Free molecular software for linux

Python Macromolecular Library (mmLib) is a software toolkit and library of routines for the analysis and manipulation of macromolecular structural models, implemented in the Python programming language.

Python Macromolecular Library is accessed via a layered, object-oriented application programming interface, and provides a range of useful software components for parsing mmCIF, and PDB files, a library of atomic elements and monomers, an object-oriented data structure describing biological macromolecules, and an OpenGL molecular viewer.

The mmLib data model is designed to provide easy access to the various levels of detail needed to implement high-level application programs for macromolecular crystallography, NMR, modeling, and visualization.

This includes specialized classes for proteins, DNA, amino acids, and nucleic acids. Also included is a extensive monomer library, element library, and specialized classes for performing unit cell calculations combined with a full space group library.

Biomolecule Toolkit project is an Open Source library for the structural modeling of biological macromolecules. The toolkit provides a C++ interface for common tasks in computational structural biology, to facilitate the development of molecular modeling, design, and analysis tools.
Enhancements:
Documentation updates
- Addition of an extensive discussion of the leastsquares_superposition and RMSD-calculation methods, including a description of the mathematical theory behind their operation.
- Fully documented the rotation/translation methods
- Addition of a documented example program ("gyration_radius.cpp")
Bug fixes
- Fixed copy construction bug in PDBAtomDecorator that caused compilation errors in rare situations.
- Fixed a bug in PDBFileParser that caused a compilation error in the PDBSystem copy constructor.
- Fixed a const-conversion bug in GroupedElementIterator which prevented proper interoperation of const and non-const iterator types.
- Fixed a crash-producing bug in stream output for the TypeID class.
- Fixed a math error in RMSD and superposition methods that would corrupt molecule coordinates.
- Fixed a bug that caused all default-constructed PDBAtom objects to be treated as HETATMs.
Feature additions
- Added operator[] to AtomicStructure and PolymerStructure-derived classes.
- Added protected increment() and decrement() operators to TypeID class.
- PDBFileParser can now handle PDB files with ill-formed residue numbering (i.e. Files where residue numbers are repeated in successive chains).

KMol calculates the elemental compositon and molecular weight of compounds from their chemical formula. KMol supports user defined groups and elements, unlimited nesting of subgroups, multicomponent compounds, global and per-user symbol definitions.
KMol is designed to be able to parse any chemical formula that can be
unambiguously interpreted if written as a simple character sequence (i.e.,
without subscript and superscript formating). If you can understand a chemical
formula, chances are KMol will understand it in exactly the same way.
Enhancements:
- Fixed KDE3 compilation problem. Fixed saving of user-defined weights.

Jmol is a free, open source molecule viewer for students, educators, and researchers in chemistry and biochemistry. Jmol is cross-platform, running on Linux/Unix, Mac OS X, and Windows systems.
- The JmolApplet is a web browser applet that can be integrated into web pages.
- The Jmol application is a standalone Java application that runs on the desktop.
- The JmolViewer is a development tool kit that can be integrated into other Java applications.
Main features:
- Free, open-source software licensed under the GNU Lesser General Public License
- Applet, Application, and Systems Integration Component
- Cross-platform
- Supports all major web browsers
- High-performance 3D rendering with no hardware requirements
- File formats
- Animations
- Vibrations
- basic unit-cell support
- schematic shapes for secondary structures
- measurements
- RasMol/Chime scripting language support
- JavaScript support library
- Exports to .jpg, .pdf, and PovRay
Jmol v10 is a complete rearchitecture and rewrite of Jmol, undertaken in the Spring of 2003, with the specific goal of developing Jmol into a replacement for the Chime Plug-in.
Jmol v10 retains most of the features and functionality of the previous Jmol releases while offering significant enhancments in the following areas:
- true 3D graphics engine that requires no special hardware
- 24 bit color with accurate lighting and shading
- substantially higher rendering performance
- handles large macromolecules with excellent performance
- protein/nucleic acid secondary structure graphics
- RasMol/Chime script compatibility
Enhancements:
- bug fix: isosurface color -- not operating for some isosurface types
- bug fix: isosurface "xxxx.cube" -- not assigning proper default colors
- bug fix: gamess reader MO fix
- bug fix: state save of STRUCTURE misplaced

