schrodinger.forcefield.minimizer module¶
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schrodinger.forcefield.minimizer.
minimize_structure
(mmffld_handle, st, restraints=None, constraints=None, debug_outfile=None, perturb=False, nonbond_cutoff=14.0)¶ Minimizes a single structure.
Parameters: - mmffld_handle (integer) – force field handle
- st (schrodinger.structure object) – structure
- restraints (list of Restraints) – minimization restraint list
- constraints (list of Constraints) – minimization constraint list
- debug_outfile (string) – output file name
- perturb (bool) – perturb structure prior to minimizetion
- nonbond_cutoff (float) – nonbonded cutoff value
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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)¶ Bases:
object
Class representing restraints.
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__init__
(force_constant, target_value, atom_index1, atom_index2, atom_index3, atom_index4, flat_bottom_half_width)¶ Initialize self. See help(type(self)) for accurate signature.
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class
schrodinger.forcefield.minimizer.
Constraint
(atom_index1, atom_index2, type_index1, type_index2, use_rigorous=False)¶ Bases:
object
Class representing constraints.
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__init__
(atom_index1, atom_index2, type_index1, type_index2, use_rigorous=False)¶ Initialize self. See help(type(self)) for accurate signature.
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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
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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