hh-suite/scripts/addss.pl

#!/usr/bin/perl
#
# addss.pl
# Add PSIPRED secondary structure prediction (and DSSP annotation) to an MSA or HMMER file.
# Output format is A3M (for input alignments) or HMMER (see User Guide).

#     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).

#     (C) Johannes Soeding and Michael Remmert, 2012

#     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 tempdir /;
use File::Copy;
use strict;

my $ss_cit =
"PSIPRED: Jones DT. (1999) Protein secondary structure prediction based on position-specific scoring matrices. JMB 292:195-202.";

# Module needed for aligning DSSP-sequence

$| = 1;       # Activate autoflushing on STDOUT

# Default values:
our $v = 2;    # verbose mode

my $numres   = 0;     # number of residues per line for secondary structure
my $informat = "a3m"; # input format
my $neff     = 7;     # use alignment with this diversity for PSIPRED prediction
my $program  = $0;    # name of perl script
my $pdbfile;

my $help = "
addss.pl from HHsuite $VERSION  
Add PSIPRED secondary structure prediction (and DSSP annotation) to a multiple sequence alignment (MSA) 
or HMMER (multi-)model file. 

If the input file is an MSA, the predicted secondary structure and confidence values are added as 
special annotation sequences with names >ss_pred, >ss_conf, and >ss_dssp to the top of the output 
A3M alignment. If no output file is given, the output file will have the same name as the input file, 
except for the extension being replaced by '.a3m'. Allowed input formats are A3M (default), 
A2M/FASTA (-fas, -a2m), CLUSTAL (-clu), STOCKHOLM (-sto), HMMER (-hmm).

If the input file contains HMMER models, records SSPRD and SSCON containing predicted secondary 
structure and confidence values are added to each model. In this case the output file name is 
obligatory and must be different from the input file name.

Usage: perl addss.pl <ali_file> [<outfile>] [-fas|-a3m|-clu|-sto]  
  or   perl addss.pl <hhm_file> <outfile> -hmm  
\n";

# Variable declarations
my $line;
my @seqs;    # sequences from infile (except >aa_ and >ss_pred sequences)
my $query_length;
my $header;    # header of MSA: everything before first '>'
my $name;      # query in fasta format: '>$name [^\n]*\n$qseq\n'
my $qseq;      # residues of query sequence
my $infile;
my $outfile;
my $ss_pred = "";    # psipred ss states
my $ss_conf = "";    # psipred confidence values
my $ss_dssp;         # dssp states as string
my $sa_dssp;    # relative solvent accessibility from dssp as string {A,B,C,D,E} A:absolutely buried, B:buried, E:exposed
my $aa_dssp;    # residues from dssp file as string
my $aa_astr;    # residues from infile as string
my $q_match;    # number of match states in query sequence
my $xseq;       # sequence x returned from Align.pm
my $yseq;       # sequence y returned from Align.pm
my $Sstr;       # match sequence returned from Align.pm

###############################################################################################
# Processing command line input
###############################################################################################

if ( @ARGV < 1 ) { die($help); }

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

#Input format fasta?
if    ( $options =~ s/ -fas\s/ /g ) { $informat = "fas"; }
elsif ( $options =~ s/ -a2m\s/ /g ) { $informat = "a2m"; }
elsif ( $options =~ s/ -a3m\s/ /g ) { $informat = "a3m"; }
elsif ( $options =~ s/ -clu\s/ /g ) { $informat = "clu"; }
elsif ( $options =~ s/ -sto\s/ /g ) { $informat = "sto"; }
elsif ( $options =~ s/ -hmm\s/ /g ) { $informat = "hmm"; }

if ( $options =~ s/ -v\s+(\d+) / /g ) { $v = $1; }

# Set input and output file
if ( $options =~ s/ -i\s+(\S+) // )   { $infile  = $1; }
if ( $options =~ s/ -o\s+(\S+) // )   { $outfile = $1; }
if ( $options =~ s/^\s*([^-]\S*) // ) { $infile  = $1; }
if ( $options =~ s/^\s*([^-]\S*) // ) { $outfile = $1; }

# Warn if unknown options found or no infile/outfile
if ( $options !~ /^\s*$/ ) {
	$options =~ s/^\s*(.*?)\s*$/$1/g;
	die("Error: unknown options '$options'\n");
}
if ( !$infile ) { print($help); exit(1); }

my $v2 = $v - 1;
if ( $v2 > 2 ) { $v2--; }
if ( $v2 < 0 ) { $v2 = 0; }

if ( $informat eq "hmm" && !$outfile ) {
	print(
"Error: no output file given. With the -hmm option an output file is obligatory\n"
	);
	exit(1);
}

###############################################################################################
# Reformat input alignment to a3m and psiblast-readable format and generate file with query sequence
###############################################################################################

my $inbase;    # $inbasename of infile: remove extension
my $inroot;    # $inbasename of infile: remove path and extension
if ( $infile =~ /(.*)\..*/ ) { $inbase = $1; }
else { $inbase = $infile; }    # remove extension
if ( $inbase =~ /.*\/(.*)/ ) { $inroot = $1; }
else { $inroot = $inbase; }    # remove path