Ghemical is a computational chemistry software package released under the GNU GPL. It means that full source code of the package is available, and users are free to study and modify the package. Ghemical is written in C++.
Ghemical project has a graphical user interface (which is based on GNOME), and it supports both quantum-mechanics (semi-empirical and ab initio) models and molecular mechanics models (there is an experimental Tripos 5.2-like force field for organic molecules). Also a tool for reduced protein models [1] is included. Geometry optimization, molecular dynamics and a large set of visualization tools are currently available.
Ghemical relies on external code to provide the quantum-mechanical calculations. Semi-empirical methods MNDO, MINDO/3, AM1 and PM3 come from the MOPAC7 package (Public Domain), and are included in the source distribution.
The MPQC package (GNU GPL) is used to provide ab initio methods: the methods based on Hartree-Fock theory are currently supported with basis sets ranging from STO-3G to 6-31G**.
The MPQC code is not included in the source distribution. In order to use the MPQC-based ab initio methods in Ghemical, you must first compile and install the MPQC program for your system, and then compile Ghemical using some specific settings that link the programs together; see the INSTALL file for more information. Ghemical also contains the OpenBabel package for import and export of many different file formats (as well as other tasks).
Installation
Once you have downloaded the latest release, you should extract all files from your archive file using "tar -zxvvf ghemical-1.00.tgz" or equivalently "gunzip ghemical-1.00.tgz; tar -xvvf ghemical-1.00.tar". After that please read the "INSTALL"-file you just extracted to get additional information.
Enhancements:
- bug fixes

Bioperl project is a collection of perl modules that facilitate the development of perl scripts for bioinformatics applications. As such, it does not include ready to use programs in the sense that many commercial packages and free web-based interfaces do (e.g. Entrez, SRS).
On the other hand, bioperl does provide reusable perl modules that facilitate writing perl scripts for sequence manipulation, accessing of databases using a range of data formats and execution and parsing of the results of various molecular biology programs including Blast, clustalw, TCoffee, genscan, ESTscan and HMMER. Consequently, bioperl enables developing scripts that can analyze large quantities of sequence data in ways that are typically difficult or impossible with web based systems.
In order to take advantage of bioperl, the user needs a basic understanding of the perl programming language including an understanding of how to use perl references, modules, objects and methods. If these concepts are unfamiliar the user is referred to any of the various introductory or intermediate books on perl.
Weve liked S. Holzmers Perl Core Language, Coriolis Technology Press, for example. This tutorial is not intended to teach the fundamentals of perl to those with little or no experience in the perl language. On the other hand, advanced knowledge of perl - such as how to write a object-oriented perl module - is not required for successfully using bioperl.
Bioperl is open source software that is still under active development. The advantages of open source software are well known. They include the ability to freely examine and modify source code and exemption from software licensing fees.
However, since open source software is typically developed by a large number of volunteer programmers, the resulting code is often not as clearly organized and its user interface not as standardized as in a mature commercial product.
In addition, in any project under active development, documentation may not keep up with the development of new features. Consequently the learning curve for actively developed, open source source software is sometimes steep.
Enhancements:
- Many bugfixes and enhancements were made, including support for parsing the latest NCBI BLAST text format changes, PAML 3.15 support, a Taxonomy (Bio::Species) overhaul, a Bio::Map overhaul, a Bio::SearchIO speedup, the introduction of a Build.PL installation system, and fixes for some memory leaks in Bio::Tree.
- This version requires Perl 5.6.1 or later.

Bio::NEXUS is a Perl module providing an object-oriented, Perl-based applications programming interface (API).

NEXUS is a powerful and extensible format designed for use in evolutionary analysis, including the analysis of molecular sequence data as well as classical morphological and life-history data. It is the input or output format for software such as PAUP*, MacClade, Mesquite, SIMMAP, MrBayes, Nexplorer, and so on. This package also contains the demonstration applications nexplot.pl (plot character data with a tree) and nextool.pl (allowing programmatic editing, e.g., selecting particular clades or subsets of data).

The NEXPL library of Perl software (copyright 2004 Liang, Qiu and Yang) is distributed under an open source license (see LICENSE). If you use this software, please acknowledge:
Bio::NEXUS. An Object-oriented NEXUS API in Perl. T.J. Hladish, C.L. Liang, W.-G. Qiu, P. Yang, V. Gopalan and A. Stoltzfus. Available at http://www.molevol.org/camel/software.

INSTALLATION AND TESTING

This software has been tested under Linux as well as MaxOS X 10.2 and higher, and even a few Windows installations. The package installs using the standard procedure, and runs several hundred tests:

perl Makefile.PL
make
make test
make install

For more information, or to customize, see doc/Installation.pod.