Prop3D.parsers package
Submodules
Prop3D.parsers.Electrostatics module
Prop3D.parsers.FreeSASA module
Prop3D.parsers.MODELLER module
Prop3D.parsers.MaxCluster module
Prop3D.parsers.Rosetta module
- Prop3D.parsers.Rosetta.run_minimize(pdb_file, min_type='lbfgs_armijo_nonmonotone', min_tolerance=0.001, ignore_zero_occupancy=False, parameters=None, work_dir=None)
Prop3D.parsers.SCWRL module
Prop3D.parsers.USEARCH module
Prop3D.parsers.apbs module
Prop3D.parsers.blast module
Prop3D.parsers.cath module
Prop3D.parsers.cns module
Prop3D.parsers.consurf module
Prop3D.parsers.container module
Prop3D.parsers.cx module
Prop3D.parsers.docker module
Prop3D.parsers.dssp module
Prop3D.parsers.eppic module
Prop3D.parsers.foldseek module
Prop3D.parsers.frustratometeR module
Prop3D.parsers.haddock module
Prop3D.parsers.hmmer module
Prop3D.parsers.json module
- class Prop3D.parsers.json.WebService(base_url, store, work_dir=None, download=True, clean=True, max_attempts=2)
Bases:
object- clean()
- fix_key(key)
- extension(key=None)
- parse(file_path, key)
- check_line(key, line, attempts)
Check line to test for failure. Return True if should rerun. Subclass to add functionality.
- get(key, attempts=None, last_source=None)
- download(key, fname)
- should_add_to_store(key, fname)
- class Prop3D.parsers.json.JSONApi(*args, **kwds)
Bases:
WebService- extension(key)
- parse(file_path, key)
Prop3D.parsers.mgltools module
Prop3D.parsers.mmseqs module
Prop3D.parsers.mmtf_spark module
- Prop3D.parsers.mmtf_spark.PdbToMmtfFull(pdb_path, mmtf_path, work_dir=None, job=None)
Prop3D.parsers.msms module
Prop3D.parsers.multivalue module
Prop3D.parsers.muscle module
Prop3D.parsers.openbabel module
Prop3D.parsers.pdb2pqr module
Prop3D.parsers.pdbe module
Prop3D.parsers.psize module
psize class
Get dimensions and other information from a PQR file.
Originally written by Dave Sept Additional APBS-specific features added by Nathan Baker Ported to Python/Psize class by Todd Dolinsky and subsequently hacked by Nathan Baker
PDB2PQR – An automated pipeline for the setup, execution, and analysis of Poisson-Boltzmann electrostatics calculations
Copyright (c) 2002-2011, Jens Erik Nielsen, University College Dublin; Nathan A. Baker, Battelle Memorial Institute, Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy.; Paul Czodrowski & Gerhard Klebe, University of Marburg.
All rights reserved.
Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
- Redistributions of source code must retain the above copyright notice,
this list of conditions and the following disclaimer.
- Redistributions in binary form must reproduce the above copyright notice,
this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
- Neither the names of University College Dublin, Battelle Memorial Institute,
Pacific Northwest National Laboratory, US Department of Energy, or University of Marburg nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS “AS IS” AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
- class Prop3D.parsers.psize.Psize
Bases:
objectMaster class for parsing input files and suggesting settings
- parseString(structure)
Parse the input structure as a string in PDB or PQR format
- parseInput(filename)
Parse input structure file in PDB or PQR format
- parseLines(lines)
Parse the lines
- setConstant(name, value)
Set a constant to a value; returns 0 if constant not found
- getConstant(name)
Get a constant value; raises KeyError if constant not found
- setLength(maxlen, minlen)
Compute molecule dimensions
- setCoarseGridDims(olen)
Compute coarse mesh dimensions
- setFineGridDims(olen, clen)
Compute fine mesh dimensions
- setCenter(maxlen, minlen)
Compute molecule center
- setFineGridPoints(flen)
Compute mesh grid points, assuming 4 levels in MG hierarchy
- setSmallest(n)
Compute parallel division in case memory requirement above ceiling Find the smallest dimension and see if the number of grid points in that dimension will fit below the memory ceiling Reduce nsmall until an nsmall^3 domain will fit into memory
- setProcGrid(n, nsmall)
Calculate the number of processors required to span each dimension
- setFocus(flen, np, clen)
Calculate the number of levels of focusing required for each processor subdomain
- setAll()
Set up all of the things calculated individually above
- getMax()
- getMin()
- getCharge()
- getLength()
- getCoarseGridDims()
- getFineGridDims()
- getCenter()
- getFineGridPoints()
- getSmallest()
- getProcGrid()
- getFocus()
- runPsize(filename)
Parse input PQR file and set parameters
- printResults()
Return a string with the formatted results
- Prop3D.parsers.psize.usage(rc)
Print usage information and exit with error code rc
- Prop3D.parsers.psize.main()