Projects

J-Pilot

J-Pilot is a desktop organizer application for PalmOS devices. It is meant to be an alternative to the Palm Desktop for those who run the most popular Operating Systems in the World, Linux and Unix.

Auto Kindle eBook Converter

This project was originally a quick and dirty method for me to convert my ebook collection in various formats to a kindle compatible format without worrying about the ebook source type. It takes PDF, Lit, and HTML files and converts them to .mobi.

C# Program Database (PDB) Library

A C# 4.0 library for reading Microsoft Program Database (PDB) files.

ProDy

ProDy is a free and open-source Python package for analysis and modeling of protein structural dynamics. It allows for efficient analysis of large datasets and is suitable for development or prototyping of structure-based analysis and modeling software.

molecular-view

Molecular View is a desktop application for the visualization of protein database (PDB) files. It interprets ".pdb" and ".ent" files, allowing the visualization of the correspondent 3D molecules. PDB example files can be downloaded from wwwPDB. The software also enables exporting ... [More] the 3D model to ".stl" (binary) and ".vrml" (2.0) file formats, frequently used for Rapid Prototyping physical reconstruction. The software is written in Python 2.5. Visualization Toolkit VTK 5.1 is used both for visualization and file conversion. In regards to the user interface, wxPython 2.8 was used. Molecular View is multi-platform (Windows and Linux). The team who developed Molecular View is also responsible for the 3D Medical Reconstruction software InVesalius, which is inserted into the project Rapid Pr [Less]

mmdb

MMDB is a macromolecular coordinate library, written by Eugene Krissinel. It supports reading and writing two file formats, PDB and mmCIF, and provides high-level tools for working with coordinate files: orthogonal-fractional coordinate transforms, generation of symmetry mates, editing the ... [More] molecular structure and some others. Tarballs available at: ftp://ftp.ccp4.ac.uk/opensource/ [Less]

hollow

Hollow helps to visualize and quantify voids, pockets, and channels in protein structures. It generates fake atoms that fill space inside a structure specified in the PDB format. The output is a standard PDB file containing the fake atoms. The molecular surface of these atoms is an excellent ... [More] approximation to the cavity and can be easily rendered in standard molecular visualization software such as PyMOL, VMD or Chimera. In complements programs such as HOLE, CAVER, MOLE, SPHGEN, and CASTp. [Less]

zenpdb

SummaryZenPDB is a Python module to process and analyze macromolecular structures. Macromolecular structures are represented as hierarchically nested python dictionaries, which allows to traverse and manipulate them in a pythonic way and implement structural biology algorithms compactly. This module ... [More] is also useful to establish processing pipelines. ZenPDB is currently capable of parsing and writing PDB files, but PDBML input is also planned. ZenPDB provides fast and versatile Cython implementations of important algorithms in structural biology, namely accessible surface area (ASA) and distance contact calculations by using kd-trees for nearest neighbour look-up. It is crystallography-aware and can construct crystal lattices, unit cells and biological units. DocumentationInstallationDependencies [Less]

rubypdb

This project makes it easy to access data in palm PDB database files. Because each application's record structures are different, this project lets you write a minimal amount of code: you describe the format of records in the applications you want to access, and rubypdb takes care of the rest. ... [More] The source is kept in git; releases will be available on the Downloads page, but go to http://github.com/riddochc/rubypdb/tree/master for the repository. If you have git installed, you can clone the repository with the following command: git clone git://github.com/riddochc/rubypdb.git Use the Wiki on Github, please. [Less]

pdb-tools

Introductionpdb-tools is a set of command line python scripts that manipulate wwPDB macromolecule structure files. There are many programs, both open source and proprietary, that perform similar tasks; however, most of these tools are buried within programs of larger functionality. Thus ... [More] , relatively simple calculations often involve learning a new program, compiling modules, and installing libraries. To fill a niche (and get the tasks done that I needed done), I started writing my own toolset. This has evolved into the pdb-tools suite. The suite of programs is characterized by the following philosophy: Each program should run as a stand-alone application with a standard, GNU/POSIX style command line interface. Each program should be written in such a way to allow it to be used as a library of functions for more complex programs. Programs should require a minimum of external dependencies. Most of the scripts will run "out of the box" using a python interpreter. The command line parser is designed to be flexible. It will take an arbitrarily long list of pdb files, pdb ids, text files with pdb ids, or some mixture of all three. If the pdb file or id is not in the working directory, scripts will attempt to download the pdb file from RCSB. Depending on the type of operation being done, a program will either write output files in the working directory or will print to stdout. All structure outputs are written in standard pdb format. All data outputs are in fixed-width column format. They were designed to be read by the statistics package R; however, they should be easily parsed by other graphing programs. Note: These scripts are only compatible with Python version 2.4 and above. Current functionsStructure-based calculationsGeometrycalculate protein center of mass: pdb_centermass.py calculate distance distributions: pdb_dist-filter.py, pdb_ion_dist.py calculate backbone torsion angles: pdb_torsion.py calculate secondary structure content: pdb_dssp.py(requires DSSP) calculate atom-by-atom solvent accessibility pdb_sasa.py(requires NACCESS) find disulfide bonds based on distance: pdb_disfulfide.py find residues that touch: pdb_contact.py, pdb_water-contact.py find number of atoms neighboring another: pdb_neighbors.py Energy calculationcalculate coulomb energy: pdb_coulomb.py calculate the dipole moment of the protein: pdb_moment.py calculate pKa of ionizable groups using the Solvent-Accessibility-modified Tanford-Kirkwood method pdb_satk.py (requires fortran compiler) Structure propertiesextract structure experiment properties: pdb_exper.py extract protein sequence from structure: pdb_seq.py calculate theoretical pI, MW, fraction titratable residues, charge: pdb_param.py File/structure manipulationadd polar hydrogens: pdb_addH.py (requires CHARMM) add missing heavy atoms, remove alternate conformations, etc.: pdb_clean.py (requires CHARMM) mutate a residue: pdb_mutator.py (requires CHARMM) renumber atoms: pdb_atom-renumber.py renumber residues: pdb_residue-renumber.py offset all residues by a fixed amount: pdb_offset.py center protein in xyz space: pdb_centermass.py places the asymmetric unit inside the unit cell: pdb_centerasu.py take subset of residues from file: pdb_subset.py split an NMR ensemble structure into individual files: pdb_splitnmr.py take a set of pdb files and create an individual directory for each one: pdb_pdb2dir.py load data into the b-factor column: pdb_bfactor.py Some of the programs are written as interfaces to other programs: CHARMM, DSSP and NACCESS, which must be downloaded and installed separately if their functions are desired. To use pdb_satk.py, a set of fortran packages must be compiled. Project ContributorsMike Harms Marcin Cieślik [Less]