repESP.respin_generation module

Creating resp program input for predefined ESP fitting types

This module may be useful if you require custom instructions for the resp program. Otherwise, the functions in the resp_wrapper module should be sufficient and more convenient.

class RespinGenerator

Bases: abc.ABC

Interface for creators of resp fitting instructions

This interface will be implemented differently for different types of fitting with the resp program. This module provides implementations for the most common fitting types.

An implementation of this interface is required by the prepare_respin function.

resp_type() → str

Return the human-readable description of the type of fitting

get_ivary() → repESP.respin_format.Respin.Ivary

Create the “ivary” section of the “respin” file

get_cntrl() → repESP.respin_format.Respin.Cntrl

Create the “cntrl” section of the “respin” file

class RespRespinGenerator(ivary: repESP.respin_format.Respin.Ivary)

Bases: repESP.respin_generation.RespinGenerator

Base class providing “respin” creation methods for RESP charges

get_ivary() → repESP.respin_format.Respin.Ivary

Create the “ivary” section of the “respin” file

classmethod from_respin(respin: repESP.respin_format.Respin) → RespRespinGeneratorT

Alternative initialization from a “respin” file

This alternative initializer expresses the fact that this object can be created directly from an existing “respin” file, when the contained “ivary” section expresses the desired per-atom fitting instructions.

Parameters:respin (Respin) – An object representing pre-existing instructions to the resp program.

classmethod from_methyl_and_methylene(equivalence: repESP.equivalence.Equivalence, methyl_methylene_mask: List[bool]) → RespRespinGeneratorT

Alternative initialization from chemical information

The per-atom fitting instructions in the RESP charge optimization depend on the chemical equivalence and whether a given carbon or hydrogen atom belongs to a methyl or methylene group.

Parameters:

• equivalence (Equivalence) – The chemical equivalence relations between atoms in the molecule.
• methyl_methylene_mask (typing.List[bool]) – A list, in which each value describes an atom of the molecule. The value should be True when the atom is a carbon or hydrogen atom in a methyl or methylene group and False otherwise.

Raises:

ValueError – Raised when the length of the values attribute of the equivalence argument is not equal to the length of the methyl_methylene_mask argument.

class RespStage1RespinGenerator(ivary: repESP.respin_format.Respin.Ivary)

Bases: repESP.respin_generation.RespRespinGenerator

Creator of “respin” files for 1st stage RESP fitting

The original RESP procedure is conducted in two stages and this object prepares the input for the first stage. In this stage, carbon and hydrogen atoms in methyl and methylene groups vary freely, while other atoms need to obey chemical equivalence relations. The magnitudes of charges on all atoms are constrained with hyperbolic constraints with a weight factor of 0.0005.

Parameters:ivary (Respin.Ivary) – The “ivary” section of a “respin” file for 1st stage RESP fitting.

resp_type() → str

Return the human-readable description of the type of fitting

get_cntrl() → repESP.respin_format.Respin.Cntrl

Create the “cntrl” section of the “respin” file

classmethod from_methyl_and_methylene(equivalence: repESP.equivalence.Equivalence, methyl_methylene_mask: List[bool]) → RespStage1RespinGeneratorT

See documentation in base class (RespRespinGenerator)

class RespStage2RespinGenerator(ivary: repESP.respin_format.Respin.Ivary)

Bases: repESP.respin_generation.RespRespinGenerator

Creator of “respin” files for 2nd stage RESP fitting

The original RESP procedure is conducted in two stages and this object prepares the input for the second stage. In this stage, carbon and hydrogen atoms in methyl and methylene groups are varied subject to equivalence relations and the magnitudes of the charges are constrained with hyperbolic constraints with a weight factor of 0.001. Other atoms are frozen at initial charge values, which should come from 1st stage fitting.

