Commit 0c817605 authored by eric pellegrini's avatar eric pellegrini
Browse files

Added AtomsList configurator to set a various number of atoms replicated

for all the same type of molecule
parent 9661f66a
#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
#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
#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
:author: Eric C. Pellegrini
import collections
import numpy
from MDANSE.Framework.UserDefinitionsStore import UD_STORE
from MDANSE.Framework.Configurators.IConfigurator import IConfigurator
from MDANSE.MolecularDynamics.Trajectory import find_atoms_in_molecule
class AtomsListConfigurator(IConfigurator):
This configurator allows of a given list of atom names.
The atoms has to belong to the same molecule.
:note: this configurator depends on 'trajectory'
type = 'atoms_list'
_default = None
def __init__(self, name, nAtoms=2, **kwargs):
Initializes the configurator.
:param name: the name of the configurator as it will appear in the configuration.
:type name: str
:param nAtoms: the (exact) number of atoms of the list.
:type nAtoms: int
IConfigurator.__init__(self, name, **kwargs)
self._nAtoms = nAtoms
def nAtoms(self):
return self._nAtoms
def configure(self, configuration, value):
Configure an input value.
The value must be a string that can be either an atom selection string or a valid user
:param configuration: the current configuration
:type configuration: a MDANSE.Framework.Configurable.Configurable object
:param value: the input value
:type value: str
trajConfig = configuration[self._dependencies['trajectory']]
if UD_STORE.has_definition(trajConfig["basename"],"%d_atoms_list" % self._nAtoms,value):
molecule,atoms = UD_STORE.get_definition(trajConfig["basename"],"%d_atoms_list" % self._nAtoms,value)
self["value"] = value
indexes = [find_atoms_in_molecule(trajConfig['instance'].universe,molecule, at, True) for at in atoms]
self['atoms'] = zip(*indexes)
self['n_values'] = len(self['atoms'])
def find_parent(atom, level):
Retrieve recursively the parent of a given MMTK atom at a given level.
For example, a level of 1 will return the direct parent of the atom.
:note: this is a static method
:param atom: the atom for which the parent is searched for
:type atom: MMTK.Atom object
:param level: the level of the parent
:type level: int
for _ in range(level):
atom = atom.parent
return atom
def group(self, atoms, level="atom"):
Group the selected atoms according to a given granularity and update
the configurator with the grouping results.
:param atoms: the atoms for
:type atoms: list of MMTK.Atom
:param level: the level of granularity at which the atoms should be grouped
:type level: str
groups = collections.OrderedDict()
for at in atoms:
lvl = LEVELS[level][at.topLevelChemicalObject().__class__.__name__.lower()]
parent = self.find_parent(at,lvl)
self["groups"] = groups.values()
self["n_groups"] = len(self["groups"])
if level != "atom":
self["elements"] = [["dummy"]]*self["n_groups"]
self["level"] = level
def set_contents(self):
Sets the contents of the atom selection.
self["contents"] = collections.OrderedDict()
self['index_to_symbol'] = collections.OrderedDict()
for i, group in enumerate(self["elements"]):
for j, el in enumerate(group):
self['index_to_symbol'][self["groups"][i][j]] = el
for k,v in self["contents"].items():
self["contents"][k] = numpy.array(v,dtype=numpy.int32)
self["n_atoms_per_element"] = dict([(k,len(v)) for k,v in self["contents"].items()])
self['n_selected_elements'] = len(self["contents"])
def get_information(self):
Returns some informations the atom selection.
:return: the information about the atom selection.
:rtype: str
if not self.has_key("n_selected_atoms"):
return "No configured yet"
info = []
info.append("Number of selected atoms:%d" % self["n_selected_atoms"])
info.append("Level of selection:%s" % self["level"])
info.append("Number of selected groups:%d" % self["n_groups"])
info.append("Selected elements:%s" % self["contents"].keys())
return "\n".join(info)
\ No newline at end of file
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