def main():
if len(sys.argv) < 2:
# Display the UI.
import ui
ui.launchUI()
else:
# Run in command line mode.
from optparse import OptionParser
parser = OptionParser(usage="Usage: %prog\n %prog [options] filename\n\nWhen run with no arguments, it launches the user interface. If any arguments are specified, it runs in command line mode.")
parser.add_option('--output', default='output.pdb', dest='output', metavar='FILENAME', help='output pdb file [default: output.pdb]')
parser.add_option('--add-atoms', default='all', dest='atoms', choices=('all', 'heavy', 'hydrogen', 'none'), help='which missing atoms to add: all, heavy, hydrogen, or none [default: all]')
parser.add_option('--keep-heterogens', default='all', dest='heterogens', choices=('all', 'water', 'none'), metavar='OPTION', help='which heterogens to keep: all, water, or none [default: all]')
parser.add_option('--replace-nonstandard', action='store_true', default=False, dest='nonstandard', help='replace nonstandard residues with standard equivalents')
parser.add_option('--add-residues', action='store_true', default=False, dest='residues', help='add missing residues')
parser.add_option('--water-box', dest='box', type='float', nargs=3, metavar='X Y Z', help='add a water box. The value is the box dimensions in nm [example: --water-box=2.5 2.4 3.0]')
parser.add_option('--ph', type='float', default=7.0, dest='ph', help='the pH to use for adding missing hydrogens [default: 7.0]')
parser.add_option('--positive-ion', default='Na+', dest='positiveIon', choices=('Cs+', 'K+', 'Li+', 'Na+', 'Rb+'), metavar='ION', help='positive ion to include in the water box: Cs+, K+, Li+, Na+, or Rb+ [default: Na+]')
parser.add_option('--negative-ion', default='Cl-', dest='negativeIon', choices=('Cl-', 'Br-', 'F-', 'I-'), metavar='ION', help='negative ion to include in the water box: Cl-, Br-, F-, or I- [default: Cl-]')
parser.add_option('--ionic-strength', type='float', default=0.0, dest='ionic', metavar='STRENGTH', help='molar concentration of ions to add to the water box [default: 0.0]')
(options, args) = parser.parse_args()
if len(args) == 0:
parser.error('No filename specified')
if len(args) > 1:
parser.error('Must specify a single filename')
fixer = PDBFixer(filename=sys.argv[1])
if options.residues:
fixer.findMissingResidues()
else:
fixer.missingResidues = {}
if options.nonstandard:
fixer.findNonstandardResidues()
fixer.replaceNonstandardResidues()
fixer.findMissingAtoms()
if options.atoms not in ('all', 'heavy'):
fixer.missingAtoms = {}
fixer.missingTerminals = {}
fixer.addMissingAtoms()
if options.heterogens == 'none':
fixer.removeHeterogens(False)
elif options.heterogens == 'water':
fixer.removeHeterogens(True)
if options.atoms in ('all', 'hydrogen'):
fixer.addMissingHydrogens(options.ph)
if options.box is not None:
fixer.addSolvent(boxSize=options.box*unit.nanometer, positiveIon=options.positiveIon,
negativeIon=options.negativeIon, ionicStrength=options.ionic*unit.molar)
with open(options.output, 'w') as f:
if fixer.source is not None:
f.write("REMARK 1 PDBFIXER FROM: %s\n" % fixer.source)
app.PDBFile.writeFile(fixer.topology, fixer.positions, f)
def main():
if len(sys.argv) < 2:
# Display the UI.
import ui
ui.launchUI()
else:
# Run in command line mode.
from optparse import OptionParser
parser = OptionParser(usage="Usage: %prog\n %prog [options] filename\n\nWhen run with no arguments, it launches the user interface. If any arguments are specified, it runs in command line mode.")
