def test_write(self):
"""
test writing a pdbq file
"""
writer = PdbqWriter()
writer.write('test_pdbqWriter.pdbq', self.mol, bondOrigin=('File',))
ans, errors = self.compare('Data/1crn_Hs.pdbq',
'test_pdbqWriter.pdbq')
self.assertEquals(errors, None)
self.assertEquals(ans, True)
def setup(self,
useProteinAromaticList=1,
aromaticCutOff=7.5,
maxtors=32,
autoMergeNPHS=1):
if self.chains[0].hasBonds == 0:
self.buildBondsByDistance()
self.useProteinAromaticList = useProteinAromaticList
self.aromaticCutOff = aromaticCutOff
self.maxtors = 32
self.autoMergeNPHS = autoMergeNPHS
self.bondClassifier = AutoDockBondClassifier()
self.torsionTree = None
self.message = ""
self.torscount = 0
self.possible_torscount = 0
self.TORSDOF = 0
self.resKeys = list(q.keys())
self.PdbqWriter = PdbqWriter()
#should this be here?
msg = 'initialized ' + self.name + ':\n'
#detect whether isPeptide
msg += self.checkIsPeptide()
#process charges
msg += self.checkCharges()
##process hydrogens
msg += self.checkHydrogens()
#process bonds
#this doesn't report anything???
newmsg, nphs = self.checkBonds()
msg += newmsg
#process aromaticCarbons
msg += self.checkAromatics()
return msg, nphs
sys.exit()
if not filename:
print('rotate_molecule: filename must be specified.')
usage()
sys.exit()
mol = Read(filename)[0]
if verbose: print('read ', filename)
filetype = os.path.splitext(os.path.basename(filename))[1]
if verbose: print("filetype=", filetype)
writer = None
if filetype == '.pdbqt':
writer = PdbqtWriter()
elif filetype == '.pdbq':
writer = PdbqWriter()
elif filetype == '.pdbqs':
writer = PdbqsWriter()
elif filetype == '.pdb':
writer = PdbWriter()
else:
print('Sorry! Unable to write this filetype->', filetype)
center = numpy.add.reduce(mol.allAtoms.coords) / len(mol.allAtoms)
crds = numpy.array(mol.allAtoms.coords)
center = numpy.add.reduce(crds) / len(mol.allAtoms)
crds = crds - center
crds = crds.tolist()
mol.allAtoms.updateCoords(crds)
lenCoords = len(crds)
#rotate the atoms here
if not pdbqt_filename:
print 'pdbqt_to_pdbq: pdbqt_filename must be specified.'
usage()
sys.exit()
mols = Read(pdbqt_filename)
if verbose: print 'read ', pdbqt_filename
mol = mols[0]
mol.buildBondsByDistance()
#fix number for problem files with alternative positions
mol.allAtoms.number = range(1, len(mol.allAtoms)+1)
#pdb_filename = mol.name + '.pdb'
writer = PdbqWriter()
#writer.write(pdbq_filename, mol.allAtoms, records=['ATOM', 'HETATM'])
fptr = open(pdbq_filename, 'w')
ctr = 0
for l in mol.parser.allLines:
if l.find('ATOM')==0 or l.find('HETATM')==0:
at = mol.allAtoms[ctr]
if at.autodock_element=='A':
if len(at.name)==1:
at.name='A'
else:
at.name = 'A' + at.name[1:]
writer.write_atom(fptr, mol.allAtoms[ctr])
ctr = ctr + 1
else:
fptr.write(l)
sys.exit()
if not pdbqt_filename:
print('pdbqt_to_pdbq: pdbqt_filename must be specified.')
usage()
sys.exit()
mols = Read(pdbqt_filename)
if verbose: print('read ', pdbqt_filename)
mol = mols[0]
mol.buildBondsByDistance()
#fix number for problem files with alternative positions
mol.allAtoms.number = list(range(1, len(mol.allAtoms) + 1))
#pdb_filename = mol.name + '.pdb'
writer = PdbqWriter()
#writer.write(pdbq_filename, mol.allAtoms, records=['ATOM', 'HETATM'])
fptr = open(pdbq_filename, 'w')
ctr = 0
for l in mol.parser.allLines:
if l.find('ATOM') == 0 or l.find('HETATM') == 0:
at = mol.allAtoms[ctr]
if at.autodock_element == 'A':
if len(at.name) == 1:
at.name = 'A'
else:
at.name = 'A' + at.name[1:]
writer.write_atom(fptr, mol.allAtoms[ctr])
ctr = ctr + 1
else:
fptr.write(l)
