Source code for ccpn.core.Residue

"""
"""
#=========================================================================================
# Licence, Reference and Credits
#=========================================================================================
__copyright__ = "Copyright (C) CCPN project (www.ccpn.ac.uk) 2014 - $Date: 2016-07-18 11:42:07 +0100 (Mon, 18 Jul 2016) $"
__credits__ = "Wayne Boucher, Rasmus H Fogh, Simon P Skinner, Geerten W Vuister"
__license__ = ("CCPN license. See www.ccpn.ac.uk/license"
              "or ccpnmodel.ccpncore.memops.Credits.CcpnLicense for license text")
__reference__ = ("For publications, please use reference from www.ccpn.ac.uk/license"
                " or ccpnmodel.ccpncore.memops.Credits.CcpNmrReference")

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# Last code modification:
#=========================================================================================
__author__ = "$Author: rhfogh $"
__date__ = "$Date: 2016-07-18 11:42:07 +0100 (Mon, 18 Jul 2016) $"
__version__ = "$Revision: 9696 $"

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# Start of code
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from typing import Optional

from ccpn.util import Common as commonUtil
from ccpn.core.Project import Project
from ccpn.core.Chain import Chain
from ccpn.core._implementation.AbstractWrapperObject import AbstractWrapperObject
from ccpn.core.lib import Pid
from ccpnmodel.ccpncore.api.ccp.molecule.MolSystem import Residue as ApiResidue