# Create tmpfile
my $tmpdir;
if ( $v <= 3 ) { $tmpdir = tempdir( CLEANUP => 1 ); }
else { $tmpdir = tempdir( CLEANUP => 0 ); }
my ( $tmpf, $tmpfile ) = tempfile( DIR => $tmpdir );
my $tmpfile_no_dir;
if ( $tmpfile =~ /.*\/(.*)/ ) {
	$tmpfile_no_dir = $1;
}
else {
	$tmpfile_no_dir = $tmpfile;
}

my $tmp_outfile = "$tmpfile.out";

if ( $infile eq "stdin" ) {
	my @stdin = <STDIN>;
	$infile = "$tmpfile.stdin";
	open(OUT, ">$infile");
	foreach my $line (@stdin) {
  	print OUT $line;
	}
	close(OUT);
}

############################################################################################

if ( $informat ne "hmm" ) {
	if ( !$outfile ) { $outfile = "$inbase.a3m"; }

	# Use first sequence to define match states and reformat input file to a3m and psi
	if ( $informat ne "a3m" ) {
		&HHPaths::System(
			"$hhscripts/reformat.pl -v $v2 -M first $informat a3m $infile $tmpfile.1.in.a3m"
		);
	}
	else {
		&HHPaths::System("cp $infile $tmpfile.1.in.a3m");
	}

	# Sanitise the input file - remove all '>' characters, except the one at the start of the string
	# Note that this will corrupt the file if the "header" is not separated by a newline from the
	# first line that starts with '>'
	open( INFILE, "<$tmpfile.1.in.a3m" );
	open( OUTFILE, ">$tmpfile.in.a3m" );
	while ( $line = <INFILE> ) {
		$line =~ s/([^>]+)>/$1/g;
		print OUTFILE $line;
	}
	close(INFILE);
	close(OUTFILE);

	# Read query sequence
	open( INFILE, "<$tmpfile.in.a3m" )
	  or die("ERROR: cannot open $tmpfile.in.a3m!\n");
	$/ = ">";    # set input field separator
	my $i = 0;
	$qseq   = "";
	$header = <INFILE>;
	$header =~ s />$//;
	while ( $line = <INFILE> ) {
		$line =~ s/>$//;
		if ( $line =~ /^ss_/ || $line =~ /^aa_/ ) { next; }
		$seqs[ $i++ ] = ">$line";
		if ( !$qseq ) {
			$line =~ s/^(.*)[^\n]*//;
			$name = $1;
			$qseq = $line;
			$qseq =~ s/\n//g;
		}
	}
	close(INFILE);
	$/ = "\n";    # set input field separator

	if ( $qseq =~ /\-/ ) {

		# First sequence contains gaps => calculate consensus sequence
		&HHPaths::System(
			"hhconsensus -i $tmpfile.in.a3m -s $tmpfile.sq -o $tmpfile.in.a3m > /dev/null"
		);

	}
	else {
		$query_length = ( $qseq =~ tr/A-Z/A-Z/ );
		$qseq =~ tr/A-Z//cd;    # remove everything except capital letters

		# Write query sequence file in FASTA format
		open( QFILE, ">$tmpfile.sq" )
		  or die("ERROR: can't open $tmpfile.sq: $!\n");
		printf( QFILE ">%s\n%s\n", $name, $qseq );
		close(QFILE);
	}

	# Filter alignment to diversity $neff
	if ( $v >= 1 ) { printf(STDERR "Filtering alignment to diversity $neff ...\n"); }
	&HHPaths::System(
		"hhfilter -v $v2 -neff $neff -i $tmpfile.in.a3m -o $tmpfile.in.a3m");

	# Reformat into PSI-BLAST readable file for jumpstarting
	&HHPaths::System(
		"$hhscripts/reformat.pl -v $v2 -r -noss a3m psi $tmpfile.in.a3m $tmpfile.in.psi"
	);

	open( ALIFILE, ">$tmp_outfile" )
	  || die("ERROR: cannot open $tmp_outfile: $!\n");
	printf( ALIFILE "%s", $header );

	# Add DSSP sequence (if available)
	if ( $dssp ne "" ) {
		if ( !&AppendDsspSequences("$tmpfile.sq") ) {
			if ($numres) {

				# insert a line break every $numres residues
				$ss_dssp =~ s/(\S{$numres})/$1\n/g;
			}
			printf( ALIFILE ">ss_dssp\n%s\n", $ss_dssp );
			if ( $v >= 1 ) { print(STDERR "\nAdding DSSP state sequence ...\n"); }
		}
	}

	# Secondary structure prediction with psipred
	if ( $v >= 2 ) {
		print(STDERR "Predicting secondary structure with PSIPRED ... ");
	}
	&RunPsipred("$tmpfile.sq");

	if ( open( PSIPREDFILE, "<$tmpfile.horiz" ) ) {
		$ss_conf = "";
		$ss_pred = "";

