CHARMMPARDIR) par_all36_na.prm] [file join $env(CHARMMPARDIR) par_all36_carb.prm] \
[file join $env(CHARMMPARDIR) par_all36_cgenff.prm] [file join $env(CHARMMPARDIR) toppar_all36_carb_glycopeptide.str]\
[file join $env(CHARMMPARDIR) toppar_water_ions_namd.str]]
variable DefaultThreshold 0.1
variable DefaultMaskCutoff 2
variable MPINP
variable settings
set ::MODELMAKER::settings(username) ""
variable DefaultModelSel "all"
variable DefaultModelN 1
}
proc modelmaker { args } { return [eval ::MODELMAKER::modelmaker $args] }
proc ::MODELMAKER::modelmaker_usage { } {
puts "Usage: modelmaker <command> \[args...\]"
puts "Commands:"
puts " gapfind -- find gaps in structure"
puts " full_length_model -- generate a complete template model"
puts " abinitio -- run Rosetta abinitio structure prediction"
puts " insertion -- run Rosetta structure prediction for insertion folding"
puts " analyze -- analyze results of Rosetta abinitio structure prediction"
puts " refine -- refine a structure with Rosetta using a density"
puts " pdb2seq -- get the single-letter amino acid sequence"
puts " seqsub -- extract subrange of fasta sequence"
puts " makepsf -- make a .psf file from a pdb"
puts " mdff -- run an MDFF simulation"
puts " cccolor -- calculate local cross correlations"
puts " ssanalysis -- analyze the secondary structure of the generated structures"
puts " get_empty_density -- find the unassigned empty density around a structure"
puts " model -- generate a homology model with MODELLER"
puts " fragments -- generate fragment files"
return
}
proc ::MODELMAKER::modelmaker { args } {
set nargs [llength $args]
if { $nargs == 0 } {
modelmaker_usage
error ""
}
# parse command
set command [lindex $args 0]
set args [lreplace $args 0 0]
if { $command == "gapfind" } {
return [eval ::MODELMAKER::gapfind $args]
} elseif { $command == "full_length_model" } {
return [eval ::MODELMAKER::full_length_model $args]
} elseif { $command == "abinitio" } {
return [eval ::MODELMAKER::abinitio $args]
} elseif { $command == "analyze" } {
return [eval ::MODELMAKER::analyze $args]
} elseif { $command == "insertion" } {
return [eval ::MODELMAKER::insertion $args]
} elseif { $command == "refine" } {
return [eval ::MODELMAKER::refine $args]
} elseif { $command == "pdb2seq" } {
return [eval ::MODELMAKER::pdb2seq $args]
} elseif { $command == "seqsub" } {
return [eval ::MODELMAKER::seqsub $args]
} elseif { $command == "makepsf" } {
return [eval ::MODELMAKER::makepsf $args]
} elseif { $command == "mdff" } {
return [eval ::MODELMAKER::quick_mdff $args]
} elseif { $command == "cccolor" } {
return [eval ::MODELMAKER::cccolor $args]
} elseif { $command == "get_empty_density" } {
return [eval ::MODELMAKER::get_empty_density $args]
} elseif { $command == "ssanalysis" } {
return [eval ::MODELMAKER::ssanalysis $args]
} elseif { $command == "model" } {
return [eval ::MODELMAKER::model $args]
} elseif { $command == "fragments" } {
return [eval ::MODELMAKER::fragments $args]
} else {
modelmaker_usage
error "Unrecognized command."
