schrodinger.forcefield.common module¶
OPLS context managers.
Copyright Schrodinger LLC, All Rights Reserved.
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exception
schrodinger.forcefield.common.
AtomTypingFailure
(msg='')[source]¶ Bases:
schrodinger.infra.mmcheck.MmException
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__init__
(msg='')[source]¶ Initialize with the wrapped function, arguments used, and the return code.
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args
¶
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with_traceback
()¶ Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.
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schrodinger.forcefield.common.
mmffld_environment
()[source]¶ A context manager for loading the mmffld environment.
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schrodinger.forcefield.common.
opls_force_field
(version: pymmlibs.OPLSVersion = 16, archive_path: Optional[os.PathLike] = None, bend_conj_amines: bool = False, no_cm1a_bcc: bool = False, charges_from_ct: bool = False)[source]¶ A context manager for creating a force field handle, using default precedence for loading ffld datafiles.
- Parameters
version – OPLS version number
archive_path – path to specific .opls file
bend_conj_amines – bend conjungated amine
no_cm1a_bcc – don’t use cm1a_bcc for OPLS version 16
charges_from_ct – obtain charges from ct
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schrodinger.forcefield.common.
assign_force_field
(mmffld_handle: pymmlibs.MMFfldHandle, st: schrodinger.structure._structure.Structure, apply_mmlewis: bool = True)[source]¶ 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
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schrodinger.forcefield.common.
generate_partial_charges
(st: schrodinger.structure._structure.Structure, version: pymmlibs.OPLSVersion = 16)[source]¶ 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.