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GDS2 is a module for quickly creating programs to read and/or write GDS2 files.

Create Method

new - open gds2 file

usage:
my $gds2File = new GDS2(-fileName => "filename.gds2"); ## to read
my $gds2File2 = new GDS2(-fileName => ">filename.gds2"); ## to write

fileNum - file number...

usage:

close - close gds2 file

usage:

$gds2File -> close;
-or-
$gds2File -> close(-markEnd=>1); ## experimental -- some systems have trouble closing files
$gds2File -> close(-pad=>2048); ## experimental -- pad end with s till file size is a
## multiple of number. Note: old reel to reel tapes on Calma
## systems used 2048 byte blocks

High Level Write Methods

printInitLib() - Does all the things needed to start a library, writes HEADER,BGNLIB,LIBNAME,and UNITS records

The default is to create a library with a default unit of 1 micron that has a resolution of 1000. To get this set uUnit to 0.001 (1/1000) and the dbUnit to 1/1000th of a micron (1e-9). usage: $gds2File -> printInitLib(-name => "testlib", ## required -isoDate => 0|1 ## (optional) use ISO 4 digit date 2001 vs 101 -uUnit => real number ## (optional) default is 0.001 -dbUnit => real number ## (optional) default is 1e-9 );

## defaults to current date for library date

note:

remember to close library with printEndlib()
printBgnstr - Does all the things needed to start a structure definition

usage:

$gds2File -> printBgnstr(-name => "nand3" ## writes BGNSTR and STRNAME records
-isoDate => 1|0 ## (optional) use ISO 4 digit date 2001 vs 101
);

note:

remember to close with printEndstr()

printPath - prints a gds2 path
usage:
$gds2File -> printPath(
-layer=>#,
-dataType=>#, ##optional
-pathType=>#,
-width=>#.#,
-unitWidth=>#, ## (optional) directly specify width in data base units (vs -width which is multipled by resolution)
-xy=>@array, ## array of reals
-xyInt=>@array, ## array of internal ints (optional -wks better if you are modifying an existing GDS2 file)
);

note:
layer defaults to 0 if -layer not used
pathType defaults to 0 if -pathType not used
pathType 0 = square end
1 = round end
2 = square - extended 1/2 width
4 = custom plus variable path extension...
width defaults to 0.0 if -width not used
printBoundary - prints a gds2 boundary
usage:
$gds2File -> printBoundary(
-layer=>#,
-dataType=>#,
-xy=>@array, ## array of reals
-xyInt=>@array, ## array of internal ints (optional -wks better if you are modifying an existing GDS2 file)
);

note:
layer defaults to 0 if -layer not used
dataType defaults to 0 if -dataType not used
printSref - prints a gds2 Structure REFerence
usage:
$gds2File -> printSref(
-name=>string, ## Name of structure
-xy=>@array, ## array of reals
-xyInt=>@array, ## array of internal ints (optional -wks better than -xy if you are modifying an existing GDS2 file)
-angle=>#.#, ## (optional) Default is 0.0
-mag=>#.#, ## (optional) Default is 1.0
-reflect=>0|1 ## (optional)
);

note:
best not to specify angle or mag if not needed
printAref - prints a gds2 Array REFerence
usage:
$gds2File -> printAref(
-name=>string, ## Name of structure
-columns=>#, ## Default is 1
-rows=>#, ## Default is 1
-xy=>@array, ## array of reals
-xyInt=>@array, ## array of internal ints (optional -wks better if you are modifying an existing GDS2 file)
-angle=>#.#, ## (optional) Default is 0.0
-mag=>#.#, ## (optional) Default is 1.0
-reflect=>0|1 ## (optional)
);

note:
best not to specify angle or mag if not needed
printText - prints a gds2 Text
usage:
$gds2File -> printText(
-string=>string,
-layer=>#, ## Default is 0
-textType=>#, ## Default is 0
-font=>#, ## 0-3
-top, or -middle, -bottom, ##optional vertical presentation
-left, or -center, or -right, ##optional horizontal presentation
-xy=>@array, ## array of reals
-xyInt=>@array, ## array of internal ints (optional -wks better if you are modifying an existing GDS2 file)
-x=>#.#, ## optional way of passing in x value
-y=>#.#, ## optional way of passing in y value
-angle=>#.#, ## (optional) Default is 0.0
-mag=>#.#, ## (optional) Default is 1.0
-reflect=>#, ## (optional) Default is 0
);

note:

best not to specify reflect, angle or mag if not needed

XDrawChem is a two-dimensional molecule drawing program for Unix operating systems. XDrawChem is similar in functionality to other molecule drawing programs such as ChemDraw (TM, CambridgeSoft).
It can read and write MDL Molfiles, and read ChemDraw text and binary files, to allow sharing between XDrawChem and other chemistry applications, and it can create images in popular formats like PNG and EPS. XDrawChem has been tested on Linux, SGI IRIX 6.5, Sun Solaris, Mac OS X, and Windows.
Main features:
- 100% compatible Windows 95/98/NT version
- Fixed length, fixed angle drawing.
- Automatic alignment of figures. Detects structures, text, and arrows and places them automatically.
- Can automatically draw rings and other structures - has all standard amino acids and nucleic acids in built-in library.
- Can retrieve structures from a network database based on CAS number, formula, or name.
- Can draw symbols such as partial charge, radicals, etc.
- Can read MDL Molfiles, CML [Chemical Markup Language, defined in J. Chem. Inf. Comput. Sci.39(1999), 928-942], ChemDraw(TM) binary format, ChemDraw(TM) XML text format.
- Can write MDL Molfiles, CML, ChemDraw(TM) XML text format.
- Can also read and write any format supported by the current release of OpenBabel.
- Can export pictures in PNG, Windows bitmap (*.bmp), Encapsulated PostScript (EPS), and Scalable Vector Graphics (SVG).
- Can generate 3-D structures with the help of the external program BUILD3D.
- Online help, including tool tips.
- 13C-NMR prediction, based on Bremser W, Mag. Res. Chem.23(4):271-275
- 1H-NMR prediction, based on additive rules and functional group lookup methods, described in Pretsch, Clerc, Seibl, Simon, "Tables of Spectral Data for Structure Determination of Organic Compounds", 2ed., 1989, Springer-Verlag
- Simple IR prediction.
- Simple pKa estimation.
- Octanol-water partition coefficient estimation.
- Reaction analysis: gas-phase enthalpy change estimate, 1H NMR and 13C NMR comparison.
- Integration with OpenBabel, allowing XDrawChem to read and write over 20 different chemical file formats.