/
rosetta_scoring_wrapper.tcl
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/
rosetta_scoring_wrapper.tcl
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### Wrapper for rosetta scoring
### Maximilian Scheurer, April 2016
### mail: mscheurer@ks.uiuc.edu
namespace eval ::RosettaScoring {
namespace export score_refinement
namespace export score_refinement_cluster
namespace export score_abinitio
# Set up Variable
set version 0.1
set packageDescription "RosettaVMD Plugin"
}
package provide RosettaScoring $RosettaScoring::version
proc score_refinement {args} \
{
return [eval ::RosettaScoring::score_refinement $args]
}
proc score_refinement_cluster {args} \
{
return [eval ::RosettaScoring::score_refinement_cluster $args]
}
proc score_abinitio {args} \
{
return [eval ::RosettaScoring::score_abinitio $args]
}
proc ::RosettaScoring::score_refinement {MOL max_structures jobname} \
{
#set MOL loopmodel_73-78_4OCM_B.pdb_full_length
#set max_structures 25
puts "scoring started"
set pdb [::RosettaScoring::rosetta_scoring $max_structures $jobname]
puts $pdb
puts "scoring finished"
mol delete all
#mol new ./pdb_out/${MOL}_[format %04i [lindex $pdb 0]].pdb waitfor all
for {set i 0} {$i < [llength $pdb]} {incr i} {
if { [llength $pdb] < 10000} {
mol new $::MODELMAKER::workdir/run-$jobname/pdb_out/${MOL}_[format %04i [lindex $pdb $i]].pdb
} else {
set offset [expr int(floor(log10([llength $pdb]))) + 1]
mol new $::MODELMAKER::workdir/run-$jobname/pdb_out/${MOL}_[format %0${offset}i [lindex $pdb $i]].pdb
}
[atomselect top all] writepdb $::MODELMAKER::workdir/run-$jobname/${jobname}_best[expr $i + 1].pdb
}
#animate write pdb ${MOL}_rosetta_scoring_min_$max_structures.pdb beg 0 end [expr $max_structures-1] skip 1 0
}
proc ::RosettaScoring::score_refinement_cluster {run MOL max_structures} \
{
set pdb [::RosettaScoring::rosetta_scoring_cluster_consistent $max_structures $run]
puts $pdb
for {set i 0} {$i < [llength $pdb]} {incr i} {
mol new ./pdb_out/${MOL}[lindex $pdb $i]_0001.pdb
[atomselect top all] writepdb ${MOL}_best[expr $i + 1].pdb
}
}
proc ::RosettaScoring::score_abinitio {run MOL max_structures cluster {extra 0} args} \
{
puts $MOL
#not sure why there is a need now for this difference with new cluster script...testing using the same
# if {$cluster} {
# set pdb [::RosettaScoring::rosetta_scoring_cluster_consistent $max_structures $run $extra]
# } else {
set pdb [::RosettaScoring::rosetta_scoring $max_structures $run]
# }
#set pdblist [lsort -dictionary [glob ../rosetta_output/pdb_out_aligned/*.pdb]]
#set file "../rosetta_output/pdb_out/${MOL}[lindex $pdb 0]_0001.pdb"
puts $pdb
#set file "../rosetta_output_bbfix/pdb_out/${MOL}[lindex $pdb 0]_0001.pdb"
set file "$::MODELMAKER::workdir/run-$run/pdb_out_aligned/${MOL}_[lindex $pdb 0]_0001_aligned.pdb"
#set file "../rosetta_output_bbfree/pdb_out_aligned/${MOL}[lindex $pdb 0]_0001_aligned.pdb"
mol new $file waitfor all
set sel [atomselect top "all and noh"]
puts "[file root $file]_noh.pdb"
$sel writepdb "[file root $file]_noh.pdb"
$sel delete
mol delete [molinfo top]
set top [mol new "[file root $file]_noh.pdb"]
file delete "[file root $file]_noh.pdb"
for {set i 1} {$i < [llength $pdb]} {incr i} {
#set file "../rosetta_output/pdb_out/${MOL}[lindex $pdb $i]_0001.pdb"
#set file "../rosetta_output_bbfix/pdb_out/${MOL}[lindex $pdb $i]_0001.pdb"
set file "$::MODELMAKER::workdir/run-$run/pdb_out_aligned/${MOL}_[lindex $pdb $i]_0001_aligned.pdb"
#set file "../rosetta_output_bbfree/pdb_out_aligned/${MOL}[lindex $pdb $i]_0001_aligned.pdb"
mol new $file waitfor all
set sel [atomselect top "all and noh"]
$sel writepdb "[file root $file]_noh.pdb"
$sel delete
mol delete [molinfo top]
mol addfile "[file root $file]_noh.pdb" waitfor all $top
file delete "[file root $file]_noh.pdb"
update idletasks
}
animate write pdb ${MOL}_rosetta_scoring_min_$max_structures.pdb beg 0 end [expr $max_structures-1] skip 1 $top
update idletasks
update
animate write dcd ${MOL}_rosetta_scoring_min_$max_structures.dcd beg 0 end [expr $max_structures-1] skip 1 $top
update idletasks
update
}
proc ::RosettaScoring::rosetta_scoring {length_tot jobname} {
set file_list ""
set val_list ""
set file_list [lsort -dictionary [glob $::MODELMAKER::workdir/run-$jobname/sc_out/*.sc]]
set length 0
for {set i 0} {$i < [llength $file_list]} {incr i} {
set file [open [lindex $file_list $i] r]
set log [open "$::MODELMAKER::workdir/run-$jobname/rosetta_scoring.log" w+]
while {[eof $file] != 1} {