		# Read Psipred file
		while ( $line = <PSIPREDFILE> ) {
			if    ( $line =~ /^Conf:\s+(\S+)/ ) { $ss_conf .= $1; }
			elsif ( $line =~ /^Pred:\s+(\S+)/ ) { $ss_pred .= $1; }
		}
		close(PSIPREDFILE);
		$ss_conf =~ tr/0-9/0/c;    # replace all non-numerical symbols with a 0
		if ($numres) {
			$ss_pred =~ s/(\S{$numres})/$1\n/g
			  ;                    # insert a line break every $numres residues
			$ss_conf =~ s/(\S{$numres})/$1\n/g
			  ;                    # insert a line break every $numres residues
		}
		if (length($ss_pred) > 0 && length($ss_conf) > 0) {
			printf( ALIFILE ">ss_pred PSIPRED predicted secondary structure\n%s\n", $ss_pred);
			printf( ALIFILE ">ss_conf PSIPRED confidence values\n%s\n", $ss_conf );
		}
	}

	# Append alignment sequences to psipred sequences
	for ( $i = 0 ; $i < @seqs ; $i++ ) {
		printf( ALIFILE "%s", $seqs[$i] );
	}
	close(ALIFILE);

	if ( !$outfile ) {
		$outfile = "$inbase.a3m";
	}

	if($outfile ne "stdout") {
		move( $tmp_outfile, $outfile );
	}
	else {
		open(IN, "<$tmp_outfile");
		foreach $line(<IN>) {
			print $line;
		}
		close(IN)
	}

	if ( $v >= 2 ) { print(STDERR "done \n"); }
}
##############################################################
# HMMER format
else {
	if ( !$outfile ) { 
		$outfile = "$inbase.hmm"; 
	}

	my $log2 = log(2);
	my @logoddsmat;
	my @lines;
	my $length;
	my $query;
	# empirically determined scale factor between HMMER bit score and PSI-BLAST score, 0.3 for HMMER3
	my $scale = 0.13; 
	my $acc;
	my $name;
	my $desc;
	my $nmodels = 0;

	open( INFILE, "<$infile" ) || die("ERROR: cannot open $infile: $!\n");
	open( OUTFILE, ">$tmp_outfile" ) || die("ERROR: cannot open $tmp_outfile: $!\n");

	# Read HMMER file model by model
	while ( $line = <INFILE> ) {

		# Search for start of next model
		while ( $line && $line !~ /^HMMER/ && $line !~ /^NAME / ) {
			$line = <INFILE>;
		}
		if ( $line =~ /^HMMER3/ ) {

			$scale      = 0.3;
			@logoddsmat = ();
			@lines      = ($line);

			while ( $line = <INFILE> ) {
				push( @lines, $line );
				if ( $line =~ /^LENG/ ) { last; }
			}
			$line =~ /^LENG\s+(\d+)/;
			$length = $1;    # number of match states in HMM
			$query  = "";    # query residues from NULL emission lines
			while ( $line = <INFILE> ) {
				push( @lines, $line );
				if ( $line =~ /^\s*m->m/ ) { last; }
			}
			push( @lines, $line = <INFILE> );
			if ( $line !~ /^\s*COMPO/ ) {
				die("Error: need null-model probablities (Parameter COMPO)!\n");
			}
			$line =~ s/^\s*COMPO\s+(\S.*\S)\s*$/$1/;
			my @nullmodel = split( /\s+/, $line );
			@nullmodel =
			  map { $_ = exp( -1 * $_ ) }
			  @nullmodel;    # Transform to probabilities
			push( @lines, $line = <INFILE> );   # state 0 insert emission
			push( @lines, $line = <INFILE> );   # transisitions from begin state

			while ( $line = <INFILE> ) {
				push( @lines, $line );
				if ( $line =~ /^\/\// ) { last; }
				$line =~ s/^\s*\d+\s+(\S.*\S)\s+\d+\s+(\S)\s+\S\s*$/$1/;
				$query .= $2;
				my @probs = split( /\s+/, $line );
				@probs =
				  map { $_ = exp( -1 * $_ ) }
				  @probs;                       # Transform to probabilities
				                                # calculate log-odds
				my @logodds = ();

				for ( my $a = 0 ; $a < scalar(@probs) ; $a++ ) {
					my $logodd =
					  ( log( $probs[$a] / $nullmodel[$a] ) / $log2 ) * 1000;
					push( @logodds, $logodd );
				}

				push( @logoddsmat, \@logodds );
				push( @lines,      $line = <INFILE> );
				push( @lines,      $line = <INFILE> );
			}

