def test_read_write(self, tmpdir):
"""Read a topology, write it out, and read in the output again.
Writing the topology out should make no change to the topology.
"""
path = self.processed
with tmpdir.as_cwd():
filename1 = 'processed_1.top'
filename2 = 'processed_2.top'
top1 = TOP(path)
top1.write(filename1)
# make life harder, write out again
top2 = TOP(filename1)
top2.write(filename2)
top2 = TOP(filename2)
attrs1 = [section for section in top1.found_sections if "types" in section]
attrs2 = [section for section in top1.found_sections if "types" in section]
assert attrs1 == attrs2
#attrs1 = ['atomtypes', 'pairtypes', 'bondtypes', 'constrainttypes', 'angletypes', 'dihedraltypes', 'dihedraltypes', 'cmaptypes']
#attrs1 = ['atomtypes',]
for attr in attrs1:
attr1 = getattr(top1, attr)
attr2 = getattr(top2, attr)
assert attr1 == attr2, helper(attr, attr1, attr2)
def test_read(self, tmpdir):
path = self.processed
try:
top1 = TOP(path)
except Exception as err:
raise AssertionError("Failed to read {0}. Raised:\n{1}".format(
path, str(err)))
attrs1 = [
section for section in top1.found_sections if "types" in section
]
assert attrs1
def test_equal(self):
"""
Load the same topology twice and check if __eq__ comparisions work
"""
path = self.processed
top1 = TOP(path)
top2 = TOP(path)
attrs1 = [
section for section in top1.found_sections if "types" in section
]
attrs2 = [
section for section in top1.found_sections if "types" in section
]
assert attrs1 == attrs2, "sections are not equal"
for attr in attrs1:
assert getattr(top1, attr) == getattr(top2, attr), \
"{0} not identical".format(attr)
def test_read_write(self, tmpdir):
"""Read a topology, write it out, and read in the output again.
Writing the topology out should make no change to the topology.
"""
path = self.processed
with tmpdir.as_cwd():
filename1 = 'processed_1.top'
filename2 = 'processed_2.top'
top1 = TOP(path)
top1.write(filename1)
# make life harder, write out again
top2 = TOP(filename1)
top2.write(filename2)
top2 = TOP(filename2)
attrs1 = [
section for section in top1.found_sections
if "types" in section
]
attrs2 = [
section for section in top1.found_sections
if "types" in section
]
assert attrs1 == attrs2
#attrs1 = ['atomtypes', 'pairtypes', 'bondtypes', 'constrainttypes', 'angletypes', 'dihedraltypes', 'dihedraltypes', 'cmaptypes']
#attrs1 = ['atomtypes',]
for attr in attrs1:
attr1 = getattr(top1, attr)
attr2 = getattr(top2, attr)
assert attr1 == attr2, helper(attr, attr1, attr2)
key = "{0}-{1}-{2}-{3}-{4}".format(a1, a2, a3, a4,
im.gromacs['func'])
if (key in impropers):
for i, imt in enumerate(impropers[key]):
new_impropers[key] = imt
break
print(new_impropers)
return new_impropers.values()
parser = argparse.ArgumentParser()
parser.add_argument("input")
parser.add_argument("output")
args = parser.parse_args()
top = TOP(args.input)
molname = top.molecules[0].name
mol = top.dict_molname_mol[molname]
#
# ATOMTYPES
#
atomtypes = {a.atomtype for a in mol.atoms}
top.atomtypes = [at for at in top.atomtypes if at.atype in atomtypes]
#
# BONDTYPES
#
bondtypes = {
tuple(sorted((b.atom1.atomtype, b.atom2.atomtype)))
for b in mol.bonds
def test_basic(self):
path = self.processed
top = TOP(path)
assert top.dict_molname_mol.keys() == self.molecules
if((iswitch/16)%2==1): a4="X";
key = "{0}-{1}-{2}-{3}-{4}".format(a1, a2, a3, a4, im.gromacs['func'])
if (key in impropers):
for i, imt in enumerate(impropers[key]):
new_impropers[key] = imt
break
print new_impropers
return new_impropers.values()
parser = argparse.ArgumentParser()
parser.add_argument("input")
parser.add_argument("output")
args = parser.parse_args()
top = TOP(args.input)
molname = top.molecules[0].name
mol = top.dict_molname_mol[molname]
#
# ATOMTYPES
#
atomtypes = {a.atomtype for a in mol.atoms}
top.atomtypes = [at for at in top.atomtypes if at.atype in atomtypes]
#
# BONDTYPES
#
bondtypes = {tuple(sorted((b.atom1.atomtype, b.atom2.atomtype))) for b in mol.bonds}
bondtypes_dictionary = {tuple(sorted((bt.atype1, bt.atype2))): bt for bt in top.bondtypes}
top.bondtypes = [bondtypes_dictionary[bt] for bt in bondtypes]
