/usr/share/pdb2pqr/src/inputgen.py is in pdb2pqr 2.1.1+dfsg-2.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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Create an APBS input file using psize data
Written by Todd Dolinsky based on original sed script 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.
----------------------------
"""
# User - Definable Variables: Default values
# cfac = 1.7 # Factor by which to expand mol dims to
# get coarse grid dims
# fadd = 20 # Amount to add to mol dims to get fine
# grid dims
# space = 0.50 # Desired fine mesh resolution
# gmemfac = 200 # Number of bytes per grid point required
# for sequential MG calculation
# gmemceil = 400 # Max MB allowed for sequential MG
# calculation. Adjust this to force the
# script to perform faster calculations (which
# require more parallelism).
# ofrac = 0.1 # Overlap factor between mesh partitions
# redfac = 0.25 # The maximum factor by which a domain
# dimension can be reduced during focusing
__date__ = "21 April 2007"
__author__ = "Todd Dolinsky, Nathan Baker, Yong Huang"
import string, sys
import psize
import pickle
import os.path
import utilities
class Elec:
"""
An object for the ELEC section of an APBS input file
"""
def __init__(self, pqrpath, size, method, asyncflag, istrng=0, potdx=False):
"""
Initialize the variables that can be set in this object
Users can modify any of these variables (that's why
they're here!)
"""
# If this is an async or parallel calc, we want to use
# the per-grid dime rather than the global dime.
self.dime = size.getFineGridPoints()
gmem = 200.0 * self.dime[0] * self.dime[1] * self.dime[2] / 1024.0 / 1024.0
if method == "": # method not named - use ceiling
if gmem > size.getConstant("gmemceil"): method = "mg-para"
else: method = "mg-auto"
if method == "mg-para":
self.dime = size.getSmallest()
self.method = method
self.istrng = istrng
self.glen = size.getCoarseGridDims()
self.cglen = size.getCoarseGridDims()
self.fglen = size.getFineGridDims()
self.pdime = size.getProcGrid()
self.label = ""
self.nlev = 4
self.ofrac = 0.1
self.async = 0
self.asyncflag = asyncflag
self.cgcent = "mol 1"
self.fgcent = "mol 1"
self.gcent = "mol 1"
self.mol = 1
self.lpbe = 1
self.npbe = 0
self.bcfl = "sdh"
self.ion = [[-1,1.815],[1,1.875]] # Multiple ions possible
self.pdie = 2.0
self.sdie = 78.54
self.srfm = "smol"
self.chgm = "spl2"
self.sdens = 10.0
self.srad = 1.4
self.swin = 0.3
self.temp = 298.15
self.gamma = 0.105
self.calcenergy = "total"
self.calcforce = "no"
if potdx:
self.write = [["pot", "dx", pqrpath]]
else:
self.write = [["pot", "dx", "pot"]] # Multiple write statements possible
def __str__(self):
"""
Return the elec statement as a string. Check the method
to see which keywords to use.
"""
text = "elec %s\n" % self.label
text += " %s\n" % self.method
text += " dime %i %i %i\n" % (self.dime[0], self.dime[1], self.dime[2])
if self.method == "mg-manual":
text += " glen %.3f %.3f %.3f\n" % (self.glen[0], self.glen[1], self.glen[2])
text += " gcent %s\n" % self.gcent
elif self.method == "mg-auto":
text += " cglen %.4f %.4f %.4f\n" % (self.cglen[0], self.cglen[1], self.cglen[2])
text += " fglen %.4f %.4f %.4f\n" % (self.fglen[0], self.fglen[1], self.fglen[2])
text += " cgcent %s\n" % self.cgcent
text += " fgcent %s\n" % self.fgcent
elif self.method == "mg-para":
text += " pdime %i %i %i\n" % (self.pdime[0], self.pdime[1], self.pdime[2])
text += " ofrac %.1f\n" % self.ofrac
text += " cglen %.4f %.4f %.4f\n" % (self.cglen[0], self.cglen[1], self.cglen[2])
text += " fglen %.4f %.4f %.4f\n" % (self.fglen[0], self.fglen[1], self.fglen[2])
text += " cgcent %s\n" % self.cgcent
text += " fgcent %s\n" % self.fgcent
if self.asyncflag == 1:
text += " async %i\n" % self.async
text += " mol %i\n" % self.mol
if self.lpbe: text += " lpbe\n"
else: text += " npbe\n"
text += " bcfl %s\n" % self.bcfl
if self.istrng > 0:
for ion in self.ion:
text += " ion charge %.2f conc %.3f radius %.4f\n" % (ion[0], self.istrng, ion[1])
text += " pdie %.4f\n" % self.pdie
text += " sdie %.4f\n" % self.sdie
text += " srfm %s\n" % self.srfm
text += " chgm %s\n" % self.chgm
text += " sdens %.2f\n" % self.sdens
text += " srad %.2f\n" % self.srad
text += " swin %.2f\n" % self.swin
text += " temp %.2f\n" % self.temp
text += " calcenergy %s\n" % self.calcenergy
text += " calcforce %s\n" % self.calcforce
for write in self.write:
text += " write %s %s %s\n" % (write[0], write[1], write[2])
text += "end\n"
return text
class Input:
"""
The input class. Each input object is one APBS input file.
