def __init__(self):
NTdict.__init__(self,
__CLASS__ = 'ROGscore',
__FORMAT__ = "ROGscore '%(colorLabel)s' %(colorCommentList)s"
)
# Explicitly showing instance attributes here in init.
self.colorLabel = constants.COLOR_GREEN
# Elements in this list are tuples of (color, comment).
self.colorCommentList = NTlist()
def __init__( self, table, id, **kwds ):
NTdict.__init__( self, __CLASS__ = 'NmrPipeTabRow',
table = table,
id = id,
name = 'row'+str(id),
__FORMAT__ = '%(name)s',
**kwds
)
# set defaults to None
for c in self.keys():
self.setdefault( c, None )
def __init__(self, checkID, level, modelCount ):
NTdict.__init__( self, __CLASS__ = 'CingResult',
checkID = checkID,
alternate = None,
level = level,
# comment = Whatif.explain(checkID),
)
# # Initialize the lists
# if Whatif.cingNameDict.has_key(checkID):
# self.alternate = Whatif.cingNameDict[checkID]
# for c in [ VALUE_LIST_STR, QUAL_LIST_STR]:
for c in [ constants.VALUE_LIST_STR ]:
self[c] = nTfill( None, modelCount)
def __init__( self, tabFile=None, **kwds ):
NTdict.__init__( self, __CLASS__ = 'nmrPipeTab', **kwds )
self.setdefault('noneIndicator', '-') # character to identify the None value
self.columnDefs = NTlist() # list of column definitions, implemented
# as NTdict
self.rows = NTlist()
self.nrows = 0
self.remarks = NTlist()
self.data = NTdict()
self.tabFile = tabFile
if tabFile:
self.readFile( tabFile )
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
# (RES_LEVEL, 'PDBLST', None, 'List of residues', 'List of residues'),
# (RES_LEVEL, 'PL3CHK', None, 'Side chain planarity with hydrogens attached', 'NA planarity'),
# (RES_LEVEL, 'PLNCHK', 'planarities', 'Protein side chain planarities', 'Protein SC planarity'),
# (RES_LEVEL, 'PRECHK', None, 'Missing backbone atoms.', 'Missing backbone atoms.'),
# (RES_LEVEL, 'PUCCHK', None, 'Ring puckering in Prolines', 'Ring puckering in Prolines'),
# (RES_LEVEL, 'QUACHK', 'packingQuality1','Directional Atomic Contact Analysis, aka 1st generation packing quality', 'Packing quality'),
# (RES_LEVEL, 'RAMCHK', 'ramachandran', 'Ramachandran Z-score', 'Ramachandr.' ),
# (RES_LEVEL, 'ROTCHK', 'rotamer', 'Rotamers', 'Rotamer normality'),
# (RES_LEVEL, 'SCOLST', None, 'List of symmetry contacts', 'List of symmetry contacts'),
# (RES_LEVEL, 'TO2CHK', None, 'Missing C-terminal groups', 'Missing C-terminal groups'),
# (RES_LEVEL, 'TOPPOS', None, 'Ligand without know topology', 'Ligand without know topology'),
# (RES_LEVEL, 'TORCHK', None, 'Unknown check', 'Unknown check'),
# (RES_LEVEL, 'WIOPAC', None, 'Water packing', 'Water packing')
]
cingNameDict = NTdict( zip( nTzap(nameDefs,1), nTzap(nameDefs,2)) )
nameDict = NTdict( zip( nTzap(nameDefs,1), nTzap(nameDefs,3)) )
shortNameDict = NTdict( zip( nTzap(nameDefs,1), nTzap(nameDefs,4)) )
cingNameDict.keysformat()
nameDict.keysformat()
shortNameDict.keysformat()
wiPlotList = []
# GV: moved to outer level to not always call createHtmlWhatif
wiPlotList.append( ('_01_backbone_chi','QUA/RAM/BBC/C12') )
wiPlotList.append( ('_02_bond_angle','BND/ANG/NQA/PLNCHK') )
wiPlotList.append( ('_03_steric_acc_flip','BMP/ACC/FLP/CHI') )
# Whatif id's for summary; will be keys in molecule[WHATIF_STR] dict
# Make them available to 'outside world through the Whatif class
def __init__(self):
NTdict.__init__(self)
self[ ERROR_ID ] = NTlist()
self[ WARNING_ID ] = NTlist()
self[ MESSAGE_ID ] = NTlist()
self[ DEBUG_ID ] = NTlist()
"C": 1,
"N": 1,
"H": 1,
"HN": 1,
"H1": 1,
"H2": 1,
"H3": 1,
"CA": 1,
"HA": 1,
"HA1": 1,
"HA2": 1,
"HA3": 1,
}
backBoneNucleicAtomDict = {"P": 1, "O3'": 1, "C3'": 1, "C4'": 1, "C5'": 1, "O5'": 1} # skipping 'backbone protons'
NterminalProteinAtomDict = NTdict()
NterminalProteinAtomDict.appendFromList("H1 H2 H3 H' H''".split()) # watch out; H1 does occur in nucleic acid bases.
