def mainCommand(argv):
"""
Main driver for running program from the command line.
"""
fieldNames = ('amber', 'charmm', 'parse', 'tyl06', 'peoepb', 'swanson')
validForcefields = []
validForcefields.extend(fieldNames)
validForcefields.extend((x.upper() for x in fieldNames))
description = 'This module takes a PDB file as input and performs ' +\
'optimizations before yielding a new PQR-style file in PQR_OUTPUT_PATH.\n' +\
'If PDB_PATH is an ID it will automatically be obtained from the PDB archive.'
usage = 'Usage: %prog [options] PDB_PATH PQR_OUTPUT_PATH'
parser = OptionParser(description=description,
usage=usage,
version='%prog (Version ' + __version__ + ')')
group = OptionGroup(parser, "Manditory options",
"One of the following options must be used.")
group.add_option('--ff',
dest='ff',
metavar='FIELD_NAME',
choices=validForcefields,
help='The forcefield to use - currently amber, ' +
'charmm, parse, tyl06, peoepb and swanson ' +
'are supported.')
group.add_option(
'--userff',
dest='userff',
metavar='USER_FIELD_FILE',
help=
'The user created forcefield file to use. Requires --usernames overrides --ff'
)
group.add_option(
'--clean',
dest='clean',
action='store_true',
default=False,
help='Do no optimization, atom addition, or parameter assignment, ' +
'just return the original PDB file in aligned format. ' +
'Overrides --ff and --userff')
parser.add_option_group(group)
group = OptionGroup(parser, "General options")
group.add_option('--nodebump',
dest='debump',
action='store_false',
default=True,
help='Do not perform the debumping operation')
group.add_option('--noopt',
dest='opt',
action='store_false',
default=True,
help='Do not perform hydrogen optimization')
group.add_option('--chain',
dest='chain',
action='store_true',
default=False,
help='Keep the chain ID in the output PQR file')
group.add_option(
'--assign-only',
dest='assign_only',
action='store_true',
default=False,
help=
'Only assign charges and radii - do not add atoms, debump, or optimize.'
)
group.add_option(
'--ffout',
dest='ffout',
metavar='FIELD_NAME',
choices=validForcefields,
help=
'Instead of using the standard canonical naming scheme for residue and atom names, '
+ 'use the names from the given forcefield - currently amber, ' +
'charmm, parse, tyl06, peoepb and swanson are supported.')
group.add_option(
'--usernames',
dest='usernames',
metavar='USER_NAME_FILE',
help='The user created names file to use. Required if using --userff')
group.add_option(
'--apbs-input',
dest='input',
action='store_true',
default=False,
help=
'Create a template APBS input file based on the generated PQR file. Also creates a Python '
+ 'pickle for using these parameters in other programs.')
group.add_option(
'--ligand',
dest='ligand',
metavar='PATH',
help=
'Calculate the parameters for the ligand in mol2 format at the given path. '
+ 'Pdb2pka must be compiled.')
group.add_option(
'--whitespace',
dest='whitespace',
action='store_true',
default=False,
help=
'Insert whitespaces between atom name and residue name, between x and y, and between y and z.'
)
group.add_option('--typemap',
dest='typemap',
action='store_true',
default=False,
help='Create Typemap output.')
group.add_option(
'--neutraln',
dest='neutraln',
action='store_true',
default=False,
help='Make the N-terminus of this protein neutral (default is charged). '
'Requires PARSE force field.')
group.add_option(
'--neutralc',
dest='neutralc',
action='store_true',
default=False,
help='Make the C-terminus of this protein neutral (default is charged). '
'Requires PARSE force field.')
group.add_option('-v',
'--verbose',
dest='verbose',
action='store_true',
default=False,
help='Print information to stdout.')
group.add_option(
'--drop-water',
dest='drop_water',
action='store_true',
default=False,
help=
'Drop waters before processing protein. Currently recognized and deleted are the following water types: %s'
% ', '.join(WAT.water_residue_names))
group.add_option(
'--include-header',
dest='include_header',
action='store_true',
default=False,
help='Include pdb header in pqr file. '
'WARNING: The resulting PQR file will not work with APBS versions prior to 1.5'
)
parser.add_option_group(group)
pka_group = OptionGroup(parser, "pH options")
pka_group.add_option(
'--ph-calc-method',
dest='ph_calc_method',
metavar='PH_METHOD',
choices=('propka', 'pdb2pka'),
help=
'Method used to calculate ph values. If a pH calculation method is selected, for each'
' titratable residue pH values will be calculated and the residue potentially modified'
' after comparison with the pH value supplied by --with_ph\n'
'propka - Use PROPKA to calculate pH values. Actual PROPKA results will be output to <output-path>.propka.\n'
'pdb2pka - Use PDB2PKA to calculate pH values. Requires the use of the PARSE force field.'
