def MirrorImageConf(): ac = [[-1.5846, -0.5216, 0.1338], [-1.1512, -1.5146, -0.0477 ], [-1.7781, -0.4440, 1.2120 ], [-2.5555, -0.4907, -0.3770 ], [-0.6751, 0.5855, -0.3509 ], [-1.1705, 1.5633, -0.1896 ], [-0.5293, 0.5028, -1.4463 ], [ 0.6751, 0.5854, 0.3509 ], [ 1.1705, 1.5633, 0.1895 ], [ 0.5294, 0.5028, 1.4463 ], [ 1.5846, -0.5216, -0.1338 ], [ 2.5554, -0.4908, 0.3772 ], [ 1.1510, -1.5146, 0.0475 ], [ 1.7783, -0.4438, -1.2120]] aa = [6, 1, 1, 1, 6, 1, 1, 6, 1, 1, 6, 1, 1, 1] bc = [[ -1.5845, -0.5216, -0.1338], [-1.7784, -0.4438, -1.2120 ], [-1.1509, -1.5146, 0.0474 ], [-2.5553, -0.4910, 0.3773 ], [-0.6751, 0.5855, 0.3508 ], [-0.5293, 0.5028, 1.4463 ], [-1.1705, 1.5634, 0.1895 ], [ 0.6751, 0.5855, -0.3508 ], [ 1.1705, 1.5633, -0.1893 ], [ 0.5294, 0.5030, -1.4463 ], [ 1.5845, -0.5216, 0.1338 ], [ 1.1510, -1.5146, -0.0478 ], [ 2.5555, -0.4908, -0.3770 ], [ 1.7780, -0.4441, 1.2121 ]] ba = [6, 1, 1, 1, 6, 1, 1, 6, 1, 1, 6, 1, 1, 1] a = MolecularCoordinates.MolecularGeometry(aa,ac) b = MolecularCoordinates.MolecularGeometry(ba,bc) return MolecularCoordinates.checkConformationalEquivalence(b, a, Atol=0.001)
def LongLinearChainHetConf(n):
# n represents the number of atoms in the chain
atomtypes = [i for i in range(0, n)]
atomcoor = [[i, 0, 0] for i in range(0, n)]
a = MolecularCoordinates.MolecularGeometry(atomtypes, atomcoor)
b = MolecularCoordinates.MolecularGeometry(atomtypes, atomcoor)
return MolecularCoordinates.checkConformationalEquivalence(b, a, Atol=0.5)
def LongLinearChainHetConf(n): #n represents the number of atoms in the chain atomtypes = [i for i in range(0,n)] atomcoor = [[i,0,0] for i in range(0,n)] a = MolecularCoordinates.MolecularGeometry(atomtypes,atomcoor) b = MolecularCoordinates.MolecularGeometry(atomtypes,atomcoor) return MolecularCoordinates.checkConformationalEquivalence(b, a, Atol=0.5)
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 LongLinearChainHomConf(n):
# n represents the number of atoms in the chain
# all the atom-to-atom distances should be unique by the "binary" construction of the coordinates
atomtypes = [1 for i in range(0, n)]
atomcoor = [[2 ** i, 0, 0] for i in range(0, n)]
a = MolecularCoordinates.MolecularGeometry(atomtypes, atomcoor)
b = MolecularCoordinates.MolecularGeometry(atomtypes, atomcoor)
return MolecularCoordinates.checkConformationalEquivalence(b, a, Atol=0.5)
def LongLinearChainHomConf(n): #n represents the number of atoms in the chain #all the atom-to-atom distances should be unique by the "binary" construction of the coordinates atomtypes = [1 for i in range(0,n)] atomcoor = [[2**i,0,0] for i in range(0,n)] a = MolecularCoordinates.MolecularGeometry(atomtypes,atomcoor) b = MolecularCoordinates.MolecularGeometry(atomtypes,atomcoor) return MolecularCoordinates.checkConformationalEquivalence(b, a, Atol=0.5)
def SimpleHomConf():
a = MolecularCoordinates.MolecularGeometry(
[1, 1, 1, 1, 1, 1, 1, 1],
[[0, 0, 0], [1, 0, 0], [0, 1, 0], [0, 0, 1], [0, 1, 1], [1, 0, 1], [1, 1, 0], [1, 1, 1]],
)
b = MolecularCoordinates.MolecularGeometry(
