Vim Patior

Edit file

File name : chem

Content :

#! /usr/bin/perl

# chem - a groff preprocessor for producing chemical structure diagrams

# Source file position: <groff-source>/contrib/chem/chem.pl
# Installed position: <prefix>/bin/chem

# This file is part of 'chem', which is part of 'groff'.

# 'groff' is free software; you can redistribute it and/or modify it
# under the terms of the GNU General Public License (GPL) version 2 as
# published by the Free Software Foundation.

# 'groff' 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.

# The GPL2 license text is available in the internet at
# <http://www.gnu.org/licenses/gpl-2.0.html>.

########################################################################
# settings
########################################################################

my $Program_Version = '1.0.5';

# this setting of the groff version is only used before make is run,
# otherwise 1.22.4 will set it.
my $Groff_Version_Preset='1.20preset';

# test on Perl version
require v5.6;

########################################################################
# begin
########################################################################

use warnings;
use strict;
use Math::Trig;

# for catfile()
use File::Spec;

# $Bin is the directory where this script is located
use FindBin;

my $Chem_Name;
my $Groff_Version;
my $File_chem_pic;
my $File_pic_tmac;

BEGIN {
  {
    my $before_make;		# script before run of 'make'
    {
      my $at = '@';
      $before_make = 1 if '1.22.4' eq "${at}VERSION${at}";
    }

my %at_at;

if ($before_make) {
      my $chem_dir = $FindBin::Bin;
      $at_at{'BINDIR'} = $chem_dir;
      $at_at{'G'} = '';
      $File_chem_pic = File::Spec->catfile($chem_dir, 'chem.pic');
      $File_pic_tmac = File::Spec->catfile($chem_dir, '..', 'pic.tmac');
      $Groff_Version = '';
      $Chem_Name = 'chem';
    } else {
      $Groff_Version = '1.22.4';
      $at_at{'BINDIR'} = '/usr/bin';
      $at_at{'G'} = '';
      $at_at{'PICDIR'} = '/usr/share/groff/1.22.4/pic';
      $at_at{'TMACDIR'} = '/usr/share/groff/1.22.4/tmac';
      $File_chem_pic =
	File::Spec->catfile($at_at{'PICDIR'}, 'chem.pic');
      $File_pic_tmac = File::Spec->catfile($at_at{'TMACDIR'}, 'pic.tmac');
      $Chem_Name = $at_at{'G'} . 'chem';
    }
  }
}

########################################################################
# check the parameters
########################################################################

if (@ARGV) {
  # process any FOO=bar switches
  # eval '$'.$1.'$2;' while $ARGV[0] =~ /^([A-Za-z_0-9]+=)(.*)/ && shift;
  my @filespec = ();
  my $dbl_minus;
  my $wrong;
  foreach (@ARGV) {
    next unless $_;
    if (/=/) {
      # ignore FOO=bar switches
      push @filespec, $_ if -f;
      next;
    }
    if ($dbl_minus) {
      if (-f $_) {
	push @filespec, $_ if -s $_;
      } else {
	warn "chem: argument $_ is not an existing file.\n";
	$wrong = 1;
      }
      next;
    }
    if (/^--$/) {
      $dbl_minus = 1;
      next;
    }
    if (/^-$/) {
      push @filespec, $_;
      next;
    }
    if (/^-h$/ or '--help' =~ /^$_/) {
      &usage();
      exit 0;
    }
    if (/^-v$/ or '--version' =~ /^$_/) {
      &version();
      exit 0;
    }
    if (-f $_) {
      push @filespec, $_ if -s $_;
    } else {
      $wrong = 1;
      if (/^-/) {
	warn "chem: wrong option ${_}.\n";
      } else {
	warn "chem: argument $_ is not an existing file.\n";
      }
    }
  }
  if (@filespec) {
    @ARGV = @filespec;
  } else {
    exit 0 if $wrong;
    @ARGV = ('-');
  }
} else {			# @ARGV is empty
  @ARGV = ('-') unless @ARGV;
}

########################################################################
# main process
########################################################################

my %Dc = ( 'up' => 0, 'right' => 90, 'down' => 180, 'left' => 270,
	   'ne' => 45, 'se' => 135, 'sw' => 225, 'nw' => 315,
	   0 => 'n', 90 => 'e', 180 => 's', 270 => 'w',
	   30 => 'ne', 45 => 'ne', 60 => 'ne',
	   120 => 'se', 135 => 'se', 150 => 'se',
	   210 => 'sw', 225 => 'sw', 240 => 'sw',
	   300 => 'nw', 315 => 'nw', 330 => 'nw',
	 );

my $Word_Count;
my @Words;

my $Line_No;
my $Last_Name = '';

