schrodinger.structutils.minimize module¶
A module for force field energy evaluation and minimization.
A non-conformer serial minimization should use the minimize function:
for st in structure.StructureReader('various_ligands.mae'):
minimize.minimize_structure(st)
st.append('various_ligands-mini-out.mae')
A conformer serial minimization can reduce atom-typing overhead by using the Minimizer class:
for index, st in enumerate(structure.StructureReader('conformers.mae')):
if index == 0:
min = minimize.Minimizer(struct=st)
else:
min.updateCoordinates(st)
min.minimize()
st = min.getStructure()
st.append('conformers-out.mae')
Copyright Schrodinger, LLC. All rights reserved.
-
schrodinger.structutils.minimize.
get_energy
(struct)[source]¶ Return the force field energy for a Structure. Units are kcal/mol.
- Parameters
ffld_version – One of the valid force fields
-
schrodinger.structutils.minimize.
minimize_structure
(struct, ffld_version=None, cleanup=True, **kwargs)[source]¶ Minimize the provided structure.
Additional keyword arguments will be used to set properties of the Minimizer instance. See the Minimizer.__init__() method for supported property names.
- Parameters
ffld_version (integer module constant) – The force field to use. Default is to use the force field that is selected in Maestro preferences.
cleanup (bool) – If True, attempts to automatically clean up the structure will be made. (This uses the C function
mmlewis_apply()
.) Note that this can modify the atom types of the passed in structure.kwargs – Additional keyword arguments.
-
class
schrodinger.structutils.minimize.
Minimizer
(ffld_version=None, struct=None, cleanup=True, honor_pbc=True, **kwargs)[source]¶ Bases:
object
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.
-
__init__
(ffld_version=None, struct=None, cleanup=True, honor_pbc=True, **kwargs)[source]¶ Initialize.
Additional keyword arguments will be used to set properties of the instance. See the __init__() method for supported property names.
- Parameters
ffld_version (integer module constant) – Use one of the valid force fields. Default is to use the force field that is selected in Maestro preferences.
struct (schrodinger.structure.Structure) – The structure to be minimized.
cleanup (bool) – If True, attempts to automatically clean up the structure will be made. (This uses the C function
mmlewis_apply()
.) Note that this can modify the atom types of the passed in structure.min_method (enum) – 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.
max_steps (int) – The maximum number of steps to run the mimization for. Default is 1500.
energy_criterion (float) – The energy convergence criterion. Default is 5.0e-09.
gradient_criterion (float) – The gradient convergence criterion. Default is 0.05.
verbose (bool) – Printing verbosity. Default is False.
energy_no_electrostatics (bool) – Whether to turn off electrostatics. Default is False, i.e. to use electrostatics. NOTE: Can not be modified after the instance is created
energy_lj_repulsive_only (bool) – 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
nonbonded_cutoff (float) – The cutoff for non-bonded interactions. It will be automatically scaled down for small BPC boxes. Default is 14.0.
maintain_planarity (bool) – 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
dielectric_constant (float) – The strength of the constant dielectric field used in the energy calculation. The default is 1.0 (vacuum).
no_zob_restrain (bool) – 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.
charges_from_ct (bool) – 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.
honor_pbc (bool) – Honor Periodic Boundary Conditions, if defined as properties in the structure. Default is True.
-
updateCoordinates
(struct)[source]¶ 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
()[source]¶ 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.
-
getBondedEnergyComponents
(stretch_item_list, bending_item_list, torsion_item_list, imp_torsion_item_list)[source]¶ 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.
-
getNBEnergyForTwoAtomLists
(atom_list_i, atom_list_j)[source]¶ Get the non-bonded energy components for two arbitrary list of atoms. The total Coulomb and LJ interaction energies are returned.
-
setStructure
(struct)[source]¶ 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().
-
getEnergy
(recalc=None)[source]¶ Run a zero-step minimization to calculate the energy, and return it. Also stores the energy in the structure properties. Units are kcal/mol.
- Parameters
recalc (bool) – Deprecated, and will propably go away. If previously calculated energy is needed, use the Minimizer.min_energy property.
-
setOptions
(**kwargs)[source]¶ Set Minimizer options by keyword. To be used only internally by the constructor.
-
addTorsionRestraint
(i, j, k, l, force_constant, target, flat_bottom=0.0)[source]¶ Define a torsional restraint.
