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Minimizer
A class to provide force field energy and minimization.
For simple cases the minimize_structure function can be used. Direct use of this class is mostly useful for cases where multiple conformers are to be minimized, as the updateCoordinates() method allows one to avoid running atom-typing for every conformer.
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| float |
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| float |
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Inherited from |
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min_method See the constructor method for documentation. |
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max_steps See the constructor method for documentation. |
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energy_criterion See the constructor method for documentation. |
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gradient_criterion See the constructor method for documentation. |
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verbose See the constructor method for documentation. |
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energy_no_electrostatics See the constructor method for documentation. |
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energy_lj_repulsive_only See the constructor method for documentation. |
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nonbonded_cutoff See the constructor method for documentation. |
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maintain_planarity See the constructor method for documentation. |
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no_zob_restrain See the constructor method for documentation. |
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charges_from_ct See the constructor method for documentation. |
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dielectric_constant See the constructor method for documentation. |
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min_converged Return 1 if last minimization converged, 0 if it didn't. |
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min_rms_gradient Return the RMS gradient of the last minimization. |
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min_energy Return the energy calculated in the last minimization. |
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Initialize.
Additional keyword arguments will be used to set properties of the
instance. See the __init__() method for supported property names.
Parameters
@type ffld_version: integer module constant
@param ffld_version: Use one of the valid force fields from
mmcommon_get_valid_forcefields() Default is to use the force
field that is selected in Maestro preferences.
@type struct: schrodinger.structure.Structure
@param struct:
The structure to be minimized.
@type cleanup: bool
@param cleanup:
If True, attempts to automatically clean up the structure will
be made. (This uses the C function C{mmlewis_apply()}.) Note
that this can modify the atom types of the passed in structure.
@type min_method: enum
@keyword min_method: The minimizer method. Valid values are MinBFGS,
MinAUTO and MinCG. Default is MinAUTO, which uses BFGS if number of
atoms is less than 500, CG otherwise.
@type max_steps: int
@keyword max_steps: The maximum number of steps to run the mimization
for. Default is 1500.
@type energy_criterion: float
@keyword energy_criterion: The energy convergence criterion.
Default is 5.0e-09.
@type gradient_criterion: float
@keyword gradient_criterion: The gradient convergence criterion.
Default is 0.05.
@type verbose: bool
@keyword verbose: Printing verbosity. Default is False.
@type energy_no_electrostatics: bool
@keyword energy_no_electrostatics: Whether to turn off electrostatics.
Default is False, i.e. to use electrostatics.
NOTE: Can not be modified after the instance is created
@type energy_lj_repulsive_only: bool
@keyword energy_lj_repulsive_only: Whether to use only the repulsive
portion of the Lennard-Jones term. Default is False.
NOTE: Can not be modified after the instance is created
@type nonbonded_cutoff: float
@keyword nonbonded_cutoff: The cutoff for non-bonded interactions. It
will be automatically scaled down for small BPC boxes.
Default is 14.0.
@type maintain_planarity: bool
@keyword maintain_planarity: Enable scaling of forces to artificially
maintain planarity of certain sub-structures. This sets associated
scale factors to their default values. Default is False.
NOTE: Can not be modified after the instance is created
@type dielectric_constant: float
@keyword dielectric_constant: The strength of the constant dielectric
field used in the energy calculation. The default is 1.0 (vacuum).
@type no_zob_restrain: bool
@keyword no_zob_restrain: The default (False) is to restrain zero-order
metal bonds to their input value. Setting this to True causes the
forcefield parameters to be taken from lookup results if possible.
@type charges_from_ct: bool
@keyword charges_from_ct: The default (False) is to use the
charges from the force field. Setting this to True causes the
charges from the ct to be used.
@param honor_pbc: Honor Periodic Boundary Conditions, if defined as
properties in the structure. Default is True.
