def example_valinomycin_pureLinK_vs_LinKwithDF():
# read inputs
# args = read_arguments()
# path_to_file1 = os.path.abspath(args.file_mol1)
# path_to_file2 = os.path.abspath(args.file_mol2)
path_to_file1 = "/home/ctcc2/Documents/CODE-DEV/xyz2top/xyz2top/tests/files/valinomycin_geomOpt_DFT-b3lyp_cc-pVTZ.xyz"
path_to_file2 = "/home/ctcc2/Documents/CODE-DEV/xyz2top/xyz2top/tests/files/valinomycin_geomOpt_DFT-b3lyp-noDF_cc-pVTZ.xyz"
import xyz2molecule as xyz
molecule1 = xyz.parse_XYZ(path_to_file1)
molecule2 = xyz.parse_XYZ(path_to_file2)
diff = topologyDiff(molecule1, molecule2, covRadFactor=1.3)
def test_jsonOutput_Histidine_molecule(self):
import json
with open(self.path_to_json_topology) as json_file:
json_topology = json.load(json_file)
with open(self.path_to_XYZ_format, 'r') as f:
histidine = xyz.parse_XYZ(self.path_to_XYZ_format)
histidineXYZ_Object = histidine.get_object()
for key, value in histidineXYZ_Object.iteritems():
if (key not in ['comments']):
self.assertEqual(value, json_topology["molecule"][key])
def setUp(self):
self.path_to_XYZ_format = "../../files/histidine.xyz"
self.histidine_moleculeObject = xyz.parse_XYZ(self.path_to_XYZ_format)
self.histidine_topologyObject = topology.topology(
self.histidine_moleculeObject)
#self.histidine_topologyObject.build_topology()
[
self.filename_config, self.filename_bonds, self.filename_angles,
self.filename_dihedralAngles
] = self.histidine_topologyObject.write_topology_files()
self.path_to_stored_files = "./files/"
def main():
# read inputs
args = read_arguments()
path_to_file = os.path.abspath(args.filename)
if (args.covRadFactor == None):
print "no factor for bond distance specified\n>> default covalent radius factor will apply.\n(Run './main.py --help' for more options.)"
else:
print "Covalent radius factor set to ", args.covRadFactor
if args.verbose:
print "Approximate the molecular topology stored in {} \n \
with connections detected as covalent bonds if pair-atomic \
distance goes below {} times the sum of the covalent radii.\
".format(args.filename, args.covRadFactor)
### parse_molecule_XYZ()
molecule = xyz.parse_XYZ(path_to_file)
#print molecule.get_object()
#print molecule
### compute the topology
if (args.covRadFactor != None):
molecular_topology = topology(molecule, args.covRadFactor)
else:
molecular_topology = topology(molecule)
molecular_topology.build_topology()
# print molecular_topology.get_as_JSON()
print molecular_topology
### print topology to file
jsonString = molecular_topology.get_as_JSON()
with open('./topology.json', 'w') as outfile:
outfile.write(jsonString)
print "\nZmatrix format: (not done yet)"
print molecular_topology.get_as_Zmatrix()
print "\nZmatrix format with variables: (not done yet)"
print molecular_topology.get_as_Zmatrix(useVariables=True)
print "\nCreate 3 topology files for bonds, angles and dihedrals + config.txt"
[
filename_config, filename_bonds, filename_angles,
filename_dihedralAngles
] = molecular_topology.write_topology_files()
print "files generated:" \
+ "\n\t- " + filename_config \
+ "\n\t- " + filename_bonds \
+ "\n\t- " + filename_angles \
+ "\n\t- " + filename_dihedralAngles
def setUp(self):
self.path_to_XYZ_format = "../../files/histidine.xyz"
self.maxDiff = None
self.histidine_moleculeObject = xyz.parse_XYZ(self.path_to_XYZ_format)
self.histidine_topologyObject = topology.topology(
self.histidine_moleculeObject)
def test_extracting_data_from_XYZ_format(self):
str1 = str(xyz.parse_XYZ(self.path_to_XYZ_format))
stringDATA = ""
with open(self.path_to_XYZ_format, 'r') as f:
stringDATA = f.read()
self.assertEqual(str1.strip(), stringDATA.strip())