Fixed consective HH commands, able to use file pathing across files

joshua-mae · Aug 7, 2023 · 06b0690 · 06b0690
1 parent 515c3be
commit 06b0690
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Showing 4 changed files with 61 additions and 119 deletions.
diff --git a/holebash.sh b/holebash.sh
@@ -1,13 +1,9 @@
 #!/bin/bash
 
-username=$(whoami)
-folder_dir=$(find /home/$username -type d -name "HH-Results" ! -path "/home/*/*.*")
-logs_folder="$folder_dir/logs-folder"
-inp_folder="$folder_dir/inp-folder"
-for inp_file in $inp_folder/*;
+for inp_file in $1/HH-Results/inp-folder/*;
 do 
     full_filename=$(basename $inp_file)
     file="${full_filename%.*}"
 
-    hole < $inp_file >> "$logs_folder/$file.log"
+    hole < $inp_file >> "$1/HH-Results/logs-folder/$file.log"
 done
diff --git a/holehelper.tcl b/holehelper.tcl
@@ -22,7 +22,6 @@ namespace eval ::HOLEHelper:: {
     variable output_dir
 } 
 
-
 proc holehelper_usage {} {
     vmdcon -info "Usage: holehelper <pdbfile> <psffile> <dcdfolder> <dcdstep> <molsel> <wrap> \
     <cvec> <radtype> <cp> <endrad> <outputdir>"
@@ -113,7 +112,7 @@ proc holehelper_core {args} {
     set outputdirbashpath [exec find /home/$user  -type d -name "${outputdir}" ! -path "/home/*/*.*"]
 
     if {$wrap != "no"} {
-        pbc wrap -all -sel "${molesel}" -centersel "${wrap}" \
+        pbc wrap -sel "${molesel}" -all -centersel "${wrap}" \
         -compound fragment -center com
     }   
 
@@ -147,6 +146,7 @@ proc holehelper_core {args} {
             mol addfile $dcdfiles type dcd step $step_size waitfor -1 
         }
     }
+    set top_mol [molinfo top]
     cd $outputdirbashpath
     file mkdir HH-Results
     cd $outputdirbashpath/HH-Results
@@ -186,11 +186,25 @@ proc holehelper_core {args} {
     }
 
     cd $user_holepath
-    exec sh holebash.sh
-    exec python3 sphcleaner.py
-    source sameatomcount.tcl
-
+    exec sh holebash.sh "${outputdirbashpath}"
+    exec python3 sphcleaner.py ${outputdirbashpath}
     cd $outputdirbashpath/HH-Results/sph-folder
+    set sphfilelist [lsort [glob *.sph]]
+
+    foreach sph $sphfilelist {
+        mol new $sph type pdb
+        set real_atom_count [molinfo top get numatoms]
+        set moleculeid [molinfo top]
+        set fake_atom_count 1000
+        set atom_count_diff [expr $fake_atom_count - $real_atom_count]
+        set outfile [open $sph a]
+        for { set f 0 } {$f < $atom_count_diff } { incr f} {
+            puts $outfile "ATOM      1  QSS SPH S-888"
+        }
+        close $outfile
+        mol delete $moleculeid
+    }
+
     set sphfilelist [lsort [glob *.sph]]
     mol new [lindex $sphfilelist 0] type pdb
     set top_num [molinfo top]
@@ -200,9 +214,13 @@ proc holehelper_core {args} {
     for {set f 1} {$f < $frame_nums} {incr f} {
         mol addfile [lindex $sphfilelist $f] type pdb
     }
+    cd /home/$user
+    mol top $top_mol
+
 
 }
 
+
 proc ::HOLEHelper::holehelper {} {
     variable w
     variable hh_path
@@ -388,9 +406,7 @@ proc ::HOLEHelper::holehelper {} {
 
     pack [button $w.traj -text "Run HOLE2 on Trajectory" -command ::HOLEHelper::run_hole2_traj] \
     -side top -pady 5 -padx 3 -fill x -anchor w
-
-    pack [button $w.loaded -text "Run HOLE2 On Top Mol" -command ::HOLEHelper::loaded_hole] \
-    -side top -pady 5 -padx 3 -fill x -anchor w
+
 	#-------------------------------------------------------------------------
 }
 proc ::HOLEHelper::run_hole2_single {} {
@@ -415,6 +431,9 @@ proc ::HOLEHelper::run_hole2_single {} {
     $primarycvec_y $primarycvec_z $primarycpnt_x $primarycpnt_y $primarycpnt_z \
     $endrad $output_dir
 
+
+    set top_mol [molinfo top]
+
     cd $output_dir
     file mkdir HH-Results
     cd $output_dir/HH-Results
@@ -451,6 +470,7 @@ proc ::HOLEHelper::run_hole2_single {} {
     cd $hh_path
     exec sh holebash.sh
 
+
     cd $output_dir/HH-Results/sph-folder
     set sphfilelist [lsort [glob *.sph]]
     mol new [lindex $sphfilelist 0] type pdb
@@ -459,8 +479,15 @@ proc ::HOLEHelper::run_hole2_single {} {
     set sel [atomselect top "all"]
     $sel set radius [$sel get beta]
 
+    cd /home/$user
+    mol top $top_mol
+
 }
 
+# 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
+
 proc ::HOLEHelper::run_hole2_traj {} {
     variable user
     variable hh_path
@@ -480,6 +507,8 @@ proc ::HOLEHelper::run_hole2_traj {} {
     $primarycvec_y $primarycvec_z $primarycpnt_x $primarycpnt_y $primarycpnt_z \
     $endrad $output_dir
 
