schrodinger.forcefield.minimizer module¶
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class
schrodinger.forcefield.minimizer.
Restraint
(force_constant, target_value, atom_index1, atom_index2, atom_index3, atom_index4, flat_bottom_half_width)[source]¶ Bases:
object
Class representing restraints.
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class
schrodinger.forcefield.minimizer.
Constraint
(atom_index1, atom_index2, type_index1, type_index2, use_rigorous=False)[source]¶ Bases:
object
Class representing constraints.
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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)[source]¶ Bases:
tuple
Class for assigning the mmffld minimization options.
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opls_version
: int¶ Alias for field number 0
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nonbond_cutoff
: float¶ Alias for field number 1
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max_step
: int¶ Alias for field number 2
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energy_convergence
: float¶ Alias for field number 3
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gradient_convergence
: float¶ Alias for field number 4
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line_search_method
: int¶ Alias for field number 5
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min_method
: int¶ Alias for field number 6
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no_restrain_zob
: bool¶ Alias for field number 7
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bend_conj_amines
: bool¶ Alias for field number 8
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perturb
: bool¶ Alias for field number 9
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restraints
: Optional[List[schrodinger.forcefield.minimizer.Restraint]]¶ Alias for field number 10
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constraints
: Optional[List[schrodinger.forcefield.minimizer.Constraint]]¶ Alias for field number 11
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debug_outfile
: Optional[str]¶ Alias for field number 12
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__contains__
(key, /)¶ Return key in self.
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__len__
()¶ Return len(self).
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count
(value, /)¶ Return number of occurrences of value.
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index
(value, start=0, stop=9223372036854775807, /)¶ Return first index of value.
Raises ValueError if the value is not present.
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schrodinger.forcefield.minimizer.
minimize_structure
(st: schrodinger.structure._structure.Structure, options: Optional[schrodinger.forcefield.minimizer.MinimizationOptions] = None, archive_path: Optional[os.PathLike] = None)[source]¶ 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
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schrodinger.forcefield.minimizer.
iterate_minimize_structure
(st, iteration, options=None)[source]¶ 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
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schrodinger.forcefield.minimizer.
write_restraints
(filename, restraints)[source]¶ Writes restraints into filename.
- Parameters
filename (string) – restraint filename
restraints (list of Restraints) – a list to be filled with restraints
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schrodinger.forcefield.minimizer.
read_restraints
(filename, restraints=None, constraints=None)[source]¶ 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