schrodinger.application.prepwizard2.diagnostics module

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

Bases: schrodinger.models.parameters.CompoundParam

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

A parameter of the class.

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

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.

missingChanged

A pyqtSignal emitted by instances of the class.

missingReplaced

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.find_missing_res_atoms(st)

Seaches the specified structure for missing residue atoms, and returns a list of: (atomnum, num_heavy, expected_heavy, missing_only_sidechains)

This list DOES include residues with only backbone atoms missing.

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