' Warning: Larger residues can take a very long time to run using this method. EXPERIMENTAL!'
)
pka_group.add_option(
'--with-ph',
dest='ph',
action='store',
type='float',
default=7.0,
help=
'pH values to use when applying the results of the selected pH calculation method.'
' Defaults to %default')
parser.add_option_group(pka_group)
pdb2pka_group = OptionGroup(parser, "PDB2PKA method options")
pdb2pka_group.add_option(
'--pdb2pka-out',
dest='pdb2pka_out',
action='store',
default='pdb2pka_output',
help='Output directory for PDB2PKA results. Defaults to %default')
pdb2pka_group.add_option(
'--pdb2pka-resume',
dest='pdb2pka_resume',
action="store_true",
default=False,
help='Resume run from state saved in output directory.')
pdb2pka_group.add_option(
'--pdie',
dest='pdb2pka_pdie',
default=8,
type='int',
help='Protein dielectric constant. Defaults to %default')
pdb2pka_group.add_option(
'--sdie',
dest='pdb2pka_sdie',
default=80,
type='int',
help='Solvent dielectric constant. Defaults to %default')
# pdb2pka_group.add_option('--maps', dest='maps', default=None, type='int',
# help='<1 for using provided 3D maps; 2 for genereting new maps>')
# pdb2pka_group.add_option('--xdiel', dest='xdiel', default=None, type='str',
# help='<xdiel maps>')
# pdb2pka_group.add_option('--ydiel', dest='ydiel', default=None, type='str',
# help='<ydiel maps>')
# pdb2pka_group.add_option('--zdiel', dest='zdiel', default=None, type='str',
# help='<zdiel maps>')
# pdb2pka_group.add_option('--kappa', dest='kappa', default=None, type='str',
# help='<ion-accessibility map>')
# pdb2pka_group.add_option('--smooth', dest='sd', default=None, type='float',
# help='<st.dev [A] of Gaussian smooting of 3D maps at the boundary, bandthwith=3 st.dev>')
#
# Cut off energy for calculating non-charged-charged interaction energies
#
pdb2pka_group.add_option(
'--pairene',
dest='pdb2pka_pairene',
type='float',
default=1.0,
help=
'Cutoff energy in kT for calculating non charged-charged interaction energies. Default: %default'
)
parser.add_option_group(pdb2pka_group)
propka_group = OptionGroup(parser, "PROPKA method options")
propka_group.add_option(
"--propka-reference",
dest="propka_reference",
default="neutral",
choices=('neutral', 'low-pH'),
help=
"Setting which reference to use for stability calculations. See PROPKA 3.0 documentation."
)
propka_group.add_option(
'--propka-verbose',
dest='propka_verbose',
action='store_true',
default=False,
help='Print extra proPKA information to stdout. '
'WARNING: This produces an incredible amount of output.')
parser.add_option_group(propka_group)
extensions.setupExtensionsOptions(parser)
(options, args) = parser.parse_args(argv[1:])
commandLine = ' '.join(argv[1:])
if len(args) != 2:
parser.error('Incorrect number (%d) of arguments!\nargs: %s' %
(len(args), args))
if options.assign_only or options.clean:
options.debump = options.optflag = False
userfffile = None
usernamesfile = None
if not options.clean:
if not options.usernames is None:
try:
usernamesfile = open(options.usernames, 'rU')
except IOError:
parser.error('Unable to open user names file %s' %
options.usernames)
if not options.userff is None:
try:
userfffile = open(options.userff, 'rU')
except IOError:
parser.error('Unable to open user force field file %s' %
options.userff)
if options.usernames is None:
parser.error('--usernames must be specified if using --userff')
else:
if options.ff is None:
parser.error(
'One of the manditory options was not specified.\n' +
'Please specify either --ff, --userff, or --clean')
if getFFfile(options.ff) == '':
parser.error(
'Unable to find parameter files for forcefield %s!' %
options.ff)
if options.ph < 0.0 or options.ph > 14.0:
parser.error(
'%i is not a valid pH! Please choose a pH between 0.0 and 14.0.' %
options.pH)
ph_calc_options = None
if options.ph_calc_method == 'propka':
ph_calc_options = utilities.createPropkaOptions(
options.ph,
verbose=options.propka_verbose,
reference=options.propka_reference)
if options.ph_calc_method == 'pdb2pka':
if options.ff.lower() != 'parse':
parser.error('PDB2PKA requires the PARSE force field.')
