Conversion utilities¶

amber2charmm.sh¶

A bash script for converting AMBER atom names to CHARMM names. Found in tools/conversion

del2dx¶

Converts DelPhi-format map files (electrostatic potential, etc.) to APBS OpenDX format. Found in tools/mesh

dx2mol¶

Converts OpenDX format map files to MolMol format. Found in tools/mesh

dx2uhbd¶

Converts OpenDX format map files to UHBD format. Found in tools/mesh

qcd2pqr.awk¶

An awk script for converting from UHBD QCD format to PQR format.

Benchmarking utilities¶

benchmark¶

Benchmark file I/O for reading/writing scalar data. Found in tools/mesh

spack¶

Spack <https://spack.io/>`_ configuration files for APBS, PROPKA, and PDB2PQR. See #191 <https://github.com/Electrostatics/apbs/issues/191>_ for more information. Found in tools/spack

uhbd_asc2bin¶

Converts UHBD ASCII-format files to binary format. Found in tools/mesh

WHATIF2AMBER.sed¶

A sed script for converting WHATIF atoms names to the AMBER naming scheme. Found in tools/conversion

Setup and analysis utilities¶

analysis¶

Calculates various metrics from input scalar data. Found in tools/mesh

born¶

Calculate generalized Born forces and energies. Found in tools/manip

coulomb¶

Calculate Coulomb forces and energies. Found in tools/manip

dxmath¶

Performs simple arithmetic operations with Cartesian grid data. This program takes as input a file with operations specified in a stack-based (RPN) manner. For example, a command file which adds grid1 and grid2, multiplies the result by 5.3, adds grid4, subtracts 99.3 from the whole thing, and writes the result on grid5 would have the form:

grid1
grid2 +
5.3 *
grid4 +
99.3 -
grid5 =

The file names, scalar values, and operations must be separated by tabs, line breaks, or white space. Comments can be included between the character # and a new line (in the usual shell script fashion). Found in tools/mesh

inputgen.py¶

Create an APBS input file using psize.py data. Found in tools/manip

mergedx and mergedx2¶

Combine multiple OpenDX files into a single resampled file. mergedx2 can perform a number of grid manipulation operations, including:

Combining multiple OpenDX map files
Resampling of one or more OpenDX map files (for example to alter the grid spacing of separate OpenDX files for further manipulation)
Extracting a subregion of an existing OpenDX map file.

Found in tools/mesh

mgmesh¶

Prints out acceptable combinations of nlev and dime for multigrd calculations. Found in tools/mesh

multivalue¶

This program evaluates OpenDX scalar data at a series of user-specified points and returns the value of the data at each point. Found in tools/mesh

psize.py¶

Suggest grid sizes and spacings for APBS given an input molecule. Found in tools/manip

similarity¶

Computes similarity between two scalar grid datasets. Found in tools/mesh

smooth¶

Convolve grid data with various filters. Found in tools/mesh