-
Notifications
You must be signed in to change notification settings - Fork 0
/
compare.py
222 lines (179 loc) · 7.2 KB
/
compare.py
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
#!/usr/bin/python
"""
Set of routines to calculate the RMSD between two molecular structures.
The module can be run from the command line using PDB files as input.
"""
import math
import numpy
import vector3d, util, molecule, polymer
def rmsd(crds1, crds2):
"""Returns RMSD between 2 sets of [nx3] numpy array"""
assert(crds1.shape[1] == 3)
assert(crds1.shape == crds2.shape)
n_vec = numpy.shape(crds1)[0]
correlation_matrix = numpy.dot(numpy.transpose(crds1), crds2)
v, s, w = numpy.linalg.svd(correlation_matrix)
is_reflection = (numpy.linalg.det(v) * numpy.linalg.det(w)) < 0.0
if is_reflection:
s[-1] = - s[-1]
E0 = sum(sum(crds1 * crds1)) + \
sum(sum(crds2 * crds2))
rmsd_sq = (E0 - 2.0*sum(s)) / float(n_vec)
rmsd_sq = max([rmsd_sq, 0.0])
return numpy.sqrt(rmsd_sq)
def optimal_superposition(crds1, crds2):
"""Returns best-fit rotation matrix as [3x3] numpy matrix"""
assert(crds1.shape[1] == 3)
assert(crds1.shape == crds2.shape)
correlation_matrix = numpy.dot(numpy.transpose(crds1), crds2)
v, s, w = numpy.linalg.svd(correlation_matrix)
is_reflection = (numpy.linalg.det(v) * numpy.linalg.det(w)) < 0.0
if is_reflection:
v[-1,:] = -v[-1,:]
return numpy.dot(v, w)
def get_i_residue(residues, tag):
def get_tag(residue):
tag = ""
if residue.chain_id != " " and residue.chain_id != "":
tag += residue.chain_id + ":"
tag += str(residue.num)
if residue.insert:
tag += residue.insert
return tag
# clean up tag
tag = tag.strip()
if tag[0] == ":":
tag = tag[1:]
if not tag[0].isdigit() and tag[1].isdigit():
tag = tag[0] + ":" + tag[1:]
for i, residue in enumerate(residues):
if tag.lower() == get_tag(residue).lower():
return i
raise "Can't find residue", tag
def get_superposable_all_atoms(polymer, segments):
atom_types=['CA', 'N', 'C', 'CB',
'CD', 'CD1', 'CD2', 'CE', 'CE1',
'CE2', 'CE3', 'CG', 'CG1', 'CG2',
'CH2', 'CZ', 'CZ2', 'CZ3', 'ND1',
'ND2', 'NE', 'NE1', 'NE2', 'NH1',
'NH2', 'NZ', 'O', 'OD1', 'OD2',
'OE1', 'OE2', 'OG', 'OG1', 'OH',
'OXT', 'SD', 'SG', 'CEN']
result = []
allowed_i = []
residues = polymer.residues()
for res_num_i, res_num_j in segments:
i = get_i_residue(residues, str(res_num_i))
j = get_i_residue(residues, str(res_num_j))
allowed_i.extend(range(i,j+1))
for i, residue in enumerate(residues):
if i in allowed_i:
result.extend([a for a in residue.atoms()
if a.type in atom_types])
return result
def get_superposable_atoms(polymer, segments,
atom_types=['CA', 'N', 'C', 'CB','O']):
result = []
allowed_i = []
residues = polymer.residues()
for res_num_i, res_num_j in segments:
i = get_i_residue(residues, str(res_num_i))
j = get_i_residue(residues, str(res_num_j))
allowed_i.extend(range(i,j+1))
for i, residue in enumerate(residues):
if i in allowed_i:
result.extend([a for a in residue.atoms()
if a.type in atom_types])
return result
def get_crds(atoms):
crds = numpy.zeros((len(atoms), 3), float)
for i, a in enumerate(atoms):
crds[i,0] = a.pos.x
crds[i,1] = a.pos.y
crds[i,2] = a.pos.z
return crds
def calculate_superposition_matrix(atoms1, atoms2):
def convert_to_matrix3d(numpy_matrix3d):
result = vector3d.Matrix3d()
for i in range(3):
for j in range(3):
result.setElem(i, j, numpy_rotation[j, i])
return result
numpy_rotation = optimal_superposition(get_crds(atoms1), get_crds(atoms2))
return convert_to_matrix3d(numpy_rotation)
def sum_rmsd(atoms1, atoms2):
sum_squared = 0.0
for atom1, atom2 in zip(atoms1, atoms2):
sum_squared += vector3d.pos_distance(atom1.pos, atom2.pos)**2
return math.sqrt(sum_squared/float(len(atoms1)))
def residues_rmsd(atoms1, atoms2):
sum_squared = []
for atom1, atom2 in zip(atoms1, atoms2):
each_diff = math.sqrt(vector3d.pos_distance(atom1.pos, atom2.pos)**2)
sum_squared.append(round(each_diff, 2))
return sum_squared, round(sum_rmsd(atoms1, atoms2), 2)
def get_raw_rmsd(pdb1, pdb2, segments1, segments2, atom_types):
polymer1 = polymer.Polymer(pdb1)
polymer2 = polymer.Polymer(pdb2)
atoms1 = get_superposable_atoms(polymer1, segments1, atom_types)
atoms2 = get_superposable_atoms(polymer2, segments2, atom_types)
return sum_rmsd(atoms1, atoms2)
def get_best_alignment(pdb1, pdb2, segments1, segments2, atom_types):
"""Returns rmsd and filename of transformed pdb2."""
