hh-suite/scripts/renumberpdb.pl

#!/usr/bin/perl
# renumberpdb.pl - generate a PDB file with renumbered indices that match residue indices in input sequence
# Usage:   renumberpdb.pl [options] infile [outfile] 
# Example: renumberpdb.pl d1hz4a_.a3m d1hz4a_.pdb

# (C) Johannes Soeding, 2012
#
#     HHsuite version 3.0.0 (15-03-2015)
#
#     Reference: 
#     Remmert M., Biegert A., Hauser A., and Soding J.
#     HHblits: Lightning-fast iterative protein sequence searching by HMM-HMM alignment.
#     Nat. Methods, epub Dec 25, doi: 10.1038/NMETH.1818 (2011).

#     This program is free software: you can redistribute it and/or modify
#     it under the terms of the GNU General Public License as published by
#     the Free Software Foundation, either version 3 of the License, or
#     (at your option) any later version.

#     This program is distributed in the hope that it will be useful,
#     but WITHOUT ANY WARRANTY; without even the implied warranty of
#     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
#     GNU General Public License for more details.

#     You should have received a copy of the GNU General Public License
#     along with this program.  If not, see <http://www.gnu.org/licenses/>.

#     We are very grateful for bug reports! Please contact us at [email protected]

use lib $ENV{"HHLIB"}."/scripts";
use HHPaths;   # config file with path variables for nr, blast, psipred, pdb, dssp etc.
use Align;     # Needleman-Wunsch and Smith-Waterman alignment functions
use File::Temp qw/ tempfile /;
use strict;

$|=1; # autoflush on

# Default parameters for Align.pm
our $d=3;    # gap opening penalty for Align.pm
our $dx=20;  # gap opening penalty for sequence x Align.pm
our $e=0.1;  # gap extension penalty for Align.pm
our $g=0.09; # endgap penalty for Align.pm
our $v=2;    # verbose mode
our $matrix="identity";

my $TEMPDIR = $ENV{'TEMP'};

# Global variables
my $infile;            # input file
my $outfile;           # output file
my $line;              # input line
my $nameline="";       # characters following '>' in input file
my $aaq="";            # amino acid sequence read from input file
my $outdir;            # directory path of input file
my $program=$0;        # name of perl script
my $replaceMSE=1;      # replace HETATM MSE records by ATOM MET
my $dopt=0;
my $altloc="A";
my $pdbfile;

$program=~s/.*\///;    # remove path
if (scalar(@ARGV)<1) {
    print("
 $program - generate a PDB file with renumbered indices that match residue indices in 
 input sequence
 The program reads an input sequence in FASTA/A3M which must have a SCOP domain, PDB chain, or DALI 
 domain identifier (e.g. d1hz4a_, 1hz4_A, or 1hz4A_1). It reads the corresponding PDB file from the 
 given pdb directory and  generates a new PDB file by aligning the input sequence to the sequence 
 extracted from the ATOM records of the corresponding pdb chain and renumbering the residues in 
 columns 23-26 according to the position in the input sequence.
 (HETATM records for MSE (selenomethionine) will be interpreted as ATOM records for MET in the 
 alignment. MSE will be changed to MET in the output file.)
 
 Usage:   $program [options] infile [outfile] 
 Example: $program d1hz4a_.a3m /cluster/tmp/d1hz4a_.pdb 

 Options: 
   -o <file>    output file (default: <infile_wo_extension>.pdb
   -d <pdbdir>  give directory of pdb files (default=$pdbdir)
   -a [A|B]     filter alternative location identifier (e.g. A or B)
\n"); 
    exit;
}


my $options="";
for (my $i=0; $i<@ARGV; $i++) {$options.=" $ARGV[$i] ";}

# General options
if ($options=~s/ -d\s*(\S+) / /) {$pdbdir=$1; $dopt=1;}
if ($options=~s/ -a\s*(\S+) / /) {$altloc=$1;}
if ($options=~s/ -i\s*(\S*) //) {$infile=$1;}
if ($options=~s/ -o\s*(\S*) //) {$outfile=$1;}
if ($options=~s/ -v\s+(\d+) / /g)  {$v=$1;}
if (!$infile  && $options=~s/^\s*([^-]\S*)\s* / /) {$infile=$1;} 
if (!$outfile && $options=~s/^\s*([^-]\S*)\s* / /) {$outdir=$1;} 
if (!$outfile) {
    $outfile=$infile;
    $outfile=~s/^(.*)\..*?$/$1.pdb/;
}

