def test_parsePDBQ():
"""
check that pdbq format files can be read
"""
from MolKit.pdbParser import PdbqParser
parser = PdbqParser("Data/1ent.pdbqs")
m = parser.parse()[0]
assert len(m.allAtoms)==2901
def test_parsePDBQ():
"""
check that pdbq format files can be read
"""
from MolKit.pdbParser import PdbqParser
parser = PdbqParser("Data/1ent.pdbqs")
m = parser.parse()[0]
assert len(m.allAtoms) == 2901
def Read(filename=None, alllines=None, dataformat='pdb', modelsAs='molecules'):
if not alllines and not filename:
raise AssertionError("%s invalid molecule" % filename)
elif alllines and filename:
alllines = None
elif filename:
if not os.path.exists(filename):
raise AssertionError("%s does't exist" % filename)
if alllines:
ext = dataformat
args = [None, alllines]
else:
ext = filename.split('.')[1]
args = [filename, None]
if ext == 'pdb':
parser = PdbParser(*args, modelsAs=modelsAs)
elif ext == 'pdbq':
parser = PdbqParser(*args, modelsAs=modelsAs)
elif ext == 'pdbqt':
parser = PdbqtParser(*args, modelsAs=modelsAs)
elif ext == 'pdbqs':
parser = PdbqsParser(*args, modelsAs=modelsAs)
elif ext == 'pqr':
parser = PQRParser(*args, modelsAs=modelsAs)
# FIXME: pass all lines???
elif ext == 'mol2':
parser = Mol2Parser(
filename) # ??should modelsAs be available for mol2 format??
elif ext == 'cif':
parser = MMCIFParser(filename)
elif ext == 'f2d':
parser = F2DParser(filename)
else:
print("File Format unknown can't parse it")
return []
molecules = parser.parse()
return molecules
def Read(filename, modelsAs='molecules'):
if not os.path.exists(filename):
raise AssertionError, "%s does't exist" % filename
from MolKit.pdbParser import PdbParser, PdbqParser,PdbqsParser,\
PdbqtParser, PQRParser, F2DParser
from MolKit.mol2Parser import Mol2Parser
from MolKit.mmcifParser import MMCIFParser
ext = string.split(filename, '.')
if ext[-1] == 'pdb':
parser = PdbParser(filename, modelsAs=modelsAs)
elif ext[-1] == 'pdbq':
parser = PdbqParser(filename, modelsAs=modelsAs)
elif ext[-1] == 'pdbqt':
parser = PdbqtParser(filename, modelsAs=modelsAs)
elif ext[-1] == 'pdbqs':
parser = PdbqsParser(filename, modelsAs=modelsAs)
elif ext[-1] == 'pqr':
parser = PQRParser(filename, modelsAs=modelsAs)
elif ext[-1] == 'mol2':
parser = Mol2Parser(
filename) #??should modelsAs be available for mol2 format??
elif ext[-1] == 'cif':
parser = MMCIFParser(filename, modelsAs=modelsAs)
elif ext[-1] == 'f2d':
parser = F2DParser(filename)
else:
print "File Format unknown can't parse it"
return []
molecules = parser.parse()
return molecules
def Read(filename):
from MolKit.pdbParser import PdbParser, PdbqParser, PdbqsParser, PQRParser
from MolKit.mol2Parser import Mol2Parser
ext = string.split(filename, '.')
if ext[-1] == 'pdb':
parser = PdbParser(filename)
elif ext[-1] == 'pdbq':
parser = PdbqParser(filename)
elif ext[-1] == 'pdbqs':
parser = PdbqsParser(filename)
elif ext[-1] == 'pqr':
parser = PQRParser(filename)
elif ext[-1] == 'mol2':
parser = Mol2Parser(filename)
else:
print "File Format unknown can't parse it"
return []
molecules = parser.parse()
return molecules
next_index = self.__torTree2dot(c, next_index, currLbl, allAtoms,
dotGraph, atList, verbose)
return next_index
if __name__ == '__main__':
import getopt
import sys
from MolKit.pdbParser import PdbqParser
try:
opt_list, args = getopt.getopt(sys.argv[1:], 'f:')
except getopt.GetoptError as msg:
print('torTree.py: %s' % msg)
sys.exit(2)
filename = None
for o, a in opt_list:
if o in ('-f', '--f'):
filename = a
if filename:
parser = PdbqParser(filename)
mol = parser.parse()
# make torTree and print
tt = TorTree(parser)
# run as python2.0 -i torTree.py -f <pdbq_file>
# use interpreter to examine mol and tt
return next_index
if __name__ == '__main__':
import getopt
import sys
from MolKit.pdbParser import PdbqParser
try:
opt_list, args = getopt.getopt(sys.argv[1:], 'f:')
except getopt.GetoptError, msg:
print 'torTree.py: %s' % msg
sys.exit(2)
filename = None
for o, a in opt_list:
if o in ('-f', '--f'):
filename = a
if filename:
parser = PdbqParser(filename)
mol = parser.parse()
# make torTree and print
tt = TorTree(parser)
# run as python2.0 -i torTree.py -f <pdbq_file>
# use interpreter to examine mol and tt