parser.add_option('--output', default='output.pdb', dest='output', metavar='FILENAME', help='output pdb file [default: output.pdb]')
parser.add_option('--add-atoms', default='all', dest='atoms', choices=('all', 'heavy', 'hydrogen', 'none'), help='which missing atoms to add: all, heavy, hydrogen, or none [default: all]')
parser.add_option('--keep-heterogens', default='all', dest='heterogens', choices=('all', 'water', 'none'), metavar='OPTION', help='which heterogens to keep: all, water, or none [default: all]')
parser.add_option('--replace-nonstandard', action='store_true', default=False, dest='nonstandard', help='replace nonstandard residues with standard equivalents')
parser.add_option('--add-residues', action='store_true', default=False, dest='residues', help='add missing residues')
parser.add_option('--water-box', dest='box', type='float', nargs=3, metavar='X Y Z', help='add a water box. The value is the box dimensions in nm [example: --water-box=2.5 2.4 3.0]')
parser.add_option('--ph', type='float', default=7.0, dest='ph', help='the pH to use for adding missing hydrogens [default: 7.0]')
parser.add_option('--positive-ion', default='Na+', dest='positiveIon', choices=('Cs+', 'K+', 'Li+', 'Na+', 'Rb+'), metavar='ION', help='positive ion to include in the water box: Cs+, K+, Li+, Na+, or Rb+ [default: Na+]')
parser.add_option('--negative-ion', default='Cl-', dest='negativeIon', choices=('Cl-', 'Br-', 'F-', 'I-'), metavar='ION', help='negative ion to include in the water box: Cl-, Br-, F-, or I- [default: Cl-]')
parser.add_option('--ionic-strength', type='float', default=0.0, dest='ionic', metavar='STRENGTH', help='molar concentration of ions to add to the water box [default: 0.0]')
(options, args) = parser.parse_args()
if len(args) == 0:
parser.error('No filename specified')
if len(args) > 1:
parser.error('Must specify a single filename')
fixer = PDBFixer(filename=sys.argv[1])
if options.residues:
fixer.findMissingResidues()
else:
fixer.missingResidues = {}
if options.nonstandard:
fixer.findNonstandardResidues()
fixer.replaceNonstandardResidues()
fixer.findMissingAtoms()
if options.atoms not in ('all', 'heavy'):
fixer.missingAtoms = {}
fixer.missingTerminals = {}
fixer.addMissingAtoms()
if options.heterogens == 'none':
fixer.removeHeterogens(False)
elif options.heterogens == 'water':
fixer.removeHeterogens(True)
if options.atoms in ('all', 'hydrogen'):
fixer.addMissingHydrogens(options.ph)
if options.box is not None:
fixer.addSolvent(boxSize=options.box*unit.nanometer, positiveIon=options.positiveIon,
negativeIon=options.negativeIon, ionicStrength=options.ionic*unit.molar)
with open(options.output, 'w') as f:
if fixer.source is not None:
f.write("REMARK 1 PDBFIXER FROM: %s\n" % fixer.source)
app.PDBFile.writeFile(fixer.topology, fixer.positions, f)
atomResidue = [atom.residue for atom in topology.atoms()]
nearest = sys.float_info.max
for atom in newAtoms:
p = positions-positions[atom.index]
dist = math.sqrt(min(np.dot(p[i], p[i]) for i in range(len(atomResidue)) if atomResidue[i] != atom.residue))
if dist < nearest:
nearest = dist
return nearest
if __name__=='__main__':
if len(sys.argv) < 2:
# Display the UI.
import ui
ui.launchUI()
else:
# Run in command line mode.
from optparse import OptionParser
parser = OptionParser(usage="Usage: %prog\n %prog [options] filename\n\nWhen run with no arguments, it launches the user interface. If any arguments are specified, it runs in command line mode.")
parser.add_option('--output', default='output.pdb', dest='output', metavar='FILENAME', help='output pdb file [default: output.pdb]')
parser.add_option('--add-atoms', default='all', dest='atoms', choices=('all', 'heavy', 'hydrogen', 'none'), help='which missing atoms to add: all, heavy, hydrogen, or none [default: all]')
parser.add_option('--keep-heterogens', default='all', dest='heterogens', choices=('all', 'water', 'none'), metavar='OPTION', help='which heterogens to keep: all, water, or none [default: all]')
parser.add_option('--replace-nonstandard', action='store_true', default=False, dest='nonstandard', help='replace nonstandard residues with standard equivalents')
parser.add_option('--add-residues', action='store_true', default=False, dest='residues', help='add missing residues')
parser.add_option('--water-box', dest='box', type='float', nargs=3, metavar='X Y Z', help='add a water box. The value is the box dimensions in nm [example: --water-box=2.5 2.4 3.0]')
parser.add_option('--ph', type='float', default=7.0, dest='ph', help='the pH to use for adding missing hydrogens [default: 7.0]')
parser.add_option('--positive-ion', default='Na+', dest='positiveIon', choices=('Cs+', 'K+', 'Li+', 'Na+', 'Rb+'), metavar='ION', help='positive ion to include in the water box: Cs+, K+, Li+, Na+, or Rb+ [default: Na+]')
parser.add_option('--negative-ion', default='Cl-', dest='negativeIon', choices=('Cl-', 'Br-', 'F-', 'I-'), metavar='ION', help='negative ion to include in the water box: Cl-, Br-, F-, or I- [default: Cl-]')
parser.add_option('--ionic-strength', type='float', default=0.0, dest='ionic', metavar='STRENGTH', help='molar concentration of ions to add to the water box [default: 0.0]')