# Read infile
if ($v>=3) {print("Reading $infile...\n");}

my @infile_lines;
if($infile ne "stdin") {
  open(INFILE,"<$infile") or die("Error: can't open $infile: $!\n");
  @infile_lines = <INFILE>;
  close(INFILE);
}
else {
  @infile_lines = <STDIN>;
}

# Read query sequence in infile
my $line_index = 0;
for ($line_index = 0; $line_index < scalar(@infile_lines); $line_index++) {
  $line = $infile_lines[$line_index];
  if ($line =~ /^>/ && $line !~ /^>(aa|ss)_/) {
    last;
  }
}
  
$line=~/^>(.*)/;
$nameline=$1;

# Read query sequence
for ($line_index += 1; $line_index < scalar(@infile_lines); $line_index++) {
  $line = $infile_lines[$line_index];
  if($line =~ /^>/) {
    last;
  }
  chomp($line);
  $aaq .= $line;
}

# Prepare output file if stdout
my $is_stdout_output = 0;
if ($outfile eq "stdout") {
	$is_stdout_output = 1;
	(undef, $outfile) = tempfile(UNLINK => 1, OPEN => 0, DIR => $TEMPDIR);
}

if (&MakePdbFile($nameline,$aaq,$outfile) !=0) {exit(1);}

# Print outfile to stdout if specified by the user
if ($is_stdout_output == 1) {
  open(FH, "<$outfile") or die("Error: can't open temporary $outfile: $!\n");

	while( my $line = <FH>) { 
  	print($line);
	}

  close(FH);
}

if ($v>=2) {print("Done\n");}

exit(0);



##################################################################################
# Make a pdb file $base.pdb with correct resdiue numbers from query sequence in $base.hhm 
##################################################################################
sub MakePdbFile() 
{


# >g1avo.1 a.24.8.1 (A:,B:) Proteasome activator reg(alpha) {Human (Homo sapiens)}    
    my $nameline=$_[0]; # everything in line following '>' in infile 
    my $aaq=$_[1];      # query amino acids
    my $outfile=$_[2];  # query amino acids
    my $pdbcode;        # e.g. 1hz4
    my $chain;          # chain id of query sequence for hmmfile 
    my $line;           # currently read input line
    my $header;         # PDB file header
    my @remarks;        # PDB file remarks
    my $date=`date`;
    chomp($date);
    $nameline=~/^(\S+)/;
    my $name=$1;

    # SCOP ID? (d3lkfa_,d3grs_3,d3pmga1,g1m26.1)
    if ($nameline=~/^[d-u](\d[a-z0-9]{3})([a-z0-9_.])[a-z0-9_]\b/) {
	$pdbcode=lc($1);
	$chain=uc($2);
	if ($chain eq "_") {$chain="[A ]";} else {$chain=uc($2);} 
	$header="HEADER    SCOP domain $name                    $date";
    }
    
    # DALI ID? (8fabA_0,1a0i_2)
    elsif ($nameline=~/^(\d[a-z0-9]{3})([A-Za-z0-9])?_\d+\s+\d+\.\d+.\d+.\d+.\d+.\d+/) {
	$pdbcode=lc($1);
	$chain=$2;
	if ($chain eq "") {$chain="A";}
	$header="HEADER    DALI domain $name                    $date";
    }
    
    # PDB ID? (8fab_A, 1a0i, 1a0i_2)
    elsif ($nameline=~/^(\d[a-z0-9]{3})_?(\S?)\b/) {
	$pdbcode=lc($1);
	$chain=$2;
	if ($chain eq "") {$chain="[A ]";}
	$header="HEADER    PDB chain $name                      $date";
    }

    # T0289_B or similar
    elsif ($dopt && $nameline=~/^([^_\s]+)/) {
	$pdbcode=$1;
	if ($nameline=~/^[^_\s]+_(\S)/) {$chain=$1;} else {$chain=".";}
	$header="HEADER    $pdbcode                             $date";
    }    
    else {
	die("Error: no pdb code found in sequence '$nameline'\n");
    }
 
