Documentation
PerlMol Quick Tutorial
an awk for molecules
A perl frontend to the Parse::Yapp module
Modules
Generate 3D coordinates from a connection table
Chemical atoms as objects in molecules
Chemical bonds as objects in molecules
Detect bonds in a molecule from atomic 3D coordinates and assign formal bond orders
Number the atoms in a molecule in a unique way
Class for domains in macromolecules
Molecule file I/O base class
Read and write molecules via Data::Dumper
Molecular formula reader/formatter
Wrapper Chemistry::File class for Formula patterns
MDL molfile reader/writer
Wrapper Chemistry::File class for Midas patterns
MOPAC 6 input file reader/writer
Protein Data Bank file format reader/writer
MDL Structure Data File reader/writer
SLN linear notation parser/writer
SMARTS chemical substructure pattern linear notation parser
SMILES linear notation parser/writer
Generate VRML models for molecules
XYZ molecule format reader/writer
Match molecule by formula
Represent the position of an atom using internal coordinates and convert it to Cartesian coordinates.
Build a Z-matrix from cartesian coordinates
Table of the isotopes exact mass data
Perl module for macromolecules
Select atoms in macromolecules
molecular awk interpreter
Molecule object toolkit
Abstract chemistry object
Chemical substructure pattern matching
An atom that knows how to match
A bond that knows how to match
Explicit chemical reactions
Represent a ring as a substructure of a molecule
Find the rings (cycles) in a molecule
Module to handle 3D Vector Mathematics
Perl extension for generating and using LALR parsers.
Perl modules for molecular chemistry
weighted linear regression package (line+plane fitting)
Provides
in lib/Chemistry/File/SLN/Parser.pm
in lib/Chemistry/File/VRML.pm
in lib/Math/VectorReal.pm
in lib/Parse/Yapp/Driver.pm
in lib/Parse/Yapp/Grammar.pm
in lib/Parse/Yapp/Lalr.pm
in lib/Parse/Yapp/Options.pm
in lib/Parse/Yapp/Output.pm
in lib/Parse/Yapp/Parse.pm