def __init__(self):
"""
Just add some properties.
"""
self.project = None
self.objectPath = None
self.projectList = None
self.rogScore = ROGscore()
def __init__(self):
"""
Just add some properties.
"""
self.project = None
self.objectPath = None
self.projectList = None
self.rogScore = ROGscore()
def __init__(self, name, status='keep'):
NTlist.__init__(self)
ProjectListMember.__init__(self) # Initialized objectPath
self.__CLASS__ = 'ResonanceList'
self.name = name # Name of the list
self.status = status # Status of the list; 'keep' indicates storage required
self.currentId = 0 # Id for each element of list
self._idDict = {
} # dictionary to look up id in case the list is sorted differently
self._byItem = None # if not None: list was sorted _byItem.
self.vascoResults = NTdict(
) # See applyVascoChemicalShiftCorrections # NB match with VASCO_RESULTS_STR
self.vascoApplied = False # VASCO_APPLIED_STR
self.bmrb_id = None # Will be derived from name when calling rename.
self.rogScore = ROGscore()
self.SMLhandler.SML_SAVE_ATTRIBUTE_LIST = self.SML_SAVE_ATTRIBUTE_LIST
self.rename(name) # Triggers setting self.bmrb_id
class ProjectListMember():
"""An element of ProjectList always has certain attributes to add.
"""
def __init__(self):
"""
Just add some properties.
"""
self.project = None
self.objectPath = None
self.projectList = None
self.rogScore = ROGscore()
# end def
def decriticize(self):
# nTdebug("Now in ProjectListMember#%s" % getCallerName())
# Any list
self.rogScore.reset()
for obj in self:
# nTdebug("Looking at object: %s [%r]" % (str(obj), repr(obj)))
obj.decriticize()
class ProjectListMember():
"""An element of ProjectList always has certain attributes to add.
"""
def __init__(self):
"""
Just add some properties.
"""
self.project = None
self.objectPath = None
self.projectList = None
self.rogScore = ROGscore()
# end def
def decriticize(self):
# nTdebug("Now in ProjectListMember#%s" % getCallerName())
# Any list
self.rogScore.reset()
for obj in self:
# nTdebug("Looking at object: %s [%r]" % (str(obj), repr(obj)))
obj.decriticize()
def __init__(self, name, status = 'keep'):
NTlist.__init__(self)
ProjectListMember.__init__(self) # Initialized objectPath
self.__CLASS__ = 'ResonanceList'
self.name = name # Name of the list
self.status = status # Status of the list; 'keep' indicates storage required
self.currentId = 0 # Id for each element of list
self._idDict = {} # dictionary to look up id in case the list is sorted differently
self._byItem = None # if not None: list was sorted _byItem.
self.vascoResults = NTdict() # See applyVascoChemicalShiftCorrections # NB match with VASCO_RESULTS_STR
self.vascoApplied = False # VASCO_APPLIED_STR
self.bmrb_id = None # Will be derived from name when calling rename.
self.rogScore = ROGscore()
self.SMLhandler.SML_SAVE_ATTRIBUTE_LIST = self.SML_SAVE_ATTRIBUTE_LIST
self.rename(name) # Triggers setting self.bmrb_id
class ResonanceList(NTlist, ProjectListMember):
"""
Contains ResonanceList meta data.
NB the name is not necessarily unique within even the molecule.
I.e. for PDB entry 1cjg and from NMR-STAR entry 4813 will get the resonance list name bmr4813_21.str twice from CCPN.
"""
SML_SAVE_ATTRIBUTE_LIST = 'name status bmrb_id vascoApplied vascoResults'.split() # Used in cing.core.sml.SMLNTListWithAttrHandler
# use the same spelling through out.
# NB the unusual init. Differs in that arguments aren't added to the list.
def __init__(self, name, status = 'keep'):
NTlist.__init__(self)
ProjectListMember.__init__(self) # Initialized objectPath
self.__CLASS__ = 'ResonanceList'
self.name = name # Name of the list
self.status = status # Status of the list; 'keep' indicates storage required
self.currentId = 0 # Id for each element of list
self._idDict = {} # dictionary to look up id in case the list is sorted differently
self._byItem = None # if not None: list was sorted _byItem.
self.vascoResults = NTdict() # See applyVascoChemicalShiftCorrections # NB match with VASCO_RESULTS_STR
self.vascoApplied = False # VASCO_APPLIED_STR
self.bmrb_id = None # Will be derived from name when calling rename.
self.rogScore = ROGscore()
self.SMLhandler.SML_SAVE_ATTRIBUTE_LIST = self.SML_SAVE_ATTRIBUTE_LIST
self.rename(name) # Triggers setting self.bmrb_id
#end def
def decriticize(self):
# nTdebug("Now in ResonanceList#decriticize")
# Restraints lists
self.rogScore.reset()
for dr in self:
dr.rogScore.reset()
# end for
#end def
def hasVascoCorrectionsApplied(self):
'A little bit more sophisticated routine to report no corrections of zero.'
