AtomSelectionConfigurator.py 6.23 KB
Newer Older
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
#MDANSE : Molecular Dynamics Analysis for Neutron Scattering Experiments
#------------------------------------------------------------------------------------------
#Copyright (C)
#2015- Eric C. Pellegrini Institut Laue-Langevin
#BP 156
#6, rue Jules Horowitz
#38042 Grenoble Cedex 9
#France
#pellegrini[at]ill.fr
#goret[at]ill.fr
#aoun[at]ill.fr
#
#This library is free software; you can redistribute it and/or
#modify it under the terms of the GNU Lesser General Public
#License as published by the Free Software Foundation; either
#version 2.1 of the License, or (at your option) any later version.
#
#This library is distributed in the hope that it will be useful,
#but WITHOUT ANY WARRANTY; without even the implied warranty of
#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
#Lesser General Public License for more details.
#
#You should have received a copy of the GNU Lesser General Public
#License along with this library; if not, write to the Free Software
#Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA

''' 
Created on Mar 30, 2015

30
:author: Eric C. Pellegrini
31
32
33
34
35
'''

import collections
import operator

36
from MDANSE import ELEMENTS, REGISTRY
37
from MDANSE.Framework.UserDefinitionStore import UD_STORE
38
from MDANSE.Framework.Configurators.IConfigurator import IConfigurator, ConfiguratorError
eric pellegrini's avatar
test    
eric pellegrini committed
39
from MDANSE.Framework.AtomSelectionParser import AtomSelectionParser
40

41
# The granularities at which the selection will be performed
42
43
44
45
46
47
48
LEVELS = collections.OrderedDict()
LEVELS["atom"]     = {"atom" : 0, "atomcluster" : 0, "molecule" : 0, "nucleotidechain" : 0, "peptidechain" : 0, "protein" : 0}
LEVELS["group"]    = {"atom" : 0, "atomcluster" : 1, "molecule" : 1, "nucleotidechain" : 1, "peptidechain" : 1, "protein" : 1}
LEVELS["residue"]  = {"atom" : 0, "atomcluster" : 1, "molecule" : 1, "nucleotidechain" : 2, "peptidechain" : 2, "protein" : 2}
LEVELS["chain"]    = {"atom" : 0, "atomcluster" : 1, "molecule" : 1, "nucleotidechain" : 3, "peptidechain" : 3, "protein" : 3}
LEVELS["molecule"] = {"atom" : 0, "atomcluster" : 1, "molecule" : 1, "nucleotidechain" : 3, "peptidechain" : 3, "protein" : 4}

49
class AtomSelectionConfigurator(IConfigurator):
50
51
52
53
    '''
    This configurator allows the selection of a specific set of atoms on which the analysis will be performed.

    Without any selection, all the atoms stored into the trajectory file will be selected.
54
55
56
    
    After the call to :py:meth:`~MDANSE.Framework.Configurators.AtomSelectionConfigurator.AtomSelectionConfigurator.configure` method 
    the following keys will be available for this configurator
57

58
    #. value: the input value used to configure this configurator
59
    #. indexes: the sorted (in increasing order) MMTK indexes of the selected atoms
60
    #. n_selected_atoms: the number of selected atoms
61
    #. elements: a nested-list of the chemical symbols of the selected atoms. The size of the nested list depends on the grouping_level selected via :py:class:`~MDANSE.Framework.Configurators.GroupingLevelConfigurator.GroupingLevelConfigurator` configurator.
62
    
63
    :note: this configurator depends on :py:class:`~MDANSE.Framework.Configurators.MMTKTrajectoryConfigurator.MMTKTrajectoryConfigurator` and :py:class:`~MDANSE.Framework.Configurators.GroupingLevelConfigurator.GroupingLevelConfigurator` configurators to be configured
64
    '''
65

66
    _default = "all"
67

68
    def configure(self, value):
69
        '''
70
71
        Configure an input value. 
        
72
        The value must be a string that can be either an atom selection string or a valid user definition.
73
74
75
76
        
        :param value: the input value
        :type value: str
        '''
77

78
        trajConfig = self._configurable[self._dependencies['trajectory']]
79

eric pellegrini's avatar
eric pellegrini committed
80
        if value is None:
81
            value = ['all']
82

83
84
        if isinstance(value,basestring):
            value = [value]
85
86
87

        if not isinstance(value,(list,tuple)):
            raise ConfiguratorError("Invalid input value.")
88

89
        self["value"] = value
90

91
        indexes = set()
92
93

        for v in value:
94

95
96
            if UD_STORE.has_definition(trajConfig["basename"],"atom_selection",v):
                ud = UD_STORE.get_definition(trajConfig["basename"],"atom_selection",v)
97
                indexes.update(ud["indexes"])
98
            else:
99
                parser = AtomSelectionParser(trajConfig["instance"])
100
101
                indexes.update(parser.parse(v))

102
        self["flatten_indexes"] = sorted(list(indexes))
103

104
        trajConfig = self._configurable[self._dependencies['trajectory']]
105
106

        atoms = sorted(trajConfig["universe"].atomList(), key = operator.attrgetter('index'))
107
108
        selectedAtoms = [atoms[idx] for idx in indexes]

109
        self["selection_length"] = len(self["flatten_indexes"])
110
111
        self['indexes'] = [[idx] for idx in self["flatten_indexes"]]

112
113
114
115
        self['elements'] = [[at.symbol] for at in selectedAtoms]
        self['names'] = [at.symbol for at in selectedAtoms]
        self['unique_names'] = sorted(set(self['names']))
        self['masses'] = [[ELEMENTS[n,'atomic_weight']] for n in self['names']]
116

117
    def get_natoms(self):
118

119
120
121
122
123
124
        nAtomsPerElement = {}
        for v in self["names"]:
            if nAtomsPerElement.has_key(v):
                nAtomsPerElement[v] += 1
            else:
                nAtomsPerElement[v] = 1
125

126
        return nAtomsPerElement
127

128
129
130
131
132
133
134
    def get_indexes(self):

        indexesPerElement = {}
        for i,v in enumerate(self["names"]):
            if indexesPerElement.has_key(v):
                indexesPerElement[v].extend(self['indexes'][i])
            else:
135
                indexesPerElement[v] = self['indexes'][i][:]
136

137
        return indexesPerElement
138

139
    def get_information(self):
140
        '''
141
        Returns some informations the atom selection.
142
        
143
        :return: the information about the atom selection.
144
145
        :rtype: str
        '''
146

147
148
        if not self.has_key("selection_length"):
            return "Not configured yet\n"
149

150
        info = []
151
152
        info.append("Number of selected atoms:%d" % self["selection_length"])
        info.append("Selected elements:%s" % self["unique_names"])
153

154
        return "\n".join(info)
155

156
REGISTRY["atom_selection"] = AtomSelectionConfigurator