set line [gets $file]
if {[lindex $line 0] == "SCORE:" && [regsub -all {[^0-9]} [lindex $line 1] ""] != ""} {
lappend val_list [lindex $line 1]
incr length
}
}
close $file
}
# for {set i 0} {$i < $length} {incr i} {
# set file [open [lindex $file_list $i] r]
# set rfile [read $file]
# set line [lindex [split $rfile "\n"] 2]
# if {$line == ""} {
# set line [lindex [split $rfile "\n"] 0]
# }
# set val [lindex $line 1]
# #puts "$i FILES LIST [lindex $file_list $i]"
# #puts "$i VALUES LIST [lindex $val_list $i]"
# close $file
#}
set index_sorted [lsort -real -indices $val_list]
#puts "\n$index_sorted"
set number ""
for {set i 0} {$i < [llength $index_sorted]} {incr i} {
lappend number [expr [lindex $index_sorted $i] +1 ]
puts $log "[expr [lindex $index_sorted $i] +1 ]\t[lindex $file_list [lindex $index_sorted $i]]\t[lindex $val_list [lindex $index_sorted $i]] "
}
puts "LENGTH $length"
if {$length >= $length_tot} {
return [lrange $number 0 [expr $length_tot -1]]
} else {
puts " Not enough file for chosen length_tot total file = $length: length_tot= $length_tot "
}
}
proc ::RosettaScoring::rosetta_scoring_cluster {length_tot} {
set file_list [lsort -dictionary [glob ./sc_out/*.sc]]
#set file_list [lsort -dictionary [glob ../rosetta_output_bbfix/sc_out/*.sc]]
#set file_list [lsort -dictionary [glob ../rosetta_output_bbfree/sc_out/*.sc]]
set length [llength $file_list]
set log [open "rosetta_scoring.log" w+]
for {set i 0} {$i < $length} {incr i} {
set file [open [lindex $file_list $i] r]
set rfile [read $file]
set line [lindex [split $rfile "\n"] 2]
if {$line == ""} {
set line [lindex [split $rfile "\n"] 0]
}
set val [lindex $line 1]
lappend val_list $val
#puts "$i FILES LIST [lindex $file_list $i]"
#puts "$i VALUES LIST [lindex $val_list $i]"
close $file
}
set index_sorted [lsort -real -indices $val_list]
#puts "\n$index_sorted"
set number ""
for {set i 0} {$i < [llength $index_sorted]} {incr i} {
lappend number [expr [lindex $index_sorted $i] +1 ]
puts $log "[expr [lindex $index_sorted $i] +1 ]\t[lindex $file_list [lindex $index_sorted $i]]\t[lindex $val_list [lindex $index_sorted $i]] "
}
if {$length >= $length_tot} {
return [lrange $number 0 [expr $length_tot -1]]
} else {
puts " Not enough file for chosen length_tot total file = $length: length_tot= $length_tot "
}
}
#package require Tcl 8.5
proc ::RosettaScoring::rosetta_scoring_cluster_consistent {length_tot runname {extra 0} args} {
set file_list ""
set val_list ""
set id_list ""
# set ic_val_list ""
if {$extra == 0} {
set score_name "${runname}_score"
} else {
set score_name "${runname}_${extra}_score"
}
puts $score_name
set file_list [lsort -dictionary [glob ./sc_out/*.sc]]
#set file_list [lsort -dictionary [glob ../rosetta_output_bbfix/sc_out/*.sc]]
#set file_list [lsort -dictionary [glob ../rosetta_output_bbfree/sc_out/*.sc]]
set file_id_list [] ;# for total score
# set file_id_if_list [] ;# for interface score
foreach file $file_list {
puts "file: $file"
#regexp -nocase [subst -nocommands -nobackslashes {${score_name}[0-9]*}] $file a
set a [glob ./pdb_out/*]
puts "a: $a"
# set ident [string trim $a $score_name]
set sc_length [string length $score_name]
set ident [string range $a $sc_length end]
puts "ident: $ident"
set f [open "$file" r]
set rfile [read $f]
set line [lindex [split $rfile "\n"] 2]
if {$line == ""} {
set line [lindex [split $rfile "\n"] 0]
}
set val [lindex $line 1]
# set icval [lindex $line 4]
close $f
lappend file_id_list [list $ident $file $val]
# lappend file_id_if_list [list $ident $file $icval]
}
set sort_scores [lsort -real -index 2 $file_id_list]
# set sort_if_scores [lsort -real -index 2 $file_id_if_list]
puts "finished reading and sorting."
set length [llength $file_list]
set log [open "rosetta_scoring.log" w+]
# set ic_log [open "rosetta_if_sc.log" w+]
set counter 0
foreach item $sort_scores {
if {$counter < $length_tot} {
lappend number [lindex $item 0]
}
puts $log "[lindex $item 0]\t[lindex $item 1]\t[lindex $item 2]"
incr counter
}
set counter 0
# foreach item $sort_if_scores {
# if {$counter < $length_tot} {
# lappend ic_number [lindex $item 0]
# }
# puts $ic_log "[lindex $item 0]\t[lindex $item 1]\t[lindex $item 2]"
# incr counter
# }
if {$length > $length_tot} {
# return [list [lrange $number 0 [expr $length_tot -1]] [lrange $ic_number 0 [expr $length_tot -1]]]
return [lrange $number 0 [expr $length_tot -1]]
} else {
puts " Not enough file for chosen length_tot total file = $length: length_tot= $length_tot "
}
}