		}
		else {

			$scale = 0.13;
			if ( $line !~ /^HMMER/ && $line !~ /^NAME / ) {
				last;
			}    # first line in each model must begin with 'HMMER...'
			@logoddsmat = ();
			@lines      = ($line);

			while ( $line = <INFILE> ) {
				push( @lines, $line );
				if ( $line =~ /^LENG/ ) { last; }
			}
			$line =~ /^LENG\s+(\d+)/;
			$length = $1;    # number of match states in HMM
			$query  = "";    # query residues from NULL emission lines
			while ( $line = <INFILE> ) {
				push( @lines, $line );
				if ( $line =~ /^\s*m->m/ ) { last; }
			}
			push( @lines, $line = <INFILE> );
			while ( $line = <INFILE> ) {
				push( @lines, $line );
				if ( $line =~ /^\/\// ) { last; }
				$line =~ s/^\s*\d+\s+(\S.*\S)\s*$/$1/;
				my @logodds = split( /\s+/, $line );
				push( @logoddsmat, \@logodds );
				push( @lines, $line = <INFILE> );
				$line =~ /^\s*(\S)/;
				$query .= $1;
				push( @lines, $line = <INFILE> );
			}
		}

		# Write mtx matrix
		open( MTXFILE, ">$tmpfile.mtx" ) || die("ERROR: cannot open $tmpfile.mtx: $!\n");
		printf( MTXFILE "%i\n", $length );
		printf( MTXFILE "%s\n", $query );
		printf( MTXFILE
			"2.670000e-03\n4.100000e-02\n-3.194183e+00\n1.400000e-01\n2.670000e-03\n4.420198e-02\n-3.118986e+00\n1.400000e-01\n3.176060e-03\n1.339561e-01\n-2.010243e+00\n4.012145e-01\n"
		);
		while (@logoddsmat) {
			my @logodds = @{ shift(@logoddsmat) };
			print( MTXFILE "-32768 " );
			splice( @logodds, 1, 0, -32768 / $scale )
			  ;    # insert logodds value for B
			splice( @logodds, 20, 0, -100 / $scale )
			  ;    # insert logodds value for X
			splice( @logodds, 22, 0, -32768 / $scale )
			  ;    # insert logodds value for Z
			for ( my $i = 0 ; $i < 23 ; $i++ ) {
				printf( MTXFILE "%4.0f ", $scale * $logodds[$i] );
			}
			print( MTXFILE "-32768 -400\n" );
		}
		close(MTXFILE);

		# Start Psiblast from checkpoint file tmp.chk that was generated to build the profile
		# Psipred version < 3.0
		if ( -e "$datadir/weights.dat4" ) {    
			&HHPaths::System(
				"$execdir/psipred $tmpfile.mtx $datadir/weights.dat $datadir/weights.dat2 $datadir/weights.dat3 $datadir/weights.dat4 > $tmpfile.ss"
			);
		}
		else {
			&HHPaths::System(
				"$execdir/psipred $tmpfile.mtx $datadir/weights.dat $datadir/weights.dat2 $datadir/weights.dat3 > $tmpfile.ss"
			);
		}

		# READ PSIPRED file
		if (open( PSIPRED, "$execdir/psipass2 $datadir/weights_p2.dat 1 0.98 1.09 $tmpfile.ss2 $tmpfile.ss |"))
		{
			$ss_conf = "";
			$ss_pred = "";

			# Read Psipred file
			while ( $line = <PSIPRED> ) {
				if    ( $line =~ /^Conf:\s+(\d+)/ ) { $ss_conf .= $1; }
				elsif ( $line =~ /^Pred:\s+(\S+)/ ) { $ss_pred .= $1; }
			}
			close(PSIPREDFILE);
		}

		# Add secondary structure to HMMER output file and print
		foreach $line (@lines) {
			if ( $line =~ /^SSPRD/ || $line =~ /^SSCON/ || $line =~ /^SSCIT/ ) {
				next;
			}
			if ( $line =~ /^HMM / ) {
				# insert a line break every 80 residues
				$ss_pred =~ s/(\S{80})/$1\nSSPRD /g;
				# insert a line break every 80 residues    
				$ss_conf =~ s/(\S{80})/$1\nSSCON /g;    
				printf( OUTFILE
					"SSCIT HHsearch-readable PSIPRED secondary structure prediction:\n"
				);
				printf( OUTFILE "SSPRD %s\n", $ss_pred );
				printf( OUTFILE "SSCON %s\n", $ss_conf );
				printf( OUTFILE "SSCIT %s\n", $ss_cit );
			}
			printf( OUTFILE $line );
		}
		$nmodels++;
	}

	close(OUTFILE);
	close(INFILE);

	if ( !$outfile ) {
		$outfile = "$inbase.a3m";
	}

	move( $tmp_outfile, $outfile );

	&HHPaths::System("rm $tmpfile.mtx $tmpfile.ss $tmpfile.ss2");
	if ( $v >= 2 ) {
		printf( STDERR "Added PSIPRED secondary structure to %i models\n", $nmodels );
	}
}

if ( $v <= 3 ) {
	unlink("$tmpfile.in.a3m");
	unlink("$tmpfile.in.psi");
	unlink("$tmpfile.horiz");
	unlink("$tmpfile.dssp");
}

exit;

