def test_write(self):
"""
test writing a pdbqs file
"""
writer = PdbqsWriter()
writer.write('test_pdbqsWriter.pdbqs', self.mol, bondOrigin=('File',))
ans, errors = self.compare('Data/1crn.pdbqs', 'test_pdbqsWriter.pdbqs')
self.assertEquals(errors, None)
self.assertEquals(ans, True)
if len(item.name) == 1:
item.name = 'A'
else:
item.name = 'A' + item.name[1:]
elif hasattr(item, 'autodock_element'):
item.autodock_element = item.autodock_element
if splitAcceptors and item.autodock_element in self.acceptorList:
#if item has a bond to a hydrogen:
# change acceptor type 'XA' to 'XB' for 'B'oth 'A'cceptor and 'D'onor
if 'H' in item.bonds.getAtoms().element:
#O->OB;N->NB;S->SB
item.autodock_element = item.element + 'B'
d[item.autodock_element] = 1
type_list = d.keys()
type_list.sort()
mol.types = type_list
if __name__ == "__main__":
from MolKit import Read
m = Read("/mgl/work4/rhuey/dev23/hsg1_no_conects.pdbq")[0]
solP = SolvationParameterizer()
ll = solP.addParameters(m.allAtoms)
#NB: hydrogens get 0.0 0.0
print "len(notfound) = ", len(ll)
for i in ll:
print i.full_name(),
from MolKit.pdbWriter import PdbqsWriter
writer = PdbqsWriter()
writer.write("/mgl/work4/rhuey/dev23/test_hsg1.pdbqs", m.allAtoms)
item.name = 'A'
else:
item.name = 'A' + item.name[1:]
elif hasattr(item, 'autodock_element'):
item.autodock_element = item.autodock_element
if splitAcceptors and item.autodock_element in self.acceptorList:
#if item has a bond to a hydrogen:
# change acceptor type 'XA' to 'XB' for 'B'oth 'A'cceptor and 'D'onor
if 'H' in item.bonds.getAtoms().element:
#O->OB;N->NB;S->SB
item.autodock_element = item.element + 'B'
d[item.autodock_element] = 1
type_list = d.keys()
type_list.sort()
mol.types = type_list
if __name__ == "__main__":
from MolKit import Read
m = Read("/mgl/work4/rhuey/dev23/hsg1_no_conects.pdbq")[0]
solP = SolvationParameterizer()
ll = solP.addParameters(m.allAtoms)
#NB: hydrogens get 0.0 0.0
print "len(notfound) = ", len(ll)
for i in ll:
print i.full_name(),
from MolKit.pdbWriter import PdbqsWriter
writer = PdbqsWriter()
writer.write("/mgl/work4/rhuey/dev23/test_hsg1.pdbqs", m.allAtoms)