[1, 1, 1, 1, 1, 1, 1, 1],
[[0, 0, 0], [1, 0, 0], [0, 1, 0], [0, 0, 1], [0, 1, 1], [1, 0, 1], [1, 1, 0], [1, 1, 1]],
)
return MolecularCoordinates.checkConformationalEquivalence(b, a, Atol=0.01)
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 MirrorImageConf():
ac = [
[-1.5846, -0.5216, 0.1338],
[-1.1512, -1.5146, -0.0477],
[-1.7781, -0.4440, 1.2120],
[-2.5555, -0.4907, -0.3770],
[-0.6751, 0.5855, -0.3509],
[-1.1705, 1.5633, -0.1896],
[-0.5293, 0.5028, -1.4463],
[0.6751, 0.5854, 0.3509],
[1.1705, 1.5633, 0.1895],
[0.5294, 0.5028, 1.4463],
[1.5846, -0.5216, -0.1338],
[2.5554, -0.4908, 0.3772],
[1.1510, -1.5146, 0.0475],
[1.7783, -0.4438, -1.2120],
]
aa = [6, 1, 1, 1, 6, 1, 1, 6, 1, 1, 6, 1, 1, 1]
bc = [
[-1.5845, -0.5216, -0.1338],
[-1.7784, -0.4438, -1.2120],
[-1.1509, -1.5146, 0.0474],
[-2.5553, -0.4910, 0.3773],
[-0.6751, 0.5855, 0.3508],
[-0.5293, 0.5028, 1.4463],
[-1.1705, 1.5634, 0.1895],
[0.6751, 0.5855, -0.3508],
[1.1705, 1.5633, -0.1893],
[0.5294, 0.5030, -1.4463],
[1.5845, -0.5216, 0.1338],
[1.1510, -1.5146, -0.0478],
[2.5555, -0.4908, -0.3770],
[1.7780, -0.4441, 1.2121],
]
ba = [6, 1, 1, 1, 6, 1, 1, 6, 1, 1, 6, 1, 1, 1]
a = MolecularCoordinates.MolecularGeometry(aa, ac)
b = MolecularCoordinates.MolecularGeometry(ba, bc)
return MolecularCoordinates.checkConformationalEquivalence(b, a, Atol=0.001)
def AtomTypeSwapConf():
a = MolecularCoordinates.MolecularGeometry([8, 1, 1], [[0, 0, 0], [1, 0, 0], [0, 1, 0]])
b = MolecularCoordinates.MolecularGeometry([1, 8, 1], [[0, 0, 0], [1, 0, 0], [0, 1, 0]])
return MolecularCoordinates.checkConformationalEquivalence(b, a, Atol=0.01)
def DistinctJP10Conf():
a = MolecularCoordinates.readMOLFile("JP10A.mol")
b = MolecularCoordinates.readMOLFile("JP10B.mol")
return MolecularCoordinates.checkConformationalEquivalence(b, a, Atol=0.10)
def Buckminsterfullerene():
a = MolecularCoordinates.readMOLFile("c60_c.mol")
b = MolecularCoordinates.readMOLFile("c60_c.mol")
return MolecularCoordinates.checkConformationalEquivalence(b, a, Atol=0.01)
def AtomTypeSwapConf(): a = MolecularCoordinates.MolecularGeometry([8,1,1],[[0,0,0],[1,0,0],[0,1,0]]) b = MolecularCoordinates.MolecularGeometry([1,8,1],[[0,0,0],[1,0,0],[0,1,0]]) return MolecularCoordinates.checkConformationalEquivalence(b, a, Atol=0.01)
def DistinctJP10Conf():
a = MolecularCoordinates.readMOLFile('JP10A.mol')
b = MolecularCoordinates.readMOLFile('JP10B.mol')
return MolecularCoordinates.checkConformationalEquivalence(b, a, Atol=0.10)
def Buckminsterfullerene():
a = MolecularCoordinates.readMOLFile('c60_c.mol')
b = MolecularCoordinates.readMOLFile('c60_c.mol')
return MolecularCoordinates.checkConformationalEquivalence(b, a, Atol=0.01)
def SimpleHomConf(): a = MolecularCoordinates.MolecularGeometry([1,1,1,1,1,1,1,1],[[0,0,0],[1,0,0],[0,1,0],[0,0,1],[0,1,1],[1,0,1],[1,1,0],[1,1,1]]) b = MolecularCoordinates.MolecularGeometry([1,1,1,1,1,1,1,1],[[0,0,0],[1,0,0],[0,1,0],[0,0,1],[0,1,1],[1,0,1],[1,1,0],[1,1,1]]) return MolecularCoordinates.checkConformationalEquivalence(b, a, Atol=0.01)