@type honor_pbc: bool
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Initialize needed mmlibs. This method is called by the Minimizer constructor, so if Minimizer objects are used there is no need to explicitly call it. |
Terminate the mmlibs initialized in the initialize method. It's only necessary to call this method if you want to free resources used by the underlying lib. Note that this terminate method isn't automatically called in the __del__ method of Minimizer. This is because there is significant overhead to reading the force field data and it won't be re-read as long as the library reference count is greater than zero. |
Update the coordinates of the current structure with the values from the provided struct. This allows an additional conformer to be minimized without re-running atomtyping. It is the caller's responsibility to make sure the molecules are equivalent and have the same atomtypes (i.e. same charges, connectivity). |
Minimize the provided Structure. Store results as properties in the Structure. Note that this method will require a valid product license. Currently, MacroModel, GLIDE, Impact, or PLOP will suffice. |
Get energy components for bonded terms given in an list of stretches/bend/torsions/improper torsions (given as integer numbers) in *_item_list. The *_energy_list arguments are ignored. Returns the corresponding energies as a tuple of double lists: (stretch_energy_list, bending_energy_list, torsion_energy_list, imp_torsion_energy_list). Atoms are counted starting at zero. NOTE: The API of this function may change in the next release. |
TODO: this API should be eliminated. This is currently called by test programs in /mmshare/mmlibs/mmffld/test/*.py and one could replace the use of this API by calling getInteractionEnergyComponents() see Ev:133233. Get the non-bonded energy components for two cases:
Note that atom_list_j is a list (of len(atom_list_i)) of lists. The energy components are returned in a vector of length atom_list_i of a vector (of length atom_list_j) of a vector of double which includes the following energy components: 1) A_ij *R^-12 2) -B_ij *R^-6 3) Coulomb energy 4) interatomic distance r_ij Note that this method will require a valid product license. Currently, MacroModel, GLIDE, Impact, or PLOP will suffice. Atoms are counted starting at zero. |
Get the non-bonded energy components for two arbitrary list of atoms. The total Coulomb and LJ interaction energies are returned. |
Change the structure to be minimized. This method generally won't need to be called by the end user. To minimize different molecules, it is preferable to create separate Minimizer instances. If only the coordinates of the structure changed, it is much faster to call updateCoordinates() instead of setStructure(). |
Run a zero-step minimization to calculate the energy, and return it. Also stores the energy in the structure properties. Units are kcal/mol.
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Set Minimizer options by keyword. To be used only internally by the constructor. |
Define a torsional restraint.
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Define an angle restraint.
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Define a distance restraint.
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Define a positional restraint.
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Define a frozen atom.
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Delete all the restraints for a given type (default all types).
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Return bonded energies for bonded interactions within the given atom subset.
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Return the bonded component of the interaction energy between the two given atom sets. If the second subset is not specified, instead use all other atoms from the CT.
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Given a list of atoms representing a substructure (e.g. a residue), return a tuple of:
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Return the internal energy of the the given atoms. This is the sum of all bonded interactions between the given atoms.
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Return the potential energy of the the given atoms. It is a sum of bonded interactions within the atom set and the non-bonded interactions between the atom set and the rest of the structure (honoring the NB-cutoff). By default, the internal interaction energy is also included.
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Returns the interaction energy between the two atom groups. Private method, use getInteractionEnergy() instead.
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Calculate the energy of interaction between the <subset_atoms> and the <consider_atoms>. If <consider_atoms> is not specified, then returns a sum of all interactions between the <subset_atoms> and the rest of the atoms. Note that in the default case where <consider_atoms> is None, atoms outside of the cutoff are not considered.
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min_methodSee the constructor method for documentation.
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max_stepsSee the constructor method for documentation.
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energy_criterionSee the constructor method for documentation.
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gradient_criterionSee the constructor method for documentation.
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verboseSee the constructor method for documentation.
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energy_no_electrostaticsSee the constructor method for documentation.
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energy_lj_repulsive_onlySee the constructor method for documentation.
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nonbonded_cutoffSee the constructor method for documentation.
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maintain_planaritySee the constructor method for documentation.
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no_zob_restrainSee the constructor method for documentation.
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charges_from_ctSee the constructor method for documentation.
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dielectric_constantSee the constructor method for documentation.
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min_convergedReturn 1 if last minimization converged, 0 if it didn't.
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min_rms_gradientReturn the RMS gradient of the last minimization.
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min_energyReturn the energy calculated in the last minimization.
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