##############################################################################################
# Run SS prediction starting from alignment in $tmpfile.in.psi (called by BuildAlignment)
##############################################################################################
sub RunPsipred() {

	# This is a simple script which will carry out all of the basic steps
	# required to make a PSIPRED V2 prediction. Note that it assumes that the
	# following programs are in the appropriate directories:
	# blastpgp - PSIBLAST executable (from NCBI toolkit)
	# makemat - IMPALA utility (from NCBI toolkit)
	# psipred - PSIPRED V2 program
	# psipass2 - PSIPRED V2 program

	my $infile = $_[0];
	my $basename;    #file name without extension
	my $rootname;    #basename without directory path
	if ( $infile =~ /^(.*)\..*?$/ ) { $basename = $1; }
	else { $basename = $infile; }
	if ( $basename =~ /^.*\/(.*?)$/ ) { $rootname = $1; }
	else { $rootname = $basename; }

	# Does dummy database exist?
	if ( !-e "$dummydb.phr" ) {
		if ( !-e "$dummydb" ) {
			die "Error in addss.pl: Could not find $dummydb\n";
		}

		&HHPaths::System("cp $infile $dummydb");
		&HHPaths::System("$ncbidir/formatdb -i $dummydb");
		if ( !-e "$dummydb.phr" ) {
			die "Error in addss.pl: Could not find nor create index files for $dummydb\n";
		}
	}

# Start Psiblast from checkpoint file tmp.chk that was generated to build the profile
	&HHPaths::System(
		"$ncbidir/blastpgp -b 1 -j 1 -h 0.001 -d $dummydb -i $infile -B $tmpfile.in.psi -C $tmpfile.chk 1> $tmpfile.blalog 2> $tmpfile.blalog"
	);

	#print("Predicting secondary structure...\n");
	&HHPaths::System( "echo " . "$tmpfile_no_dir" . ".chk > $tmpfile.pn\n" );
	&HHPaths::System( "echo " . "$tmpfile_no_dir" . ".sq  > $tmpfile.sn\n" );
	&HHPaths::System("$ncbidir/makemat -P $tmpfile");

	# Start Psiblast from checkpoint file tmp.chk that was generated to build the profile
	if ( -e "$datadir/weights.dat4" ) {    # Psipred version < 3.0
		&HHPaths::System(
			"$execdir/psipred $tmpfile.mtx $datadir/weights.dat $datadir/weights.dat2 $datadir/weights.dat3 $datadir/weights.dat4 > $tmpfile.ss"
		);
	}
	else {
		&HHPaths::System(
			"$execdir/psipred $tmpfile.mtx $datadir/weights.dat $datadir/weights.dat2 $datadir/weights.dat3 > $tmpfile.ss"
		);
	}

	&HHPaths::System(
		"$execdir/psipass2 $datadir/weights_p2.dat 1 0.98 1.09 $tmpfile.ss2 $tmpfile.ss > $tmpfile.horiz"
	);

	# Remove temporary files
	if ( $v <= 3 ) {
		unlink(
			split ' ',
				"$tmpfile.pn $tmpfile.sn $tmpfile.mn $tmpfile.chk $tmpfile.blalog $tmpfile.mtx $tmpfile.aux $tmpfile.ss $tmpfile.ss2 $tmpfile.sq"
		);
	}
	return;
}

##############################################################################################
# Read query sequence and extract dssp sequence
##############################################################################################
sub AppendDsspSequences() {
	my $qfile = $_[0];

	my $line;      #input line
	my $name;      #name of sequence in in file, e.g. d1g8ma1
	my $qrange;    #chain and residue range of query sequence
	my $aas = "";  #amino acids from in file for each $name

	my $dsspfile;
	my $pdbfile;
	my $pdbcode
	  ;    #pdb code for accessing dssp file; shortened from in code, e.g. 1g8m
	my @ss_dssp = ();    #dssp states for residues (H,E,L)
	my @sa_dssp = ();    #dssp states for residues (H,E,L)
	my @aa_dssp = ();    #residues in dssp file
	my @aa_astr = ();    #residues from infile
	my $length;          #length of sequence

	# Default parameters for Align.pm
	our $d      = 3;            # gap opening penatlty for Align.pm
	our $e      = 0.1;          # gap extension penatlty for Align.pm
	our $g      = 0.09;         # endgap penatlty for Align.pm
	our $matrix = "identity";

	# Read query sequence -> $name, $nameline, $range, $aas
	open( QFILE, "<$qfile" ) || die("cannot open $qfile: $!");
	while ( $line = <QFILE> ) {
		if ( $line =~ />(\S+)/ ) {
			$name = $1;

			# SCOPe ID? (d3lkfa_,d3grs_3,d3pmg.1)
			if ( $line =~ /^>(d[a-z0-9]{4}[a-z0-9_.][a-z0-9_])/ )
			{
				$pdbcode = $1;
				$qrange  = "";
			}