NterminalNucleicAtomDict = NTdict()
NterminalNucleicAtomDict.appendFromList("HOP2 HOP3".split())
def isNterminalAtom(atmDef):
"""
Return True if atom belongs to N-terminal category.
Needs to be called by valid atmDef or 0 will be returned.
"""
if atmDef is None or atmDef.residueDef is None: # Fixes 2ksi
# nTdebug("%s called without atom/residue definition." % getCallerName())
return 0
if atmDef.residueDef.hasProperties("protein"):
def __init__(self):
NTdict.__init__(self)
self[ERROR_ID] = NTlist()
self[WARNING_ID] = NTlist()
self[MESSAGE_ID] = NTlist()
self[DEBUG_ID] = NTlist()
directories = cdefs.directories
moleculeDirectories = cdefs.validationDirectories
validationDirectories = cdefs.validationDirectories
htmlDirectories = cdefs.htmlDirectories
cingPaths = cdefs.cingPaths
outlierColor = '#CC66FF' # iWeb lavender
plotParameters = NTdict(
#default
dihedralDefault = NTdict(
min = 0.0,
max = 360.0,
mticksize= 10,
ticksize = 60,
# color = 'green',
color = '#990099', # iWeb plum
outlier = outlierColor,
average = 'blue',
lower = 'orange',
upper = 'orange'
),
)
plotParameters.PHI = plotParameters.dihedralDefault.copy()
plotParameters.PHI.min = -180
plotParameters.PHI.max = 180
plotParameters.PHI.xlabelLat = '$\phi 1$' # Latex
plotParameters.PSI = plotParameters.PHI.copy()
plotParameters.PHI.xlabelLat = '$\psi 1$' # Latex
config = NTdict(
XPLOR = xplorPath,
# (waterrefine) xplor stuff, directories, etc.
refinePath = refinePath,
topparPath = os.path.join(refinePath,'toppar'),
protocolsPath = os.path.join(refinePath,'explicit_solvent'),
parameterFiles = [ 'parallhdg5.3-merge.pro',
'parallhdg5.3.sol',
'par_axis_aria.pro',
'ion.param',
],
topologyFiles = [ 'topallhdg5.3-merge.pro',
'topallhdg5.3.sol',
'top_axis_aria.pro',
'ion.top',
],
directories = NTdict(
converted = 'Converted',
analyzed = 'Analyzed', # analyzed from refine
annealed = 'Annealed', # annealed from template
template = 'Template', # extended structure at random
refined = 'Refined', # from analyzed
tables = 'Tables',
jobs = 'Jobs',
psf = 'PSF',
toppar = 'Toppar'
)
)
class NmrPipeTable( NTdict ):
"""
NmrPipeTable class
implemented as NTdict of NTdict's, i.e.
