def __init__(self, name, ranges=None, root='.', **kwds):
NTtree.__init__(self, __CLASS__='Projects', name=name, ranges=ranges, root=root, **kwds)
self.entries = self._children
self.next_id = 0
self.moleculeMap = None
self.rmsds = None # pairwise rmsd comparisons
self.mkdir()
def __init__(self, name, *args, **kwds):
NTtree.__init__(
self,
__CLASS__="MolDef",
convention=constants.INTERNAL,
name=name,
residueDict={}, # contains definitions of residues, sorted by convention
)
self.residues = self._children
for arg in args:
self.update(arg)
# end for
self.update(kwds)
self.__FORMAT__ = "=== MolDef %(name)s (%(convention)r) ===\n" + "residues: %(residues)s\n"
def __init__(self, name, **kwds):
NTtree.__init__(
self,
__CLASS__="DihedralDef",
convention=constants.INTERNAL,
name=name,
aliases=[],
residueDef=None,
atoms=[], # List of atoms: (i, name) tuple
# i: -1=previous residue
# 0=current residue
# 1=next residue
karplus=None, # Karplus parameters: (A,B,C,teta) tuple
)
self.update(kwds)
self.__FORMAT__ = (
"=== DihedralDef %(residueDef)s.%(name)s (%(convention)r) ===\n"
+ "atoms: %(atoms)s\n"
+ "karplus: %(karplus)s"
)
def __init__(self, name, **kwds):
NTtree.__init__(
self,
__CLASS__="ResidueDef",
convention=constants.INTERNAL,
name=name, # used to refer to this residueDef: should be unique
commonName=name, # used to name residue; default later changed to constants.IUPAC if exists
shortName="_",
canBeModified=True, # ResidueDef can be modified; i.e. AtomDefs added;
# set to False on import for non-protein and non-nucleic CING definitions
shouldBeSaved=True,
# ResidueDef requires saving with project; set to False on import for default CING definitions
comment=None,
nameDict={constants.INTERNAL_0: name, constants.INTERNAL_1: name},
atomDict={},
# contains definition of atoms, sorted by convention, dynamically created on initialization
dihedrals=NTlist(),
properties=[], # list of properties for residue
)
if self.nameDict.has_key(constants.IUPAC):
self.commonName = self.nameDict[constants.IUPAC]
# update the defaults with any arguments to the initialization
self.update(kwds)
self.properties = []
# NB atoms is a derived attribute (from _children), no need to save it explicitly
self.atoms = self._children
self.__FORMAT__ = (
"=== ResidueDef %(name)s (%(convention)r) ===\n"
+ "commonName: %(commonName)s\n"
+ "shortName: %(shortName)s\n"
+ "comment: %(comment)s\n"
+ "atoms: %(atoms)s\n"
+ "dihedrals: %(dihedrals)s\n"
+ "properties: %(properties)s"
)
def __init__(self, name, **kwds):
# print '>>', args, kwds
NTtree.__init__(
self,
__CLASS__="AtomDef",
convention=constants.INTERNAL,
name=name, # Internal name
nameDict={constants.INTERNAL_0: name, constants.INTERNAL_1: name}, # default initialization, to be
# updated later.
aliases=[], # list of aliases,
canBeModified=True,
residueDef=None, # ResidueDef instance
topology=[], # List of bound atoms: (i, name) tuple
# i: -1=previous residue; 0=current residue; 1=next residue
NterminalTopology=[], # special case for N-terminal atoms
CterminalTopology=[], # special case for C-terminal atoms
pseudo=None, # Corresponding pseudo atom (for real atoms)
pseudoId=DEFAULT_PSEUDO_ATOM_ID_UNDEFINED,
real=[], # List of corresponding real atoms (for pseudo atoms)
type=None, # Cyana type of atom
spinType=None, # NMR spin type; i.e. 1H, 13C ...
shift=None, # NTdict with average and sd
hetatm=False, # PDB HETATM type
)
self.properties = [] # List with properties
self.update(kwds)
self.__FORMAT__ = (
"=== %(name)s (%(convention)r) ===\n"
+ "topology: %(topology)s\n"
+ "pseudo: %(pseudo)s\n"
+ "real: %(real)s\n"
+ "spinType: %(spinType)s\n"
+ "hetatm: %(hetatm)s\n"
+ "properties: %(properties)s"
)