}
return
}
proc ::MODELMAKER::insertion_usage { } {
variable DefaultNStruct
variable DefaultWorkDir
puts "Usage: modelmaker insertion -model <full length template pdb> -fragfiles <list of fragment files> \
-sel <list of atomselection texts with selections to fold> -fasta <fasta file> \
?options?"
puts "Options:"
puts " -jobname <name prefix for job> (default: taken from -model)> "
puts " -nstruct <number of structures to predict> (default: $DefaultNStruct)> "
puts " -workdir <working/project directory for job> (default: $DefaultWorkDir)>"
puts " -np <Number of processors to use. MPI version only> "
}
proc ::MODELMAKER::insertion { args } {
variable rosettaEXE
variable rosettadbpath
variable DefaultNStruct
variable rosettaPath
variable DefaultWorkDir
variable MPINP
global rosettapath
global rosettaDBpath
global platform
set rosettapath $rosettaPath
set rosettaDBpath $rosettadbpath
set platform $rosettaEXE
set nargs [llength [lindex $args 0]]
if {$nargs == 0} {
insertion_usage
error ""
}
foreach {name val} $args {
switch -- $name {
-jobname { set arg(jobname) $val }
-model { set arg(model) $val }
-sel { set arg(sel) $val }
-fasta { set arg(fasta) $val }
-fragfiles { set arg(fragfiles) $val }
-nstruct { set arg(nstruct) $val }
-workdir { set arg(workdir) $val }
-np { set arg(np) $val }
default { puts "Unknown argument $name"; return }
}
}
if { [info exists arg(model)] } {
set model [file rootname [file tail $arg(model)]]
} else {
error "A full model pdb file must be specified!"
}
if { [info exists arg(sel)] } {
set sel [list $arg(sel)]
} else {
error "An atomselection text must be specified!"
}
if { [info exists arg(fragfiles)] } {
set fragfiles $arg(fragfiles)
} else {
error "At least two fragment files must be specified!"
}
if { [info exists arg(fasta)] } {
#NOTE: Right now, because of RosettaVMD package, this needs to be the fasta name without the .fasta
#extension. Need to change RosettaVMD to not require this.
set fasta [string range $arg(fasta) 0 [expr [string last ".fasta" $arg(fasta)] - 1 ]]
} else {
error "A fasta file must be specified!"
}
if { [info exists arg(nstruct)] } {
set nstruct $arg(nstruct)
} else {
set nstruct $DefaultNStruct
}
if { [info exists arg(jobname)] } {
set jobname $arg(jobname)
} else {
set jobname $model
}
if { [info exists arg(np)] } {
set MPINP $arg(np)
} elseif { [string match "*mpi.*" $rosettaEXE] } {
error "number of processors (-np) must be specified when using MPI version of Rosetta!"
}
if { [info exists arg(workdir)] } {
set ::MODELMAKER::workdir $arg(workdir)
} else {
set ::MODELMAKER::workdir $DefaultWorkDir
}
# if { [file exists $::MODELMAKER::workdir] } {
# puts "The working directory already exists!"
# exit 1
# }
if {![file exists $::MODELMAKER::workdir]} { file mkdir $::MODELMAKER::workdir }
## preparing files ##
# folder with all the files needed for setup/run
file mkdir $::MODELMAKER::workdir/setup-$jobname
file mkdir $::MODELMAKER::workdir/run-$jobname
set tmpmol [mol new $arg(model)]
set tmpsel [atomselect $tmpmol "noh"]
$tmpsel writepdb "$::MODELMAKER::workdir/setup-$jobname/[file tail $arg(model)]"
file copy -force $fasta.fasta $::MODELMAKER::workdir/setup-$jobname
foreach fragfile $fragfiles {
puts $fragfile
file copy -force $fragfile $::MODELMAKER::workdir/setup-$jobname
}
set currentPWD [pwd]
start_rosetta_insertion $jobname $model $sel $fragfiles $fasta $nstruct
set temp_mol [mol new $arg(model)]
set temp_sel [atomselect $temp_mol all]
set resstart [lindex [lsort -integer [$temp_sel get resid]] 0]
foreach pdb [glob "$::MODELMAKER::workdir/run-$jobname/pdb_out/*"] {
set full_mol [mol new $pdb]
set full_sel [atomselect $full_mol all]
renumber $full_sel $resstart
$full_sel writepdb $pdb
mol delete $full_mol
}
}
proc ::MODELMAKER::refine_usage { } {
variable DefaultNStruct
variable DefaultCluster
variable DefaultNPerTask
variable DefaultTestRun
variable DefaultWorkDir
variable DefaultScore
variable DefaultRefineMode
puts "Usage: modelmaker refine -model <full length template pdb> \
-sel <list of atomselection texts with selections to fold> -anchor <anchor residue for coordinate restraints> \
-density <density file to refine against in .mrc format> -res <resolution of the density in Angstroms> \
?options?"