ph_calc_options = {
'output_dir': options.pdb2pka_out,
'clean_output': not options.pdb2pka_resume,
'pdie': options.pdb2pka_pdie,
'sdie': options.pdb2pka_sdie,
'pairene': options.pdb2pka_pairene
}
if options.ligand is not None:
try:
options.ligand = open(options.ligand, 'rU')
except IOError:
parser.error('Unable to find ligand file %s!' % options.ligand)
if options.neutraln and (options.ff is None
or options.ff.lower() != 'parse'):
parser.error('--neutraln option only works with PARSE forcefield!')
if options.neutralc and (options.ff is None
or options.ff.lower() != 'parse'):
parser.error('--neutralc option only works with PARSE forcefield!')
text = """
--------------------------
PDB2PQR - a Python-based structural conversion utility
--------------------------
Please cite your use of PDB2PQR as:
Dolinsky TJ, Nielsen JE, McCammon JA, Baker NA.
PDB2PQR: an automated pipeline for the setup, execution,
and analysis of Poisson-Boltzmann electrostatics calculations.
Nucleic Acids Research 32 W665-W667 (2004).
"""
sys.stdout.write(text)
path = args[0]
pdbFile = getPDBFile(path)
pdblist, errlist = readPDB(pdbFile)
if len(pdblist) == 0 and len(errlist) == 0:
parser.error("Unable to find file %s!" % path)
if len(errlist) != 0 and options.verbose:
print "Warning: %s is a non-standard PDB file.\n" % path
print errlist
outpath = args[1]
options.outname = outpath
#In case no extensions were specified or no extensions exist.
if not hasattr(options,
'active_extensions') or options.active_extensions is None:
options.active_extensions = []
#I see no point in hiding options from extensions.
extensionOpts = options
#TODO: The ideal would be to pass a file like object for the second
# argument and add a third for names then
# get rid of the userff and username arguments to this function.
# This would also do away with the redundent checks and such in
# the Forcefield constructor.
try:
header, lines, missedligands = runPDB2PQR(
pdblist,
options.ff,
outname=options.outname,
ph=options.ph,
verbose=options.verbose,
selectedExtensions=options.active_extensions,
ph_calc_method=options.ph_calc_method,
ph_calc_options=ph_calc_options,
extensionOptions=extensionOpts,
clean=options.clean,
neutraln=options.neutraln,
neutralc=options.neutralc,
ligand=options.ligand,
assign_only=options.assign_only,
chain=options.chain,
drop_water=options.drop_water,
debump=options.debump,
opt=options.opt,
typemap=options.typemap,
userff=userfffile,
usernames=usernamesfile,
ffout=options.ffout,
commandLine=commandLine,
include_old_header=options.include_header)
except PDB2PQRError as er:
print er
sys.exit(2)
# Print the PQR file
outfile = open(outpath, "w")
outfile.write(header)
# Adding whitespaces if --whitespace is in the options
for line in lines:
if options.whitespace:
if line[0:4] == 'ATOM':
newline = line[0:6] + ' ' + line[6:16] + ' ' + line[
16:38] + ' ' + line[38:46] + ' ' + line[46:]
outfile.write(newline)
elif line[0:6] == 'HETATM':
newline = line[0:6] + ' ' + line[6:16] + ' ' + line[
16:38] + ' ' + line[38:46] + ' ' + line[46:]
outfile.write(newline)
else:
outfile.write(line)
outfile.close()
if options.input:
from src import inputgen
from src import psize
method = "mg-auto"
size = psize.Psize()
size.parseInput(outpath)
size.runPsize(outpath)
async = 0 # No async files here!
input = inputgen.Input(outpath, size, method, async, potdx=True)
input.printInputFiles()
input.dumpPickle()
pickleToJSON(outpath)
def mainCommand(argv):
"""
Main driver for running program from the command line.
