schrodinger.forcefield.minimizer module

class schrodinger.forcefield.minimizer.Restraint(force_constant, target_value, atom_index1, atom_index2, atom_index3, atom_index4, flat_bottom_half_width)

Bases: object

Class representing restraints.

__init__(force_constant, target_value, atom_index1, atom_index2, atom_index3, atom_index4, flat_bottom_half_width)

class schrodinger.forcefield.minimizer.Constraint(atom_index1, atom_index2, type_index1, type_index2, use_rigorous=False)

Bases: object

Class representing constraints.

__init__(atom_index1, atom_index2, type_index1, type_index2, use_rigorous=False)

class schrodinger.forcefield.minimizer.MinimizationOptions(opls_version: int = 16, nonbond_cutoff: float = 14.0, max_step: int = 1500, energy_convergence: float = 5e-09, gradient_convergence: float = 0.05, line_search_method: int = 1, min_method: int = 0, no_restrain_zob: bool = False, bend_conj_amines: bool = False, perturb: bool = False, restraints: Optional[List[schrodinger.forcefield.minimizer.Restraint]] = None, constraints: Optional[List[schrodinger.forcefield.minimizer.Constraint]] = None, debug_outfile: Optional[str] = None)

Bases: tuple

Class for assigning the mmffld minimization options.

opls_version: int

Alias for field number 0

nonbond_cutoff: float

Alias for field number 1

max_step: int

Alias for field number 2

energy_convergence: float

Alias for field number 3

gradient_convergence: float

Alias for field number 4

line_search_method: int

Alias for field number 5

min_method: int

Alias for field number 6

no_restrain_zob: bool

Alias for field number 7

bend_conj_amines: bool

Alias for field number 8

perturb: bool

Alias for field number 9

restraints: Optional[List[schrodinger.forcefield.minimizer.Restraint]]

Alias for field number 10

constraints: Optional[List[schrodinger.forcefield.minimizer.Constraint]]

Alias for field number 11

debug_outfile: Optional[str]

Alias for field number 12

__contains__(key, /)

Return key in self.

__len__()

Return len(self).

count(value, /)

Return number of occurrences of value.

index(value, start=0, stop=9223372036854775807, /)

Return first index of value.

Raises ValueError if the value is not present.

schrodinger.forcefield.minimizer.minimize_structure(st: schrodinger.structure._structure.Structure, options: Optional[schrodinger.forcefield.minimizer.MinimizationOptions] = None, archive_path: Optional[os.PathLike] = None)

Minimizes a single structure. For minimizing multiple structures, the performance improves drastically if the forcefield handle instantiation happens outside the iteration loop.

Parameters

• st – structure

• options – mmffld minimization options

• archive_path – path to specific .opls file

Returns

minimization results

Return type

mm.MinimizeResults

schrodinger.forcefield.minimizer.iterate_minimize_structure(st, iteration, options=None)

Minimize a single structure multiple times. This function instantiates the forcefield handle before the iteration loop and hence increases the performance by eliminating instantiation repetitions.

Parameters

• st (schrodinger.structure object) – structure

• iteration (int) – iteration number

• options (MinimizationOptions namedtuple) – mmffld minimization options

Returns

minimization results

Return type

mm.MinimizeResults

schrodinger.forcefield.minimizer.minimize_substructure(st: schrodinger.structure._structure.Structure, atoms_to_minimize: Iterable[schrodinger.structure._structure._StructureAtom]) → schrodinger.structure._structure.Structure

Given a structure, minimizes the specified atoms in it, and returns it

Parameters

• st – The structure containing the atoms to be minimized

• atoms_to_minimize – The subset of atoms in the structure to be minimize

Returns

The structure with the atoms minimized

schrodinger.forcefield.minimizer.minimize_ligands(st: schrodinger.structure._structure.Structure, **kwargs) → schrodinger.structure._structure.Structure

Given a structure, returns that structure with all the ligands minimized

Parameters

• st – The structure containing ligands to be minimized

• **kwargs – Any options to supply to analyze.find_ligands

Returns

The structure with the ligands minimized

schrodinger.forcefield.minimizer.write_restraints(filename, restraints)

Writes restraints into filename.

Parameters

• filename (string) – restraint filename

• restraints (list of Restraints) – a list to be filled with restraints

schrodinger.forcefield.minimizer.read_restraints(filename, restraints=None, constraints=None)

Reads restraints and constraints arguments from a file and creates separate lists for Restraint and Constraint objects.

Parameters

• filename (string) – restraint/constraint filename

• restraints (list of Restraints) – a list to be filled with restraints

• constraints (list of Constraints) – a list to be filled with constraints