Free chemical elements software for linux

GChemPaint is a 2D chemical structures editor for the Gnome desktop.

GChemPaint should enable embedding some chemistry in files from other programs using Bonobo.

SVG::Element is a Perl module to generate the element bits for SVG.pm.

SVG.pm makes it possible to generate fully-functional SVG images in perl.
100% of the SVG tags are supported, and any new arbitrary element tag can be
added by users by declaring it.

***THERE ARE FIVE WAYS TO IMPLEMENT SVG MODULE IN PERL***

1/ Systems with CPAN support (all Unix/Linux/BSD/Mac):
-----------------------------------------------------
Install the new distribution via the Perl CPAN module:
In a shell:

/home/somewhere% perl -MCPAN -e"install SVG"

2/ (WIN) install Perl from Active State or equivalent:
-----------------------------------------------------
Make sure you already have perl or get it here: http://www.activestate.com
On the command line:
C:> ppm
PPM> set repository tmp http://roasp.com/PPM/SVG/
PPM> install SVG
PPM> quit
C:>

3/ Use Source RPMs.
Download the source RPM of your choice.
In a shell:
/hom/somewhere/% rpm -ihv SVG-source-rpm-name
You may be prompted for the root password

4/ The hard way (requires make or nmake, tar, gunzip, and gcc):
---------------------------------------------------------------
This method was tested in DOS, Windows, AS400, Linux, Unix, BSD, Mac.
Hard-headed users can directly get the distribution from
http://www.roasp.com/PPM/SVG/SVG-2.27.tar.gz or
http://www.roasp.com/PPM/SVG/ .
First download the source.
Then, in a shell:
/home/somewhere% gunzip SVG-2.27.tar.gz
/home/somewhere% tar-xvf SVG-2.27.tar
cd SVG-2.1
make
make test
make install


5/ If all the above fail, there is still a (cumbersome) way:
-----------------------------------------------------------
You have to install to a local dirctory and explicitly call the module
by using one of the following line in your calling program:

#using use lib
use lib path/where/the/release/is/located;

-or-

#using BEGIN block at the beginning of the file
BEGIN {
push @INC path/to/svg.pm-file; #where the SVG.pm file lives
push @INC path/to/svg.pm-file/SVG; # where the Utils.pm file lives
}
#Refer to the Perl manual for more details.

YAPE::Regex::Element contains sub-classes for YAPE::Regex elements.

SYNOPSIS

use YAPE::Regex MyExt::Mod;
# this sets up inheritence in MyExt::Mod
# see YAPE::Regex documentation

YAPE MODULES

The YAPE hierarchy of modules is an attempt at a unified means of parsing and extracting content. It attempts to maintain a generic interface, to promote simplicity and reusability. The API is powerful, yet simple. The modules do tokenization (which can be intercepted) and build trees, so that extraction of specific nodes is doable.

Methods for YAPE::Regex::Element

This class contains fallback methods for the other classes.
my $str = $obj->text;
Returns a string representation of the content of the regex node itself, not any nodes contained in it. This is undef for non-text nodes.
my $str = $obj->string;
Returns a string representation of the regex node itself, not any nodes contained in it.
my $str = $obj->fullstring;
Returns a string representation of the regex node, including any nodes contained in it.
my $quant = $obj->quant;
Returns a string with the quantity, and a ? if the node is non-greedy. The quantity is one of *, +, ?, {M,N}, or an empty string.
my $ng = $obj->ngreed;
Returns a ? if the node is non-greedy, and an empty string otherwise.

Methods for YAPE::Regex::anchor

This class represents anchors. Objects have the following methods:
my $anchor = YAPE::Regex::anchor->new($type,$q,$ng);
Creates a YAPE::Regex::anchor object. Takes three arguments: the anchor (^, A, $, Z, z, B, b, or G), the quantity, and the non-greedy flag. The quantity should be an empty string.
my $anc = YAPE::Regex::anchor->new(A, , ?);
# /A?/
my $type = $anchor->type;
Returns the string anchor.
Methods for YAPE::Regex::macro
This class represents character-class macros. Objects have the following methods:
my $macro = YAPE::Regex::macro->new($type,$q,$ng);
Creates a YAPE::Regex::macro object. Takes three arguments: the macro (w, W, d, D, s, or S), the quantity, and the non-greedy flag.
my $macro = YAPE::Regex::macro->new(s, {3,5});
# /s{3,5}/
my $text = $macro->text;
Returns the macro.
print $macro->text; # s
my $type = $macro->type;
Returns the string macro.

Methods for YAPE::Regex::oct

This class represents octal escapes. Objects have the following methods:
my $oct = YAPE::Regex::oct->new($type,$q,$ng);
Creates a YAPE::Regex::oct object. Takes three arguments: the octal number (as a string), the quantity, and the non-greedy flag.
my $oct = YAPE::Regex::oct->new(040);
# / 40/
my $text = $oct->text;
Returns the octal escape.
print $oct->text; # 40
my $type = $oct->type;
Returns the string oct.

