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lib/SmotifTF/GetSMotifsfromPDB.pm  view on Meta::CPAN

              SmotifTF::PDB::PDBCoordinateSectionParse::GetPDBHetatmRecordFields($line);
        }
        else {
            die  "There was error: unexpected line-start\n\t$line";
            
        }
        unless ( ( exists( $$HashRef_CoordRecord{'AtomName'} ) )
            && ( exists( $$HashRef_CoordRecord{'ResidueNumber'} ) )
            && ( exists( $$HashRef_CoordRecord{'ResidueInsertionCode'} ) ) )
        {
            die
"There was error: no atom name or res num or insertion code in returned hash\n\t$line\n";
           # return;
        }
        my $AtomType = $$HashRef_CoordRecord{'AtomName'};
        next PDBLINE unless ( $AtomType eq 'CA' );
        my $num           = $$HashRef_CoordRecord{'ResidueNumber'};
        my $insert        = $$HashRef_CoordRecord{'ResidueInsertionCode'};
        my $residuenumber = $num . $insert;
        $residuenumber =~ s/\s+//g;
        if ( $residuenumber eq $motifstart ) {
            $InRange = 1;
            $count++;
        }
        if ($InRange) {
            $count++;
            if ( $count == $ss1lng + 1 ) {
                $loopstart = $residuenumber;
            }
            if ( $count == ( $ss1lng + $looplength ) ) {
                $loopend = $residuenumber;
                last;
            }
        }
        else {
            next PDBLINE;
        }

    }    #end PDBLINE loop

    return ( $loopstart, $loopend );

}
################################################################
##### CHECKED
#####################MUST CHANGE THIS SUBROUTINE TO WORK WITH PDB FILE
sub checklength {
    my ( $start, $end, $ressequence, $sssequence, $ArrayRef_coordchain ) = @_
      ; #smotif start residue, end residue, aa sequence, secondary structure sequence, pdb coord records for chain
    unless ( defined($start)
        && defined($end)
        && defined($ressequence)
        && defined($sssequence)
        && defined($ArrayRef_coordchain) )
    {
        die "There was error: arguments for checklength subroutine\n";
       # return;
    }
    my $checklength;

    #count insertions in the start-end range
    my $numinsertions = 0;
    my $InRange       = 0;
    my $rescount      = 0;
    my %CAcoords;
    my $firstresnum = 'NA';
    my $lastresnum  = 'NA';
  PDBLINE: foreach my $line (@$ArrayRef_coordchain) {

        #get the coordinate line info for any ATOM or HETATM record
        next PDBLINE unless ( $line =~ /^(ATOM|HETATM)/ );
        my ($HashRef_CoordRecord);
        if ( $line =~ /^ATOM/ ) {
            $HashRef_CoordRecord =
              SmotifTF::PDB::PDBCoordinateSectionParse::GetPDBAtomRecordFields($line);
        }
        elsif ( $line =~ /^HETATM/ ) {
            $HashRef_CoordRecord =
              SmotifTF::PDB::PDBCoordinateSectionParse::GetPDBHetatmRecordFields($line);
        }
        else {
            die "There was error: unexpected line-start\n\t$line\n";
           # return;
        }
        unless ( ( exists( $$HashRef_CoordRecord{'AtomName'} ) )
            && ( exists( $$HashRef_CoordRecord{'ResidueNumber'} ) )
            && ( exists( $$HashRef_CoordRecord{'ResidueInsertionCode'} ) ) )
        {
            die
"There was error: no atom name or res num or insertion code in returned hash\n\t$line\n";
           # return;
        }

        #check the CA atoms
        my $AtomType = $$HashRef_CoordRecord{'AtomName'};
        next PDBLINE unless ( $AtomType eq 'CA' );

        #get the current residue PDB number (number and insert code)
        #when the smotif start residue/insert code is encountered, set InRange=1
        my $num           = $$HashRef_CoordRecord{'ResidueNumber'};
        my $insert        = $$HashRef_CoordRecord{'ResidueInsertionCode'};
        my $residuenumber = $num . $insert;
        $residuenumber =~ s/\s+//g;
        if ( $residuenumber eq $start ) {
            $InRange = 1;
        }

        #if the parseing is in the coordinates for the smotif
        if ($InRange) {

            #check to see if there is an insertion code.
            #this is used to count the number of insertions.
            if ( $insert !~ /\s+/ ) { $numinsertions++; }
            if ( $insert =~ /\s+/ ) {

                #set first and last PDB residue numbers
                if ( $firstresnum eq 'NA' ) {
                    $firstresnum = $num;
                }
                $lastresnum = $num;
            }