    my $i;          # index for residues in scop sequence
    my $l;          # index for residue record in pdb file: l-1'st character in $aapdb <=> l'th record of $pdbline
    my @pdbline;    # $pdbline[$l][$natom] = line in pdb file for l'th residue in $aapdb and atom N, CB, or O 
    my $natom;      # runs from 0 up to 2 (N, CB, O)
    my $res;        # residue in pdb line
    my $atom;       # atom code in pdb file (N, CA, CB, O, ...)
    my $aapdb="";   # template amino acids from ATOM record of pdb file
    my $col;        # column of alignment query (from hhm file) versus pdb-residues
    my $nres;       # residue number in pdb file
    
    if ($v>=3) {print("Looking for pdb file with pdb code $pdbcode ...\n");}
    $pdbfile = &OpenPDBfile($pdbcode);
    if ($v>=3) {print("Opening pdb file $pdbfile ...\n");}
    if ($pdbfile eq "") {return 1;}
   
    $l=0;
    $nres=-1e6;
    while ($line=<PDBFILE>) {
# ATOM      1  N   GLY A   1     -19.559   8.872   4.925  1.00 16.44           N
# ATOM      2  CA  GLY A   1     -19.004   8.179   6.112  1.00 14.30           C
	if ($line=~/^ENDMDL/) {last;} # if file contains NMR models read only first

	if ($line=~/^ATOM  \s*\d+ (....)[ $altloc](\w{3}) $chain\s*(-?\d+\w?).*/ ||
	    $line=~/^HETATM\s*\d+ (....)[ $altloc](MSE) $chain\s*(-?\d+\w?).*/) {
	    $atom=$1;
	    $res=$2;
	    # New residue?
	    if ($3 ne $nres) {  # $3<$nres if new chain (A:,B:)
 		$nres=$3;
		$l++;
		$res=&Three2OneLetter($res);
		$aapdb.=$res;
		$natom=0;
	    }
	    if ($replaceMSE) {
		$line=~s/^(HETATM\s*\d+ )SE(...MSE)/$1 S$2/ && $line=~s/SE(\s*)$/ S$1/;
		$line=~s/^HETATM(\s*\d+ .....)MSE/ATOM  $1MET/;
	    }
	    $pdbline[$l][$natom++]=$line;
	}
    }
    close (PDBFILE);

    # Align scop query sequence ($aaq) with query sequence in pdb ($aapdb)	
    my $xseq=$aaq;
    my $yseq=$aapdb;
    my ($imin,$imax,$lmin,$lmax);
    my $Sstr;
    my $score;  
    my (@i,@l);    # The aligned characters are returend in $j[$col] and $l[$col]
    if ($v>=3) {print("Aligning query sequence with sequence from pdb ATOM records \n");}	
    $score=&AlignNW(\$xseq,\$yseq,\@i,\@l,\$imin,\$imax,\$lmin,\$lmax,\$Sstr);  
    
    # DEBUG
    if ($v>=3) {print("Generating renumbered pdbfile \n");}	
    
    # Set remarks etc.
    my $author ="AUTHOR    J. Soeding    johannes\@soeding.com";
    push(@remarks,"REMARK    This file was generated by $program. Its residue numbers refer");
    push(@remarks,"REMARK    to the following SEQRES sequence, for which $program was called:");
    push(@remarks,"REMARK    >$nameline");
    $line=uc($aaq);
    while ($line) {
	$line=~s/^(\S{1,60})//;
	push(@remarks,"REMARK    $1");
    }

    # Print scop-pdb file
    if (!open (OUTFILE,">$outfile")) {warn("Error: can't open $outfile: $!\n"); return 3;}
    printf(OUTFILE "%-80.80s\n",$header);
    printf(OUTFILE "%-80.80s\n",$author);
    foreach my $remark (@remarks) {printf(OUTFILE "%-80.80s\n",$remark);}
    my $match=0; 
    my $len=length($aaq);
    for ($col=0; $col<@i; $col++) {
	if ($i[$col] && $l[$col]) {
	    $match++;
	    for ($natom=0; $natom<scalar(@{$pdbline[$l[$col]]}); $natom++) {
		$pdbline[$l[$col]][$natom]=~/(^......\s*\d+ .....\w{3} $chain).{5}(.*)/;
		if ($v>=4) {printf("%s%4i %s\n",$1,$i[$col],$2);}
		$line=sprintf("%s%4i %s\n",$1,$i[$col],$2);
#		$pdbline[$l[$col]][$natom]=~/(^......\s*\d+ .....\w{3} $chain).{4}(.*)/;
#		if ($v>=4) {printf("%s%4i%s\n",$1,$i[$col],$2);}
#		$line=sprintf("%s%4i%s\n",$1,$i[$col],$2);
		print(OUTFILE $line);
	    }
	}
    }
    $line=~/^ATOM\s+(\d+)......(.........)/;
    printf(OUTFILE "TER   %5i      %s                                                    \n",1+$1,$2);
    print(OUTFILE "END                                                                             \n");
    close (OUTFILE);

