schrodinger.forcefield.minimizer module

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
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)

Initialize self. See help(type(self)) for accurate signature.

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)

Initialize self. See help(type(self)) for accurate signature.

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
schrodinger.forcefield.minimizer.setup_mmffld_min(mmffld_handle)

Initializes the mmffld handle for structural minimization. This function is used in the parameter fitting module of ffbuilder.

Parameters:mmffld_handle (integer) – the force field handle with parameters loaded