"""
fieldNames = ('amber','charmm','parse', 'ty106','peopb','swanson')
validForcefields = []
validForcefields.extend(fieldNames)
validForcefields.extend((x.upper() for x in fieldNames))
description = 'This module takes a PDB file as input and performs ' +\
'optimizations before yielding a new PQR-style file in PQR_OUTPUT_PATH.\n' +\
'If PDB_PATH is an ID it will automatically be obtained from the PDB archive.'
usage = 'Usage: %prog [options] PDB_PATH PQR_OUTPUT_PATH'
parser = OptionParser(description=description, usage=usage, version='%prog (Version ' + __version__ + ')')
group = OptionGroup(parser,"Manditory options", "One of the following options must be used.")
group.add_option('--ff', dest='ff', metavar='FIELD_NAME', choices=validForcefields,
help='The forcefield to use - currently amber, ' +
'charmm, parse, tyl06, peoepb and swanson ' +
'are supported.')
group.add_option('--userff', dest='userff', metavar='USER_FIELD_FILE',
help='The user created forcefield file to use. Requires --usernames overrides --ff')
group.add_option('--clean', dest='clean', action='store_true', default=False,
help='Do no optimization, atom addition, or parameter assignment, ' +
'just return the original PDB file in aligned format. ' +
'Overrides --ff and --userff')
parser.add_option_group(group)
group = OptionGroup(parser,"General options")
group.add_option('--nodebump', dest='debump', action='store_false', default=True,
help='Do not perform the debumping operation')
group.add_option('--noopt', dest='opt', action='store_false', default=True,
help='Do not perform hydrogen optimization')
group.add_option('--chain', dest='chain', action='store_true', default=False,
help='Keep the chain ID in the output PQR file')
group.add_option('--assign-only', dest='assign_only', action='store_true', default=False,
help='Only assign charges and radii - do not add atoms, debump, or optimize.')
group.add_option('--ffout', dest='ffout', metavar='FIELD_NAME',choices=validForcefields,
help='Instead of using the standard canonical naming scheme for residue and atom names, ' +
'use the names from the given forcefield - currently amber, ' +
'charmm, parse, tyl06, peoepb and swanson ' +
'are supported.')
group.add_option('--usernames', dest='usernames', metavar='USER_NAME_FILE',
help='The user created names file to use. Required if using --userff')
group.add_option('--with-ph', dest='pH', action='store', type='float',
help='Use propka to calculate pKas and apply them to the molecule given the pH value. ' +
'Actual PropKa results will be output to <output-path>.propka.')
group.add_option('--apbs-input', dest='input', action='store_true', default=False,
help='Create a template APBS input file based on the generated PQR file. Also creates a Python ' +
'pickle for using these parameters in other programs.')
group.add_option('--ligand', dest='ligand', metavar='PATH',
help='Calculate the parameters for the ligand in mol2 format at the given path. ' +
'Pdb2pka must be compiled.')
group.add_option('--whitespace', dest='whitespace', action='store_true', default=False,
help='Insert whitespaces between atom name and residue name, between x and y, and between y and z.')
group.add_option('--typemap', dest='typemap', action='store_true', default=False,
help='Create Typemap output.')
group.add_option('--neutraln', dest='neutraln', action='store_true', default=False,
help='Make the N-terminus of this protein neutral (default is charged). ' +
'Requires PARSE force field.')
group.add_option('--neutralc', dest='neutralc', action='store_true', default=False,
help='Make the C-terminus of this protein neutral (default is charged). ' +
'Requires PARSE force field.')
group.add_option('-v', '--verbose', dest='verbose', action='store_true', default=False,
help='Print information to stdout.')
