Mol_Volume calculates the volume of a macromolecule by a method somewhat akin to the Monte Carlo method, namely, by measuring how many vertices of a dense regular grid happen to be within the probe radius of the molecule's atoms. The volume is then calculated as V = V_grid * N_near / N_total = N_near * V_per_node.
PDBCat can be used to manipulate and process PDB files using commonly available text-processing tools such as Perl, awk, etc. The Brookhaven Protein Data Bank stores atomic coordinate information for protein structures in a column-based format which is designed to be read easily read by FORTRAN programs. PDBCat converts the ATOM and HETATM records of PDB files from this column-based format to a field-based one that is more easily processed by standard Unix tools.
SODIUM places the required number of sodium ions around a (simulated) system of electric charges, e.g., the atoms of a biological macromolecule (protein, DNA, protein/DNA complex). The ions are placed in the nodes of a cubic grid in which the electrostatic energy achieves the smallest values. The energy is re-computed after placement of each ion. A simple Coulombic formula is used for the energy. The coordinates of the placed ions are printed out in the PDB format for further usage. Trivial modifications to the program should allow the placement of any combination of multivalent ions of different charges.
PHPLOT is a PHP graphics class for creating charts and plots. It works with PHP5 (but older versions can use PHP4). PHPlot uses the PHP GD extension to produce PNG, GIF, or JPEG images. TrueType fonts (TTF) are optional, or built-in GD fonts can be used. The available plot types are: area, bars, line/points, lines, pie, points, squared, stacked-bars, and thin bar-line. Labels, tick marks, plot legend, X/Y axes, and more are all configurable. Images can be imported as a background, multiple graphs can be drawn on one image, and images can be saved to disk or returned to a browser.
vtkFlRenderWindowInteractor is a class which enables you to create applications with full VTK and FLTK integration and interaction. This means that VTK renders to your FLTK UI, and your FLTK UI interacts with the VTK pipelines. Standard VTK interactor styles and picking work by default. This code has been tested successfully on Linux, SGI Irix, Sun Solaris, and Windows (NT, 2000, and XP).
Linguaphile is a simple command line language translator. It is open source, platform independent, and programmed in Perl. Linguaphile currently supports the following languages: Afrikaans, Alawa, Albanian, Arrernte, Basque, Belarusian, Bulgarian, Catalan, Croatian, Czech, Danish, Dutch, English, Esperanto, Estonian, Finnish, French, Galician, German, Greek, Hawaiian, Hungarian, Icelandic, Indonesian, Interlingua, Irish, Italian, Kala Lagaw Ya, Korean, Kriol, Latvian, Lithuanian, Malay, Maltese, Maori, Norwegian, Pitjantjatjara, Polish, Portuguese, Romanian, Russian, Samoan, Serbian, Slovak, Slovenian, Spanish, Swahili, Swedish, Thai, Tok Pisin, Turkish, Ukrainian, Warlpiri, and Welsh. The Spanish to English translation is the most useful at this stage.
A practical lambda-calculator is a normal-order evaluator for the untyped lambda-calculus, extended with convenient commands and shortcuts to make programming in it more productive. Shortcuts are distinguished constants that represent terms. Commands define new shortcuts, activate tracing of all reductions, compare terms modulo alpha-conversion, print all defined shortcuts and evaluation flags, etc. Terms to evaluate and commands are entered at a read-eval-print-loop (REPL) "prompt" or "included" from a file by a special command. A Haskell branch is an embedding of the lambda calculator (as a domain-specific language) into Haskell. The calculator can be used interactively within Hugs or GHCi.