                        # SCOP ID? (d3lkfa_,d3grs_3,d3pmga1,g1m26.1)
			elsif ( $line =~
/^>[defgh](\d[a-z0-9]{3})[a-z0-9_.][a-z0-9_]\s+[a-z]\.\d+\.\d+\.\d+\s+\((\S+)\)/
			  )
			{
				$pdbcode = $1;
				$qrange  = $2;
			}

			# PDB ID? (8fab_A, 1a0i)
                        elsif ( $line =~ /^>(\d[A-Za-z0-9]{3})_?(\S?)\s/ ) {
				$pdbcode = $1;
				if ( $2 ne "" ) { $qrange = "$2:"; }
				else { $qrange = "-"; }
			}

			# DALI ID? (8fabA_0,1a0i_2)
			elsif ( $line =~
/^>(\d[a-z0-9]{3})[A-Za-z0-9]?_\d+\s+\d+\.\d+.\d+.\d+.\d+.\d+\s+\((\S+)\)/
			  )
			{
				$pdbcode = $1;
				$qrange  = $2;
			}

			else {
				if ( $v >= 3 ) {
					print( STDERR
						"Warning: no pdb code found in sequence name '$name'\n"
					);
				}
				close(QFILE);
				return
				  1;   # no astral/DALI/pdb sequence => no dssp states available
			}
			$aas = "";

		}
		else {
			chomp($line);
			$line =~ tr/a-z \t/A-Z/d;
			$aas .= $line;
		}
	}
	close(QFILE);
	if ( $v >= 3 ) {
		printf( STDERR "Searching DSSP state assignments: name=%s  range=%s\n",
			$name, $qrange);
	}

	# Try to open dssp file
        $pdbcode =~ tr/[A-Z]/[a-z]/;
	my $dsspfile = "$dsspdir/$pdbcode.dssp";
	if ( -e $dsspfile ) {
		( $aa_dssp, $ss_dssp, $sa_dssp ) = &readDSSP( $dsspfile, $qrange );
		if ( length($aa_dssp) <= 20 ) {

		   #dssp file is erroneous or chain identifiers in $qrange are erroneous
			if ( $v >= 3 ) {
				printf( STDERR "Warning in $program: Found only "
					  . length($aa_dssp)
					  . " residues in $dsspfile matching $qrange!\n" );
			}

			$aa_dssp = "";
		}
	}
	else {
		if ( $v >= 3 ) {
			printf( STDERR "Warning in $program: Cannot open $dsspfile!\n" );
		}
	}

	if ( $aa_dssp eq "" ) {
		$pdbfile = &OpenPDBfile($pdbcode);
		if ( $pdbfile eq "" ) { return 1; }
		$dsspfile = $tmpfile . ".dssp";
		# Thanks to Stefan Bienert for this patch
		&HHPaths::System("$dssp -i $pdbfile -o $dsspfile 2> /dev/null");

		if ( !-e $dsspfile ) {
			if ( $v >= 3 ) {
				printf( STDERR "Warning in $program: dssp couldn't generate file from $pdbfile. Skipping $name\n");
			}
			return 1;
		}
		else {
			( $aa_dssp, $ss_dssp, $sa_dssp ) = &readDSSP( $dsspfile, $qrange );
			if ( length($aa_dssp) <= 20 ) {
				if ( $v >= 3 ) {
					printf( STDERR 
						"Warning in $program: Found only %i residues in newly calculated $dsspfile matching $qrange!\n", 
						length($aa_dssp)
					);
				}

				# Read in whole DSSP file
				( $aa_dssp, $ss_dssp, $sa_dssp ) = &readDSSP( $dsspfile, "" );
			}
		}
	}

	if ( length($aa_dssp) == 0 ) {
		print(STDERR "WARNING: no residues found in $dsspfile\n");
		return 1;
	}

	if ( length($aa_dssp) <= 20 ) {
		printf(STDERR "WARNING: only %i residues found in $dsspfile\n", length($aa_dssp) );
		return 1;
	}

	# Postprocess $aa_dssp etc
	$aa_dssp =~ tr/a-z/CCCCCCCCCCCCCCCCCCCCCCCCCC/;
	$ss_dssp =~ tr/ I/CC/;
	$ss_dssp =~ s/ \S /   /g;
	$ss_dssp =~ s/ \S\S /    /g;

	# Align query with dssp sequence
	$aa_astr = $aas;
	$xseq    = $aas;
	$yseq    = $aa_dssp;
	my ( $imax, $imin, $jmax, $jmin );
	my ( @i, @j );
	# For long sequences extremely slow... should be replaced
	my $score = &AlignNW( \$xseq, \$yseq, \@i, \@j, \$imin, \$imax, \$jmin, \$jmax, \$Sstr );

	# Initialize strings (=arrays) for dssp states with "----...-"
	my @ss_dssp_ali = ();    # $ss_dssp_ali[$i] is dssp state aligned to $aa_astr[$i]
	my @sa_dssp_ali = ();    # $sa_dssp_ali[$i] is solvent accessibility string
	my @aa_dssp_ali = ();    # $aa_dssp_ali[$i] is dssp residue aligned to $aa_astr[$i]
	
