schrodinger.application.prepwizard2.diagnostics module

class schrodinger.application.prepwizard2.diagnostics.Problems(*args, _param_type=<object object>, **kwargs)

Bases: CompoundParam

invalid_types: List[Tuple[int, int, int]]

A parameter of the class.

missing_atoms: List[Tuple[int, int, int, bool]]

A parameter of the class.

missing_loops: List[Tuple[Residue, Residue, str]]

A parameter of the class.

overlapping: List[Tuple[int, int]]

A parameter of the class.

alternates: List[Tuple[int, float]]

A parameter of the class.

alternatesChanged

A pyqtSignal emitted by instances of the class.

alternatesReplaced

A pyqtSignal emitted by instances of the class.

invalid_typesChanged

A pyqtSignal emitted by instances of the class.

invalid_typesReplaced

A pyqtSignal emitted by instances of the class.

missing_atomsChanged

A pyqtSignal emitted by instances of the class.

missing_atomsReplaced

A pyqtSignal emitted by instances of the class.

missing_loopsChanged

A pyqtSignal emitted by instances of the class.

missing_loopsReplaced

A pyqtSignal emitted by instances of the class.

overlappingChanged

A pyqtSignal emitted by instances of the class.

overlappingReplaced

A pyqtSignal emitted by instances of the class.

schrodinger.application.prepwizard2.diagnostics.get_problems(st)

schrodinger.application.prepwizard2.diagnostics.get_atoms_with_improper_atom_types(st)

Returns a list of (atomnum, expected_valence, actual_valence) items. expected_valence is None for atom types of 150 or above.

schrodinger.application.prepwizard2.diagnostics.get_overlapping_atoms(st)

schrodinger.application.prepwizard2.diagnostics.find_residues_with_multiple_occupancies(st)

Find residues that have at least one atom with multiple occupancies (alternate states).

Parameters:

st (structure.Structure) – Protein structure

Returns:

List of (Atom index, average occupancy)

Return type:

list