puts "Options:"
puts " -mode <refinement mode (backbone, sidechain, or cartesian> (default: $DefaultRefineMode)"
puts " -jobname <name prefix for job> (default: taken from -model) "
puts " -workdir <working/project directory for job> (default: $DefaultWorkDir)"
puts " -nstruct <number of structures to predict> (default: $DefaultNStruct) "
puts " -bestN <number of structures with best scores to save> (default: same as -nstruct) "
puts " -score <Rosetta density score; lower values indicate lower weight> (default: $DefaultScore) "
puts " -np <Number of processors to use. MPI version only> "
}
proc ::MODELMAKER::refine { args } {
variable rosettaEXE
variable rosettadbpath
variable DefaultNStruct
variable rosettaPath
variable DefaultWorkDir
variable DefaultScore
variable MPINP
variable DefaultRefineMode
global rosettapath
global rosettaDBpath
global platform
global packagePath
set packagePath $::env(RosettaVMDDIR)
set rosettapath $rosettaPath
set rosettaDBpath $rosettadbpath
set platform $rosettaEXE
set nargs [llength [lindex $args 0]]
if {$nargs == 0} {
refine_usage
error ""
}
foreach {name val} $args {
switch -- $name {
-jobname { set arg(jobname) $val }
-model { set arg(model) $val }
-sel { set arg(sel) $val }
-anchor { set arg(anchor) $val }
-nstruct { set arg(nstruct) $val }
-density { set arg(density) $val }
-res { set arg(res) $val }
-score { set arg(score) $val }
-bestN { set arg(bestN) $val }
-workdir { set arg(workdir) $val }
-mode { set arg(mode) $val }
-np { set arg(np) $val }
default { puts "Unknown argument $name"; return }
}
}
if { [info exists arg(model)] } {
set model [file rootname [file tail $arg(model)]]
} else {
error "A full model pdb file must be specified!"
}
if { [info exists arg(sel)] } {
set sel [list $arg(sel)]
} else {
error "An atomselection text must be specified!"
}
if { [info exists arg(anchor)] } {
set anchor $arg(anchor)
} else {
error "An anchor residue id must be specified!"
}
if { [info exists arg(density)] } {
set density [string range $arg(density) 0 [expr [string last ".mrc" $arg(density)] - 1 ]]
} else {
error "A density file must be specified!"
}
if { [info exists arg(res)] } {
set res $arg(res)
} else {
error "The resolution of the density must be specified!"
}
if { [info exists arg(mode)] } {
set mode $arg(mode)
} else {
set mode $DefaultRefineMode
}
if { [info exists arg(score)] } {
set score $arg(score)
} else {
set score $DefaultScore
}
if { [info exists arg(nstruct)] } {
set nstruct $arg(nstruct)
} else {
set nstruct $DefaultNStruct
}
if { [info exists arg(bestN)] } {
set bestN $arg(bestN)
} else {
set bestN $nstruct
}
if { [info exists arg(jobname)] } {
set jobname $arg(jobname)
} else {
set jobname $model
}
if { [info exists arg(np)] } {
set MPINP $arg(np)
} elseif { [string match "*mpi.*" $rosettaEXE] } {
error "number of processors (-np) must be specified when using MPI version of Rosetta!"