element (row-0, INDEX) indexed as
tab[0].INDEX or tab[0]['INDEX']
tab = NmrPipeTable() # Empty table
tab = NmrPipeTable( 'tabFile' ) # table from tabFile
METHODS:
addColumn( name, fmt = "%s", default=None ):
Add column 'name' to table; set values to 'default'
hideColumn( *cNames )
Hide column(s) cNames
showColumn( *cNames )
Show columns cNames
addRow( **kwds ):
Add row to table, optional kwds can be used to set values
readFile( tabFile ):
Read table from tabFile
write( stream=sys.stdout ):
Write table to stream
writeFile( tabFile) :
Open tabFile, write table and close tabFile
"""
def __init__( self, tabFile=None, **kwds ):
NTdict.__init__( self, __CLASS__ = 'nmrPipeTab', **kwds )
self.setdefault('noneIndicator', '-') # character to identify the None value
self.columnDefs = NTlist() # list of column definitions, implemented
# as NTdict
self.rows = NTlist()
self.nrows = 0
self.remarks = NTlist()
self.data = NTdict()
self.tabFile = tabFile
if tabFile:
self.readFile( tabFile )
#end if
#end def
def format(self): # pylint: disable=W0221
return sprintf(
'''=== NmrPipeTable "%s" ===
columns: %s
nrows: %d''', self.tabFile, self.columnDefs.zap('name'), self.nrows
)
def addRow( self, **kwds ):
"""
Add row to table, optional kwds can be used to set values
"""
row = NmrPipeTabRow( table=self, id=self.nrows, **kwds )
self[ self.nrows ] = row
self.rows.append( row )
self.nrows += 1
return row
#end def
def addColumn( self, name, fmt = "%s", default=None ):
"""
Add column 'name' to table; set values to 'default'
return columnDef, or None on error
"""
if name in self:
nTerror('NmrPipeTable.addColumn: column "%s" already exists\n', name )
return None
#end if
col = NTdict( name=name,
fmt=fmt,
id=len(self.columnDefs),
hide=False,
__FORMAT__ = '%(name)s'
)
self.columnDefs.append( col )
self[name] = col
for row in self:
row[name] = default
#end for
return col
#end def
def column( self, cName ):
"""Return list of values of column cName or None on error
"""
if cName not in self:
return None
col = NTlist()
for row in self:
col.append( row[cName] )
#end for
return col
#end def
def hideColumn( self, *cNames ):
"""
Hide column(s) cNames
"""
for c in cNames:
if not c in self:
nTerror('NmrPipeTable.hideColumn: column "%s" not defined\n', c)
else:
self[c].hide = True
#end if
#end for
#end def
def showColumn( self, *cNames ):
"""
Show column(s) cNames
"""
for c in cNames:
if not c in self:
nTerror('NmrPipeTable.showColumn: column "%s" not defined\n', c)
else:
self[c].hide = False
#end if
#end for
#end def
def readFile( self, tabFile ):
"""
Read table from tabFile
"""
# nTmessage('Reading nmrPipe table file %s', tabFile )
#end if
for line in AwkLike( tabFile, minNF = 1, commentString = '#' ):
if ( line.dollar[1] == 'REMARK' and line.NF > 1 ):
self.remarks.append( line.dollar[2:] )
elif ( line.dollar[1] == 'VARS' ):
for v in line.dollar[2:]:
self.addColumn( name=v )
#end for
elif ( line.dollar[1] == 'FORMAT' ):
i = 0
for f in line.dollar[2:]:
self.columnDefs[i].fmt=f
i += 1
#end for
elif ( line.dollar[1] == 'DATA' and line.NF > 3 ):
self.data[line.dollar[2]] = line.dollar[3:]
elif ( line.NF == len( self.columnDefs ) ):
row = self.addRow()
for i in range( 0, line.NF ):
col = self.columnDefs[i]
if (line.dollar[i+1] == self.noneIndicator):
row[col.name] = None
else:
# derive conversion function from fmt field
if (col.fmt[-1:] in ['f','e','E','g','G']):
func = float
elif (col.fmt[-1:] in ['d','o','x','X']):
func = int
else:
func = str
#end if
row[ col.name ] = func( line.dollar[i+1] )
#endif
#end for
else:
pass
#end if
#end for
self.tabFile = tabFile
#end def
def write( self, stream=sys.stdout):
"""
Write tab to stream
"""
for r in self.remarks:
fprintf( stream, 'REMARK %s\n', r )
#end for
fprintf( stream, '\n' )
for d,v in self.data.iteritems():
fprintf( stream, 'DATA %s %s\n', d, v ) # Note: only ONE space between DATA and identifier!!!
#end for
fprintf( stream, '\n' )
fprintf( stream, 'VARS ' )
for c in self.columnDefs:
if not c.hide:
fprintf( stream, '%s ', c.name )
#end for
fprintf( stream, '\n' )
fprintf( stream, 'FORMAT ' )
for c in self.columnDefs:
if not c.hide:
fprintf( stream, '%s ', c.fmt )
#end for
fprintf( stream, '\n' )
fprintf( stream, '\n' )
for row in self:
fprintf( stream, '%s\n', row )
#end for
#end def
def writeFile( self, tabFile) :
"""
Write table to tabFile.
Return True on error
"""
fp = open( tabFile, 'w' )
if fp is None:
nTerror('NmrPipeTable.writeFile: error opening "%s"', tabFile)
return True
self.write( fp )
fp.close()
# nTdebug('==> Written nmrPipe table file "%s"', tabFile )
return False
#end def
#iteration overrides: loop over row indices or rows
def keys( self ):
return range( 0, self.nrows )
#end def
def __iter__( self ):
for row in self.rows:
yield row
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 io.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