Methods for YAPE::Regex::hex

This class represents hexadecimal escapes. Objects have the following methods:
my $hex = YAPE::Regex::hex->new($type,$q,$ng);
Creates a YAPE::Regex::hex object. Takes three arguments: the hexadecimal number (as a string), the quantity, and the non-greedy flag.
my $hex = YAPE::Regex::hex->new(20,{2,});
# /x20{2,}/
my $text = $hex->text;
Returns the hexadecimal escape.
print $hex->text; # x20
my $type = $hex->type;
Returns the string hex.

Methods for YAPE::Regex::utf8hex

This class represents UTF hexadecimal escapes. Objects have the following methods:
my $hex = YAPE::Regex::utf8hex->new($type,$q,$ng);
Creates a YAPE::Regex::utf8hex object. Takes three arguments: the hexadecimal number (as a string), the quantity, and the non-greedy flag.
my $utf8hex = YAPE::Regex::utf8hex->new(beef,{0,4});
# /x{beef}{2,}/
my $text = $utf8hex->text;
Returns the hexadecimal escape.
print $utf8hex->text; # x{beef}
my $type = $utf8hex->type;
Returns the string utf8hex.

Methods for YAPE::Regex::backref

This class represents back-references. Objects have the following methods:
my $bref = YAPE::Regex::bref->new($type,$q,$ng);
Creates a YAPE::Regex::bref object. Takes three arguments: the number of the back-reference, the quantity, and the non-greedy flag.
my $bref = YAPE::Regex::bref->new(2,,?);
# /2?/
my $text = $bref->text;
Returns the backescape.
print $bref->text; # 2
my $type = $bref->type;
Returns the string backref.

Methods for YAPE::Regex::ctrl

This class represents control character escapes. Objects have the following methods:
my $ctrl = YAPE::Regex::ctrl->new($type,$q,$ng);
Creates a YAPE::Regex::ctrl object. Takes three arguments: the control character, the quantity, and the non-greedy flag.
my $ctrl = YAPE::Regex::ctrl->new(M);
# /cM/
my $text = $ctrl->text;
Returns the control character escape.
print $ctrl->text; # cM
my $type = $ctrl->type;
Returns the string ctrl.

Methods for YAPE::Regex::named

This class represents named characters. Objects have the following methods:
my $ctrl = YAPE::Regex::named->new($type,$q,$ng);
Creates a YAPE::Regex::named object. Takes three arguments: the name of the character, the quantity, and the non-greedy flag.
my $named = YAPE::Regex::named->new(GREEK SMALL LETTER BETA);
# /N{GREEK SMALL LETTER BETA}/
my $text = $named->text;
Returns the character escape text.
print $named->text; # N{GREEK SMALL LETTER BETA}
my $type = $named->type;
Returns the string named.

Chemtool project is a small program for drawing chemical structures on Linux and Unix systems using the GTK toolkit under X11.
Chemtool relies on transfig by Brian Smith for postscript printing and exporting files in PicTeX and EPS formats. Its companion program, XFig, is recommended for enhancing the output of chemtool, and for creation of 2D diagrams and schematics in general.
Both are included with most distributions of Linux, and are available through a number of websites including www.xfig.org. If you want to import chemtool drawings into word processing programs other than LaTeX, you will probably want to add a preview bitmap to them, as neither StarOffice/OpenOffice nor that software from Redmond seem to be able to display postscript inserts on screen without them.
For this purpose, using either ps2epsi, which comes with ghostscript, or epstool, a part of gsview is recommended. Since chemtool-1.6, this option is supported directly (through the equivalent function offered by recent versions of transfig).
Chemtool was originally written by Thomas Volk, then a student of chemistry and biology at the university of Ulm, Germany. His version, which was described in an article in the german periodical LinuxMagazin, was using plain X11.
The bond types available in chemtool are:
- a single bond
- a double bond (with one line shorter than the other)
- a double bond (having the shorter line on the opposite side)
- a centered double bond
- a triple bond (with the flanking lines shorter than the center)
- a wedge-shaped bond
- a dashed wedge-shaped bond
- a wavy line
- a dashed wide line
- a half arrow
- an arrow
- a wide bond
- a circle
- a dotted line
- a single bond that cuts out a segment from any bond it crosses
- a triple bond (with equal line lengths)
- a quadruple bond
Enhancements:
- PNG export, kprinter support, and a few new template structures were added.
- Screen rendering of complex labels was improved.
- Several problems with text input in UTF8-enabled locales were fixed.
- Arrowhead size in EPS output and the appearance of arrowheads, superscripts, and national characters in SVG output were fixed.