BioSimSpace.Protocol.ATMMinimisation

class BioSimSpace.Protocol.ATMMinimisation(system=None, data=None, steps=10000, core_alignment=True, com_distance_restraint=True, restraint=None, force_constant=10 kcal mol-1 Å-2, positional_restraint_width=0.5000 A, align_k_distance=2.5 kcal mol-1 Å-2, align_k_theta=10.0000 kcal/mol, align_k_psi=10.0000 kcal/mol, soft_core_umax=1000.0000 kcal/mol, soft_core_u0=500.0000 kcal/mol, soft_core_a=0.0625, com_k=25 kcal mol-1 Å-2, com_restraint_width=5.0000 A)

Minimisation protocol for ATM simulations.

__init__(system=None, data=None, steps=10000, core_alignment=True, com_distance_restraint=True, restraint=None, force_constant=10 kcal mol-1 Å-2, positional_restraint_width=0.5000 A, align_k_distance=2.5 kcal mol-1 Å-2, align_k_theta=10.0000 kcal/mol, align_k_psi=10.0000 kcal/mol, soft_core_umax=1000.0000 kcal/mol, soft_core_u0=500.0000 kcal/mol, soft_core_a=0.0625, com_k=25 kcal mol-1 Å-2, com_restraint_width=5.0000 A)

Parameters:

• system (System) – A prepared ATM system.

• data (dict) – The ATM data dictionary.

• core_alignment (bool) – Whether to use rigid core restraints to align the two ligands.

• align_k_distance (int, float, str, GeneralUnit) – The force constant for the distance portion of the alignment restraint (kcal/(mol A^2)).

• align_k_theta (int, float, str, Energy) – The force constant for the angular portion of the alignment restaint (kcal/mol).

• align_k_psi (int, float, str, Energy) – The force constant for the dihedral portion of the alignment restraint (kcal/mol).

• com_distance_restraint (bool) – Whether to use a center of mass distance restraint. This restraint applies to the protein/host and both ligands, and is used to maintain the relative positions of all of them.

• com_k (int, float, str, GeneralUnit) – The force constant for the center of mass distance restraint (kcal/mol/A^2).

• com_restraint_width (int, float, str, :class:`Length <BioSimSpace.Types.Length>) – The width (tolerance) of the center of mass distance restraint (A).

• restraint (str, [int]) –

  The type of restraint to perform. This should be one of the following options:

  ”backbone”

  Protein backbone atoms. The matching is done by a name template, so is unreliable on conversion between molecular file formats.

  ”heavy”

  All non-hydrogen atoms that aren’t part of water molecules or free ions.

  ”all”

  All atoms that aren’t part of water molecules or free ions.

  Alternatively, the user can pass a list of atom indices for more fine-grained control. If None, then no restraints are used.

• force_constant (GeneralUnit, float) – The force constant for the restraint potential. If a ‘float’ is passed, then default units of ‘kcal_per_mol / angstrom**2’ will be used.

• positional_restraint_width (Length, float) – The width of the flat-bottom potential used for coordinate restraint in Angstroms.

• pos_restrained_atoms ([int]) – The atoms to be restrained.

soft_core_umaxint, float, str, Energy

The Umax value for the ATM softcore potential (kcal/mol).

soft_core_u0int, float, str, Energy

The uh value for the ATM softcore potential (kcal/mol).

soft_core_aint, float, str, Energy

The a value for the ATM softcore potential.

Methods

__init__([system, data, steps, ...])
getAlignKDistance()	Return the align_k_distance value.
getAlignKPsi()	Return the align_k_psi value.
getAlignKTheta()	Return the align_k_theta value.
getCOMDistanceRestraint()	Return CMCM restraint boolean.
getCOMWidth()	Return the com_restraint_width value.
getCOMk()	Return the com_k value.
getCoreAlignment()	Return core alignment boolean.
getData()	Return the ATM data dictionary.
getForceConstant()	Return the force constant for the restraint.
getPosRestWidth()	Return the width of the position restraint.
getRestraint()	Return the type of restraint.
getSoftCoreA()	Return the soft_core_a value.
getSoftCoreU0()	Return the soft_core_u0 value.
getSoftCoreUmax()	Return the soft_core_umax value.
getSteps()	Return the number of minimisation steps.
restraints()	Return a list of the supported restraint keywords.
setAlignKDistance(align_k_distance)	Set the align_k_distance value.
setAlignKPsi(align_k_psi)	Set the align_k_psi value.
setAlignKTheta(align_k_theta)	Set the align_k_theta value.
setCOMDistanceRestraint(com_distance_restraint)	Set the CMCM restraint flag.
setCOMWidth(com_restraint_width)	Set the com_restraint_width value.
setCOMk(com_k)	Set the com_k value.
setCoreAlignment(core_alignment)	Set the core alignment flag.
setForceConstant(force_constant)	Set the force constant for the restraint.
setPosRestWidth(positional_restraint_width)	Set the width of the position restraint.
setRestraint(restraint)	Set the type of restraint.
setSoftCoreA(soft_core_a)	Set the soft_core_a value.
setSoftCoreU0(soft_core_u0)	Set the soft_core_u0 value.
setSoftCoreUmax(soft_core_umax)	Set the soft_core_umax value.
setSteps(steps)	Set the number of minimisation steps.

getAlignKDistance()

Return the align_k_distance value.

