Package schrodinger :: Package application :: Package msv :: Package io :: Module seqio :: Class StructureConverter
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Class StructureConverter

object --+
         |
        StructureConverter

Instance Methods [hide private]
 
__init__(self, ct)
x.__init__(...) initializes x; see help(type(x)) for signature
bool
_structureResidueIsValid(self, res, valid_atom_indices, capping_groups)
Takes a residue, a set of valid atom indices and a set of capping groups and returns a bool indicating whether it the residue is valid
 
makeSequences(self)
Note that disulfide bonds might be between chains, so need to be calculated at the ct level
 
findDisulfideBonds(self, seqs)
Finds intra- and inter-chain disulfide bonds.

Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __str__, __subclasshook__

Static Methods [hide private]
bool
sequenceIsValid(residues)
Test whether given sequence is valid.
Properties [hide private]

Inherited from object: __class__

Method Details [hide private]

__init__(self, ct)
(Constructor)

 

x.__init__(...) initializes x; see help(type(x)) for signature

Overrides: object.__init__
(inherited documentation)

_structureResidueIsValid(self, res, valid_atom_indices, capping_groups)

 

Takes a residue, a set of valid atom indices and a set of capping groups and returns a bool indicating whether it the residue is valid

Parameters:
Returns: bool
Whether the residue is valid or not

sequenceIsValid(residues)
Static Method

 

Test whether given sequence is valid. A sequence is considered valid if it contains at least one residue with C-alpha atom.

Parameters:
  • residues (structure.Residue iterator) - Input sequence
Returns: bool
True if seq is valid.