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PerlMol-0.26_00.ppm
River stage zero No dependents
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Documentation

Chemistry::Tutorial
PerlMol Quick Tutorial
mok
an awk for molecules
yapp
A perl frontend to the Parse::Yapp module

Modules

Chemistry::Atom
Chemical atoms as objects in molecules
Chemistry::Bond
Chemical bonds as objects in molecules
Chemistry::Bond::Find
Detect bonds in a molecule from atomic 3D coordinates and assign formal bond orders
Chemistry::Canonicalize
Number the atoms in a molecule in a unique way
Chemistry::Domain
Class for domains in macromolecules
Chemistry::File
Molecule file I/O base class
Chemistry::File::Dumper
Read and write molecule via Data::Dumper
Chemistry::File::Formula
Molecular formula reader/formatter
Chemistry::File::FormulaPattern
Wrapper Chemistry::File class for Formula patterns
Chemistry::File::MDLMol
MDL molfile reader/writer
Chemistry::File::MidasPattern
Wrapper Chemistry::File class for Midas patterns
Chemistry::File::Mopac
MOPAC 6 input file reader/writer
Chemistry::File::PDB
Protein Data Bank file format reader/writer
Chemistry::File::SDF
MDL Structure Data File reader/writer
Chemistry::File::SLN
SLN linear notation parser/writer
Chemistry::File::SMARTS
SMARTS chemical substructure pattern linear notation parser
Chemistry::File::SMILES
SMILES linear notation parser/writer
Chemistry::File::XYZ
XYZ molecule format reader/writer
Chemistry::FormulaPattern
Match molecule by formula
Chemistry::InternalCoords
Represent the position of an atom using internal coordinates and convert it to Cartesian coordinates.
Chemistry::InternalCoords::Builder
Build a Z-matrix from cartesian coordinates
Chemistry::MacroMol
Perl module for macromolecules
Chemistry::MidasPattern
Select atoms in macromolecules
Chemistry::Mok
molecular awk interpreter
Chemistry::Mol
Molecule object toolkit
Chemistry::Obj
Abstract chemistry object
Chemistry::Pattern
Chemical substructure pattern matching
Chemistry::Pattern::Atom
Chemistry::Pattern::Bond
Chemistry::Ring
Represent a ring as a substructure of a molecule
Chemistry::Ring::Find
Find the rings (cycles) in a molecule
Math::VectorReal
Module to handle 3D Vector Mathematics
Parse::Yapp
Perl extension for generating and using LALR parsers.
PerlMol
Perl modules for molecular chemistry
Statistics::Regression
weighted linear regression package (line+plane fitting)

Provides

Chemistry::File::SLN::Parser
in lib/Chemistry/File/SLN/Parser.pm
Math::MatrixReal
in lib/Math/VectorReal.pm
Parse::Yapp::Driver
in lib/Parse/Yapp/Driver.pm
Parse::Yapp::Grammar
in lib/Parse/Yapp/Grammar.pm
Parse::Yapp::Lalr
in lib/Parse/Yapp/Lalr.pm
Parse::Yapp::Options
in lib/Parse/Yapp/Options.pm
Parse::Yapp::Output
in lib/Parse/Yapp/Output.pm
Parse::Yapp::Parse
in lib/Parse/Yapp/Parse.pm