}
if { [info exists arg(workdir)] } {
set ::MODELMAKER::workdir $arg(workdir)
} else {
set ::MODELMAKER::workdir $DefaultWorkDir
}
# if { [file exists $::MODELMAKER::workdir] } {
# puts "The working directory already exists!"
# exit 1
# }
if {![file exists $::MODELMAKER::workdir]} { file mkdir $::MODELMAKER::workdir }
## preparing files ##
# folder with all the files needed for setup/run
file mkdir $::MODELMAKER::workdir/setup-$jobname
file mkdir $::MODELMAKER::workdir/run-$jobname
set tmpmol [mol new $arg(model)]
set tmpsel [atomselect $tmpmol "noh"]
$tmpsel writepdb "$::MODELMAKER::workdir/setup-$jobname/[file tail $arg(model)]"
if { $mode == "cartesian" } {
set csflag 1
} else {
set csflag 0
}
if { $mode == "sidechain" } {
start_rosetta_refine_sidechains_density $jobname $model $sel $anchor $density $res $score $bestN $nstruct
} else {
start_rosetta_refine $jobname $model $sel $anchor $csflag $density $res $score $bestN $nstruct
}
set inmol [mol new $arg(model)]
foreach pdb [glob -nocomplain $::MODELMAKER::workdir/run-$jobname/*_best*.pdb] {
set outmol [mol new $pdb]
regen_segnames $inmol $outmol
set sel [atomselect $outmol all]
$sel writepdb $pdb
$sel delete
}
}
proc ::MODELMAKER::abinitio_usage { } {
variable DefaultNStruct
variable DefaultCluster
variable DefaultNPerTask
variable DefaultTestRun
variable DefaultWorkDir
puts "Usage: modelmaker abinitio -model <full length template pdb> -fragfiles <list of fragment files> \
-sel <list of atomselection texts with selections to fold> -anchor <atomselection text for anchor residue for coordinate restraints> \
?options?"
puts "Options:"
puts " -jobname <name prefix for job> (default: taken from -model)> "
puts " -workdir <working/project directory for job> (default: $DefaultWorkDir)>"
puts " -nstruct <number of structures to predict> (default: $DefaultNStruct)> "
puts " -testrun <test run flag (0 or 1)> (default: $DefaultTestRun)> "
puts " -np <Number of processors to use. MPI version only> "
}
proc ::MODELMAKER::abinitio { args } {
variable rosettaEXE
variable rosettadbpath
variable DefaultNStruct
variable DefaultCluster
variable DefaultNPerTask
variable DefaultTestRun
variable rosettaPath
variable DefaultWorkDir
variable MPINP
global rosettapath
global rosettaDBpath
global platform
set rosettapath $rosettaPath
set rosettaDBpath $rosettadbpath
set platform $rosettaEXE
set nargs [llength [lindex $args 0]]
if {$nargs == 0} {
abinitio_usage
error ""
}
foreach {name val} $args {
switch -- $name {
-jobname { set arg(jobname) $val }
-model { set arg(model) $val }
-sel { set arg(sel) $val }
-anchor { set arg(anchor) $val }
-fragfiles { set arg(fragfiles) $val }
-nstruct { set arg(nstruct) $val }
-cluster { set arg(cluster) $val }
-npertask { set arg(npertask) $val }
-testrun { set arg(testrun) $val }
-workdir { set arg(workdir) $val }
-np { set arg(np) $val }
default { puts "Unknown argument $name"; return }
}
}
if { [info exists arg(model)] } {
set model [file rootname [file tail $arg(model)]]
} else {
error "A full model pdb file must be specified!"
}
if { [info exists arg(sel)] } {
set sel [list $arg(sel)]
} else {
error "An atomselection text must be specified!"
}
if { [info exists arg(anchor)] } {
set anchor $arg(anchor)
} else {
error "An anchor residue id must be specified!"
}
if { [info exists arg(fragfiles)] } {
set fragfiles $arg(fragfiles)
} else {
error "Two fragment files must be specified!"
