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multiple HH commands and custom file names
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@joshua-mae
joshua-mae committed Aug 7, 2023
1 parent 06b0690 commit 8c868a6
Showing 1 changed file with 42 additions and 27 deletions.
69 changes: 42 additions & 27 deletions holehelper.tcl
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Original file line number Diff line number Diff line change
Expand Up @@ -20,6 +20,7 @@ namespace eval ::HOLEHelper:: {
variable primarycpnt_y
variable primarycpnt_z
variable output_dir
variable output_file_name
}

proc holehelper_usage {} {
Expand Down Expand Up @@ -58,17 +59,20 @@ proc holehelper_core {args} {
set cpoint [lindex $args 8]
set edrad [lindex $args 9]
set outputdir [lindex $args 10]
set filenames [lindex $args 11]

# Need to make sure file names are unique

# Need to make sure file names are unique

set pdbbashpath [exec find /home/$user -type f -name "${pdbfile}" ! -path "*/\.*"]
set psfbashpath [exec find /home/$user -type f -name "${psffile}" ! -path "*/\.*"]
set dcdbashpath [exec find /home/$user -type d -name "${dcd_folder}" ! -path "/home/*/*.*"]

if {($pdbfile != "no") && ($psffile == "no") && ($dcd_folder == "no")} {
if {[file extension $pdbbashpath] != ".pdb"} {
error "Needs proper pdb file"
}
}

} elseif {($pdbfile != "no") && ($psffile != "no") && ($dcd_folder != "no")} {
if {[file extension $pdbbashpath] != ".pdb"} {
error "Needs proper pdb file"
Expand All @@ -79,6 +83,7 @@ proc holehelper_core {args} {
if {[file isdirectory $dcd_folder] != 1} {
error "Needs proper dcd directory"
}

} elseif {($pdbfile != "no") && ($psffile != "no") && ($dcd_folder == "no")} {

if {[file extension $pdbbashpath] != ".pdb"} {
Expand Down Expand Up @@ -111,11 +116,6 @@ proc holehelper_core {args} {

set outputdirbashpath [exec find /home/$user -type d -name "${outputdir}" ! -path "/home/*/*.*"]

if {$wrap != "no"} {
pbc wrap -sel "${molesel}" -all -centersel "${wrap}" \
-compound fragment -center com
}

if {$edrad != "no"} {
if {[string is double -strict $edrad] != 1} {
error "Needs proper end radius"
Expand Down Expand Up @@ -146,14 +146,19 @@ proc holehelper_core {args} {
mol addfile $dcdfiles type dcd step $step_size waitfor -1
}
}
set top_mol [molinfo top]
if {$wrap != "no"} {
pbc wrap -sel "${molesel}" -all -centersel "${wrap}" \
-compound fragment -center com
}

cd $outputdirbashpath
file mkdir HH-Results
cd $outputdirbashpath/HH-Results
file mkdir pdb-folder
file mkdir inp-folder
file mkdir sph-folder
file mkdir logs-folder
set top_mol [molinfo top]

set frame_nums [molinfo top get numframes]

Expand All @@ -166,15 +171,15 @@ proc holehelper_core {args} {
# Writing out the pdbs

cd $outputdirbashpath/HH-Results/pdb-folder
animate write pdb "HoleHelper-PDB-${f}.pdb" beg $f end $f waitfor -1 sel $sel
animate write pdb "${filenames}-PDB-${f}.pdb" beg $f end $f waitfor -1 sel $sel

# Writing the inp files for the bash script to read

cd ../inp-folder
set outfile [open "HoleHelper-INP-${f}.inp" w+]
puts $outfile "coord ${outputdirbashpath}/HH-Results/pdb-folder/HoleHelper-PDB-${f}.pdb"
set outfile [open "${filenames}-INP-${f}.inp" w+]
puts $outfile "coord ${outputdirbashpath}/HH-Results/pdb-folder/${filenames}-PDB-${f}.pdb"
puts $outfile "radius ${user_holepath}/rad/${radtype}.rad"
puts $outfile "sphpdb ${outputdirbashpath}/HH-Results/sph-folder/HoleHelper-SPH-${f}.sph"
puts $outfile "sphpdb ${outputdirbashpath}/HH-Results/sph-folder/${filenames}-SPH-${f}.sph"
puts $outfile "cvect ${cvec}"
if {$cpoint != "no"} {
puts $outfile "cpoint ${cpoint}"
Expand Down Expand Up @@ -216,11 +221,8 @@ proc holehelper_core {args} {
}
cd /home/$user
mol top $top_mol


}


proc ::HOLEHelper::holehelper {} {
variable w
variable hh_path
Expand All @@ -240,6 +242,8 @@ proc ::HOLEHelper::holehelper {} {
variable primarycpnt_y
variable primarycpnt_z
variable output_dir "/home/$user"
variable output_file_name


if { [winfo exists .holehelper] } {
wm deiconify $w
Expand All @@ -251,7 +255,7 @@ proc ::HOLEHelper::holehelper {} {
grid columnconfigure $w 0 -weight 1
grid rowconfigure $w 0 -weight 1

wm geometry $w 510x600
wm geometry $w 510x575

set file_window $w.fileoptions
ttk::labelframe $file_window -borderwidth 2 -relief ridge -text "File Options"
Expand Down Expand Up @@ -396,8 +400,14 @@ proc ::HOLEHelper::holehelper {} {
}] -row 0 -column 2 -sticky w
grid columnconfigure $output_window.files 1 -weight 1

frame $output_window.naming
grid [label $output_window.naming.namelabel -text "PDB/INP/SPH File Name: "] \
-row 1 -column 0 -sticky e
grid [entry $output_window.naming.namepath -textvariable \
::HOLEHelper::output_file_name -width 30 -justify left] -row 1 -column 1

pack $output_window -side top -pady 5 -padx 3 -fill x -anchor w
pack $output_window.files -side top -padx 0 -pady 2 -expand 1 -fill x
pack $output_window.files $output_window.naming -side top -padx 0 -pady 2 -expand 1 -fill x