# from init()
my $First_Time = 1;
my $Last_Type;
my $Dir;			# direction
my %Types = (
	     'RING' => 'R',
	     'MOL' => 'M',
	     'BOND' => 'B',
	     'OTHER' => 'O'	# manifests
	    );

# from setparams()
my %Params;

# from ring()
my $Nput;
my $Aromatic;
my %Put;
my %Dbl;

my %Labtype;
my %Define = ();

my $File_Name = '';
my $Line = '';

&main();

{
  my $is_pic = '';
  my $is_chem = '';
  my $former_line = '';

##########
  # main()
  #
  sub main {
    my $count_minus = 0;
    my @stdin = ();
    my $stdin = 0;

# for centralizing the pic code
    open TMAC, "<$File_pic_tmac" and print <TMAC>;
    close TMAC;

foreach (@ARGV) {
      $count_minus++ if /^-$/;
    }

foreach my $arg (@ARGV) {
      &setparams(1.0);
      next unless $arg;
      $Line_No = 0;
      $is_pic = '';
      $is_chem = '';
      if ($arg eq '-') {
	$File_Name = 'standard input';
	if ($stdin) {
	  &main_line($_) foreach @stdin;
	} else {
	  $stdin = 1;
	  if ($count_minus <= 1) {
	    while (<STDIN>) {
	      &main_line($_);
	    }
	  } else {
	    @stdin = ();
	    while (<STDIN>) {
	      push @stdin, $_;
	      &main_line($_);
	    }
	  }
	}
### main()
      } else {			# $arg is not -
	$File_Name = $arg;
	open FILE, "<$arg";
	&main_line($_) while <FILE>;
	close FILE;
      }				# if $arg
      if ($is_pic) {
	printf ".PE\n";
      }
    }
  } # main()

##########
  # main_line()
  #
  sub main_line {
    my $line = $_[0];
#    $Last_Type = $Types{'OTHER'};
#    $Last_Type = '';
    my $stack;
    $Line_No++;
    chomp $line;

$line = $former_line . $line if $former_line;
    if ($line =~ /^(.*)\\$/) {
      $former_line = $1;
      return 1;
    } else {
      $former_line = '';
    }
    $Line = $line;

{
      @Words = ();
      my $s = $line;
      $s =~ s/^\s*//;
      $s =~ s/\s+$//;
      return 1 unless $s;
      $s = " $s";
      $s =~ s/\s+#.*$// if $is_pic;
      return 1 unless $s;
      $line = $s;
      $line =~ s/^\s*|\s*$//g;
      my $bool = 1;
      while ($bool) {
	$s =~ /^([^"]*)\s("[^"]*"?\S*)(.*)$/;
	if (defined $1) {
	  my $s1 = $1;
	  my $s2 = $2;
	  $s = $3;
	  $s1 =~ s/^\s*|\s*$//g;
	  push @Words, split(/\s+/, $s1) if $s1;
	  push @Words, $s2;
	}
	if ($s !~ /\s"/) {
	  $s =~ s/^\s*|\s*$//g;
	  push @Words, split(/\s+/, $s) if $s;
	  $bool = 0;
	}
      }

#      @Words = split(/\s+/, $s);
      return 1 unless @Words;
#      foreach my $i (0..$#Words) {
#	if ($Words[$i] =~ /^\s*#/) {
#	  $#Words = $i - 1;
#	  last;
#	}
#      }
#      return 1 unless @Words;
    }

if ($line =~ /^([\.']\s*PS\s*)|([\.']\s*PS\s.+)$/) {
      # .PS
      unless ($is_pic) {
	$is_pic = 'running';
	print "$line\n";
      }
      return 1;
    }
### main_line()
    if ( $line =~ /^([\.']\s*PE\s*)|([\.']\s*PE\s.+)$/ ) {
      # .PE
      $is_chem = '';
      if ($is_pic) {
	$is_pic = '';
	print "$line\n";
      }
      return 1;
    }
    if ($line =~ /^[\.']\s*cstart\s*$/) {
      # line: '.cstart'
      if ($is_chem) {
	&error("additional '.cstart'; chem is already active.");
	return 1;
      }
      unless ($is_pic) {
	&print_ps();
	$is_pic = 'by chem';
      }
      $is_chem = '.cstart';
      &init();
      return 1;
    }
### main_line()
    if ($line =~ /^\s*begin\s+chem\s*$/) {
      # line: 'begin chem'
      if ($is_pic) {
	if ($is_chem) {
	  &error("additional 'begin chem'; chem is already active.");
	  return 1;
	}
	$is_chem = 'begin chem';
	&init();
      } else {
	print "$line\n";
      }
      return 1;
    }
    if ($line =~ /^[\.']\s*cend\s*/) {
      # line '.cend'
      if ($is_chem) {
	&error("you end chem with '.cend', but started it with 'begin chem'.")
	  if $is_chem eq 'begin chem';
	if ($is_pic eq 'by chem') {
	  &print_pe();
	  $is_pic = '';
	}
	$is_chem = '';
      } else {
	print "$line\n";
      }
      return 1;
    }
    if ($line =~ /^\s*end\s*$/) {
      # line: 'end'
      if ($is_chem) {
	&error("you end chem with 'end', but started it with '.cstart'.")
	  if $is_chem eq '.cstart';
	if ($is_pic eq 'by chem') {
	  &print_pe();
	  $is_pic = '';
	}
	$is_chem = '';
      } else {
	print "$line\n";
      }
      return 1;
    }