- Parameters
j, k, l (i,) – atoms defining the restraint
force_constant (float) – force constant
target (float) – target value
flat_bottom (float) – flat-bottom half width (default 0.0)
-
addAngleRestraint
(i, j, k, force_constant, target, flat_bottom=0.0)[source]¶ Define an angle restraint.
- Parameters
j, k (i,) – atoms defining the restraint
force_constant (float) – force constant
target (float) – target value
flat_bottom (float) – flat-bottom half width (default 0.0)
-
addDistanceRestraint
(i, j, force_constant, target, flat_bottom=0.0)[source]¶ Define a distance restraint.
- Parameters
j (i,) – atoms defining the restraint
force_constant (float) – force constant
target (float) – target value
flat_bottom (float) – flat-bottom half width (default 0.0)
-
addPosRestraint
(i, force_constant, flat_bottom=0.0)[source]¶ Define a positional restraint.
- Parameters
i (int) – atom defining the restraint
force_constant (float) – force constant
flat_bottom (float) – flat-bottom half width (default 0.0)
-
deleteAllRestraints
(rest_type=0)[source]¶ Delete all the restraints for a given type (default all types).
- Parameters
rest_type (mm Constant) – One of: - mm.MMFfldTorsionRest - mm.MMFfldPosRest - mm.MMFfldPosFrozen - mm.MMFfldAllRestType
-
property
min_method
¶ See the constructor method for documentation.
-
property
max_steps
¶ See the constructor method for documentation.
-
property
energy_criterion
¶ See the constructor method for documentation.
-
property
gradient_criterion
¶ See the constructor method for documentation.
-
property
verbose
¶ See the constructor method for documentation.
-
property
energy_no_electrostatics
¶ See the constructor method for documentation.
-
property
energy_lj_repulsive_only
¶ See the constructor method for documentation.
-
property
nonbonded_cutoff
¶ See the constructor method for documentation.
-
property
maintain_planarity
¶ See the constructor method for documentation.
-
property
no_zob_restrain
¶ See the constructor method for documentation.
-
property
charges_from_ct
¶ See the constructor method for documentation.
-
property
dielectric_constant
¶ See the constructor method for documentation.
-
property
min_energy
¶ Return the energy calculated in the last minimization.
-
getBondedEnergies
(atom_subset)[source]¶ Return bonded energies for bonded interactions within the given atom subset.
- Parameters
atom_subset (List of atom indices.) – Atoms to calculate bonded energies for.
- Returns
(stretch-energy, bend-energy, torsion-energy, imp-tor-energy)
- Return type
tuple
-
getBondedInteractionEnergy
(atomset1, atomset2=None, verbose=False)[source]¶ 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.
- Parameters
atomset1 (List of atom indices.) – Atoms from the first subset.
atomset2 (List of atom indices.) – Atoms from the second subset.
- Returns
The bonded interaction energy.
- Return type
float
-
getNonBondedEnergies
(atom_subset, verbose=False)[source]¶ Given a list of atoms representing a substructure (e.g. a residue), return a tuple of:
the sum of non-bonded energies WITHIN the set.
the sum of non-bonded energies between the set atoms and everything else.
- Parameters
atom_subset (list(int)) – Atoms indicies to calculate non-bonded energies for
- Returns
(internal non-bonded energy in kcal/mol, non-bonded interaction energy in kcal/mol)
- Return type
tuple
-
getSelfEnergy
(atom_subset, include_intra_nb=True)[source]¶ Return the internal energy of the the given atoms. This is the sum of all bonded interactions between the given atoms.
- Parameters
atom_subset (List of atom indices.) – Atoms to calculate self-energy for.
include_intra_nb (bool) – If True, include non-bonded interaction energy within the given subset. If False, include only bonded interactions.
- Returns
Total self-energy
- Return type
float
-
getInteractionEnergy
(subset_atoms, consider_atoms=None, include_bonded=False, verbose=False)[source]¶ 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.
- Parameters
subset_atoms (List of atom indices.) – First atom set.
consider_atoms (List of atom indices.) – Second atom set (optional)
include_bonded (Boolean.) – Whether to also include bonded terms. By default, only non-bonded interactions are included, even if the atom sets are covalently bonded, and any bonded interactions are excluded.
- Returns
Interaction energy betwen the given atom sets (or between the given atom sets and the rest of the structure).
- Return type
float
-