Source code for ccpn.core.Model

# Licence, Reference and Credits
__copyright__ = "Copyright (C) CCPN project ( 2014 - $Date: 2016-07-18 06:32:18 +0100 (Mon, 18 Jul 2016) $"
__credits__ = "Wayne Boucher, Rasmus H Fogh, Simon P Skinner, Geerten W Vuister"
__license__ = ("CCPN license. See"
              "or ccpnmodel.ccpncore.memops.Credits.CcpnLicense for license text")
__reference__ = ("For publications, please use reference from"
                " or ccpnmodel.ccpncore.memops.Credits.CcpNmrReference")

# Last code modification:
__author__ = "$Author: rhfogh $"
__date__ = "$Date: 2016-07-18 06:32:18 +0100 (Mon, 18 Jul 2016) $"
__version__ = "$Revision: 9684 $"

# Start of code

from typing import Sequence
import numpy
import collections
from ccpn.core._implementation.AbstractWrapperObject import AbstractWrapperObject
from ccpn.core.Project import Project
from ccpn.core.StructureEnsemble import StructureEnsemble
from ccpn.util import Common as commonUtil
from ccpnmodel.ccpncore.api.ccp.molecule.MolStructure import Model as ApiModel

[docs]class Model(AbstractWrapperObject): """ ccpn.Model - Structural Model, or one member of the structure ensemble.""" #: Short class name, for PID. shortClassName = 'MD' # Attribute it necessary as subclasses must use superclass className className = 'Model' _parentClass = StructureEnsemble #: Name of plural link to instances of class _pluralLinkName = 'models' #: List of child classes. _childClasses = [] # Qualified name of matching API class _apiClassQualifiedName = ApiModel._metaclass.qualifiedName() # CCPN properties @property def _apiModel(self) -> ApiModel: """ API Model matching Model""" return self._wrappedData @property def _key(self) -> str: """id string - ID number converted to string""" return str(self._wrappedData.serial) @property def serial(self) -> int: """ID number of Model, used in Pid and to identify the Model. """ return self._wrappedData.serial @property def _parent(self) -> StructureEnsemble: """StructureEnsemble containing Model.""" return self._project._data2Obj[self._wrappedData.structureEnsemble] structureEnsemble = _parent @property def title(self) -> str: """title of Model (not used in PID).""" return @title.setter def title(self, value): = value @property def comment(self) -> str: """Free-form text comment""" return self._wrappedData.details @comment.setter def comment(self, value:str): self._wrappedData.details = value @property def coordinateData(self) -> numpy.ndarray: """ atomCount * 3 numpy array of coordinates. """ data = self.structureEnsemble.coordinateData return data[self._wrappedData.index] @coordinateData.setter def coordinateData(self, value): data = self.structureEnsemble.coordinateData data[self._wrappedData.index] = value @property def occupancyData(self) -> numpy.ndarray: """ atomCount length numpy array of occupancies. """ data = self.structureEnsemble.occupancyData return data[self._wrappedData.index] @occupancyData.setter def occupancyData(self, value): data = self.structureEnsemble.occupancyData data[self._wrappedData.index] = value @property def bFactorData(self) -> numpy.ndarray: """ atomCount length numpy array of B factors. """ data = self.structureEnsemble.bFactorData return data[self._wrappedData.index] @bFactorData.setter def bFactorData(self, value): data = self.structureEnsemble.bFactorData data[self._wrappedData.index] = value @property def atomNameData(self) -> numpy.ndarray: """atomCount length numpy array of model-specific atom names.""" raise NotImplementedError("atomNameData not implemented yet") @atomNameData.setter def atomNameData(self, value): raise NotImplementedError("atomNameData not implemented yet") @classmethod def _getAllWrappedData(cls, parent: StructureEnsemble)-> list: """get wrappedData - all Model children of parent StructureEnsemble""" return parent._wrappedData.sortedModels()
def _newModel(self:StructureEnsemble, title:str=None, comment:str=None, coordinateData:numpy.ndarray=None, bFactorData:Sequence[float]=None, occupancyData:Sequence[float]=None) -> Model: """Create new Model CoordinateData can be a numpy.ndarray of the right shape, or any nested list or tuple representation that contains the right number of elements""" defaults = collections.OrderedDict((('title', None), ('comment', None), ('coordinateData', None), ('bFactorData', None), ('occupancyData', None) ) ) structureEnsemble = self._wrappedData self._startFunctionCommandBlock('newModel', values=locals(), defaults=defaults, parName='newModel') self._project.blankNotification() # delay notifiers till model is fully ready try: if coordinateData: atomCount = structureEnsemble.nAtoms # Sanity check - filter out (most?) wrongly shaped arrays if hasattr(coordinateData, 'shape'): if coordinateData.shape != (atomCount,3): raise ValueError("numpy.ndarray input not of correct shape (%s,3)" % atomCount) else: if len(coordinateData) not in (atomCount, 3*atomCount): raise ValueError("nested sequence input does not match %s*3 array" % atomCount) coordinateData = commonUtil.flattenIfNumpy(coordinateData, shape=(atomCount,3)) newApiModel = structureEnsemble.newModel(name=title, details=comment) if coordinateData: newApiModel.setSubmatrixData('coordinates', coordinateData) if occupancyData: newApiModel.setSubmatrixData('occupancies', occupancyData) if bFactorData: newApiModel.setSubmatrixData('bFactors', bFactorData) # remove cached matrices, which are now out of date: for tag in ('_coordinateData', '_occupancyData', '_bFactorData'): if hasattr(self, tag): delattr(self, tag) finally: self._project.unblankNotification() self._project._appBase._endCommandBlock() result = self._project._data2Obj.get(newApiModel) # Do creation notifications result._finaliseAction('create') # return result # Connections to parents: StructureEnsemble.newModel = _newModel del _newModel # Notifiers: # Must be done with API notifiers as it rewuires a predelete notifier. def _flushCachedData(project:Project, apiModel:ApiModel): """Flush cached data to ensure up-to-date data are saved""" structureEnsemble = project._data2Obj[apiModel].structureEnsemble structureEnsemble._flushCachedData() Project._apiNotifiers.append( ('_flushCachedData', {}, ApiModel._metaclass.qualifiedName(), 'preDelete'), )