### main_line()
    if (! $is_chem) {
      print "$line\n";
      return 1;
    }
    if ($line =~ /^[.']/) {
      # groff request line
      print "$line\n";
      return 1;
    }

if ($Words[0] eq 'pic') {
      # pic pass-thru
      return 1 if $#Words == 0;
      my $s = $line;
      $s =~ /^\s*pic\s*(.*)$/;
      $s = $1;
      print "$s\n" if $s;
      $Last_Type = $Types{'OTHER'};
      $Define{ $Words[2] } = 1 if $#Words >= 2 && $Words[1] eq 'define';
      return 1;
    }

if ($Words[0] eq 'textht') {
      if ($#Words == 0) {
	&error("'textht' needs a single argument.");
	return 0;
      }
      &error("only the last argument is taken for 'textht', " .
	     "all others are ignored.")
	unless $#Words <= 1 or ($#Words == 2 && $Words[1] =~ /^=/);
      $Params{'textht'} = $Words[$#Words];
      return 1;
    }
### main_line()
    if ($Words[0] eq 'cwid') {	# character width
      if ($#Words == 0) {
	&error("'cwid' needs a single argument.");
	return 0;
      }
      &error("only the last argument is taken for 'cwid', " .
	     "all others are ignored.")
	unless $#Words <= 1 or ($#Words == 2 && $Words[1] =~ /^=/);
      $Params{'cwid'} = $Words[$#Words];
      return 1;
    }
    if ($Words[0] eq 'db') {	# bond length
      if ($#Words == 0) {
	&error("'db' needs a single argument.");
	return 0;
      }
      &error("only the last argument is taken for 'db', " .
	     "all others are ignored.")
	unless $#Words <= 1 or ($#Words == 2 && $Words[1] =~ /^=/);
      $Params{'db'} = $Words[$#Words];
      return 1;
    }
    if ($Words[0] eq 'size') {	# size for all parts of the whole diagram
      my $size;
      if ($#Words == 0) {
	&error("'size' needs a single argument.");
	return 0;
      }
      &error("only the last argument is taken for 'size', " .
	     "all others are ignored.")
	unless $#Words <= 1 or ($#Words == 2 && $Words[1] =~ /^=/);
      if ($Words[$#Words] <= 4) {
	$size = $Words[$#Words];
      } else {
	$size = $Words[$#Words] / 10;
      }
      &setparams($size);
      return 1;
    }

### main_line()
    print "\n#", $Line, "\n";  		      # debugging, etc.
    $Last_Name = '';
#    $Last_Type = $Types{'OTHER'};
#    $Last_Type = '';

if ($Words[0] =~ /^[A-Z].*:$/) {
      # label;  falls thru after shifting left
      my $w = $Words[0];
      $Last_Name = $w;
      $Last_Name =~ s/:$//;
      print "$w";
      shift @Words;
      if (@Words) {
	print " ";
	$line =~ s/^\s*$w\s*//;
      } else {
	print "\n";
	return 1;
      }
    }

if ($Words[0] eq 'define') {
      print "$line\n";
      $Define{ $Words[1] } = 1 if $#Words >= 1;
      $Last_Type = $Types{'OTHER'};
      return 1;
    }
    if ($Words[0] =~ /^[\[\]{}]/) {
      print "$line\n";
      $Last_Type = $Types{'OTHER'};
      return 1;
    }

if ($Words[0] =~ /^"/) {
      print 'Last: ', $line, "\n";
      $Last_Type = $Types{'OTHER'};
      return 1;
    }

if ($Words[0] =~ /bond/) {
      &bond($Words[0]);
      return 1;
    }

if ($#Words >= 1) {
      if ($Words[0] =~ /^(double|triple|front|back)$/ &&
	  $Words[1] eq 'bond') {
	my $w = shift @Words;
	$Words[0] = $w . $Words[0];
	&bond($Words[0]);
	return 1;
      }
      if ($Words[0] eq 'aromatic') {
	my $temp = $Words[0];
	$Words[0] = $Words[1] ? $Words[1] : '';
	$Words[1] = $temp;
      }
    }

