Split NMR-style multiple model pdb files into individual models: Difference between revisions
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This one-liner splits the file models.pdb into individual pdb files | This one-liner splits the file models.pdb into individual pdb files named model_###.pdb. | ||
grep -n 'MODEL\|ENDMDL' models.pdb | cut -d: -f 1 | \ | |||
awk '{if(NR%2) printf "sed -n %d,",$1+1; else printf "%dp models.pdb > model_%03d.pdb\n", $1-1,NR/2;}' | bash -sf | |||
== Bash script == | |||
i=1 | |||
while read -a line; do | |||
echo "${line[@]}" >> model_${i}.pdb | |||
[[ ${line[0]} == ENDMDL ]] && ((i++)) | |||
done < /path/to/file.pdb | |||
== Awk script == | |||
Should be called as | |||
awk -f script.awk < models.pdb | |||
BEGIN {file = 0; filename = "model_" file ".pdb"} | |||
/ENDMDL/ {getline; file ++; filename = "model_" file ".pdb"} | |||
{print $0 > filename} | |||
== Perl script == | == Perl script == | ||
$base='1g9e';open(IN,"<$base.pdb");@indata = <IN>;$i=0; | $base='1g9e';open(IN,"<$base.pdb");@indata = <IN>;$i=0; | ||
foreach $line(@indata) { | |||
if($line =~ /^MODEL/) {++$i;$file="${base}_$i.pdb";open(OUT,">$file");next} | |||
if($line =~ /^ENDMDL/) {next} | |||
if($line =~ /^ATOM/ || $line =~ /^HETATM/) {print OUT "$line"} | |||
} | |||
== Python script == | |||
For this kludgy version using Python 2.x, you need to paste the entire PDB file into the script where it says "PASTE YOUR PDB FILE TEXT HERE". | |||
You can fork [https://github.com/fomightez/structurework/blob/master/python_scripts/super_basic_multiple_model_PDB_file_splitter.py the code here at Github]. | |||
(A more full-featured version there that you can just point at your file [,or a folder of files,] using an argument on the command line can be found [https://github.com/fomightez/structurework/blob/master/python_scripts/multiple_model_PDB_file_splitter.py here at Github]. ) | |||
if | PDB_text = """ | ||
PASTE YOUR PDB FILE TEXT HERE | |||
""" | |||
model_number = 1 | |||
new_file_text = "" | |||
for line in filter(None, PDB_text.splitlines()): | |||
line = line.strip () #for better control of ends of lines | |||
if line == "ENDMDL": | |||
# save file with file number in name | |||
output_file = open("model_" + str(model_number) + ".pdb", "w") | |||
output_file.write(new_file_text.rstrip('\r\n')) #rstrip to remove trailing newline | |||
output_file.close() | |||
# reset everything for next model | |||
model_number += 1 | |||
new_file_text = "" | |||
elif not line.startswith("MODEL"): | |||
new_file_text += line + '\n' | |||
Back to [[Useful scripts (aka smart piece of code)]] |
Latest revision as of 20:14, 3 June 2016
This assumes that you have a correctly formatted pdb file that contains both MODEL and ENDMDL records.
Bash/awk one-liner[edit | edit source]
This one-liner splits the file models.pdb into individual pdb files named model_###.pdb.
grep -n 'MODEL\|ENDMDL' models.pdb | cut -d: -f 1 | \ awk '{if(NR%2) printf "sed -n %d,",$1+1; else printf "%dp models.pdb > model_%03d.pdb\n", $1-1,NR/2;}' | bash -sf
Bash script[edit | edit source]
i=1 while read -a line; do echo "${line[@]}" >> model_${i}.pdb [[ ${line[0]} == ENDMDL ]] && ((i++)) done < /path/to/file.pdb
Awk script[edit | edit source]
Should be called as
awk -f script.awk < models.pdb
BEGIN {file = 0; filename = "model_" file ".pdb"} /ENDMDL/ {getline; file ++; filename = "model_" file ".pdb"} {print $0 > filename}
Perl script[edit | edit source]
$base='1g9e';open(IN,"<$base.pdb");@indata = <IN>;$i=0; foreach $line(@indata) { if($line =~ /^MODEL/) {++$i;$file="${base}_$i.pdb";open(OUT,">$file");next} if($line =~ /^ENDMDL/) {next} if($line =~ /^ATOM/ || $line =~ /^HETATM/) {print OUT "$line"} }
Python script[edit | edit source]
For this kludgy version using Python 2.x, you need to paste the entire PDB file into the script where it says "PASTE YOUR PDB FILE TEXT HERE".
You can fork the code here at Github.
(A more full-featured version there that you can just point at your file [,or a folder of files,] using an argument on the command line can be found here at Github. )
PDB_text = """ PASTE YOUR PDB FILE TEXT HERE """ model_number = 1 new_file_text = "" for line in filter(None, PDB_text.splitlines()): line = line.strip () #for better control of ends of lines if line == "ENDMDL": # save file with file number in name output_file = open("model_" + str(model_number) + ".pdb", "w") output_file.write(new_file_text.rstrip('\r\n')) #rstrip to remove trailing newline output_file.close() # reset everything for next model model_number += 1 new_file_text = "" elif not line.startswith("MODEL"): new_file_text += line + '\n'