	# sum up to len+1 because 0'th element in @ss_dssp and @aa_dssp is dummy "-" 
	for ( my $i = 0 ; $i <= length($aa_astr) ; $i++ ) {    
		$ss_dssp_ali[$i] = "-";
		$sa_dssp_ali[$i] = "-";
		$aa_dssp_ali[$i] = "-";
	}

	# To each residue (from i=0 to len-1) of input sequence $aa_astr assign aligned dssp state
	@ss_dssp = split( //, $ss_dssp );
	@sa_dssp = split( //, $sa_dssp );
	@aa_dssp = split( //, $aa_dssp );
	@aa_astr = split( //, $aa_astr );
	my $len = 0;

	#add a gap symbol at beginning -> first residue is at 1!
	unshift( @aa_dssp, "-" );

	#add a gap symbol at beginning -> first residue is at 1!
	unshift( @ss_dssp, "-" );

	#add a gap symbol at beginning -> first residue is at 1!
	unshift( @sa_dssp, "-" );

	#add a gap symbol at beginning -> first residue is at 1!
	unshift( @aa_astr, "-" );

	for ( my $col = 0 ; $col < @i ; $col++ ) {
		if ( $i[$col] > 0 ) {
			# count match states (for score/len calculation)
			if ( $j[$col] > 0 ) {
				$len++;
			}
			$ss_dssp_ali[ $i[$col] ] = $ss_dssp[ $j[$col] ];
			$sa_dssp_ali[ $i[$col] ] = $sa_dssp[ $j[$col] ];
			$aa_dssp_ali[ $i[$col] ] = $aa_dssp[ $j[$col] ];
		}

		if ( $v >= 4 ) {
			printf(
				"%s %3i   %s %3i\n",
				$aa_astr[ $i[$col] ], $i[$col],
				$aa_dssp[ $j[$col] ], $j[$col]
			);
		}
	}

	shift(@ss_dssp_ali);    # throw out first "-"
	shift(@sa_dssp_ali);    # throw out first "-"
	shift(@aa_dssp_ali);    # throw out first "-"
	$aa_dssp = join( "", @aa_dssp_ali );
	$ss_dssp = join( "", @ss_dssp_ali );
	$sa_dssp = join( "", @sa_dssp_ali );

	# Debugging output
	if ( $v >= 4 ) {
		printf( STDOUT "DSSP: %s: length=%-3i  score/len:%-5.3f\n",
			$name, $len, $score / $len );
	}

	if ( $v >= 4 ) {
		printf( "IN:    %s\n", $xseq );
		printf( "MATCH: %s\n", $Sstr );
		printf( "DSSP:  %s\n", $yseq );
		printf("\n");
		printf(">ss_dssp $name\n$ss_dssp\n");
		printf(">sa_dssp $name\n$sa_dssp\n");
		printf(">aa_dssp $name\n$aa_dssp\n");
		printf(">aa_astra $name\n$aa_astr\n\n");
	}

	if ( $score / $len < 0.5 ) {
		printf( STDERR "\nWARNING: in $name: alignment score with dssp residues too low: Score/len=%f.\n\n",
			$score / $len
		);
		printf( STDERR "IN:    %s\n", $xseq );
		printf( STDERR "MATCH: %s\n", $Sstr );
		printf( STDERR "DSSP:  %s\n", $yseq );
		return 1;
	}

	return 0;
}

################################################################################################
### Return solvent accessibility code
################################################################################################
sub sa2c () {
	my %maxsa = (
		A => 106,
		B => 160,
		C => 135,
		D => 163,
		E => 194,
		F => 197,
		G => 84,
		H => 184,
		I => 169,
		K => 205,
		L => 164,
		M => 188,
		N => 157,
		P => 136,
		Q => 198,
		R => 248,
		S => 130,
		T => 142,
		V => 142,
		W => 227,
		X => 180,
		Y => 222,
		Z => 196
	);    # maximum solvent accessiblity
	if ( $_[1] =~ /[a-z]/ ) { return "F"; }    # disulphide bridge
	if ( !defined $maxsa{ $_[1] } ) { return "-"; }    # no amino acid
	my $rsa = $_[0] / $maxsa{ $_[1] };

#printf("aa=%s  sa=%5.1f  max_sa=%5.1f  rsa=%5.3f\n",$_[1],$_[0],$maxsa{$_[1]},$rsa);
	if    ( $rsa <= 0.02 ) { return "A"; }
	elsif ( $rsa <= 0.14 ) { return "B"; }
	elsif ( $rsa <= 0.33 ) { return "C"; }
	elsif ( $rsa <= 0.55 ) { return "D"; }
	else { return "E"; }
}