parser.add_option_group(group)
extentionsGroup = extensions.setupExtensionsOptions(parser)
(options, args) = parser.parse_args()
if len(args) != 2:
parser.error('Incorrect number (%d) of arguments!\nargv: %s, args: %s' % (len(args),argv, args))
# Append Numeric/Numpy path to sys.path if the user specified a non-standard location during configuration
sys.argv=argv
package_path = PACKAGE_PATH
if package_path != "":
sys.path.extend(package_path.split(":"))
if (not options.pH is None) and (options.pH < 0.0 or options.pH > 14.0):
parser.error('%i is not a valid pH! Please choose a pH between 0.0 and 14.0.' % options.pH)
if options.assign_only or options.clean:
options.debump = options.optflag = False
userfffile = None
usernamesfile = None
if not options.clean:
if not options.usernames is None:
try:
usernamesfile = open(options.usernames, 'rU')
except IOError:
parser.error('Unable to open user names file %s' % options.usernames)
if not options.userff is None:
try:
userfffile = open(options.userff, 'rU')
except IOError:
parser.error('Unable to open user force field file %s' % options.userff)
if options.usernames is None:
parser.error('--usernames must be specified if using --userff')
else:
if options.ff is None:
parser.error('One of the manditory options was not specified.\n' +
'Please specify either --ff, --userff, or --clean')
if getFFfile(options.ff) == '':
parser.error('Unable to find parameter files for forcefield %s!' % options.ff)
if not options.ligand is None:
try:
options.ligand = open(options.ligand, 'rU')
except IOError:
parser.error('Unable to find ligand file %s!' % options.ligand)
if options.neutraln and (options.ff != 'parse' or not options.userff is None):
parser.error('--neutraln option only works with PARSE forcefield!')
if options.neutralc and (options.ff != 'parse' or not options.userff is None):
parser.error('--neutralc option only works with PARSE forcefield!')
text = "\n--------------------------\n"
text += "PDB2PQR - a Python-based structural conversion utility\n"
text += "--------------------------\n"
text += "Please cite your use of PDB2PQR as:\n"
text += " Dolinsky TJ, Nielsen JE, McCammon JA, Baker NA.\n"
text += " PDB2PQR: an automated pipeline for the setup, execution,\n"
text += " and analysis of Poisson-Boltzmann electrostatics calculations.\n"
text += " Nucleic Acids Research 32 W665-W667 (2004).\n\n"
sys.stdout.write(text)
path = args[0]
file = getPDBFile(path)
pdblist, errlist = readPDB(file)
if len(pdblist) == 0 and len(errlist) == 0:
#TODO: Why are we doing this?
# try:
# os.remove(path)
# except OSError:
# pass
parser.error("Unable to find file %s!" % path)
if len(errlist) != 0 and options.verbose:
print "Warning: %s is a non-standard PDB file.\n" % path
print errlist
outpath = args[1]
options.outname = outpath
#In case no extensions were specified.
if options.active_extentions is None:
options.active_extentions = []
#Filter out the options specifically for extentions.
#Passed into runPDB2PQR, but not used by any extention yet.
extentionOpts = ExtentionOptions()
if extentionsGroup is not None:
for opt in extentionsGroup.option_list:
if opt.dest == 'active_extentions':
continue
setattr(extentionOpts, opt.dest,
getattr(options, opt.dest))
#TODO: The ideal would be to pass a file like object for the second
# argument and get rid of the userff and username arguments to this function.
# This would also do away with the redundent checks and such in
# the Forcefield constructor.
header, lines, missedligands = runPDB2PQR(pdblist,
options.ff,
outname = options.outname,
ph = options.pH,
verbose = options.verbose,
extentions = options.active_extentions,
ententionOptions = extentionOpts,
clean = options.clean,
neutraln = options.neutraln,
neutralc = options.neutralc,
ligand = options.ligand,
assign_only = options.assign_only,
chain = options.chain,
debump = options.debump,
opt = options.opt,
typemap = options.typemap,
userff = userfffile,
usernames = usernamesfile,
ffout = options.ffout)
# Print the PQR file
outfile = open(outpath,"w")
outfile.write(header)
# Adding whitespaces if --whitespace is in the options
for line in lines:
if options.whitespace:
if line[0:4] == 'ATOM':
newline = line[0:16] + ' ' + line[16:38] + ' ' + line[38:46] + ' ' + line[46:]
outfile.write(newline)
elif line[0:6] == 'HETATM':
newline = line[0:16] + ' ' + line[16:38] + ' ' + line[38:46] + ' ' + line[46:]
outfile.write(newline)
else:
outfile.write(line)
outfile.close()
if options.input:
from src import inputgen
from src import psize
method = "mg-auto"
size = psize.Psize()
size.parseInput(outpath)
size.runPsize(outpath)
async = 0 # No async files here!
input = inputgen.Input(outpath, size, method, async)
input.printInputFiles()
input.dumpPickle()
def mainCommand(argv):
"""
Main driver for running program from the command line.
