Search results for "module:Chemistry::File"
Chemistry::File - Molecule file I/O base class
The main use of this module is as a base class for other molecule file I/O modules (for example, Chemistry::File::PDB). Such modules should override and extend the Chemistry::File methods as needed. You only need to care about the methods here if if ...
MERKYS/Chemistry-Mol-0.39 - 13 Jul 2022 08:36:38 UTC
Chemistry::File::VRML - Generate VRML models for molecules
This module generates a VRML (Virtual Reality Modeling Language) representation of a molecule, which can then be visualized with any VRML viewer. This is a PerlMol file I/O plugin, and registers the 'vrml' format with Chemistry::Mol. Note however tha...
ITUB/Chemistry-File-VRML-0.10 - 16 May 2005 21:17:49 UTC
Chemistry::File::SLN - SLN linear notation parser/writer
This module parses a SLN (Sybyl Line Notation) string. This is a File I/O driver for the PerlMol project. <http://www.perlmol.org/>. It registers the 'sln' format with Chemistry::Mol, and recognizes filenames ending in '.sln'. Optional attributes for...
ITUB/Chemistry-File-SLN-0.11 - 29 Mar 2005 16:42:04 UTC
Chemistry::File::PDB - Protein Data Bank file format reader/writer
This module reads and writes PDB files. The PDB file format is commonly used to describe proteins, particularly those stored in the Protein Data Bank (<http://www.rcsb.org/pdb/>). The current version of this module only reads the following record typ...
ITUB/Chemistry-File-PDB-0.23 - 10 May 2009 21:58:55 UTC
Chemistry::File::XYZ - XYZ molecule format reader/writer
This module reads XYZ files. It automatically registers the 'xyz' format with Chemistry::Mol, so that XYZ files may be identified and read by Chemistry::Mol->read(). The XYZ format is not strictly defined and there are various versions floating aroun...
ITUB/Chemistry-File-XYZ-0.11 - 03 Aug 2004 00:23:58 UTC
Chemistry::File::CML - Chemical Markup Language reader/writer
Chemical Markup Language reader/writer. This module automatically registers the 'cml' format with Chemistry::Mol. This version reads and writer only some of the information available in CML files. It does not read stereochemistry yet, but this is env...
MERKYS/Chemistry-File-CML-0.14 - 02 Mar 2023 14:47:33 UTC
Chemistry::File::SDF - MDL Structure Data File reader/writer
MDL SDF (V2000) reader. This module automatically registers the 'sdf' format with Chemistry::Mol. The parser returns a list of Chemistry::Mol objects. SDF data can be accessed by the $mol->attr method. Attribute names are stored as a hash ref at the ...
MERKYS/Chemistry-File-MDLMol-0.24 - 03 Feb 2022 16:09:12 UTC
Chemistry::File::Mopac - MOPAC 6 input file reader/writer
This module reads and writes MOPAC 6 input files. It can handle both internal coordinates and cartesian coordinates. It also extracts molecules from summary files, defined as those files that match /SUMMARY OF/ in the third line. Perhaps a future ver...
ITUB/Chemistry-File-Mopac-0.15 - 02 Jul 2004 18:22:49 UTC
Chemistry::File::MDLMol - MDL molfile reader/writer
MDL Molfile (V2000) reader/writer. This module automatically registers the 'mdl' format with Chemistry::Mol. The first three lines of the molfile are stored as $mol->name, $mol->attr("mdlmol/line2"), and $mol->attr("mdlmol/comment"). This version onl...
MERKYS/Chemistry-File-MDLMol-0.24 - 03 Feb 2022 16:09:12 UTC
Chemistry::File::SMARTS - SMARTS chemical substructure pattern linear notation parser
This module parse a SMARTS (SMiles ARbitrary Target Specification) string, generating a Chemistry::Pattern object. It is a file I/O driver for the PerlMol toolkit; it's not called directly but by means of the Chemistry::Pattern->parse class method. F...
ITUB/Chemistry-File-SMARTS-0.22 - 16 May 2005 22:22:44 UTC
Chemistry::File::SMILES - SMILES linear notation parser/writer
This module parses a SMILES (Simplified Molecular Input Line Entry Specification) string. This is a File I/O driver for the PerlMol project. <http://www.perlmol.org/>. It registers the 'smiles' format with Chemistry::Mol. This parser interprets anyth...
ITUB/Chemistry-File-SMILES-0.47 - 08 Jul 2010 03:16:39 UTC
Chemistry::File::Dumper - Read and write molecules via Data::Dumper
This module hooks the Data::Dumper Perl core module to the Chemistry::File API, allowing you to dump and undump Chemistry::Mol objects easily. This module automatically registers the "dumper" format with Chemistry::Mol. For purposes of automatic file...
MERKYS/Chemistry-Mol-0.39 - 13 Jul 2022 08:36:38 UTC
Chemistry::File::Formula - Molecular formula reader/formatter
This module converts a molecule object to a string with the formula and back. It registers the 'formula' format with Chemistry::Mol. Besides its obvious use, it is included in the Chemistry::Mol distribution because it is a very simple example of a C...
MERKYS/Chemistry-Mol-0.39 - 13 Jul 2022 08:36:38 UTC
Chemistry::File::QChemOut - Q-Chem ouput molecule format reader
This module reads Q-Chem output files. It automatically registers the 'qchemout' format with Chemistry::Mol, so that Q-Chem outuput files may be identified and read using Chemistry::Mol->read(). The current version of this reader simply extracts the ...
ITUB/Chemistry-File-QChemOut-0.10 - 04 Oct 2006 16:20:37 UTC
Chemistry::File::OPTIMADE - OPTIMADE reader
OPTIMADE structure representation reader....
MERKYS/Chemistry-File-OPTIMADE-0.11 - 21 Oct 2022 10:42:34 UTC
Chemistry::File::MidasPattern - Wrapper Chemistry::File class for Midas patterns
This is a wrapper class for reading Midas Patterns using the standard Chemistry::Mol I/O interface. This allows Midas patterns to be used interchangeably with other pattern languages such as SMARTS in the context of programs such as mok. All of the r...
ITUB/Chemistry-MidasPattern-0.11 - 16 May 2005 23:06:55 UTC
Chemistry::File::FormulaPattern - Wrapper Chemistry::File class for Formula patterns
This is a wrapper class for reading Formula Patterns using the standard Chemistry::Mol I/O interface. This allows Formula patterns to be used interchangeably with other pattern languages such as SMARTS in the context of programs such as mok. All of t...
ITUB/Chemistry-FormulaPattern-0.10 - 11 Aug 2004 23:09:39 UTC
Chemistry::File::InternalCoords - Internal coordinates (z-matrix) molecule format reader/writer
This is a subclass of Chemistry::File for reading and writing the zmatriz (aka Z-matrix aka InternalCoords) molecule data format. It registers the 'zmat' file extension with Chemistry::Mol. For example, here is hydrogen: H H 1 B1 B1 0.70000000 and wa...
DAVIDRW/Chemistry-File-InternalCoords-0.03 - 07 Apr 2007 23:59:47 UTC
Chemistry::Mol - Molecule object toolkit
This package, along with Chemistry::Atom and Chemistry::Bond, includes basic objects and methods to describe molecules. The core methods try not to enforce a particular convention. This means that only a minimal set of attributes is provided by defau...
MERKYS/Chemistry-Mol-0.39 - 13 Jul 2022 08:36:38 UTC