}
if { [info exists arg(nstruct)] } {
set nstruct $arg(nstruct)
} else {
set nstruct $DefaultNStruct
}
if { [info exists arg(cluster)] } {
set cluster $arg(cluster)
} else {
set cluster $DefaultCluster
}
if { [info exists arg(npertask)] } {
set npertask $arg(npertask)
} else {
set npertask $DefaultNPerTask
}
if { [info exists arg(testrun)] } {
set testrun $arg(testrun)
} else {
set testrun $DefaultTestRun
}
if { [info exists arg(jobname)] } {
set jobname $arg(jobname)
} else {
set jobname $model
}
if { [info exists arg(np)] } {
set MPINP $arg(np)
} elseif { [string match "*mpi.*" $rosettaEXE] } {
error "number of processors (-np) must be specified when using MPI version of Rosetta!"
}
if { [info exists arg(workdir)] } {
set ::MODELMAKER::workdir $arg(workdir)
} else {
set ::MODELMAKER::workdir $DefaultWorkDir
}
# if { [file exists $::MODELMAKER::workdir] } {
# puts "The working directory already exists!"
# exit 1
# }
if {![file exists $::MODELMAKER::workdir]} { file mkdir $::MODELMAKER::workdir }
## preparing files ##
# folder with all the files needed for setup/run
file mkdir $::MODELMAKER::workdir/setup-$jobname
file mkdir $::MODELMAKER::workdir/run-$jobname
set tmpmol [mol new $arg(model)]
set tmpsel [atomselect $tmpmol "noh"]
$tmpsel writepdb "$::MODELMAKER::workdir/setup-$jobname/[file tail $arg(model)]"
foreach fragfile [lindex $fragfiles 0] {
file copy -force $fragfile $::MODELMAKER::workdir/setup-$jobname
}
start_rosetta_abinitio $jobname $model $sel $anchor $fragfiles $nstruct $cluster $npertask $testrun
}
proc ::MODELMAKER::analyze_usage { } {
variable DefaultCluster
variable DefaultAlignTemplate
variable DefaultInsertion
variable DefaultKmin
variable DefaultKmax
puts "Usage: modelmaker analyze -model <full length template pdb> -nstruct <number of structures to analyze> \
-comps <list of analysis tasks> ?options?"
puts "Options:"
puts " -jobname <name prefix for job> (default: taken from -model)> "
puts " -bestN <best N structures to analyze> (default: same as -nstruct)> "
puts " -align_template <selection text of template PDB for alignment> (default: $DefaultAlignTemplate)> "
puts " -align_rosetta <selection text of predicted models for alignment> (default: taken from -align_template)> "
puts " -insertion <analyzing output from insertion? 'yes' or 'no'> (default: $DefaultInsertion)"
#change these to more user-friendly designations and explain caveats
puts " -cluster <clustering mode to use. 0 for Rosetta, 1 for Python> (default: $DefaultCluster)> "
puts " -kmin <Min number of clusters for silhouette calc, cluster mode 1 only> (default: $DefaultKmin)> "
puts " -kmax <Max number of clusters for silhouette calc, cluster mode 1 only> (default: $DefaultKmax)> "
}
proc ::MODELMAKER::analyze { args } {
variable rosettaEXE
variable rosettadbpath
variable DefaultCluster
variable rosettaPath
variable DefaultAlignTemplate
variable DefaultInsertion
variable DefaultKmin
variable DefaultKmax
set nargs [llength [lindex $args 0]]
if {$nargs == 0} {
analyze_usage
error ""
}
foreach {name val} $args {
switch -- $name {
-jobname { set arg(jobname) $val }
-model { set arg(model) $val }
-template { set arg(template) $val }
-nstruct { set arg(nstruct) $val }
-cluster { set arg(cluster) $val }
-bestN { set arg(bestN) $val }
-align_template { set arg(align_template) $val }
-align_rosetta { set arg(align_rosetta) $val }
-comps { set arg(comps) $val }
-insertion { set arg(insertion) $val }
-kmin { set arg(kmin) $val }
-kmax { set arg(kmax) $val }
default { puts "Unknown argument $name"; return }
}
}
puts $arg(model)
if { [info exists arg(model)] } {
set model [string range $arg(model) 0 [expr [string last ".pdb" $arg(model)] - 1 ]]
} else {
error "A full model pdb file must be specified!"