"""
fieldNames = ('amber','charmm','parse', 'tyl06','peoepb','swanson')
validForcefields = []
validForcefields.extend(fieldNames)
validForcefields.extend((x.upper() for x in fieldNames))
description = 'This module takes a PDB file as input and performs ' +\
'optimizations before yielding a new PQR-style file in PQR_OUTPUT_PATH.\n' +\
'If PDB_PATH is an ID it will automatically be obtained from the PDB archive.'
usage = 'Usage: %prog [options] PDB_PATH PQR_OUTPUT_PATH'
parser = OptionParser(description=description, usage=usage, version='%prog (Version ' + __version__ + ')')
group = OptionGroup(parser,"Manditory options", "One of the following options must be used.")
group.add_option('--ff', dest='ff', metavar='FIELD_NAME', choices=validForcefields,
help='The forcefield to use - currently amber, ' +
'charmm, parse, tyl06, peoepb and swanson ' +
'are supported.')
group.add_option('--userff', dest='userff', metavar='USER_FIELD_FILE',
help='The user created forcefield file to use. Requires --usernames overrides --ff')
group.add_option('--clean', dest='clean', action='store_true', default=False,
help='Do no optimization, atom addition, or parameter assignment, ' +
'just return the original PDB file in aligned format. ' +
'Overrides --ff and --userff')
parser.add_option_group(group)
group = OptionGroup(parser,"General options")
group.add_option('--nodebump', dest='debump', action='store_false', default=True,
help='Do not perform the debumping operation')
group.add_option('--noopt', dest='opt', action='store_false', default=True,
help='Do not perform hydrogen optimization')
group.add_option('--chain', dest='chain', action='store_true', default=False,
help='Keep the chain ID in the output PQR file')
group.add_option('--assign-only', dest='assign_only', action='store_true', default=False,
help='Only assign charges and radii - do not add atoms, debump, or optimize.')
group.add_option('--ffout', dest='ffout', metavar='FIELD_NAME',choices=validForcefields,
help='Instead of using the standard canonical naming scheme for residue and atom names, ' +
'use the names from the given forcefield - currently amber, ' +
'charmm, parse, tyl06, peoepb and swanson are supported.')
group.add_option('--usernames', dest='usernames', metavar='USER_NAME_FILE',
help='The user created names file to use. Required if using --userff')
group.add_option('--apbs-input', dest='input', action='store_true', default=False,
help='Create a template APBS input file based on the generated PQR file. Also creates a Python ' +
'pickle for using these parameters in other programs.')
group.add_option('--ligand', dest='ligand', metavar='PATH',
help='Calculate the parameters for the ligand in mol2 format at the given path. ' +
'Pdb2pka must be compiled.')
group.add_option('--whitespace', dest='whitespace', action='store_true', default=False,
help='Insert whitespaces between atom name and residue name, between x and y, and between y and z.')
group.add_option('--typemap', dest='typemap', action='store_true', default=False,
help='Create Typemap output.')
group.add_option('--neutraln', dest='neutraln', action='store_true', default=False,
help='Make the N-terminus of this protein neutral (default is charged). '
'Requires PARSE force field.')
group.add_option('--neutralc', dest='neutralc', action='store_true', default=False,
help='Make the C-terminus of this protein neutral (default is charged). '
'Requires PARSE force field.')
group.add_option('-v', '--verbose', dest='verbose', action='store_true', default=False,
help='Print information to stdout.')
group.add_option('--drop-water', dest='drop_water', action='store_true', default=False,
help='Drop waters before processing protein. Currently recognized and deleted are the following water types: %s' % ', '.join(WAT.water_residue_names))
group.add_option('--include-header', dest='include_header', action='store_true', default=False,
help='Include pdb header in pqr file. '
'WARNING: The resulting PQR file will not work with APBS versions prior to 1.5')
parser.add_option_group(group)
pka_group = OptionGroup(parser,"pH options")
pka_group.add_option('--ph-calc-method', dest='ph_calc_method', metavar='PH_METHOD', choices=('propka', 'propka31', 'pdb2pka'),
help='Method used to calculate ph values. If a pH calculation method is selected, for each'
' titratable residue pH values will be calculated and the residue potentially modified'
' after comparison with the pH value supplied by --with_ph\n'
'propka - Use PROPKA to calculate pH values. Actual PROPKA results will be output to <output-path>.propka.\n'
'propka31 - Use PROPKA 3.1 to calculate pH values. Actual PROPKA results will be output to <output-path>.propka.\n'
'pdb2pka - Use PDB2PKA to calculate pH values. Requires the use of the PARSE force field.'