if ($Words[0] =~ /ring|benz/) {
      &ring($Words[0]);
      return 1;
    }
    if ($Words[0] eq 'methyl') {
      # left here as an example
      $Words[0] = 'CH3';
    }
### main_line()
    if ($Words[0] =~ /^[A-Z]/) {
      &molecule();
      return 1;
    }
    if ($Words[0] eq 'left') {
      my %left;			# not used
      $left{++$stack} = &fields(1, $#Words);
      printf (("Last: [\n"));
      return 1;
    }
    if ($Words[0] eq 'right') {
      &bracket();
      $stack--;
      return 1;
    }
    if ($Words[0] eq 'label') {	# prints the vertex numbers in a ring
      if ( exists $Labtype{$Words[1]} and
	   $Labtype{$Words[1]} =~ /^$Types{'RING'}/ ) {
	my $v = substr($Labtype{$Words[1]}, 1, 1);
	$Words[1] = '' unless $Words[1];
	foreach my $i ( 1..$v ) {
	  printf "\"\\s-3%d\\s0\" at 0.%d<%s.C,%s.V%d>\n", $i, $v + 2,
	    $Words[1], $Words[1], $i;
	}
      } else {
	&error("$Words[1] is not a ring.");
      }
      return 1;
    }

if ( exists $Define{ $Words[0] } ) {
      print $line, "\n";
      $Last_Type = $Types{'OTHER'};
      return 1;
    }
    return 1 unless $line;
#    print STDERR "# $Line\n";
#    &error('This is not a chem command.  To include a command for pic, ' .
#           "add 'pic' as the first word to the command.");
    print $line, "\n";
    $Last_Type = $Types{'OTHER'};
    1;
  } # main_line()

}

########################################################################
# functions
########################################################################

##########
# atom(<string>)
#
sub atom {
  # convert CH3 to atom(...)
  my ($s) = @_;
  my ($i, $n, $nsub, $cloc, $nsubc, @s);
  if ($s eq "\"\"") {
    return $s;
  }
  $n = length($s);
  $nsub = $nsubc = 0;
  $cloc = index($s, 'C');
  if (! defined($cloc) || $cloc < 0) {
    $cloc = 0;
  }
  @s = split('', $s);
  $i = 0;
  foreach (@s) {
    unless (/[A-Z]/) {
      $nsub++;
      $nsubc++ if $i < $cloc;
      $i++;
    }
  }
  $s =~ s/([0-9]+\.[0-9]+)|([0-9]+)/\\s-3\\d$&\\u\\s+3/g;
  if ($s =~ /([^0-9]\.)|(\.[^0-9])/) { # centered dot
    $s =~ s/\./\\v#-.3m#.\\v#.3m#/g;
  }
  sprintf( "atom(\"%s\", %g, %g, %g, %g, %g, %g)",
	   $s, ($n - $nsub / 2) * $Params{'cwid'}, $Params{'textht'},
	   ($cloc - $nsubc / 2 + 0.5) * $Params{'cwid'}, $Params{'crh'},
	   $Params{'crw'}, $Params{'dav'}
	 );
} # atom()

##########
# bond(<type>)
#
sub bond {
  my ($type) = @_;
  my ($i, $moiety, $from, $leng);
  $moiety = '';
  for ($i = 1; $i <= $#Words; $i++) {
    if ($Words[$i] eq ';') {
      &error("a colon ';' must be followed by a space and a single word.")
       if $i != $#Words - 1;
      $moiety = $Words[$i + 1] if $#Words > $i;
      $#Words = $i - 1;
      last;
    }
  }
  $leng = $Params{'db'};	# bond length
  $from = '';
  for ($Word_Count = 1; $Word_Count <= $#Words; ) {
    if ($Words[$Word_Count] =~
	/(\+|-)?\d+|up|down|right|left|ne|se|nw|sw/) {
      $Dir = &cvtdir($Dir);
    } elsif ($Words[$Word_Count] =~ /^leng/) {
      $leng = $Words[$Word_Count + 1] if $#Words > $Word_Count;
      $Word_Count += 2;
    } elsif ($Words[$Word_Count] eq 'to') {
      $leng = 0;
      $from = &fields($Word_Count, $#Words);
      last;
    } elsif ($Words[$Word_Count] eq 'from') {
      $from = &dofrom();
      last;
    } elsif ($Words[$Word_Count] =~ /^#/) {
      $Word_Count = $#Words + 1;
      last;
    } else {
      $from = &fields($Word_Count, $#Words);
      last;
    }
  }
### bond()
  if ($from =~ /( to )|^to/) {	# said "from ... to ...", so zap length
    $leng = 0;
  } elsif (! $from) {		# no from given at all
    $from = 'from Last.' . &leave($Last_Type, $Dir) . ' ' .
      &fields($Word_Count, $#Words);
  }
  printf "Last: %s(%g, %g, %s)\n", $type, $leng, $Dir, $from;
  $Last_Type = $Types{'BOND'};
  $Labtype{$Last_Name} = $Last_Type if $Last_Name;
  if ($moiety) {
    @Words = ($moiety);
    &molecule();
  }
} # bond()

