Get free Perl modules, designed for molecular chemistry applications. Use these modules to simplify your code and improve productivity.
PerlMol is a chemoinformatics and computational chemistry toolkit that consists of a collection of Perl modules. The toolkit is designed with the philosophy that simple tasks should be easy to accomplish. Users can write one-liners using PerlMol to perform molecular operations.
Among the features offered by PerlMol are methods and objects for representing molecules, atoms, and bonds in Perl, substructure matching, and the ability to read and write files in several formats. It's worth noting that PerlMol is distributed and licensed under the Artistic License and GPL.
Some of the other key functions provided by this tool include basic functions such as clone molecule, delete atoms and bonds, and combine/separate molecules. Geometric functions include the ability to calculate distances, angles, dihedrals from cartesian coordinates, find the shortest distance between two molecules, Cartesian coordinates from internal coordinates, and more.
Topological functions include creating bonds from cartesian coordinates, auto-assigning formal bond orders, ring perception (including SSSR), detecting aromaticity, substructure matching, formula matching, and canonicalization/topological symmetry perception.
Input/output and file formats are also well-covered with this tool. It offers 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, and others.
Users will also appreciate the data features like relative atomic masses and exact isotope masses, while the mini-language Mok ("an AWK for molecules") offers users a suite of molecular operations to choose from.
Overall, PerlMol offers an extensive suite of features for chemoinformatics and computational chemistry. It serves as a useful tool for those looking to perform molecular operations in Perl.
Among the features offered by PerlMol are methods and objects for representing molecules, atoms, and bonds in Perl, substructure matching, and the ability to read and write files in several formats. It's worth noting that PerlMol is distributed and licensed under the Artistic License and GPL.
Some of the other key functions provided by this tool include basic functions such as clone molecule, delete atoms and bonds, and combine/separate molecules. Geometric functions include the ability to calculate distances, angles, dihedrals from cartesian coordinates, find the shortest distance between two molecules, Cartesian coordinates from internal coordinates, and more.
Topological functions include creating bonds from cartesian coordinates, auto-assigning formal bond orders, ring perception (including SSSR), detecting aromaticity, substructure matching, formula matching, and canonicalization/topological symmetry perception.
Input/output and file formats are also well-covered with this tool. It offers 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, and others.
Users will also appreciate the data features like relative atomic masses and exact isotope masses, while the mini-language Mok ("an AWK for molecules") offers users a suite of molecular operations to choose from.
Overall, PerlMol offers an extensive suite of features for chemoinformatics and computational chemistry. It serves as a useful tool for those looking to perform molecular operations in Perl.
What's New
Version 0.3500: N/A