polymer1 = polymer.Polymer(pdb1)
atoms1 = get_superposable_atoms(polymer1, segments1, atom_types)
polymer2 = polymer.Polymer(pdb2)
atoms2 = get_superposable_atoms(polymer2, segments2, atom_types)
center1 = molecule.get_center(atoms1)
polymer1.transform(vector3d.Translation(-center1))
polymer2.transform(vector3d.Translation(-molecule.get_center(atoms2)))
polymer2.transform(calculate_superposition_matrix(atoms1, atoms2))
rmsd = sum_rmsd(atoms1, atoms2)
return rmsd
def get_best_alignment_with_residues(pdb1, pdb2, segments1, segments2, atom_types):
polymer1 = polymer.Polymer(pdb1)
atoms1 = get_superposable_atoms(polymer1, segments1, atom_types)
polymer2 = polymer.Polymer(pdb2)
atoms2 = get_superposable_atoms(polymer2, segments2, atom_types)
center1 = molecule.get_center(atoms1)
polymer1.transform(vector3d.Translation(-center1))
polymer2.transform(vector3d.Translation(-molecule.get_center(atoms2)))
polymer2.transform(calculate_superposition_matrix(atoms1, atoms2))
residue_rmsd, overall_rmsd = residues_rmsd(atoms1, atoms2)
return residue_rmsd, overall_rmsd
def get_best_alignment_with_all_residues(pdb1, pdb2, segments1, segments2, atom_types):
polymer1 = polymer.Polymer(pdb1)
atoms1 = get_superposable_atoms(polymer1, segments1, atom_types)
polymer2 = polymer.Polymer(pdb2)
atoms2 = get_superposable_atoms(polymer2, segments2, atom_types)
center1 = molecule.get_center(atoms1)
polymer1.transform(vector3d.Translation(-center1))
polymer2.transform(vector3d.Translation(-molecule.get_center(atoms2)))
polymer2.transform(calculate_superposition_matrix(atoms1, atoms2))
allatoms1 = get_superposable_all_atoms(polymer1, segments1)
allatoms2 = get_superposable_all_atoms(polymer2, segments1)
residue_rmsd, overall_rmsd = residues_rmsd(allatoms1, allatoms2)
return residue_rmsd, overall_rmsd
def get_total_num_atoms(pdb1, segment1):
polymer1 = polymer.Polymer(pdb1)
atoms1 = get_superposable_all_atoms(polymer1, segment1)
return len(atoms1)
def get_rmsd(pdb1, pdb2, segments1, segments2, atom_types):
polymer1 = polymer.Polymer(pdb1)
atoms1 = get_superposable_atoms(polymer1, segments1, atom_types)
polymer2 = polymer.Polymer(pdb2)
atoms2 = get_superposable_atoms(polymer2, segments2, atom_types)
center1 = molecule.get_center(atoms1)
polymer1.transform(vector3d.Translation(-center1))
polymer2.transform(vector3d.Translation(-molecule.get_center(atoms2)))
crds1 = get_crds(atoms1)
crds2 = get_crds(atoms2)
return rmsd(crds1, crds2)
def segments_str(segments):
residues = []
for i, j in segments:
if i == j:
residues.append(str(i))
else:
residues.append("%s-%s" % (i,j))
return ', '.join(residues)