##########
# bracket()
#
sub bracket {
  my $t;
  printf (("]\n"));
  if ($Words[1] && $Words[1] eq ')') {
    $t = 'spline';
  } else {
    $t = 'line';
  }
  printf "%s from last [].sw+(%g,0) to last [].sw to last [].nw to last " .
    "[].nw+(%g,0)\n", $t, $Params{'dbrack'}, $Params{'dbrack'};
  printf "%s from last [].se-(%g,0) to last [].se to last [].ne to last " .
    "[].ne-(%g,0)\n", $t, $Params{'dbrack'}, $Params{'dbrack'};
  if ($Words[2] && $Words[2] eq 'sub') {
    printf "\" %s\" ljust at last [].se\n", &fields(3, $#Words);
  }
} # bracket()

##########
# corner(<dir>)
#
# Return the corner name next to the given angle.
#
sub corner {
  my ($d) = @_;
  $Dc{ (45 * int(($d + 22.5) / 45)) % 360 };
} # corner()

##########
# cvtdir(<dir>)
#
# Maps "[pointing] somewhere" to degrees.
#
sub cvtdir {
  my ($d) = @_;
  if ($Words[$Word_Count] eq 'pointing') {
    $Word_Count++;
  }
  if ($Words[$Word_Count] =~ /^[+\\-]?\d+/) {
    return ( $Words[$Word_Count++] % 360 );
  } elsif ($Words[$Word_Count] =~ /left|right|up|down|ne|nw|se|sw/) {
    return ( $Dc{$Words[$Word_Count++]} % 360 );
  } else {
    $Word_Count++;
    return $d;
  }
} # cvtdir()

##########
# dblring(<v>)
#
sub dblring {
  my ($v) = @_;
  my ($d, $v1, $v2);
  # should canonicalize to i,i+1 mod v
  $d = $Words[$Word_Count];
  for ($Word_Count++; $Word_Count <= $#Words &&
       $Words[$Word_Count] =~ /^[1-9]/; $Word_Count++) {
    $v1 = substr($Words[$Word_Count], 0, 1);
    $v2 = substr($Words[$Word_Count], 2, 1);
    if ($v2 == $v1 + 1 || $v1 == $v && $v2 == 1) { # e.g., 2,3 or 5,1
      $Dbl{$v1} = $d;
    } elsif ($v1 == $v2 + 1 || $v2 == $v && $v1 == 1) {	# e.g., 3,2 or 1,5
      $Dbl{$v2} = $d;
    } else {
      &error(sprintf("weird %s bond in\n\t%s", $d, $_));
    }
  }
} # dblring()

##########
# dofrom()
#
sub dofrom {
  my $n;
  $Word_Count++;			# skip "from"
  $n = $Words[$Word_Count];
  if (defined $Labtype{$n}) {	# "from Thing" => "from Thing.V.s"
    return 'from ' . $n . '.' . &leave($Labtype{$n}, $Dir);
  }
  if ($n =~ /^\.[A-Z]/) {	# "from .V" => "from Last.V.s"
    return 'from Last' . $n . '.' . &corner($Dir);
  }
  if ($n =~ /^[A-Z][^.]*\.[A-Z][^.]*$/) { # "from X.V" => "from X.V.s"
    return 'from ' . $n . '.' . &corner($Dir);
  }
  &fields($Word_Count - 1, $#Words);
} # dofrom()

##########
# error(<string>)
#
sub error {
  my ($s) = @_;
  printf STDERR "chem: error in %s on line %d: %s\n",
    $File_Name, $Line_No, $s;
} # error()

##########
# fields(<n1>, <n2>)
#
sub fields {
  my ($n1, $n2) = @_;
  if ($n1 > $n2) {
    return '';
  }
  my $s = '';
  foreach my $i ($n1..$n2) {
    if ($Words[$i] =~ /^#/) {
      last;
    }
    $s = $s . $Words[$i] . ' ';
  }
  $s;
} # fields()