Parameters:ivary (Respin.Ivary) – The “ivary” section of a “respin” file for 2nd stage RESP fitting.

resp_type() → str

Return the human-readable description of the type of fitting

get_cntrl() → repESP.respin_format.Respin.Cntrl

Create the “cntrl” section of the “respin” file

classmethod from_methyl_and_methylene(equivalence: repESP.equivalence.Equivalence, methyl_methylene_mask: List[bool]) → RespStage2RespinGeneratorT

See documentation in base class (RespRespinGenerator)

class FitHydrogensOnlyRespinGenerator(equivalence: repESP.equivalence.Equivalence, molecule: repESP.types.Molecule[repESP.types.Atom][repESP.types.Atom])

Bases: repESP.respin_generation.RespinGenerator

Supports creation of “respin” files for fitting only hydrogen atoms

The generated “respin” file instructs resp to perform fitting in which only hydrogen atoms are free to vary, subject to equivalence relations.

Parameters:

• equivalence (Equivalence) – The equivalence relations between atoms of the molecule.
• molecule (Molecule[Atom]) – The molecule which charges are being fitted. Only atom identities are required.

resp_type() → str

Return the human-readable description of the type of fitting

get_ivary() → repESP.respin_format.Respin.Ivary

Create the “ivary” section of the “respin” file

get_cntrl() → repESP.respin_format.Respin.Cntrl

Create the “cntrl” section of the “respin” file

class EquivalenceOnlyRespinGenerator(equivalence: repESP.equivalence.Equivalence)

Bases: repESP.respin_generation.RespinGenerator

Supports creation of “respin” files with no constraints beyond equivalence

The generated “respin” file instructs resp to perform fitting in which atoms are free to vary, subject only to equivalence relations.

Parameters:equivalence (Equivalence) – The equivalence relations between atoms of the molecule.

resp_type() → str

Return the human-readable description of the type of fitting

get_ivary() → repESP.respin_format.Respin.Ivary

Create the “ivary” section of the “respin” file

get_cntrl() → repESP.respin_format.Respin.Cntrl

Create the “cntrl” section of the “respin” file

class FrozenAtomsRespinGenerator(equivalence: repESP.equivalence.Equivalence, frozen_atoms: List[int])

Bases: repESP.respin_generation.RespinGenerator

Supports creation of “respin” files excluding selected atoms from fitting

The generated “respin” file instructs resp to perform fitting in which atoms are free to vary (subject to equivalence relations) unless they are explicitly excluded from the fitting by being listed in the frozen_atoms argument.

Parameters:

• equivalence (Equivalence) – The equivalence relations between atoms of the molecule.
• frozen_atoms (typing.List[int]) – List of zero-based indices of atoms in the molecule which are to be excluded from the fitting.

resp_type() → str

Return the human-readable description of the type of fitting

get_ivary() → repESP.respin_format.Respin.Ivary

Create the “ivary” section of the “respin” file

get_cntrl() → repESP.respin_format.Respin.Cntrl

Create the “cntrl” section of the “respin” file

prepare_respin(respin_generator: repESP.respin_generation.RespinGenerator, total_charge: int, molecule: repESP.types.Molecule[repESP.types.Atom][repESP.types.Atom], title: Optional[str] = None, subtitle: Optional[str] = None, read_charges: bool = False) → repESP.respin_format.Respin

Create resp program instructions based on input options

This function allows to create resp program instructions from higher-level abstractions.

Parameters:

• respin_generator (RespinGenerator) – An object implementing the RespinGenerator interface. This object expresses a given type of charge fitting through instructions understood by resp. Implementations of this interface for common fitting types are provided in this module.
• total_charge (int) – The total charge of the molecule.
• molecule (Molecule[Atom]) – The molecule which charges are being fitted. Only atom identities are required.
• title (Optional[str], optional) – The title for the optimization. If set to None (default), a default title will be used, referencing the repESP library and the type of the fitting as given by the respin_generator used.
• subtitle (Optional[str], optional) – The subttitle for the fitted structure. If set to None (default), a default generic subtitle will be used.
• read_charges (bool, optional) –

  If this option is set to True, resp will require initial charges for the fitting. Defaults to False.

  Note

  It is the responsibility of the respin_generator to instruct resp to read initial charges when they affect the result of the optimization. This parameter should only be used when the user wishes to aid the optimization by supplying an initial guess.

Returns:

An object representing the fitting instructions for the resp program.

Return type:

Respin