}
if { [info exists arg(template)] } {
# get the full path of the template file
set dir [file dirname $arg(template)]
if { $dir == "." } {
set dir [pwd]
}
set template "$dir/$arg(template)"
} else {
error "A template pdb file must be specified!"
}
#can we determine this automatically?
if { [info exists arg(nstruct)] } {
set nstruct $arg(nstruct)
} else {
error "Number of structures to analyze must be specified!"
}
#This is pretty cumbersome for the user and fairly opaque. Will have to find a succinct way of listing the
#possibilities and summarizing functionality in the usage command...
#Also, like fragment files, is a list of lists so the user will have to do somehing like
#{{fragfile1 fragfile2}} if they want just one list....
if { [info exists arg(comps)] } {
set comps $arg(comps)
} else {
error "Analysis tasks must be specified!"
}
if { [info exists arg(align_template)] } {
set align_template $arg(align_template)
} else {
set align_template "$DefaultAlignTemplate"
}
if { [info exists arg(align_rosetta)] } {
set align_rosetta $arg(align_rosetta)
} else {
set align_rosetta $align_template
}
if { [info exists arg(bestN)] } {
set bestN $arg(bestN)
} else {
set bestN $nstruct
}
if { [info exists arg(jobname)] } {
set jobname $arg(jobname)
} else {
set jobname $model
}
if { [info exists arg(insertion)] } {
set insertion $arg(insertion)
} else {
set insertion $DefaultInsertion
}
if { [info exists arg(cluster)] } {
set cluster $arg(cluster)
} else {
set cluster $DefaultCluster
}
if { [info exists arg(kmin)] } {
set kmin $arg(kmin)
} else {
set kmin $DefaultKmin
}
if { [info exists arg(kmax)] } {
set kmax $arg(kmax)
} else {
set kmax $DefaultKmax
}
if { [info exists arg(workdir)] } {
set ::MODELMAKER::workdir $arg(workdir)
} else {
set ::MODELMAKER::workdir [pwd]/workdir
}
if { ![file exists $::MODELMAKER::workdir] } {
puts "The working directory does not exist!"
exit 1
}
global rosettapath
global rosettaDBpath
global platform
global packagePath
global vmdexe
#can we avoid this or make it optional?
global gnuplotexe
set rosettapath $rosettaPath
set rosettaDBpath $rosettadbpath
set platform $rosettaEXE
set packagePath $::env(RosettaVMDDIR)
#assumes in PATH which should be reasonable requirement
set vmdexe "vmd"
set gnuplotexe "gnuplot"
switch $insertion {
"yes" {
set modelname "$model\_S"
set insert_model $model
}
"no" {
set modelname $model
set insert_model ""
}
}
analyze_abinitio $jobname $modelname $template $bestN $nstruct $cluster $align_template \
$align_rosetta $comps $kmin $kmax {*}$insert_model
}
proc ::MODELMAKER::renumber { sel start } {
if { [$sel num] == 0 } {
puts "Error in renumber: empty selection!"
return
}
set oresid [ $sel get resid ]
set delta [ expr $start - [ lindex $oresid 0] ]
set nresid { }
foreach r $oresid {
lappend nresid [ expr $r + $delta ]
}
$sel set resid $nresid
}
proc ::MODELMAKER::full_length_model_usage { } {
variable DefaultResStart
puts "Usage: modelmaker full_length_model -template <template pdb> -fragfiles <list of fragment files> \
-fasta <fasta file> ?options?"
puts "Options:"
puts " -resstart <id of first residue> (default: $DefaultResStart)> "
}
proc ::MODELMAKER::full_length_model { args } {
variable rosettaEXE
variable DefaultResStart
variable rosettaPath
set nargs [llength [lindex $args 0]]
if {$nargs == 0} {
full_length_model_usage
error ""
}
foreach {name val} $args {
switch -- $name {
-template { set arg(template) $val }
-fragfiles { set arg(fragfiles) $val }
-fasta { set arg(fasta) $val }
-resstart { set arg(resstart) $val }
default { puts "Unknown argument $name"; return }
}
}
if { [info exists arg(template)] } {
set template $arg(template)
} else {
error "A template pdb file must be specified!"