    # Warn?
    if ($v>=2 || ($v>=1 && $len-$match>5)) {
	if ($v>=1 && $len-$match>1) {
	    printf("\nWARNING: could not find coordinates for %i query residues:\n",$len-$match);
	} else { printf("\n"); }
	$nameline=~/^(\S+)/;
	printf("%-14.14s $xseq\n","Q $1:");
	printf("%-14.14s $Sstr\n","Identities:");
	printf("%-14.14s $yseq\n","T $pdbcode"."_$chain:");
	printf("\n");
	if ($v>=4) {
	    for ($col=0; $col<@l && $col<200; $col++) {
		printf("%3i  %3i  %3i\n",$col,$i[$col],$l[$col]);
	    }
	}
    }

    return 0;
}
# End MakePdbFile()


##################################################################################
# Convert three-letter amino acid code into one-letter code
##################################################################################
sub Three2OneLetter {
    my $res=uc($_[0]);
    if    ($res eq "GLY") {return "G";}
    elsif ($res eq "ALA") {return "A";}
    elsif ($res eq "VAL") {return "V";}
    elsif ($res eq "LEU") {return "L";}
    elsif ($res eq "ILE") {return "I";}
    elsif ($res eq "MET") {return "M";}
    elsif ($res eq "PHE") {return "F";}
    elsif ($res eq "TYR") {return "Y";}
    elsif ($res eq "TRP") {return "W";}
    elsif ($res eq "ASN") {return "N";}
    elsif ($res eq "ASP") {return "D";}
    elsif ($res eq "GLN") {return "Q";}
    elsif ($res eq "GLU") {return "E";}
    elsif ($res eq "CYS") {return "C";}
    elsif ($res eq "PRO") {return "P";}
    elsif ($res eq "SER") {return "S";}
    elsif ($res eq "THR") {return "T";}
    elsif ($res eq "LYS") {return "K";}
    elsif ($res eq "HIS") {return "H";}
    elsif ($res eq "ARG") {return "R";}
    elsif ($res eq "SEC") {return "U";}
    elsif ($res eq "ASX") {return "B";}
    elsif ($res eq "GLX") {return "Z";}
    elsif ($res eq "KCX") {return "K";}
    elsif ($res eq "MSE") {return "M";} # SELENOMETHIONINE 
    elsif ($res eq "SEP") {return "S";} # PHOSPHOSERINE 
    else                  {return "X";}
}

# Find the pdb file with $pdbcode in pdb directory 
sub OpenPDBfile() {
 
    my $pdbcode=lc($_[0]);
    if (! -e "$pdbdir") {
	print(STDERR "Error in $program: pdb directory '$pdbdir' does not exist!\n"); 
	return 1;
    }
    if (-e "$pdbdir/all") {$pdbfile="$pdbdir/all/";}
    elsif (-e "$pdbdir/divided") {$pdbfile="$pdbdir/divided/".substr($pdbcode,1,2)."/";}
    else {$pdbfile="$pdbdir/";}
    if ($pdbdir=~/divided.?$/) {$pdbfile.=substr($pdbcode,1,2)."/";}
    if    (-e $pdbfile."pdb$pdbcode.ent")   {$pdbfile.="pdb$pdbcode.ent";}
    elsif (-e $pdbfile."pdb$pdbcode.ent.gz") {$pdbfile="gunzip -c $pdbfile"."pdb$pdbcode.ent.gz |";}
    elsif (-e $pdbfile."pdb$pdbcode.ent.Z") {$pdbfile="gunzip -c $pdbfile"."pdb$pdbcode.ent.Z |";}
    elsif (-e $pdbfile."$pdbcode.pdb")      {$pdbfile.="$pdbcode.pdb";}
    else {
	printf(STDERR "Error in $program: Cannot find pdb file $pdbfile"."pdb$pdbcode.ent!\n"); 
	return "";
    }
    if (!open (PDBFILE, "$pdbfile")) {
	printf(STDERR "Error in $program: Cannot open pdb file: $!\n"); 
	return "";
    }
    return $pdbfile;
}