mirror of
https://github.com/Electrostatics/apbs.git
synced 2026-06-04 12:44:23 +08:00
179 lines
3.7 KiB
ReStructuredText
179 lines
3.7 KiB
ReStructuredText
--------------------
|
|
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`
|
|
|
|
^^^^^
|
|
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 :file:`tools/spack`
|
|
|
|
^^^^^^^^^^^^
|
|
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`
|
|
|