' Warning: Larger residues can take a very long time to run using this method. EXPERIMENTAL!')
pka_group.add_option('--with-ph', dest='ph', action='store', type='float', default=7.0,
help='pH values to use when applying the results of the selected pH calculation method.'
' Defaults to %default')
parser.add_option_group(pka_group)
pdb2pka_group = OptionGroup(parser,"PDB2PKA method options")
pdb2pka_group.add_option('--pdb2pka-out', dest='pdb2pka_out', action='store', default='pdb2pka_output',
help='Output directory for PDB2PKA results. Defaults to %default')
pdb2pka_group.add_option('--pdb2pka-resume', dest='pdb2pka_resume', action="store_true", default=False,
help='Resume run from state saved in output directory.')
pdb2pka_group.add_option('--pdie', dest='pdb2pka_pdie', default=8,type='int',
help='Protein dielectric constant. Defaults to %default')
pdb2pka_group.add_option('--sdie', dest='pdb2pka_sdie', default=80, type='int',
help='Solvent dielectric constant. Defaults to %default')
# pdb2pka_group.add_option('--maps', dest='maps', default=None, type='int',
# help='<1 for using provided 3D maps; 2 for genereting new maps>')
# pdb2pka_group.add_option('--xdiel', dest='xdiel', default=None, type='str',
# help='<xdiel maps>')
# pdb2pka_group.add_option('--ydiel', dest='ydiel', default=None, type='str',
# help='<ydiel maps>')
# pdb2pka_group.add_option('--zdiel', dest='zdiel', default=None, type='str',
# help='<zdiel maps>')
# pdb2pka_group.add_option('--kappa', dest='kappa', default=None, type='str',
# help='<ion-accessibility map>')
# pdb2pka_group.add_option('--smooth', dest='sd', default=None, type='float',
# help='<st.dev [A] of Gaussian smooting of 3D maps at the boundary, bandthwith=3 st.dev>')
#
# Cut off energy for calculating non-charged-charged interaction energies
#
pdb2pka_group.add_option('--pairene',dest='pdb2pka_pairene',type='float',default=1.0,
help='Cutoff energy in kT for calculating non charged-charged interaction energies. Default: %default')
parser.add_option_group(pdb2pka_group)
propka_group = OptionGroup(parser,"PROPKA method options")
propka_group.add_option("--propka-reference", dest="propka_reference", default="neutral", choices=('neutral','low-pH'),
help="Setting which reference to use for stability calculations. See PROPKA 3.0 documentation.")
propka_group.add_option('--propka-verbose', dest='propka_verbose', action='store_true', default=False,
help='Print extra proPKA information to stdout. '
'WARNING: This produces an incredible amount of output.')
parser.add_option_group(propka_group)
extensions.setupExtensionsOptions(parser)
(options, args) = parser.parse_args(argv[1:])
commandLine = ' '.join(argv[1:])
if len(args) != 2:
parser.error('Incorrect number (%d) of arguments!\nargs: %s' % (len(args), args))
if options.assign_only or options.clean:
options.debump = options.optflag = False
userfffile = None
usernamesfile = None
if not options.clean:
if not options.usernames is None:
try:
usernamesfile = open(options.usernames, 'rU')
except IOError:
parser.error('Unable to open user names file %s' % options.usernames)
if not options.userff is None:
try:
userfffile = open(options.userff, 'rU')
except IOError:
parser.error('Unable to open user force field file %s' % options.userff)
if options.usernames is None:
parser.error('--usernames must be specified if using --userff')
else:
if options.ff is None:
parser.error('One of the manditory options was not specified.\n' +
'Please specify either --ff, --userff, or --clean')
if getFFfile(options.ff) == '':
parser.error('Unable to find parameter files for forcefield %s!' % options.ff)
if options.ph < 0.0 or options.ph > 14.0:
parser.error('%i is not a valid pH! Please choose a pH between 0.0 and 14.0.' % options.pH)
ph_calc_options = None
if options.ph_calc_method == 'propka':
ph_calc_options = utilities.createPropkaOptions(options.ph,
verbose=options.propka_verbose,
reference=options.propka_reference)
elif options.ph_calc_method == 'propka31':
import propka.lib
ph_calc_options, _ = propka.lib.loadOptions('--quiet')
elif options.ph_calc_method == 'pdb2pka':
if options.ff.lower() != 'parse':
parser.error('PDB2PKA requires the PARSE force field.')
