Subversion Repositories wimsdev

#!/bin/sh

exec perl <<'EOF'

use strict "vars";

use warnings;

push (@ARGV,split(' ', $ENV{'wims_exec_parm'})) if ($ENV{'wims_exec_parm'});

my ($file)=shift @ARGV;

my @valence1=('Li','Na','K','F','Cl','Br','I','At');

my @valence2=('Be','Mg','Ca','Sr','Ba','O','Se','Te','Mn','Hg','Zn','Cu','S');

my @valence3=('B','Al','N','P','As','Fe');

my @valence4=('C','Si','Ge','Sn','A','Q');

my @other=('H');

my ($nbatom, $nbbond);

my $cnt=1; my $nH=0;

my %hash = ();

my $hash = \%hash;

my %bond=();

my $bond = \%bond;

my %atom = ();

my $atom = \%atom;

my $cntmax=10000;

my @a=();

open(IN, "$file");

while(<IN>) {

  @a=split(" ", $_);

  if($cnt==4){

    $nbatom=$a[0]; $nbbond=$a[1];$cntmax=4+$nbatom;

  };

  if($cnt>4 && $cnt <= $cntmax) {

    $hash->{$cnt-4}{name}=$a[3];

    if(!$atom->{$a[3]}) { $atom->{$a[3]}=1} else { $atom->{$a[3]} ++}

    if ( grep { $_ eq $a[3] } @valence4 ){ $hash->{$cnt-4}{hydrogen}=4}

    elsif ( grep { $_ eq $a[3] } @valence1 ){ $hash->{$cnt-4}{hydrogen}=1}

    elsif ( grep { $_ eq $a[3] } @valence2 ){ $hash->{$cnt-4}{hydrogen}=2}

    elsif ( grep { $_ eq $a[3] } @valence3 ){ $hash->{$cnt-4}{hydrogen}=3}

    elsif ( grep { $_ eq $a[3] } @other) {}

    else {

      #die( "$a[3]")

    }

  }

  my $tt;

  if ($cnt > $cntmax && $cnt <= $cntmax + $nbbond) {

    if (!($hash->{$a[0]}{name} =~ /H\b/) && !($hash->{$a[1]}{name} =~ /H\b/)) {

      $hash->{$a[0]}{'hydrogen'}-= $a[2];

      $hash->{$a[1]}{'hydrogen'}-= $a[2];

      $bond->{$cnt}=$a[0] . ',' . $a[1];

      $tt=$cnt<= $cntmax ? $cnt: $cnt-$cntmax;

      $bond->{$a[0]}=!$bond->{$a[0]} ? $tt: $bond->{$a[0]}.','. $tt;

      $bond->{$a[1]}=!$bond->{$a[1]} ? $tt: $bond->{$a[1]}.','. $tt;

    }

    if (!($hash->{$a[0]}{name} =~ /H\b/) && ($hash->{$a[1]}{name} =~ /H\b/)) {

      $hash->{$a[0]}{'hydrogenfichier'}++;

    }

    if (!($hash->{$a[1]}{name} =~ /H\b/) && ($hash->{$a[0]}{name} =~ /H\b/)) {

      $hash->{$a[1]}{'hydrogenfichier'}++;

    }

  }

  if ($_ =~s /M  CHG//) {

    @a=split(" ", $_);

    my $cc=1;

    for my $ion (@a) {

      if ($cc%2==0) {

        $hash->{$ion}{'hydrogen'} += $a[$cc];

      }

      $cc++;

    }

  };

  $cnt ++;

}

close IN;

my $nbhydrogen='';

for my $at (sort {$a<=>$b} keys %hash){

  $hash{$at}{'hydrogen'}=0 if (!(defined $hash{$at}{'hydrogen'}) || $hash{$at}{'hydrogen'}<0);

  $nH = $nH+ $hash{$at}{'hydrogen'};

  $nbhydrogen .= "$at,$hash->{$at}{name},$hash->{$at}{'hydrogen'}\n";

}

my $nbhydrogenfichier='';

for my $at (sort {$a<=>$b} keys %hash){

  if(!($hash->{$at}{name} =~ /H\b/)){

    $hash{$at}{'hydrogenfichier'}=0 if (!(defined $hash{$at}{'hydrogenfichier'})

      || $hash{$at}{'hydrogenfichier'}<0);

    $nbhydrogenfichier .= "$at,$hash->{$at}{name},$hash->{$at}{'hydrogenfichier'}\n";

  }

}

$atom{'H'}=$nH;

my $formula=$atom{'C'} > 0 ? 'C' : '' ;

$formula .= $atom{'C'} if $atom{'C'} > 1;

$formula .= 'H' if $atom{'H'} > 0;

$formula .= $atom{'H'} if $atom{'H'} > 1;

for my $at (sort keys %atom){

  next if (!(defined ($atom{$at})) || $atom{$at}==0 );

  next if ($at=~'C\b' || $at=~'H\b');

  $formula .= $atom{$at}==1? $at : $at . $atom{$at};

}

my $bondprint="";

for my $bd (sort {$a<=>$b} keys %bond){

  next if (!(defined ($bond{$bd})));

  if($bd <= $nbatom){

    $bondprint .= "atom $bd,$bond{$bd}\n";

  } else {

    my $bd1=$bd-$nbatom-4; $bondprint .= "bond $bd1,$bond{$bd}\n";

  }

}

print "$formula,[$nbhydrogen],[$nbhydrogenfichier],[$bondprint]";

EOF