+    set top_mol [molinfo top]
+
     cd $output_dir
     file mkdir HH-Results
     cd $output_dir/HH-Results
@@ -524,89 +553,28 @@ proc ::HOLEHelper::run_hole2_traj {} {
         close $outfile
     }
 
+
     cd $hh_path
-    exec sh holebash.sh
-    exec python3 sphcleaner.py
-    source sameatomcount.tcl
+    exec sh holebash.sh "${output_dir}"
+    exec python3 sphcleaner.py ${output_dir}
 
     cd $output_dir/HH-Results/sph-folder
     set sphfilelist [lsort [glob *.sph]]
-    mol new [lindex $sphfilelist 0] type pdb
-    set top_num [molinfo top]
-    mol modstyle 0 $top_num VDW
-    set sel [atomselect top "all"]
-    $sel set radius [$sel get beta]
-    for {set f 1} {$f < $frame_nums} {incr f} {
-        mol addfile [lindex $sphfilelist $f] type pdb
-    }
-}
-
-proc ::HOLEHelper::loaded_hole {} {
-    variable user
-    variable primarypdb
-    variable wrapping_filler ""
-    variable hh_path
-	variable primarycvec_x
-	variable primarycvec_y
-	variable primarycvec_z
-	variable radius 
-	variable endrad
-	variable primarycpnt_x
-	variable primarycpnt_y
-	variable primarycpnt_z
-    variable output_dir
 
-    set molecule_sel_lst [molinfo top get selection]
-    set cleaned_sel [lindex $molecule_sel_lst 0]
-    set final_mol_sel [atomselect top "${cleaned_sel}"]
-
-    error_checker $cleaned_sel $wrapping_filler $primarycvec_x \
-    $primarycvec_y $primarycvec_z $primarycpnt_x $primarycpnt_y $primarycpnt_z \
-    $endrad $output_dir
-
-    cd $output_dir
-    file mkdir HH-Results
-    cd $output_dir/HH-Results
-    file mkdir pdb-folder
-    file mkdir inp-folder
-    file mkdir sph-folder
-    file mkdir logs-folder
-    set frame_nums [molinfo top get numframes]
-
-    set com [measure center $final_mol_sel]
-    set com_x [lindex $com 0]
-    set com_y [lindex $com 1]
-    set com_z [lindex $com 2]
-
-    for { set f 0 } { $f < $frame_nums } { incr f} {
-
-
-        # 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 $final_mol_sel
-
-        # Writing the inp files for the bash script to read
-
-        cd ../inp-folder
-        set outfile [open "HoleHelper-INP-${f}.inp" w+]
-        puts $outfile "coord ${output_dir}/HH-Results/pdb-folder/HoleHelper-PDB-${f}.pdb"
-        puts $outfile "radius ${hh_path}/rad/${radius}.rad"
-        puts $outfile "sphpdb ${output_dir}/HH-Results/sph-folder/HoleHelper-SPH-${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} ${primarycpnt_z}"
-        }
-        if {$endrad != ""} {
-            puts $outfile "endrad ${endrad}"
+    foreach sph $sphfilelist {
+        mol new $sph type pdb
+        set real_atom_count [molinfo top get numatoms]
+        set moleculeid [molinfo top]
+        set fake_atom_count 1000
+        set atom_count_diff [expr $fake_atom_count - $real_atom_count]
+        set outfile [open $sph a]
+        for { set f 0 } {$f < $atom_count_diff } { incr f} {
+            puts $outfile "ATOM      1  QSS SPH S-888"
         }
         close $outfile
+        mol delete $moleculeid
     }
 
-    cd $hh_path
-    exec sh holebash.sh
-    exec python3 sphcleaner.py
-    source sameatomcount.tcl
     cd $output_dir/HH-Results/sph-folder
     set sphfilelist [lsort [glob *.sph]]
     mol new [lindex $sphfilelist 0] type pdb
@@ -617,7 +585,9 @@ proc ::HOLEHelper::loaded_hole {} {
     for {set f 1} {$f < $frame_nums} {incr f} {
         mol addfile [lindex $sphfilelist $f] type pdb
     }
-
+    cd /home/$user
+    mol top $top_mol
+
 }
 
 proc ::HOLEHelper::error_checker {molsel pbccond cvx cvy cvz cpx cpy cpz ed outdir} {

diff --git a/sameatomcount.tcl b/sameatomcount.tcl
diff --git a/sphcleaner.py b/sphcleaner.py
@@ -1,5 +1,6 @@
 import glob
-import subprocess
+import sys
+import os
 
 def readsphfile(sphfile): 
     '''
@@ -22,14 +23,9 @@ def readsphfile(sphfile):
     fi.close()
 
 def main():
-    user_name = subprocess.run(['whoami'],shell=True, capture_output=True,text=True)
-    readable_user_name = user_name.stdout
-    cleaned_user_name = readable_user_name.strip()
-    cli_func = subprocess.run([f'find /home/{cleaned_user_name} -type d -name "HH-Results" ! -path "/home/*/*.*"'],shell=True, capture_output=True,text=True)
-    sph_path = cli_func.stdout
-    sph_path = sph_path.strip()
-    sph_path += "/sph-folder/"
-    holelist = sorted(glob.glob(f'{sph_path}*.sph'))
+
+    os.chdir(f'{sys.argv[1]}/HH-Results/sph-folder')
+    holelist = sorted(glob.glob('*.sph'))
 
     for sphfile in holelist:
         readsphfile(sphfile)