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--------------------
Conversion utilities
--------------------
.. todo:: Update this documentation with the *new APBS syntax* (see :ref:`new_input_format`).
^^^^^^^^^^^^^^^
amber2charmm.sh
^^^^^^^^^^^^^^^
A bash script for converting AMBER atom names to CHARMM names.
Found in :file:`tools/conversion`
^^^^^^
del2dx
^^^^^^
Converts DelPhi-format map files (electrostatic potential, etc.) to APBS OpenDX format.
Found in :file:`tools/mesh`
^^^^^^
dx2mol
^^^^^^
Converts OpenDX format map files to MolMol format.
Found in :file:`tools/mesh`
^^^^^^^
dx2uhbd
^^^^^^^
Converts OpenDX format map files to UHBD format.
Found in :file:`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 :file:`tools/mesh`
^^^^^^^^^^^^
uhbd_asc2bin
^^^^^^^^^^^^
Converts UHBD ASCII-format files to binary format.
Found in :file:`tools/mesh`
^^^^^^^^^^^^^^^^
WHATIF2AMBER.sed
^^^^^^^^^^^^^^^^
A sed script for converting WHATIF atoms names to the AMBER naming scheme.
Found in :file:`tools/conversion`
----------------------------
Setup and analysis utilities
----------------------------
^^^^^^^^
analysis
^^^^^^^^
Calculates various metrics from input scalar data.
Found in :file:`tools/mesh`
^^^^
born
^^^^
Calculate generalized Born forces and energies.
Found in :file:`tools/manip`
^^^^^^^
coulomb
^^^^^^^
Calculate Coulomb forces and energies.
Found in :file:`tools/manip`
.. _dxmath:
^^^^^^
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:
.. code-block:: mathematica
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 :file:`tools/mesh`
^^^^^^^^^^^
inputgen.py
^^^^^^^^^^^
Create an APBS input file using :ref:`psize` data.
Found in :file:`tools/manip`
^^^^^^^^^^^^^^^^^^^^
mergedx and mergedx2
^^^^^^^^^^^^^^^^^^^^
Combine multiple OpenDX files into a single resampled file.
:program:`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 :file:`tools/mesh`
^^^^^^
mgmesh
^^^^^^
Prints out acceptable combinations of :doc:`input/old/elec/nlev` and :doc:`input/old/elec/dime` for multigrd calculations.
Found in :file:`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 :file:`tools/mesh`
.. _psize:
^^^^^^^^
psize.py
^^^^^^^^
Suggest grid sizes and spacings for APBS given an input molecule.
Found in :file:`tools/manip`
^^^^^^^^^^
similarity
^^^^^^^^^^
Computes similarity between two scalar grid datasets.
Found in :file:`tools/mesh`
^^^^^^
smooth
^^^^^^
Convolve grid data with various filters.
Found in :file:`tools/mesh`
|