##########
# init()
#
sub init {
  if ($First_Time) {
    printf "copy \"%s\"\n", $File_chem_pic;
    printf "\ttextht = %g; textwid = .1; cwid = %g\n",
      $Params{'textht'}, $Params{'cwid'};
    printf "\tlineht = %g; linewid = %g\n",
      $Params{'lineht'}, $Params{'linewid'};
    $First_Time = 0;
  }
  printf "Last: 0,0\n";
  $Last_Type = $Types{'OTHER'};
  $Dir = 90;
} # init()

##########
# leave(<last>, <d>)
#
sub leave {
  my ($last, $d) = @_;
  my ($c, $c1);
  # return vertex of $last in direction $d
  if ( $last eq $Types{'BOND'} ) {
    return 'end';
  }
  $d %= 360;
  if ( $last =~ /^$Types{'RING'}/ ) {
    return &ringleave($last, $d);
  }
  if ( $last eq $Types{'MOL'} ) {
    if ($d == 0 || $d == 180) {
      $c = 'C';
    } elsif ($d > 0 && $d < 180) {
      $c = 'R';
    } else {
      $c = 'L';
    }
    if (defined $Dc{$d}) {
      $c1 = $Dc{$d};
    } else {
      $c1 = &corner($d);
    }
    return sprintf('%s.%s', $c, $c1);
  }
  if ( $last eq $Types{'OTHER'} ) {
    return &corner($d);
  }
  'c';
} # leave()

##########
# makering(<type>, <pt>, <v>)
#
sub makering {
  my ($type, $pt, $v) = @_;
  my ($i, $j, $a, $r, $rat, $fix, $c1, $c2);
  if ($type =~ /flat/) {
    $v = 6;
    # vertices
    ;
  }
  $r = $Params{'ringside'} / (2 * sin(pi / $v));
  printf "\tC: 0,0\n";
  for ($i = 0; $i <= $v + 1; $i++) {
    $a = (($i - 1) / $v * 360 + $pt) / 57.29578; # 57. is $deg
    printf "\tV%d: (%g,%g)\n", $i, $r * sin($a), $r * cos($a);
  }
  if ($type =~ /flat/) {
    printf "\tV4: V5; V5: V6\n";
    $v = 5;
  }
  # sides
  if ($Nput > 0) {
    # hetero ...
    for ($i = 1; $i <= $v; $i++) {
      $c1 = $c2 = 0;
      if ($Put{$i} ne '') {
	printf "\tV%d: ellipse invis ht %g wid %g at V%d\n",
	  $i, $Params{'crh'}, $Params{'crw'}, $i;
	printf "\t%s at V%d\n", $Put{$i}, $i;
	$c1 = $Params{'cr'};
      }
      $j = $i + 1;
      if ($j > $v) {
	$j = 1;
      }
### makering()
      if ($Put{$j} ne '') {
	$c2 = $Params{'cr'};
      }
      printf "\tline from V%d to V%d chop %g chop %g\n", $i, $j, $c1, $c2;
      if ($Dbl{$i} ne '') {
	# should check i<j
	if ($type =~ /flat/ && $i == 3) {
	  $rat = 0.75;
	  $fix = 5;
	} else {
	  $rat = 0.85;
	  $fix = 1.5;
	}
	if ($Put{$i} eq '') {
	  $c1 = 0;
	} else {
	  $c1 = $Params{'cr'} / $fix;
	}
	if ($Put{$j} eq '') {
	  $c2 = 0;
	} else {
	  $c2 = $Params{'cr'} / $fix;
	}
	printf "\tline from %g<C,V%d> to %g<C,V%d> chop %g chop %g\n",
	  $rat, $i, $rat, $j, $c1, $c2;
	if ($Dbl{$i} eq 'triple') {
	  printf "\tline from %g<C,V%d> to %g<C,V%d> chop %g chop %g\n",
	    2 - $rat, $i, 2 - $rat, $j, $c1, $c2;
	}
      }
    }
### makering()
  } else {
    # regular
    for ($i = 1; $i <= $v; $i++) {
      $j = $i + 1;
      if ($j > $v) {
	$j = 1;
      }
      printf "\tline from V%d to V%d\n", $i, $j;
      if ($Dbl{$i} ne '') {
	# should check i<j
	if ($type =~ /flat/ && $i == 3) {
	  $rat = 0.75;
	} else {
	  $rat = 0.85;
	}
	printf "\tline from %g<C,V%d> to %g<C,V%d>\n",
	  $rat, $i, $rat, $j;
	if ($Dbl{$i} eq 'triple') {
	  printf "\tline from %g<C,V%d> to %g<C,V%d>\n",
	    2 - $rat, $i, 2 - $rat, $j;
	}
      }
    }
  }
### makering()
  # punt on triple temporarily
  # circle
  if ($type =~ /benz/ || $Aromatic > 0) {
    if ($type =~ /flat/) {
      $r *= .4;
    } else {
      $r *= .5;
    }
    printf "\tcircle rad %g at 0,0\n", $r;
  }
} # makering()

