def MM4ReadMOLWrite():
""" A test of MM4 reading and MOL, XYZ writing
"""
mg1 = MolecularCoordinates.readMM4File("JP10stochFixedStruct.out", 1)
mg2 = MolecularCoordinates.readMM4File("JP10stochFixedStruct.out", 295)
mg1a = MolecularCoordinates.readMM4File("JP10stochFixedStruct.out", 253)
mg1.writeMOLFile("JP10_MM4_1.mol", "JP10_MM4_1")
mg2.writeMOLFile("JP10_MM4_8.mol", "JP10_MM4_8")
mg1a.writeMOLFile("JP10_MM4_7.mol", "JP10_MM4_7")
mg1.perceiveConnectivity()
mg1.writeMOLFile("JP10_MM4_1_conn.mol", "JP10_MM4_1", connectivity=True)
mg1.writeXYZFile("JP10_MM4_1.xyz", "JP10_MM4_1")
print MolecularCoordinates.checkConformationalEquivalence(mg1, mg1a, Atol=0.02)
atomMap = {
1: 1,
2: 2,
3: 3,
4: 4,
5: 5,
6: 6,
7: 7,
8: 8,
9: 9,
10: 10,
11: 11,
12: 12,
13: 13,
14: 14,
15: 15,
16: 16,
17: 17,
18: 18,
19: 19,
20: 20,
21: 21,
22: 22,
23: 23,
24: 24,
25: 25,
26: 26,
} # "correct" mapping
(distDevAbs, distDevRel) = MolecularCoordinates.calcDistanceDeviationsGivenMapping(mg1, mg1a, atomMap)
distDevAbsMax = MolecularCoordinates.dictionaryMaxAbs(distDevAbs)
distDevRelMax = MolecularCoordinates.dictionaryMaxAbs(distDevRel)
print distDevAbsMax
def MM4ReadMOLWrite():
""" A test of MM4 reading and MOL, XYZ writing
"""
mg1=MolecularCoordinates.readMM4File('JP10stochFixedStruct.out',1)
mg2=MolecularCoordinates.readMM4File('JP10stochFixedStruct.out',295)
mg1a=MolecularCoordinates.readMM4File('JP10stochFixedStruct.out',253)
mg1.writeMOLFile('JP10_MM4_1.mol', 'JP10_MM4_1')
mg2.writeMOLFile('JP10_MM4_8.mol', 'JP10_MM4_8')
mg1a.writeMOLFile('JP10_MM4_7.mol', 'JP10_MM4_7')
mg1.perceiveConnectivity()
mg1.writeMOLFile('JP10_MM4_1_conn.mol', 'JP10_MM4_1', connectivity=True)
mg1.writeXYZFile('JP10_MM4_1.xyz', 'JP10_MM4_1')
print MolecularCoordinates.checkConformationalEquivalence(mg1, mg1a, Atol=0.02)
atomMap = {1:1, 2:2, 3:3, 4:4, 5:5, 6:6, 7:7, 8:8, 9:9, 10:10, 11:11, 12:12, 13:13, 14:14, 15:15, 16:16, 17:17, 18:18, 19:19, 20:20, 21:21, 22:22, 23:23, 24:24, 25:25, 26:26} #"correct" mapping
(distDevAbs,distDevRel) = MolecularCoordinates.calcDistanceDeviationsGivenMapping(mg1, mg1a, atomMap)
distDevAbsMax = MolecularCoordinates.dictionaryMaxAbs(distDevAbs)
distDevRelMax = MolecularCoordinates.dictionaryMaxAbs(distDevRel)
print distDevAbsMax
#uses MoleCoor #argv[1] = input file path #argv[2] = output file name #argv[3] = molecule name #argv[4] = $RMG/source/MoleCoor path import sys sys.path.append(sys.argv[4])#add $RMG/source/MoleCoor to the PYTHONPATH so that import statements below work properly import MolecularCoordinates mg = MolecularCoordinates.readMM4File(sys.argv[1],1) mg.writeXYZFile(sys.argv[2],sys.argv[3])
#uses MoleCoor #argv[1] = input file path #argv[2] = output file name #argv[3] = molecule name #argv[4] = $RMG/source/MoleCoor path import sys sys.path.insert(1, sys.argv[4])#add $RMG/source/MoleCoor to the PYTHONPATH so that import statements below work properly import MolecularCoordinates mg = MolecularCoordinates.readMM4File(sys.argv[1],1) mg.writeXYZFile(sys.argv[2],sys.argv[3])