return self.vascoApplied and self.hasVascoCorrectionsApplicable()
#end def
def hasVascoCorrectionsApplicable(self):
'A little bit more sophisticated routine to report no corrections of zero.'
for atomId in self.vascoResults.keys():
ntvalue = self.vascoResults[ atomId ]
rerefValue = ntvalue.value
rerefError = ntvalue.error
useCorrection = math.fabs(rerefValue) >= VASCO_CERTAINTY_FACTOR_CUTOFF * rerefError # sync with molecule code.
if useCorrection:
return True
# end if
# end for
return False
#end def
def __str__(self):
return sprintf('<%s "%s">' % (self.__CLASS__, self.name))
# return self.toVascoHtmlList() # modify when needed.
def toVascoHtmlList(self, showHeader = False):
'If showIndividualApplication the output will be multiple lines.'
s = ''
if showHeader:
s += '<h3>'
s += self.name
if self.vascoApplied:
s += ' (applied)'
else:
s += ' (ignored)'
s += '</h3>\n'
s += '<ul>\n'
for atomId in self.vascoResults.keys():
ntvalue = self.vascoResults[ atomId ]
s += '<li>'
atomClassId = getDeepByKeys(vascoMapAtomIdToHuman, atomId)
if atomClassId == None:
atomClassId = atomId
s += '%s: %s' % ( atomClassId, ntvalue)
rerefValue = ntvalue.value
rerefError = ntvalue.error
useCorrection = math.fabs(rerefValue) >= VASCO_CERTAINTY_FACTOR_CUTOFF * rerefError
if useCorrection:
s += ' applied'
else:
s += ' not applied'
# end if
s += '</li>\n'
# end for
s += '</ul>\n'
return s
#end def
def __repr__(self):
return self.__str__()
#end def
def rename(self, newName):
'Please use this rename instead of directly renaming so BMRB ID detection can kick in.'
self.name = newName
# Detect the id from strings like: bmr4020_21.str
pattern = re.compile( '^.*(bmr\d+).*$' )
match = pattern.match( self.name )
if match:
bmrb_idStr = match.group(1)[3:]
self.bmrb_id = int(bmrb_idStr)
if is_bmrb_code(self.bmrb_id):
# nTdebug("-0- Autodetected BMRB ID %s from new name: %s" % (self.bmrb_id, self.name))
return self
# end if
nTerror("Did not detect valid BMRB ID from new name: %s." % self.name)
return self
# end if
# nTdebug("-2- No BMRB ID was matched from new name: %s" % self.name)
# return self.projectList.rename(self.name, newName)
return self
#end def
def append(self, item): # pylint: disable=W0221
'Append'
# if not hasattr(self, 'currentId'): # for deepcopy
# self.currentId = 0
item.id = self.currentId
item.parent = self # being able to go from restraint to restraint list is important.
NTlist.append(self, item)
self._idDict[item.id] = item
self.currentId += 1
#end def
def save(self, path = None):
"""
Create a SML file
Return self or None on error
Sort the list on id before saving, to preserve (original) order from save to restore.
"""
# sort the list on id number
NTsort( self, byItem='id', inplace=True)
if not path:
path = self.objectPath
if self.SMLhandler.toFile(self, path) != self:
nTerror('%s.save: failed creating "%s"' % (self.__CLASS__, path))
return None
#end if
# restore original sorting
if self._byItem:
NTsort( self, byItem=self._byItem, inplace=True)
nTdetail('==> Saved %s to "%s"', self, path)
return self
#end def
def sort(self, byItem='id' ):
"Sort the list byItem; store the byItem "
NTsort( self, byItem, inplace=True)
self._byItem = byItem
return self
#end def
def getId(self, id):
"""Return restraint instance with id
Returns None on error
"""
if not self._idDict.has_key(id):
nTerror('ResonanceList.getId: invalid id (%d)', id)
return None
#end if
return self._idDict[id]
#end def
def format(self, showAll = False):
if not showAll:
return
rTxtList = []
for r in self:
rTxtList.append( r.format() )
msg = '\n'
msg += '\n'.join(rTxtList)
return msg
class ResonanceList(NTlist, ProjectListMember):
"""
Contains ResonanceList meta data.
NB the name is not necessarily unique within even the molecule.
I.e. for PDB entry 1cjg and from NMR-STAR entry 4813 will get the resonance list name bmr4813_21.str twice from CCPN.