##########
# molecule()
#
sub molecule {
  my ($n, $type);
  if ($#Words >= 0) {
    $n = $Words[0];
    if ($n eq 'BP') {
      $Words[0] = "\"\" ht 0 wid 0";
      $type = $Types{'OTHER'};
    } else {
      $Words[0] = &atom($n);
      $type = $Types{'MOL'};
    }
  }
  $n =~ s/[^A-Za-z0-9]//g;	# for stuff like C(OH3): zap non-alnum
  if ($#Words < 1) {
    printf "Last: %s: %s with .%s at Last.%s\n",
      $n, join(' ', @Words), &leave($type, $Dir + 180),
	&leave($Last_Type, $Dir);
### molecule()
  } else {
    if (! $Words[1]) {
      printf "Last: %s: %s with .%s at Last.%s\n",
	$n, join(' ', @Words), &leave($type, $Dir + 180),
	  &leave($Last_Type, $Dir);
    } elsif ($#Words >= 1 and $Words[1] eq 'below') {
      $Words[2] = '' if ! $Words[2];
      printf "Last: %s: %s with .n at %s.s\n", $n, $Words[0], $Words[2];
    } elsif ($#Words >= 1 and $Words[1] eq 'above') {
      $Words[2] = '' if ! $Words[2];
      printf "Last: %s: %s with .s at %s.n\n", $n, $Words[0], $Words[2];
    } elsif ($#Words >= 2 and $Words[1] eq 'left' && $Words[2] eq 'of') {
      $Words[3] = '' if ! $Words[3];
      printf "Last: %s: %s with .e at %s.w+(%g,0)\n",
	$n, $Words[0], $Words[3], $Params{'dew'};
    } elsif ($#Words >= 2 and $Words[1] eq 'right' && $Words[2] eq 'of') {
      $Words[3] = '' if ! $Words[3];
      printf "Last: %s: %s with .w at %s.e-(%g,0)\n",
	$n, $Words[0], $Words[3], $Params{'dew'};
    } else {
      printf "Last: %s: %s\n", $n, join(' ', @Words);
    }
  }

$Last_Type = $type;
  if ($Last_Name) {
    #    $Last_Type = '';
    $Labtype{$Last_Name} = $Last_Type;
  }
 $Labtype{$n} = $Last_Type;
} # molecule()

##########
# print_hash(<hash_or_ref>)
#
# print the elements of a hash or hash reference
#
sub print_hash {
  my $hr;
  my $n = scalar @_;
  if ($n == 0) {
    print STDERR "empty hash\n;";
    return 1;
  } elsif ($n == 1) {
    if (ref($_[0]) eq 'HASH') {
      $hr = $_[0];
    } else {
      warn 'print_hash(): the argument is not a hash or hash reference;';
      return 0;
    }
  } else {
    if ($n % 2) {
      warn 'print_hash(): the arguments are not a hash;';
      return 0;
    } else {
      my %h = @_;
      $hr = \%h;
    }
  }

### print_hash()
  unless (%$hr) {
    print STDERR "empty hash\n";
    return 1;
  }
  print STDERR "hash (ignore the ^ characters):\n";
  for my $k (sort keys %$hr) {
    my $hk = $hr->{$k};
    print STDERR "  $k => ";
    if (defined $hk) {
      print STDERR "^$hk^";
    } else {
      print STDERR "undef";
    }
    print STDERR "\n";
  }

1;
}				# print_hash()

##########
# print_pe()
#
sub print_pe {
  print ".PE\n";
} # print_pe()

##########
# print_ps()
#
sub print_ps {
  print ".PS\n";
} # print_ps()

##########
# putring(<v>)
#
sub putring {
  # collect "put Mol at n"
  my ($v) = @_;
  my ($m, $mol, $n);
  $Word_Count++;
  $mol = $Words[$Word_Count++];
  if ($Words[$Word_Count] eq 'at') {
    $Word_Count++;
  }
  $n = $Words[$Word_Count];
  if ($n !~ /^\d+$/) {
    $n =~ s/(\d)+$/$1/;
    $n = 0 if $n !~ /^\d+$/;
    error('use single digit as argument for "put at"');
  }
  if ($n >= 1 && $n <= $v) {
    $m = $mol;
    $m =~ s/[^A-Za-z0-9]//g;
    $Put{$n} = $m . ':' . &atom($mol);
  } elsif ($n == 0) {
    error('argument of "put at" must be a single digit');
  } else {
    error('argument of "put at" is too large');
  }
  $Word_Count++;
} # putring()

