Package schrodinger :: Package protein :: Module pdbname :: Class Substructure

Class Substructure

object --+
         |
        Substructure

Holds the information about a substructure

Instance Methods

[hide private]

__init__(self, definition, restype, atom_types)
Create a Substructure object

list

getMatches(self, struct)
Return a list of lists of atoms that match this substructure.

extendToIncludeSideChainAtoms(self, st, match)
For the given UNK residue match, add all atoms bound to the beta carbon (side-chain) that are not part of the backbone (known substructure).

list

fixResName(self, struct, atoms)
Update the residue name of the matching atoms.

list

fixAtomNames(self, struct, atoms)
Update the matching atoms to the proper PDB atom names.

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

Properties

[hide private]

Inherited from object: __class__

Method Details

[hide private]

init(self, definition, restype, atom_types)
(Constructor)

Create a Substructure object

Parameters:

definition (str) - MacroModel-style substructure expression.
restype (str) - 4-letter residue type ("ALA ", "VAL ", etc).
data - PDB atom names separated by ";" for example: " H ; N ". The order of the PDB names must match the order of the atoms in the substructure definition.
atom_types (str)

Overrides: object.__init__

getMatches(self, struct)

Return a list of lists of atoms that match this substructure.

Returns: list: Each item of the returned list is a list of atom indexes that match this substructure.

fixResName(self, struct, atoms)

Update the residue name of the matching atoms.

Parameters:

struct (schrodinger.structure.Structure) - The structure to operate on. This structure is modified in-place.
atoms (int) - List of atoms from this match

Returns: list

Each item of the returned list is a list of atom indexes that match this substructure.

fixAtomNames(self, struct, atoms)

Update the matching atoms to the proper PDB atom names.

Parameters:

struct (schrodinger.structure.Structure) - The structure to operate on. This structure is modified in-place.
atoms (int) - List of atoms from this match

Returns: list

Each item of the returned list is a list of atom indexes that match this substructure.

Class Substructure

__init__(self, definition, restype, atom_types) (Constructor)

getMatches(self, struct)

fixResName(self, struct, atoms)

fixAtomNames(self, struct, atoms)

init(self, definition, restype, atom_types)
(Constructor)