"""
def __init__(self, pqrpath, size, method, asyncflag, istrng=0, potdx=False):
"""
Initialize the input file class. Each input file contains
a PQR name, a list of elec objects, and a list of strings
containing print statements. For starters assume two
ELEC statements are needed, one for the inhomgenous and
the other for the homogenous dielectric calculations.
Users can edit the elec statements and the print statements.
This assumes you have already run psize, either by
size.runPsize(/path/to/pqr) or
size.parseString(string)
size.setAll()
Parameters
pqrpath: The path to the PQR file (string)
size: The Psize object (psize)
method: The method (para, auto, manual, async) to use
asyncflag: 1 if async is desired, 0 otherwise
"""
self.pqrpath = pqrpath
self.asyncflag = asyncflag
# Initialize variables to default elec values
elec1 = Elec(pqrpath, size, method, asyncflag, istrng, potdx)
if not potdx:
elec2 = Elec(pqrpath, size, method, asyncflag, istrng, potdx)
setattr(elec2, "sdie", 2.0)
setattr(elec2, "write", [])
else:
elec2 = ""
self.elecs = [elec1, elec2]
self.pqrname = os.path.basename(pqrpath)
if not potdx:
self.prints = ["print elecEnergy 2 - 1 end"]
else:
self.prints = ["print elecEnergy 1 end"]
def __str__(self):
"""
Return the text of the input file
"""
text = "read\n"
text += " mol pqr %s\n" % self.pqrname
text += "end\n"
for elec in self.elecs:
text += str(elec)
for prints in self.prints:
text += prints
text += "\nquit\n"
return text
def printInputFiles(self):
"""
Make the input file(s) associated with this object
"""
base_pqr_name = utilities.getPQRBaseFileName(self.pqrpath)
if self.asyncflag == 1:
outname = base_pqr_name + "-para.in"
# Temporarily disable async flag
for elec in self.elecs:
elec.asyncflag = 0
file = open(outname, "w")
file.write(str(self))
file.close()
# Now make the async files
elec = self.elecs[0]
nproc = elec.pdime[0] * elec.pdime[1] * elec.pdime[2]
for i in range(int(nproc)):
outname = base_pqr_name + "-PE%i.in" % i
for elec in self.elecs:
elec.asyncflag = 1
elec.async = i
file = open(outname, "w")
file.write(str(self))
file.close()
else:
outname = base_pqr_name + ".in"
file = open(outname, "w")
file.write(str(self))
file.close()
def dumpPickle(self):
"""
Make a Python pickle associated with the APBS input parameters
"""
base_pqr_name = utilities.getPQRBaseFileName(self.pqrpath)
outname = base_pqr_name + "-input.p"
pfile = open(outname, "w")
pickle.dump(self, pfile)
pfile.close()
def splitInput(filename):
"""
Split the parallel input file into multiple async file names
Parameters
filename: The path to the original parallel input
file (string)
"""
nproc = 0
file = open(filename, 'rU')
text = ""
while 1:
line = file.readline()
if line == "": break
text += line
line = string.strip(line)
if line.startswith("pdime"): # Get # Procs
words = string.split(line)
nproc = int(words[1]) * int(words[2]) * int(words[3])
if nproc == 0:
sys.stderr.write("%s is not a valid APBS parallel input file!\n" % filename)
sys.stderr.write("The inputgen script was unable to asynchronize this file!\n")
sys.exit(2)
base_pqr_name = utilities.getPQRBaseFileName(filename)
for i in range(nproc):
outname = base_pqr_name + "-PE%i.in" % i
outtext = string.replace(text, "mg-para\n","mg-para\n async %i\n" % i)
outfile = open(outname, "w")
outfile.write(outtext)
outfile.close()
def usage():
"""
Display the usage information for this script
"""
size = psize.Psize()
usage = "\n"
usage = usage + "Use this script to generate new APBS input files or split an existing\n"
usage = usage + "parallel input file into multiple async files.\n\n"
usage = usage + "Usage: inputgen.py [opts] <filename>\n"
usage = usage + "Optional Arguments:\n"
usage = usage + " --help : Display this text\n"