##########
# ring(<type>)
#
sub ring {
  my ($type) = @_;
  my ($typeint, $pt, $verts, $i, $other, $fused, $withat);
  $pt = 0;			# points up by default
  if ($type =~ /([1-8])$/) {
    $verts = $1;
  } elsif ($type =~ /flat/) {
    $verts = 5;
  } else {
    $verts = 6;
  }
  $fused = $other = '';
  for ($i = 1; $i <= $verts; $i++) {
    $Put{$i} = $Dbl{$i} = '';
  }
  $Nput = $Aromatic = $withat = 0;
  for ($Word_Count = 1; $Word_Count <= $#Words; ) {
    if ($Words[$Word_Count] eq 'pointing') {
      $pt = &cvtdir(0);
    } elsif ($Words[$Word_Count] eq 'double' ||
	     $Words[$Word_Count] eq 'triple') {
      &dblring($verts);
    } elsif ($Words[$Word_Count] =~ /arom/) {
      $Aromatic++;
      $Word_Count++;		# handled later
### ring()
    } elsif ($Words[$Word_Count] eq 'put') {
      &putring($verts);
      $Nput++;
    } elsif ($Words[$Word_Count] =~ /^#/) {
      $Word_Count = $#Words + 1;
      last;
    } else {
      if ($Words[$Word_Count] eq 'with' || $Words[$Word_Count] eq 'at') {
	$withat = 1;
      }
      $other = $other . ' ' . $Words[$Word_Count];
      $Word_Count++;
    }
  }
  $typeint = $Types{'RING'} . $verts . $pt; # RING | verts | dir
  if ($withat == 0) {
    # join a ring to something
    if ( $Last_Type =~ /^$Types{'RING'}/ ) {
      # ring to ring
      if (substr($typeint, 2) eq substr($Last_Type, 2)) {
	# fails if not 6-sided
	$fused = 'with .V6 at Last.V2';
      }
    }
    # if all else fails
    $fused = sprintf('with .%s at Last.%s',
	  &leave($typeint, $Dir + 180), &leave($Last_Type, $Dir));
  }
  printf "Last: [\n";
  &makering($type, $pt, $verts);
  printf "] %s %s\n", $fused, $other;
  $Last_Type = $typeint;
  $Labtype{$Last_Name} = $Last_Type if $Last_Name;
} # ring()

##########
# ringleave(<last>, <d>)
#
sub ringleave {
  my ($last, $d) = @_;
  my ($rd, $verts);
  # return vertex of ring in direction d
  $verts = substr($last, 1, 1);
  $rd = substr($last, 2);
  sprintf('V%d.%s', int( (($d - $rd) % 360) / (360 / $verts)) + 1,
	  &corner($d));
} # ringleave()

##########
# setparams(<scale>)
#
sub setparams {
  my ($scale) = @_;
  $Params{'lineht'} = $scale * 0.2;
  $Params{'linewid'} = $scale * 0.2;
  $Params{'textht'} = $scale * 0.16;
  $Params{'db'} = $scale * 0.2;	# bond length
  $Params{'cwid'} = $scale * 0.12;	# character width
  $Params{'cr'} = $scale * 0.08; # rad of invis circles at ring vertices
  $Params{'crh'} = $scale * 0.16; # ht of invis ellipse at ring vertices
  $Params{'crw'} = $scale * 0.12; # wid	
  $Params{'dav'} = $scale * 0.015; # vertical shift up for atoms in atom macro
  $Params{'dew'} = $scale * 0.02; # east-west shift for left of/right of
  $Params{'ringside'} = $scale * 0.3; # side of all rings
  $Params{'dbrack'} = $scale * 0.1; # length of bottom of bracket
} # setparams()

##########
# usage()
#
# Print usage information for --help.
#
sub usage {
  print "\n";
  &version();
  print <<EOF;

Usage: $Chem_Name [option]... [filespec]...

$Chem_Name is a groff preprocessor for producing chemical structure
diagrams.  The output suits to the pic preprocessor.

"filespec" is one of
  "filename"       name of a readable file
  "-"              for standard input

All available options are

-h --help         print this usage message.
-v --version      print version information.

EOF
} # usage()

##########
# version()
#
# Get version information from version.sh and print a text with this.
#
sub version {
  $Groff_Version = $Groff_Version_Preset unless $Groff_Version;
  print <<EOF;
$Chem_Name $Program_Version (Perl version)
is part of groff version $Groff_Version.
$Copyright
GNU groff and chem come with ABSOLUTELY NO WARRANTY.
You may redistribute copies of groff and its subprograms
under the terms of the GNU General Public License.
EOF
} # version()

1;
### Emacs settings
# Local Variables:
# mode: CPerl
# End: