File: Entity.py

package info (click to toggle)
python-biopython 1.68%2Bdfsg-3~bpo8%2B1
  • links: PTS, VCS
  • area: main
  • in suites: jessie-backports
  • size: 46,856 kB
  • sloc: python: 160,306; xml: 93,216; ansic: 9,118; sql: 1,208; makefile: 155; sh: 63
file content (298 lines) | stat: -rw-r--r-- 8,748 bytes parent folder | download | duplicates (2)
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
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
# Copyright (C) 2002, Thomas Hamelryck (thamelry@binf.ku.dk)
# This code is part of the Biopython distribution and governed by its
# license.  Please see the LICENSE file that should have been included
# as part of this package.

"""
Base class for Residue, Chain, Model and Structure classes.

It is a simple container class, with list and dictionary like properties.
"""

from copy import copy

from Bio.PDB.PDBExceptions import PDBConstructionException


class Entity(object):
    """
    Basic container object. Structure, Model, Chain and Residue
    are subclasses of Entity. It deals with storage and lookup.
    """
    def __init__(self, id):
        self.id = id
        self.full_id = None
        self.parent = None
        self.child_list = []
        self.child_dict = {}
        # Dictionary that keeps additional properties
        self.xtra = {}

    # Special methods

    def __len__(self):
        "Return the number of children."
        return len(self.child_list)

    def __getitem__(self, id):
        "Return the child with given id."
        return self.child_dict[id]

    def __delitem__(self, id):
        "Remove a child."
        return self.detach_child(id)

    def __contains__(self, id):
        "True if there is a child element with the given id."
        return (id in self.child_dict)

    def __iter__(self):
        "Iterate over children."
        for child in self.child_list:
            yield child

    # Public methods

    def get_level(self):
        """Return level in hierarchy.

        A - atom
        R - residue
        C - chain
        M - model
        S - structure
        """
        return self.level

    def set_parent(self, entity):
        "Set the parent Entity object."
        self.parent = entity

    def detach_parent(self):
        "Detach the parent."
        self.parent = None

    def detach_child(self, id):
        "Remove a child."
        child = self.child_dict[id]
        child.detach_parent()
        del self.child_dict[id]
        self.child_list.remove(child)

    def add(self, entity):
        "Add a child to the Entity."
        entity_id = entity.get_id()
        if self.has_id(entity_id):
            raise PDBConstructionException(
                "%s defined twice" % str(entity_id))
        entity.set_parent(self)
        self.child_list.append(entity)
        self.child_dict[entity_id] = entity

    def insert(self, pos, entity):
        "Add a child to the Entity at a specified position."
        entity_id = entity.get_id()
        if self.has_id(entity_id):
            raise PDBConstructionException(
                "%s defined twice" % str(entity_id))
        entity.set_parent(self)
        self.child_list[pos:pos] = [entity]
        self.child_dict[entity_id] = entity

    def get_iterator(self):
        "Return iterator over children."
        for child in self.child_list:
            yield child

    def get_list(self):
        "Return a copy of the list of children."
        return copy(self.child_list)

    def has_id(self, id):
        """True if a child with given id exists."""
        return (id in self.child_dict)

    def get_parent(self):
        "Return the parent Entity object."
        return self.parent

    def get_id(self):
        "Return the id."
        return self.id

    def get_full_id(self):
        """Return the full id.

        The full id is a tuple containing all id's starting from
        the top object (Structure) down to the current object. A full id for
        a Residue object e.g. is something like:

        ("1abc", 0, "A", (" ", 10, "A"))

        This corresponds to:

        Structure with id "1abc"
        Model with id 0
        Chain with id "A"
        Residue with id (" ", 10, "A")

        The Residue id indicates that the residue is not a hetero-residue
        (or a water) because it has a blank hetero field, that its sequence
        identifier is 10 and its insertion code "A".
        """
        if self.full_id is None:
            entity_id = self.get_id()
            l = [entity_id]
            parent = self.get_parent()
            while parent is not None:
                entity_id = parent.get_id()
                l.append(entity_id)
                parent = parent.get_parent()
            l.reverse()
            self.full_id = tuple(l)
        return self.full_id

    def transform(self, rot, tran):
        """
        Apply rotation and translation to the atomic coordinates.

