PerlMol Free Perl modules for molecular chemistry
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calculate parse module perl module calculation module parse module

PerlMol Description

Free Perl modules for molecular chemistry PerlMol is a collection of Perl modules for chemoinformatics and computational chemistry with the philosophy that "simple things should be simple". It should be possible to write one-liners that use this toolkit to do meaningful "molecular munging". The PerlMol toolkit provides methods and objects for representing bonds, ,olecules and atoms in Perl; doing substructure matching; and reading and writing files in various formats.NOTE: PerlMol is licensed and distributed under the terms of the Artistic License and GNU General Public License (GPL).Here are some key features of "Clozure CL":Basic functions· Clone molecules· Delete atoms and bonds· Combine/separate molecules (connected graphs)Geometric functions· Calculate distances, angles, and dihedrals from cartesian coordinates· Find shortest distance between two molecules· Cartesian coordinates from internal coordinates· Z-matrix builder: create an internal coordinate representation of a molecule from scratch using the Cartesian coordinates· 3D molecule structure builder: generate atomic coordinates from a connection table· Calculate the centroid and best-fit plane of a ringTopological functions· Create bonds from cartesian coordinates· Automatically assign formal bond orders· Ring perception (including SSSR)· Detect aromaticity· Substructure matching· Formula matching· Canonicalization / topological symmetry perception· Z-matrix builder: create an internal coordinate representation of a molecule from scratch using the Cartesian coordinatesInput/output and file formats· MDL Molfile parser/writer· MDL SDF file parser/writer· PDB file parser/writer· SMILES parser/writer· Unique SMILES generator· SMARTS parser· Sybyl Line Notation (SLN) parser/writer· Midas/Chimera atom specification language parser· Formula parser/formatter· Formula pattern parser· Mopac input file parser/writer· XYZ format file parser/writer· VRML format file writer· Perl Data::Dumper file format· A "printf" for molecules and atomsData· Relative atomic masses· Exact isotope massesMini-language· Mok - "an AWK for molecules" Requirements: · Perl What's New in This Release: · New: Chemistry-File-VRML 0.10 · New: Chemistry-3DBuilder 0.10 · Added formal_radical atom property. · Compatibility with Storable-2.14, which already takes care of weak references. · calc_implicit_hydrogens, add_implicit_hydrogens · Fixed $atom->bonds duplication on $mol->separate (bug 1173237) · New method: safe_clone · Fixed spurious warnings in sprout_hydrogens (bug 1157393) · Added a test for incompatible Chemistry::File::SMILES versions. · Read one molecule at a time using the Chemistry-Mol-0.30 interface. · New special variable $FH · Added support for Chemistry::3DBuilder (-3 command-line option) · Add #line to the generated code so that errors give more meaningful line numbers. · Fixed parsing bug where the first block used an explicit pattern language Restructured Chemistry::Mok to be more object-oriented: · WARNING: the mok object is now a hash reference instead of an array reference. This may affect derived classes. · Fixed memory leak that prevented the last atom from being garbage collected. · Added the original SMARTS string as the $patt->name property. · Added support for atom mapping numbers · Changed parse_file to read_mol · Read multi-model files (each model read as one molecule) · Read chain id and insertion code · Fixed mapping bug for overlap => 0 · Chain support. · Be more lenient with whitespace. · Refactored parsing and execution. · Added support for charges and radicals. · Add implicit hydrogens on read. · Support for some query properties: atom lists, bond topology, and bond types. · Added natural abundance table

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