schrodinger.forcefield.common module

OPLS context managers.

Copyright Schrodinger LLC, All Rights Reserved.

exception schrodinger.forcefield.common.AtomTypingFailure(msg='')

Bases: schrodinger.infra.mmcheck.MmException

__init__(msg='')

Initialize with the wrapped function, arguments used, and the return code.

args

with_traceback()

Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

schrodinger.forcefield.common.mmffld_environment()

A context manager for loading the mmffld environment.

class schrodinger.forcefield.common.ForceFieldOptions(version: int = 16, archive_path: Optional[os.PathLike] = None, bend_conj_amines: bool = False, no_cm1a_bcc: bool = False, charges_from_ct: bool = False, no_restrain_zob: bool = False, nonbond_cutoff: float = 14.0)

Bases: tuple

Class for assigning the mmffld force field options.

version: int

Alias for field number 0

archive_path: Optional[os.PathLike]

Alias for field number 1

bend_conj_amines: bool

Alias for field number 2

no_cm1a_bcc: bool

Alias for field number 3

charges_from_ct: bool

Alias for field number 4

no_restrain_zob: bool

Alias for field number 5

nonbond_cutoff: float

Alias for field number 6

__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.common.opls_force_field(ffld_options: Optional[schrodinger.forcefield.common.ForceFieldOptions] = None, **kwargs) → int

A context manager for creating a force field handle, using default precedence for loading ffld datafiles.

Parameters

• ffld_options – common.ForceFieldOptions object with options that affect ffld params

• kwargs – Allows passing ffld_option keywords seaparately to the function. See options for common.ForceFieldOptions for available options.

Returns

mmffld handle

schrodinger.forcefield.common.assign_force_field(mmffld_handle: pymmlibs.MMFfldHandle, st: schrodinger.structure._structure.Structure, apply_mmlewis: bool = True)

A context manager to runs typing by loading the structure into mmffld. Note: If cm1a is turned on, enterMol calculates charges which is a fairly lengthy operation.

Parameters

• handle – mmffld handle

• st – structure to assign atom types

• apply_mmlewis – whether to apply mmlewis to the incoming structure

Raises

AtomTypingFailure – if mmffld_enterMol() fails

schrodinger.forcefield.common.generate_partial_charges(st: schrodinger.structure._structure.Structure, version: pymmlibs.OPLSVersion = 16)

Generates partial charges for a given structure. Results will be stored in the PARTIAL_CHARGE_PROP atom-level property.

Parameters

st – Structure for which partial charges are generated.