# Find the pdb file with $pdbcode in pdb directory
sub OpenPDBfile() {

	my $pdbcode = lc( $_[0] );
	if ( !-e "$pdbdir" ) {
		if ( $v >= 3 ) {
			print( STDERR
"Warning 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 $pdbfile . "$pdbcode.ent" ) { $pdbfile .= "$pdbcode.ent"; }
	elsif ( -e $pdbfile . "pdb$pdbcode.ent" ) { $pdbfile .= "pdb$pdbcode.ent"; }
	elsif ( -e $pdbfile . "pdb$pdbcode.ent.gz" ) {
		$pdbfile .= "pdb$pdbcode.ent.gz";
	}
	elsif ( -e $pdbfile . "pdb$pdbcode.ent.Z" ) {
		$pdbfile .= "pdb$pdbcode.ent.Z";
	}
	elsif ( -e $pdbfile . "$pdbcode.pdb" ) { $pdbfile .= "$pdbcode.pdb"; }
        elsif ( -e $pdbfile . "$pdbcode.cif" ) { $pdbfile .= "$pdbcode.cif"; }
	else {
		if ( $v >= 3 ) {
			printf( STDERR "Warning in $program: Cannot find pdb file $pdbfile"
				  . "pdb$pdbcode.ent!\n" );
		}
		return "";
	}

	if ( !open( PDBFILE, "$pdbfile" ) ) {
		if ( $v >= 3 ) {
			printf( STDERR "Error in $program: Cannot open pdb file: $!\n" );
		}
		return "";
	}

	if ( $pdbfile =~ /\.(Z|gz)$/i ) {
		my $tmp_pdb_filename;
		(undef, $tmp_pdb_filename) = tempfile(UNLINK => 1, OPEN => 0);
		&HHPaths::System("gunzip -c $pdbfile > $tmp_pdb_filename");
		return "$tmp_pdb_filename";
	}
	else {
		return "$pdbfile";
	}
}

#....+....1....+....2....+....3....+....4
#  #  RESIDUE AA STRUCTURE BP1 BP2  ACC  etc.
#  623  630 A R     <        0   0  280  etc.
#  624        !*             0   0    0  etc.
#  625    8 B A              0   0  105  etc.
#  626    9 B P    >>  -     0   0   71  etc.
#  292   28SA K  H  4 S+     0   0   71  etc.  (1qdm.dssp)
#  293   29SA K  H  > S+     0   0   28  etc.

sub readDSSP() {
	my $dsspfile = $_[0];
	my $qrange   = $_[1];

	my $aa_dssp = "";
	my $sa_dssp = "";
	my $ss_dssp = "";

	open( DSSPFILE, "<$dsspfile" );
	my $line;
	while ( $line = <DSSPFILE> ) {
		if ( $line =~ /^\s*\#\s*RESIDUE\s+AA/ ) { last; }
	}
	while ( $line = <DSSPFILE> ) {
		if ( $line =~ /^.{5}(.{5})(.)(.)\s(.).\s(.).{18}(...)/ ) {
			my $thisres = $1;
			my $icode   = $2;
			my $chain   = $3;
			my $aa      = $4;
			my $ss      = $5;
			my $sa      = $6;
			my $range   = $qrange;
			if ( $aa eq "!" ) { next; }    # missing residues!
			$thisres =~ tr/ //d;
			$chain   =~ tr/ //d;
			$icode   =~ tr/ //d;
			$sa      =~ tr/ //d;

			my $contained = 0;
			if ( $qrange ne "" ) {
				do {

					#syntax (A:56S-135S)
					if (   $range =~ s/^(\S):(-?\d+)[A-Z]-(\d+)([A-Z])//
						&& $chain eq $1
						&& $icode eq $4
						&& $2 <= $thisres
						&& $thisres <= $3 )
					{
						$contained = 1;
					}

					#syntax (R:56-135)
					elsif ($range =~ s/^(\S):(-?\d+)[A-Z]?-(\d+)[A-Z]?//
						&& $chain eq $1
						&& $2 <= $thisres
						&& $thisres <= $3 )
					{
						$contained = 1;
					}

					#syntax (56-135)
					elsif ($range =~ s/^(-?\d+)[A-Z]-(\d+)([A-Z])//
						&& $chain eq ""
						&& $icode eq $3
						&& $1 <= $thisres
						&& $thisres <= $2 )
					{
						$contained = 1;
					}

					#syntax (56-135)
					elsif ($range =~ s/^(-?\d+)[A-Z]?-(\d+)[A-Z]?//
						&& $chain eq ""
						&& $1 <= $thisres
						&& $thisres <= $2 )
					{
						$contained = 1;
					}

					#syntax (A:) or (A:,2:)
					elsif ( $range =~ s/^(\S):// && $chain eq $1 ) {
						$contained = 1;
					}

					#syntax (-)
					elsif ( $range =~ s/^-$// && $chain eq "" ) {
						$contained = 1;
					}
					$range =~ s/^,//;
				} while ( $contained == 0 && $range ne "" );

				if ( $contained == 0 ) {
					next;
				}
			}
			$aa_dssp .= $aa;
			$ss_dssp .= $ss;
			$sa_dssp .= &sa2c( $sa, $aa );
		}
	}

	close DSSPFILE;
	return ( $aa_dssp, $ss_dssp, $sa_dssp );
}