"""
SML_SAVE_ATTRIBUTE_LIST = 'name status bmrb_id vascoApplied vascoResults'.split(
) # Used in cing.core.sml.SMLNTListWithAttrHandler
# use the same spelling through out.
# NB the unusual init. Differs in that arguments aren't added to the list.
def __init__(self, name, status='keep'):
NTlist.__init__(self)
ProjectListMember.__init__(self) # Initialized objectPath
self.__CLASS__ = 'ResonanceList'
self.name = name # Name of the list
self.status = status # Status of the list; 'keep' indicates storage required
self.currentId = 0 # Id for each element of list
self._idDict = {
} # dictionary to look up id in case the list is sorted differently
self._byItem = None # if not None: list was sorted _byItem.
self.vascoResults = NTdict(
) # See applyVascoChemicalShiftCorrections # NB match with VASCO_RESULTS_STR
self.vascoApplied = False # VASCO_APPLIED_STR
self.bmrb_id = None # Will be derived from name when calling rename.
self.rogScore = ROGscore()
self.SMLhandler.SML_SAVE_ATTRIBUTE_LIST = self.SML_SAVE_ATTRIBUTE_LIST
self.rename(name) # Triggers setting self.bmrb_id
#end def
def decriticize(self):
# nTdebug("Now in ResonanceList#decriticize")
# Restraints lists
self.rogScore.reset()
for dr in self:
dr.rogScore.reset()
# end for
#end def
def hasVascoCorrectionsApplied(self):
'A little bit more sophisticated routine to report no corrections of zero.'
return self.vascoApplied and self.hasVascoCorrectionsApplicable()
#end def
def hasVascoCorrectionsApplicable(self):
'A little bit more sophisticated routine to report no corrections of zero.'
for atomId in self.vascoResults.keys():
ntvalue = self.vascoResults[atomId]
rerefValue = ntvalue.value
rerefError = ntvalue.error
useCorrection = math.fabs(
rerefValue
) >= VASCO_CERTAINTY_FACTOR_CUTOFF * rerefError # sync with molecule code.
if useCorrection:
return True
# end if
# end for
return False
#end def
def __str__(self):
return sprintf('<%s "%s">' % (self.__CLASS__, self.name))
# return self.toVascoHtmlList() # modify when needed.
def toVascoHtmlList(self, showHeader=False):
'If showIndividualApplication the output will be multiple lines.'
s = ''
if showHeader:
s += '<h3>'
s += self.name
if self.vascoApplied:
s += ' (applied)'
else:
s += ' (ignored)'
s += '</h3>\n'
s += '<ul>\n'
for atomId in self.vascoResults.keys():
ntvalue = self.vascoResults[atomId]
s += '<li>'
atomClassId = getDeepByKeys(vascoMapAtomIdToHuman, atomId)
if atomClassId == None:
atomClassId = atomId
s += '%s: %s' % (atomClassId, ntvalue)
rerefValue = ntvalue.value
rerefError = ntvalue.error
useCorrection = math.fabs(
rerefValue) >= VASCO_CERTAINTY_FACTOR_CUTOFF * rerefError
if useCorrection:
s += ' applied'
else:
s += ' not applied'
# end if
s += '</li>\n'
# end for
s += '</ul>\n'
return s
#end def
def __repr__(self):
return self.__str__()
#end def
def rename(self, newName):
'Please use this rename instead of directly renaming so BMRB ID detection can kick in.'
self.name = newName
# Detect the id from strings like: bmr4020_21.str
pattern = re.compile('^.*(bmr\d+).*$')
match = pattern.match(self.name)
if match:
bmrb_idStr = match.group(1)[3:]
self.bmrb_id = int(bmrb_idStr)
if is_bmrb_code(self.bmrb_id):
# nTdebug("-0- Autodetected BMRB ID %s from new name: %s" % (self.bmrb_id, self.name))
return self
# end if
nTerror("Did not detect valid BMRB ID from new name: %s." %
self.name)
return self
# end if
# nTdebug("-2- No BMRB ID was matched from new name: %s" % self.name)
# return self.projectList.rename(self.name, newName)
return self
#end def
def append(self, item): # pylint: disable=W0221
'Append'
# if not hasattr(self, 'currentId'): # for deepcopy
# self.currentId = 0
item.id = self.currentId
item.parent = self # being able to go from restraint to restraint list is important.
NTlist.append(self, item)
self._idDict[item.id] = item
self.currentId += 1
#end def
def save(self, path=None):
"""
Create a SML file
Return self or None on error
Sort the list on id before saving, to preserve (original) order from save to restore.
"""
# sort the list on id number
NTsort(self, byItem='id', inplace=True)
if not path:
path = self.objectPath
if self.SMLhandler.toFile(self, path) != self:
nTerror('%s.save: failed creating "%s"' % (self.__CLASS__, path))
return None
#end if
# restore original sorting
if self._byItem:
NTsort(self, byItem=self._byItem, inplace=True)
nTdetail('==> Saved %s to "%s"', self, path)
return self
#end def
def sort(self, byItem='id'):
"Sort the list byItem; store the byItem "
NTsort(self, byItem, inplace=True)
self._byItem = byItem
return self
#end def
def getId(self, id):
"""Return restraint instance with id
Returns None on error
"""
if not self._idDict.has_key(id):
nTerror('ResonanceList.getId: invalid id (%d)', id)
return None
#end if
return self._idDict[id]
#end def
def format(self, showAll=False):
if not showAll:
return
rTxtList = []
for r in self:
rTxtList.append(r.format())
msg = '\n'
msg += '\n'.join(rTxtList)
return msg
