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
|
'''
Experimental MMTF (Macromolecular Transmission Format) support
'''
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
try:
from itertools import izip
as_str = str
except ImportError:
# python3
izip = zip
as_str = lambda s: s if isinstance(s, str) else s.decode()
#####################################################################
ss_map = {
0: 'H', # pi helix
1: 'L', # bend
2: 'H', # alpha helix
3: 'S', # extended
4: 'H', # 3-10 helix
5: 'S', # bridge
6: 'L', # turn
7: 'L', # coil
}
#####################################################################
def _to_chempy(data, use_auth=True):
'''
Construct a "chempy" model (molecule) from decoded MMTF data.
'''
from itertools import islice
from chempy import models, Atom, Bond
def add_bond(i1, i2, order, offset=0):
bond = Bond()
bond.order = order
bond.index = [i1 + offset, i2 + offset]
model.add_bond(bond)
coord_iter = data.get_table_iter([
'xCoordList',
'yCoordList',
'zCoordList',
])
atom_iter = data.get_table_iter([
'bFactorList',
'occupancyList',
'altLocList',
'atomIdList',
], [0.0, 1.0, '', -1])
group_iter = data.get_table_iter([
'groupTypeList',
'sequenceIndexList',
'groupIdList',
'insCodeList',
'secStructList',
])
chain_list_iter = enumerate(data.get_table_iter([
'chainIdList',
'chainNameList',
'groupsPerChain',
]))
groupList = data.get('groupList')
symmetry = (
data.get('unitCell', None),
as_str(data.get('spaceGroup', '')),
)
model_output = []
for n_chains in data.get_iter('chainsPerModel'):
model = models.Indexed()
model_output.append(model)
if symmetry[0] is not None:
model.cell, model.spacegroup = symmetry
for (chain_idx, (segi, chain, n_groups)) in islice(chain_list_iter, n_chains):
for (groupType, label_seq_id, auth_seq_id, ins_code, ss_info) in \
islice(group_iter, n_groups):
group = groupList[groupType]
resn = as_str(group[b'groupName'])
group_bond_iter = izip(
group[b'bondAtomList'][0::2],
group[b'bondAtomList'][1::2],
group[b'bondOrderList'],
)
offset = len(model.atom)
for (i1, i2, order) in group_bond_iter:
add_bond(i1, i2, order, offset)
group_atom_iter = izip(
group[b'atomNameList'],
group[b'elementList'],
group[b'formalChargeList'],
)
for (name, elem, formal_charge) in group_atom_iter:
atom = Atom()
(atom.b, atom.q, atom.alt, atom.id) = next(atom_iter)
atom.coord = next(coord_iter)
atom.symbol = as_str(elem)
atom.name = as_str(name)
atom.resn = resn
atom.hetatm = label_seq_id == -1
atom.formal_charge = formal_charge
atom.segi = segi
atom.chain = chain
atom.ss = ss_map.get(ss_info, '')
if use_auth or label_seq_id is None:
atom.resi = auth_seq_id
atom.ins_code = ins_code or ''
else:
atom.resi = label_seq_id + 1
model.add_atom(atom)
model_atom_max = 0
model_atom_min = 0
model_iter = iter(model_output)
bondAtomList_iter = data.get_iter('bondAtomList')
for order in data.get_iter('bondOrderList'):
i1 = next(bondAtomList_iter)
i2 = next(bondAtomList_iter)
if i1 >= model_atom_max or i2 >= model_atom_max:
model = next(model_iter)
model_atom_min = model_atom_max
model_atom_max += len(model.atom)
add_bond(i1, i2, order, -model_atom_min)
return model_output
#####################################################################
from .io import MmtfReader
MmtfReader.to_chempy = _to_chempy
#####################################################################
|
