Split NMR-style multiple model pdb files into individual models: Difference between revisions

Split NMR-style multiple model pdb files into individual models (edit)

Revision as of 17:08, 16 December 2010

89 bytes removed , 16 December 2010

no edit summary

Pozharski

67

edits

@@ Line 8: / Line 8: @@
 This one-liner splits the file models.pdb into individual pdb files named model_###.pdb.
-'''grep -n 'MODEL\|ENDMDL' models.pdb | '''
+  grep -n 'MODEL\|ENDMDL' models.pdb | cut -d: -f 1 | \
-'''cut -d: -f 1 | '''
+  awk '{if(NR%2) printf "sed -n %d,",$1+1; else printf "%dp > model_%03d.pdb\n", $1-1,NR/2;}' |  bash -sf
-'''awk '{if(NR%2) printf "sed -n %d,",$1+1; else printf "%dp > model_%03d.pdb\n", $1-1,NR/2;}' | '''
-'''bash -sf'''
 == Bash script ==
-'''i=1'''
+  i=1
+  while read -a line; do
-'''while read -a line; do'''
+    echo "${line[@]}" >> model_${i}.pdb
+    [[ ${line[0]} == ENDMDL ]] && ((i++))
-'''    echo "${line[@]}" >> model_${i}.pdb'''
+  done < /path/to/file.pdb
-'''    [[ ${line[0]} == ENDMDL ]] && ((i++))'''
-'''done < /path/to/file.pdb'''
@@ Line 30: / Line 24: @@
 Should be called as
-awk -f script.awk < models.pdb
+  awk -f script.awk < models.pdb
-'''BEGIN {file = 0; filename = "model_"  file ".pdb"}'''
+  BEGIN {file = 0; filename = "model_"  file ".pdb"}
+  /ENDMDL/ {getline; file ++; filename = "model_" file ".pdb"}
-'''/ENDMDL/ {getline; file ++; filename = "model_" file ".pdb"}'''
+  {print $0 > filename}
-'''{print $0 > filename}'''
 == Perl script ==
-'''$base='1g9e';open(IN,"<$base.pdb");@indata = <IN>;$i=0;'''
+  $base='1g9e';open(IN,"<$base.pdb");@indata = <IN>;$i=0;
+  foreach $line(@indata) {
-'''foreach $line(@indata) {'''
+  if($line =~ /^MODEL/) {++$i;$file="${base}_$i.pdb";open(OUT,">$file");next}
+  if($line =~ /^ENDMDL/) {next}
-'''if($line =~ /^MODEL/) {++$i;$file="${base}_$i.pdb";open(OUT,">$file");next}'''
+  if($line =~ /^ATOM/ || $line =~ /^HETATM/) {print OUT "$line"}
+  }
-'''if($line =~ /^ENDMDL/) {next}'''
-'''if($line =~ /^ATOM/ || $line =~ /^HETATM/) {print OUT "$line"}'''
-'''}'''
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