        Example:
                >>> rotation=rotmat(pi, Vector(1, 0, 0))
                >>> translation=array((0, 0, 1), 'f')
                >>> entity.transform(rotation, translation)

        @param rot: A right multiplying rotation matrix
        @type rot: 3x3 Numeric array

        @param tran: the translation vector
        @type tran: size 3 Numeric array
        """
        for o in self.get_list():
            o.transform(rot, tran)

    def copy(self):
        shallow = copy(self)

        shallow.child_list = []
        shallow.child_dict = {}
        shallow.xtra = copy(self.xtra)

        shallow.detach_parent()

        for child in self.child_list:
            shallow.add(child.copy())
        return shallow


class DisorderedEntityWrapper(object):
    """
    This class is a simple wrapper class that groups a number of equivalent
    Entities and forwards all method calls to one of them (the currently selected
    object). DisorderedResidue and DisorderedAtom are subclasses of this class.

    E.g.: A DisorderedAtom object contains a number of Atom objects,
    where each Atom object represents a specific position of a disordered
    atom in the structure.
    """
    def __init__(self, id):
        self.id = id
        self.child_dict = {}
        self.selected_child = None
        self.parent = None

    # Special methods

    def __getattr__(self, method):
        "Forward the method call to the selected child."
        if not hasattr(self, 'selected_child'):
            # Avoid problems with pickling
            # Unpickling goes into infinite loop!
            raise AttributeError
        return getattr(self.selected_child, method)

    def __getitem__(self, id):
        "Return the child with the given id."
        return self.selected_child[id]

    # XXX Why doesn't this forward to selected_child?
    # (NB: setitem was here before getitem, iter, len, sub)
    def __setitem__(self, id, child):
        "Add a child, associated with a certain id."
        self.child_dict[id] = child

    def __contains__(self, id):
        "True if the child has the given id."
        return (id in self.selected_child)

    def __iter__(self):
        "Return the number of children."
        return iter(self.selected_child)

    def __len__(self):
        "Return the number of children."
        return len(self.selected_child)

    def __sub__(self, other):
        """Subtraction with another object."""
        return self.selected_child - other

    # Public methods

    def get_id(self):
        "Return the id."
        return self.id

    def disordered_has_id(self, id):
        """True if there is an object present associated with this id."""
        return (id in self.child_dict)

    def detach_parent(self):
        "Detach the parent"
        self.parent = None
        for child in self.disordered_get_list():
            child.detach_parent()

    def get_parent(self):
        "Return parent."
        return self.parent

    def set_parent(self, parent):
        "Set the parent for the object and its children."
        self.parent = parent
        for child in self.disordered_get_list():
            child.set_parent(parent)

    def disordered_select(self, id):
        """Select the object with given id as the currently active object.

        Uncaught method calls are forwarded to the selected child object.
        """
        self.selected_child = self.child_dict[id]

    def disordered_add(self, child):
        "This is implemented by DisorderedAtom and DisorderedResidue."
        raise NotImplementedError

    def is_disordered(self):
        """
        Return 2, indicating that this Entity is a collection of Entities.
        """
        return 2

    def disordered_get_id_list(self):
        "Return a list of id's."
        # sort id list alphabetically
        return sorted(self.child_dict)

    def disordered_get(self, id=None):
        """Get the child object associated with id.

        If id is None, the currently selected child is returned.
        """
        if id is None:
            return self.selected_child
        return self.child_dict[id]

    def disordered_get_list(self):
        "Return list of children."
        return list(self.child_dict.values())