#-------------------------------------------------------------------------

Expand All @@ -424,6 +434,8 @@ proc ::HOLEHelper::run_hole2_single {} {
variable primarycpnt_y
variable primarycpnt_z
variable output_dir
variable output_file_name


# Utilizes PBC wrap to wrap a molecule if necessary

Expand All @@ -448,15 +460,15 @@ proc ::HOLEHelper::run_hole2_single {} {
}
set sel [atomselect top $mol_sel]
cd $output_dir/HH-Results/pdb-folder
animate write pdb "HoleHelper-PDB-0.pdb" beg 0 end 0 waitfor -1 sel $sel
animate write pdb "${output_file_name}-PDB-0.pdb" beg 0 end 0 waitfor -1 sel $sel

# Bash script needs an inp file in order to run

cd $output_dir/HH-Results/inp-folder
set outfile [open "HoleHelper-INP-0.inp" w+]
puts $outfile "coord ${output_dir}/HH-Results/pdb-folder/HoleHelper-PDB-0.pdb"
set outfile [open "${output_file_name}-INP-0.inp" w+]
puts $outfile "coord ${output_dir}/HH-Results/pdb-folder/${output_file_name}-PDB-0.pdb"
puts $outfile "radius ${hh_path}/rad/${radius}.rad"
puts $outfile "sphpdb ${output_dir}/HH-Results/sph-folder/HoleHelper-SPH-0.sph"
puts $outfile "sphpdb ${output_dir}/HH-Results/sph-folder/${output_file_name}-SPH-0.sph"
puts $outfile "ignore hoh tip wat"
puts $outfile "cvect ${primarycvec_x} ${primarycvec_y} ${primarycvec_z}"
if {($primarycpnt_x != "") && ($primarycpnt_x != "") && ($primarycpnt_x != "")} {
Expand All @@ -468,7 +480,7 @@ proc ::HOLEHelper::run_hole2_single {} {
close $outfile

cd $hh_path
exec sh holebash.sh
exec sh holebash.sh "$output_dir"


cd $output_dir/HH-Results/sph-folder
Expand All @@ -486,11 +498,12 @@ proc ::HOLEHelper::run_hole2_single {} {

# pbc wrap -all -sel "segname 12 13 14 15 16 17" -centersel "segname 12" -compound fragment -center com
# pbc wrap -all -sel "segname 0 1 2 3 4 5" -centersel "segname 0" -compound fragment -center com
#pbc wrap -all -sel "segname 6 7 8 9 10 11" -centersel "segname 11" -compound fragment -center com
# pbc wrap -all -sel "segname 6 7 8 9 10 11" -centersel "segname 11" -compound fragment -center com

proc ::HOLEHelper::run_hole2_traj {} {
variable user
variable hh_path
variable primarypsf
variable mol_sel
variable wrapping_condition
variable primarycvec_x
Expand All @@ -502,6 +515,8 @@ proc ::HOLEHelper::run_hole2_traj {} {
variable primarycpnt_y
variable primarycpnt_z
variable output_dir
variable output_file_name


error_checker $mol_sel $wrapping_condition $primarycvec_x \
$primarycvec_y $primarycvec_z $primarycpnt_x $primarycpnt_y $primarycpnt_z \
Expand Down Expand Up @@ -534,15 +549,15 @@ proc ::HOLEHelper::run_hole2_traj {} {
# Writing out the pdbs

cd $output_dir/HH-Results/pdb-folder
animate write pdb "HoleHelper-PDB-${f}.pdb" beg $f end $f waitfor -1 sel $sel
animate write pdb "${output_file_name}-PDB-${f}.pdb" beg $f end $f waitfor -1 sel $sel

# Writing the inp files for the bash script to read

cd ../inp-folder
set outfile [open "HoleHelper-INP-${f}.inp" w+]
puts $outfile "coord ${output_dir}/HH-Results/pdb-folder/HoleHelper-PDB-${f}.pdb"
set outfile [open "${output_file_name}-INP-${f}.inp" w+]
puts $outfile "coord ${output_dir}/HH-Results/pdb-folder/${output_file_name}-PDB-${f}.pdb"
puts $outfile "radius ${hh_path}/rad/${radius}.rad"
puts $outfile "sphpdb ${output_dir}/HH-Results/sph-folder/HoleHelper-SPH-${f}.sph"
puts $outfile "sphpdb ${output_dir}/HH-Results/sph-folder/${output_file_name}-SPH-${f}.sph"
puts $outfile "cvect ${primarycvec_x} ${primarycvec_y} ${primarycvec_z}"
if {($primarycpnt_x != "") && ($primarycpnt_x != "") && ($primarycpnt_x != "")} {
puts $outfile "cpoint ${primarycpnt_x} ${primarycpnt_y} ${primarycpnt_z}"
Expand Down

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