usage = usage + " --split : Split an existing parallel input file to multiple\n"
usage = usage + " async input files.\n"
usage = usage + " --potdx : Create an input to compute an electrostatic potential map.\n"
usage = usage + " --method=<value> : Force output file to write a specific APBS ELEC\n"
usage = usage + " method. Options are para (parallel), auto\n"
usage = usage + " (automatic), manual (manual), or async (asynchronous).\n"
usage = usage + " solve. async will result in multiple input files.\n"
usage = usage + " --cfac=<value> : Factor by which to expand molecular dimensions to\n"
usage = usage + " get coarse grid dimensions.\n"
usage = usage + " [default = %g]\n" % size.getConstant("cfac")
usage = usage + " --fadd=<value> : Amount to add to molecular dimensions to get fine\n"
usage = usage + " grid dimensions.\n"
usage = usage + " [default = %g]\n" % size.getConstant("fadd")
usage = usage + " --space=<value> : Desired fine mesh resolution\n"
usage = usage + " [default = %g]\n" % size.getConstant("space")
usage = usage + " --gmemfac=<value> : Number of bytes per grid point required\n"
usage = usage + " for sequential MG calculation\n"
usage = usage + " [default = %g]\n" % size.getConstant("gmemfac")
usage = usage + " --gmemceil=<value> : Max MB allowed for sequential MG\n"
usage = usage + " calculation. Adjust this to force the\n"
usage = usage + " script to perform faster calculations (which\n"
usage = usage + " require more parallelism).\n"
usage = usage + " [default = %g]\n" % size.getConstant("gmemceil")
usage = usage + " --ofrac=<value> : Overlap factor between mesh partitions\n"
usage = usage + " [default = %g]\n" % size.getConstant("ofrac")
usage = usage + " --redfac=<value> : The maximum factor by which a domain\n"
usage = usage + " dimension can be reduced during focusing\n"
usage = usage + " [default = %g]\n" % size.getConstant("redfac")
usage = usage + " --istrng=<value> : Ionic strength (M). Na+ anc Cl- ions will be used\n"
sys.stderr.write(usage)
sys.exit(2)
def main():
import getopt
filename = ""
shortOptList = ""
longOptList = ["help","split","potdx","method=","cfac=","space=","gmemceil=","gmemfac=","ofrac=","redfac=","istrng="]
try:
opts, args = getopt.getopt(sys.argv[1:], shortOptList, longOptList)
except getopt.GetoptError, details:
sys.stderr.write("Option error (%s)!\n" % details)
usage()
if len(args) != 1:
sys.stderr.write("Invalid argument list!\n")
usage()
else:
filename = args[0]
method = ""
size = psize.Psize()
async = 0
split = 0
istrng = 0
potdx = 0
for o, a in opts:
if o == "--help":
usage()
if o == "--split": split = 1
if o == "--potdx": potdx = 1
if o == "--method":
if a == "para":
sys.stdout.write("Forcing a parallel calculation\n")
method = "mg-para"
elif a == "auto":
sys.stdout.write("Forcing a sequential calculation\n")
method = "mg-auto"
elif a == "async":
sys.stdout.write("Forcing an asynchronous calculation\n")
method = "mg-para"
async = 1
elif a == "manual":
sys.stdout.write("Forcing a manual calculation\n")
method = "mg-manual"
else:
sys.stdout.write("Incorrect method argument: %s\n" % a)
sys.stdout.write("Defaulting to memory dependent result\n")
if o == "--cfac":
size.setConstant("cfac", float(a))
if o == "--space":
size.setConstant("space", float(a))
if o == "--gmemfac":
size.setConstant("gmemfac", int(a))
if o == "--gmemceil":
size.setConstant("gmemceil", int(a))
if o == "--ofrac":
size.setConstant("ofrac", float(a))
if o == "--redfac":
size.setConstant("redfac", float(a))
if o == "--istrng":
istrng = float(a)
if split == 1:
splitInput(filename)
else:
size.runPsize(filename)
input = Input(filename, size, method, async, istrng, potdx)
input.printInputFiles()
if __name__ == "__main__": main()
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