}
if { [info exists arg(fragfiles)] } {
set fragfiles $arg(fragfiles)
} else {
error "A list of two fragment files must be specified!"
}
if { [info exists arg(fasta)] } {
set fasta $arg(fasta)
} else {
error "A fasta file must be specified!"
}
if { [info exists arg(resstart)] } {
set resstart $arg(resstart)
} else {
set resstart $DefaultResStart
}
set name [file rootname [file tail $template]]
set mol [mol new $template]
set sel [atomselect $mol "protein and noh"]
format_pdb $sel "$name.formatted.pdb"
#this assume only 9 and 3 length fragment files and in a specific order. Can
#we implement some logic to look at the provided files and determine what all we have?
exec [glob $rosettaPath/full_length_model.$rosettaEXE] -in:file:fasta $fasta \
-loops:frag_files [lindex $fragfiles 0] [lindex $fragfiles 1] none \
-loops:frag_sizes 9 3 1 \
-in:file::s "$name.formatted.pdb" \
-overwrite >> $name-full_length_model.log
file delete "$name.formatted.pdb"
set full_mol [mol new ${name}.formatted.pdb_full_length.pdb]
set chain [lindex [$sel get chain] 0]
set segname [lindex [$sel get segname] 0]
set full_sel [atomselect $full_mol all]
if {$chain != ""} { $full_sel set chain $chain }
if {$segname != ""} { $full_sel set segname $segname }
renumber $full_sel $resstart
$full_sel writepdb ${name}_full_length.pdb
mol delete $full_mol
file delete ${name}.formatted.pdb_full_length.pdb
}
proc ::MODELMAKER::gapfind_usage { } {
variable defaultGapfindSel
puts "Usage: mdodelmaker gapfind ?options?"
puts "Options:"
puts " -i <input pdb> "
puts " -sel <atom selection text> (default: $defaultGapfindSel)"
puts " -mol <molid> (find gaps in already loaded molecule)"
}
proc ::MODELMAKER::gapfind { args } {
variable defaultGapfindSel
set nargs [llength [lindex $args 0]]
if {$nargs == 0} {
gapfind_usage
error ""
}
foreach {name val} $args {
switch -- $name {
-i { set arg(i) $val }
-sel { set arg(sel) $val }
-mol { set arg(mol) $val }
default { puts "Unknown argument $name"; return }
}
}
if { [info exists arg(i)] && [info exists arg(mol)] } {
error "only an input pdb OR a mol id can be specified at one time"
} elseif { ![info exists arg(i)] && ![info exists arg(mol)] } {
error "either an input pdb OR a mol id must be specified"
}
if { [info exists arg(i)] } {
set inputpdb $arg(i)
} else {
set inputpdb ""
}
if { [info exists arg(sel)] } {
set inputsel $arg(sel)
} else {
set inputsel $defaultGapfindSel
}
if { [info exists arg(mol)] } {
set inputmol $arg(mol)
} else {
set inputmol ""
}
if { $inputpdb != ""} {
set MOLID [mol new $inputpdb]
} else {
set MOLID $inputmol ;
}
set molname [molinfo $MOLID get name]
set chains [lsort -unique [[atomselect $MOLID $inputsel] get chain]]
foreach chain $chains {
puts $chain
set counter 0
set sel [atomselect $MOLID "chain $chain"]
set residues [lsort -integer -unique [$sel get resid]]
set missing []
#set first [lindex $residues 0]
set first 1
set last [lindex $residues end]
set delta [expr $last - $first]
for {set i $first} {$i <= $delta} {incr i} {
set d [expr $i - $first - $counter]
if {$i != [lindex $residues $d]} {
lappend missing $i
incr counter
}
}
if {1} {