[docs]class Residue(AbstractWrapperObject): """A molecular Residue, contained in a Chain, and containing Atoms.""" #: Short class name, for PID. shortClassName = 'MR' # Attribute it necessary as subclasses must use superclass className className = 'Residue' _parentClass = Chain #: Name of plural link to instances of class _pluralLinkName = 'residues' #: List of child classes. _childClasses = [] # Qualified name of matching API class _apiClassQualifiedName = ApiResidue._metaclass.qualifiedName() # CCPN properties @property def _apiResidue(self) -> ApiResidue: """ API residue matching Residue""" return self._wrappedData @property def sequenceCode(self) -> str: """Residue sequence code and id (e.g. '1', '127B') """ obj = self._wrappedData objSeqCode = obj.seqCode result = (obj.seqInsertCode or '').strip() if objSeqCode is not None: result = str(objSeqCode) + result return result @property def _key(self) -> str: """Residue ID. Identical to sequenceCode.residueType. Characters translated for pid""" return Pid.createId(self.sequenceCode, self.residueType) @property def _parent(self) -> Chain: """Chain containing residue.""" return self._project._data2Obj[self._wrappedData.chain] chain = _parent @property def residueType(self) -> str: """Residue type name string (e.g. 'ALA')""" return self._wrappedData.code3Letter or '' @property def shortName(self) -> str: return self._wrappedData.chemCompVar.chemComp.code1Letter or '?' @property def linking(self) -> str: """linking (substitution pattern) code for residue Allowed values are: For linear polymers: 'start', 'end', 'middle', 'single', 'break', 'cyclic' For other molecules: 'nonlinear' 'cyclic' and 'break' are used at the end of linear polymer stretches to signify, respectively, that the polymer is cyclic, or that the residue is bound to an unknown residue or to a cap, so that the linear polymer chain does not continue.""" molType = self._wrappedData.molType if molType in ('protein', 'DNA', 'RNA'): linkString = self._wrappedData.linking if linkString == 'none': return 'single' elif linkString in ('start', 'end'): return linkString else: assert linkString == 'middle', ("Illegal API linking value for linear polymer: %s" % linkString) # NBNB TBD FIXME - This does (MAY?) not deal properly with capped residues nextResidue = self.nextResidue previousResidue = self.previousResidue if previousResidue is None: if nextResidue is None: return 'single' else: return 'break' elif nextResidue is None: return 'break' else: # NBNB The detection of 'cyclic' only works if residues are given in # sequential order. This is not given - but is unlikely ever to break. seqId = self._wrappedData.seqId if (previousResidue._wrappedData.seqId > seqId and previousResidue._wrappedData.linking == 'middle'): return 'cyclic' elif (nextResidue._wrappedData.seqId < seqId and nextResidue._wrappedData.linking == 'middle'): return 'cyclic' else: return 'middle' else: # All other types have linking 'non-linear' in the wrapper return 'nonlinear' return self._wrappedData.linking @linking.setter def linking(self, value:str): # NBNB TBD FIXME - this will not work as intended when value is 'nonlinear' if value in ('break', 'cyclic'): value = 'middle' elif value == 'single': value = 'none' self._wrappedData.linking = value @property def residueVariant(self) -> Optional[str]: """NEF convention Residue variant descriptor (protonation state etc.) for residue""" # NBNB TBD FIXME not implemented yet, pending sorting out the NEF standard on this point return None @property def descriptor(self) -> str: """variant descriptor (protonation state etc.) for residue, as defined in the CCPN V2 ChemComp description.""" return self._wrappedData.descriptor @descriptor.setter def descriptor(self, value:str): self._wrappedData.descriptor = 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 nextResidue(self) -> Optional['Residue']: """Next residue in sequence, if any, otherwise None""" apiResidue = self._wrappedData molResidue = apiResidue.molResidue.nextMolResidue if molResidue is None: result = None else: result = self._project._data2Obj.get( apiResidue.chain.findFirstResidue(seqId=molResidue.serial)) # return result @property def previousResidue(self) -> Optional['Residue']: """Previous residue in sequence, if any,otherwise None""" apiResidue = self._wrappedData molResidue = apiResidue.molResidue.previousMolResidue if molResidue is None: result = None else: result = self._project._data2Obj.get( apiResidue.chain.findFirstResidue(seqId=molResidue.serial)) # return result
[docs] def rename(self, sequenceCode:str=None): """Reset Residue.sequenceCode (residueType is immutable). Renaming to None sets the sequence code to the seqId (serial number equivalent) """ apiResidue = self._wrappedData self._startFunctionCommandBlock('rename', sequenceCode) self._project.blankNotification() try: if sequenceCode is None: seqCode = apiResidue.seqId seqInsertCode = ' ' else: # Parse values from sequenceCode code, ss, offset = commonUtil.parseSequenceCode(sequenceCode) if code is None or offset is not None: raise ValueError("Illegal value for Residue.sequenceCode: %s" % sequenceCode) seqCode = code seqInsertCode = ss or ' ' previous = apiResidue.chain.findFirstResidue(seqCode=seqCode, seqInsertCode=seqInsertCode) if (previous not in (None, apiResidue)): raise ValueError("New sequenceCode %s clashes with existing Residue %s" % (sequenceCode, self._project._data2Obj.get(previous))) apiResidue.seqCode = seqCode apiResidue.seqInsertCode = seqInsertCode self._finaliseAction('rename') self._finaliseAction('change') finally: self._project._appBase._endCommandBlock() self._project.unblankNotification()
# Implementation functions @classmethod def _getAllWrappedData(cls, parent: Chain)-> list: """get wrappedData (MolSystem.Residues) for all Residue children of parent Chain""" # NB this is not the sort we want - sorted elsewhere return parent._apiChain.sortedResidues()
def getter(self:Residue) -> Residue: apiResidue = self._wrappedData nextApiMolResidue = apiResidue.molResidue.nextMolResidue if nextApiMolResidue is None: return None else: return self._project._data2Obj.get( apiResidue.chain.findFirstResidue(seqId=nextApiMolResidue.serial)) Residue.nextResidue = property(getter, None, None, "Next sequentially connected Residue") def getter(self:Residue) -> Residue: apiResidue = self._wrappedData previousApiMolResidue = apiResidue.molResidue.previousMolResidue if previousApiMolResidue is None: return None else: return self._project._data2Obj.get( apiResidue.chain.findFirstResidue(seqId=previousApiMolResidue.serial)) Residue.previousResidue = property(getter, None, None, "Previous sequentially connected Residue") del getter # Connections to parents: # No 'new' function - chains are made elsewhere # Notifiers: Project._apiNotifiers.extend( ( ('_finaliseApiRename', {}, ApiResidue._metaclass.qualifiedName(), 'setSeqCode'), ('_finaliseApiRename', {}, ApiResidue._metaclass.qualifiedName(), 'setSeqInsertCode'), ) )