Search results for "ITUB"
Ivan Tubert-Brohman (ITUB)
mok - an awk for molecules
The purpose of mok is to read all the molecules found in the files that are given in the command line, and for each molecule execute the CODE that is given. The CODE is given in Perl and it has at its disposal all of the methods of the PerlMol toolki...
ITUB/Chemistry-Mok-0.25 - 16 May 2005 21:55:57 UTC - Search in distribution- Chemistry::Mok - molecular awk interpreter
pflow - command line utility for printing the call graph of a fortran program
This is a simplified Perl version of the FLOW program <http://www.netlib.org/floppy/contents.html#link13>. It takes Fortran 77 source code and prints a call graph. The output looks something like this: MAIN EXTSUB * 1 SUB1 SUB11 SUB12 SUB2 SUB1 (1) S...
ITUB/CallGraph-0.55 - 07 May 2004 20:09:54 UTC - Search in distribution- CallGraph - create, navigate, and dump the call graph for a program
- CallGraph::Node - represent a subroutine as a node in a call graph
- CallGraph::Dumper - Dump a call graph into a string representation
- 1 more result from CallGraph »
annopod - a perldoc with annotations
The "annopod" program works exactly the same as perldoc, except that it looks for a local annotation database and inserts the annotations just before rendering the POD. It works by using a local note database that can be downloaded from http://annocp...
ITUB/AnnoCPAN-Perldoc-0.10 - 22 Jul 2005 02:43:17 UTC - Search in distribution- AnnoCPAN::Perldoc - Integrate AnnoCPAN notes locally into perldoc
AnnoCPAN - Annotated CPAN documentation
Background Let's start by listing some of the resources at the disposal of the Perl community. * CPAN is a wonderful archive and distribution system for Perl modules. * search.cpan.org is a very nice web interface for searching and browsing the CPAN ...
ITUB/AnnoCPAN-0.22 - 02 Aug 2005 04:33:32 UTC - Search in distribution- AnnoCPAN - Annotated CPAN documentation
- AnnoCPAN::Dist - CPAN distribution extracting and munging
- AnnoCPAN::Control - Main AnnoCPAN Web Interface Control Module
- 8 more results from AnnoCPAN »
podindex - build index from pods
This is a simple wrapper script around Pod::Index::Builder. It parses the POD files given as arguments, finds all X<> entries, generates an index and prints it to standard output....
ITUB/Pod-Index-0.14 - 16 Oct 2005 00:29:18 UTC - Search in distribution- Pod::Index - Index and search PODs using Xlt> entries.
- Pod::Index::Entry - Represents Pod search result
- Pod::Index::Search - Search for keywords in an indexed pod
- 2 more results from Pod-Index »
PerlMol - 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". ...
ITUB/PerlMol-0.3500 - 24 May 2005 23:19:23 UTC - Search in distribution
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 - Search in distribution- Chemistry::File - Molecule file I/O base class
- Chemistry::Atom - Chemical atoms as objects in molecules
- Chemistry::Tutorial - PerlMol Quick Tutorial
- 4 more results from Chemistry-Mol »
Pod::HtmlEasy - Generate personalized HTML from PODs.
The purpose of this module is to generate HTML data from POD in a easy and personalized mode. By default the HTML generated is similar to the CPAN site style for module documentation....
GLEACH/Pod-HtmlEasy-v1.1.11a - 23 Aug 2014 02:12:52 UTC - Search in distribution
Fortran::Format - Read and write data according to a standard Fortran 77 FORMAT
This is a Perl implementation of the Fortran 77 formatted input/output facility. One possible use is for producing input files for old Fortran programs, making sure that their column-oriented records are rigorously correct. Fortran formats may also h...
ITUB/Fortran-Format-0.90 - 16 Sep 2005 22:43:01 UTC - Search in distribution
IO::All::LWP - IO::All interface to LWP
This module acts as glue between IO::All and LWP, so that files can be read and written through the network using the convenient <IO:All> interface. Note that this module is not "use"d directly: you just use IO::All, which knows when to autoload IO::...
ITUB/IO-All-LWP-0.14 - 29 Mar 2007 07:34:08 UTC - Search in distribution- IO::All::HTTP - Extends IO::All to HTTP URLs
- IO::All::FTP - Extends IO::All to FTP URLs
- IO::All::HTTPS - Extends IO::All for HTTPS URLs
Test::Spelling - Check for spelling errors in POD files
Test::Spelling lets you check the spelling of a "POD" file, and report its results in standard Test::More fashion. This module requires a spellcheck program such as Hunspell <http://hunspell.github.io/>, aspell, spell, or, ispell. We suggest using Hu...
CAPOEIRAB/Test-Spelling-0.25 - 29 May 2019 01:12:24 UTC - Search in distribution
Chemistry::Pattern - Chemical substructure pattern matching
This module implements basic pattern matching for molecules. The Chemistry::Pattern class is a subclass of Chemistry::Mol, so patterns have all the properties of molecules and can come from reading the same file formats. Of course there are certain f...
ITUB/Chemistry-Pattern-0.27 - 10 May 2009 21:00:10 UTC - Search in distribution- Chemistry::Pattern::Atom - An atom that knows how to match
- Chemistry::Pattern::Bond - A bond that knows how to match
Chemistry::Reaction - Explicit chemical reactions
This package, along with Chemistry::Pattern, provides an implementation of explicit chemical reactions. An explicit chemical reaction is a representation of the transformation that takes place in a given chemical reaction. In an explicit chemical rea...
ITUB/Chemistry-Reaction-0.02 - 26 Sep 2004 19:20:27 UTC - Search in distribution
Chemistry::Smiles - SMILES parser (deprecated)
NOTE: THIS MODULE IS DEPRECATED! Use Chemistry::File::SMILES instead. This object-oriented module parses a SMILES (Simplified Molecular Input Line Entry Specification) string. It can either return the molecule as a Chemistry::Mol object or be used vi...
ITUB/Chemistry-Smiles-0.13 - 27 Feb 2004 23:47:08 UTC - Search in distribution
Chemistry::Ring - Represent a ring as a substructure of a molecule
This module provides some basic methods for representing a ring. A ring is a subclass of molecule, because it has atoms and bonds. Besides that, it has some useful geometric methods for finding the centroid and the ring plane, and methods for aromati...
MERKYS/Chemistry-Ring-0.21 - 16 Dec 2022 08:35:04 UTC - Search in distribution- Chemistry::Ring::Find - Find the rings (cycles) in a molecule
Chemistry::MidasPattern - Select atoms in macromolecules
This module partially implements a pattern matching engine for selecting atoms in macromolecules by using Midas/Chimera patterns. See <http://www.cmpharm.ucsf.edu/~troyer/troff2html/midas/Midas-uh-3.html#sh -2.1> for a detailed description of this la...
ITUB/Chemistry-MidasPattern-0.11 - 16 May 2005 23:06:55 UTC - Search in distribution- Chemistry::File::MidasPattern - Wrapper Chemistry::File class for Midas patterns
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 - Search in distribution
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 - Search in distribution
Chemistry::Domain - Class for domains in macromolecules
A domain is a substructure of a larger molecule. It is typically used to represent aminoacid residues within a protein, or bases within a nucleic acid, but you could use it for any arbitrary substructure such as functional groups and rings. A domain ...
ITUB/Chemistry-MacroMol-0.06 - 03 Jul 2004 19:22:04 UTC - Search in distribution- Chemistry::MacroMol - Perl module for macromolecules
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 - Search in distribution- Chemistry::File::SDF - MDL Structure Data File reader/writer