ph_calc_options = {'output_dir': options.pdb2pka_out,
'clean_output': not options.pdb2pka_resume,
'pdie': options.pdb2pka_pdie,
'sdie': options.pdb2pka_sdie,
'pairene': options.pdb2pka_pairene}
if options.ligand is not None:
try:
options.ligand = open(options.ligand, 'rU')
except IOError:
parser.error('Unable to find ligand file %s!' % options.ligand)
if options.neutraln and (options.ff is None or options.ff.lower() != 'parse'):
parser.error('--neutraln option only works with PARSE forcefield!')
if options.neutralc and (options.ff is None or options.ff.lower() != 'parse'):
parser.error('--neutralc option only works with PARSE forcefield!')
text = """
--------------------------
PDB2PQR - a Python-based structural conversion utility
--------------------------
Please cite your use of PDB2PQR as:
Dolinsky TJ, Nielsen JE, McCammon JA, Baker NA.
PDB2PQR: an automated pipeline for the setup, execution,
and analysis of Poisson-Boltzmann electrostatics calculations.
Nucleic Acids Research 32 W665-W667 (2004).
"""
sys.stdout.write(text)
path = args[0]
pdbFile = getPDBFile(path)
pdblist, errlist = readPDB(pdbFile)
if len(pdblist) == 0 and len(errlist) == 0:
parser.error("Unable to find file %s!" % path)
if len(errlist) != 0 and options.verbose:
print("Warning: %s is a non-standard PDB file.\n" % path)
print(errlist)
outpath = args[1]
options.outname = outpath
#In case no extensions were specified or no extensions exist.
if not hasattr(options, 'active_extensions' ) or options.active_extensions is None:
options.active_extensions = []
#I see no point in hiding options from extensions.
extensionOpts = options
#TODO: The ideal would be to pass a file like object for the second
# argument and add a third for names then
# get rid of the userff and username arguments to this function.
# This would also do away with the redundent checks and such in
# the Forcefield constructor.
try:
header, lines, missedligands, _ = runPDB2PQR(pdblist,
options.ff,
outname = options.outname,
ph = options.ph,
verbose = options.verbose,
selectedExtensions = options.active_extensions,
ph_calc_method = options.ph_calc_method,
ph_calc_options = ph_calc_options,
extensionOptions = extensionOpts,
clean = options.clean,
neutraln = options.neutraln,
neutralc = options.neutralc,
ligand = options.ligand,
assign_only = options.assign_only,
chain = options.chain,
drop_water = options.drop_water,
debump = options.debump,
opt = options.opt,
typemap = options.typemap,
userff = userfffile,
usernames = usernamesfile,
ffout = options.ffout,
commandLine = commandLine,
include_old_header = options.include_header)
except PDB2PQRError as er:
print(er)
sys.exit(2)
# Print the PQR file
outfile = open(outpath,"w")
outfile.write(header)
# Adding whitespaces if --whitespace is in the options
for line in lines:
if options.whitespace:
if line[0:4] == 'ATOM':
newline = line[0:6] + ' ' + line[6:16] + ' ' + line[16:38] + ' ' + line[38:46] + ' ' + line[46:]
outfile.write(newline)
elif line[0:6] == 'HETATM':
newline = line[0:6] + ' ' + line[6:16] + ' ' + line[16:38] + ' ' + line[38:46] + ' ' + line[46:]
outfile.write(newline)
else:
outfile.write(line)
outfile.close()
if options.input:
from src import inputgen
from src import psize
method = "mg-auto"
size = psize.Psize()
size.parseInput(outpath)
size.runPsize(outpath)
async = 0 # No async files here!
input = inputgen.Input(outpath, size, method, async, potdx=True)
input.printInputFiles()
input.dumpPickle()