Returns:

align_k_distance – The align_k_distance value in kcal/mol angstrom**2.

Return type:

GeneralUnit

getAlignKPsi()

Return the align_k_psi value.

Returns:

align_k_psi – The align_k_psi value in kcal/mol.

Return type:

Energy

getAlignKTheta()

Return the align_k_theta value.

Returns:

align_k_theta – The align_k_theta value in kcal/mol.

Return type:

Energy

getCOMDistanceRestraint()

Return CMCM restraint boolean.

Returns:

com_distance_restraint – Whether to use the CMCM restraint.

Return type:

bool

getCOMWidth()

Return the com_restraint_width value.

Returns:

com_restraint_width – The com_restraint_width value in angstroms.

Return type:

Length

getCOMk()

Return the com_k value.

Returns:

com_k – The com_k value in kcal/mol A**2.

Return type:

GeneralUnit

getCoreAlignment()

Return core alignment boolean.

Returns:

core_alignment – Whether to use core alignment.

Return type:

bool

getData()

Return the ATM data dictionary.

Returns:

data – The ATM data dictionary.

Return type:

dict

getForceConstant()

Return the force constant for the restraint.

Returns:

force_constant – The force constant for the restraint, in units of kcal_per_mol/angstrom**2.

Return type:

float, str, class:GeneralUnit

getPosRestWidth()

Return the width of the position restraint.

Returns:

positional_restraint_width – The width of the position restraint.

Return type:

Length

getRestraint()

Return the type of restraint.

Returns:

restraint – The type of restraint, either a keyword or a list of atom indices.

Return type:

str, [int]

getSoftCoreA()

Return the soft_core_a value.

Returns:

soft_core_a – The soft_core_a value.

Return type:

float

getSoftCoreU0()

Return the soft_core_u0 value.

Returns:

soft_core_u0 – The soft_core_u0 value in kcal/mol.

Return type:

Energy

getSoftCoreUmax()

Return the soft_core_umax value.

Returns:

soft_core_umax – The soft_core_umax value in kcal/mol.

Return type:

Energy

getSteps()

Return the number of minimisation steps.

Returns:

steps – The number of minimisation steps.

Return type:

int

classmethod restraints()

Return a list of the supported restraint keywords.

Returns:

restraints – A list of the supported restraint keywords.

Return type:

[str]

setAlignKDistance(align_k_distance)

Set the align_k_distance value.

Parameters:

align_k_distance (int, float, str, GeneralUnit, float) – Length value for the alignment restraint kcal/mol angstrom**2.

setAlignKPsi(align_k_psi)

Set the align_k_psi value.

Parameters:

align_k_psi (int, float, str, Energy) – Force constant for the alignment dihedral constraint in kcal/mol.

setAlignKTheta(align_k_theta)

Set the align_k_theta value.

Parameters:

align_k_theta (int, float, str, Energy) – Force constant for the alignment angular constraint in kcal/mol.

setCOMDistanceRestraint(com_distance_restraint)

Set the CMCM restraint flag.

Parameters:

com_distance_restraint (bool) – Whether to use the CMCM restraint.

setCOMWidth(com_restraint_width)

Set the com_restraint_width value.

Parameters:

com_restraint_width (int, float, str, :class:`Length <BioSimSpace.Types.Length>) – The com_restraint_width value in angstroms.

setCOMk(com_k)

Set the com_k value.

Parameters:

com_k (int, float, str, :class:`GeneralUnit <BioSimSpace.Types._GeneralUnit>) – The force constant for the CM-CM force in kcal/mol A**2.

setCoreAlignment(core_alignment)

Set the core alignment flag.

Parameters:

core_alignment (bool) – Whether to use core alignment.

setForceConstant(force_constant)

Set the force constant for the restraint.

Parameters:

force_constant (int, float, str, GeneralUnit, float) – The force constant for the restraint, in units of kcal_per_mol/angstrom**2.

setPosRestWidth(positional_restraint_width)

Set the width of the position restraint.

Parameters:

positional_restraint_width (int, float, str, Length) – The width of the position restraint.

setRestraint(restraint)

Set the type of restraint.

Parameters:

restraint (str, [int]) –

The type of restraint to perform. This should be one of the following options:

”backbone”

Protein backbone atoms. The matching is done by a name template, so is unreliable on conversion between molecular file formats.

”heavy”

All non-hydrogen atoms that aren’t part of water molecules or free ions.

”all”

All atoms that aren’t part of water molecules or free ions.

Alternatively, the user can pass a list of atom indices for more fine-grained control.

setSoftCoreA(soft_core_a)

Set the soft_core_a value.

Parameters:

soft_core_a (float) – The softcore a value.

setSoftCoreU0(soft_core_u0)

Set the soft_core_u0 value.

Parameters:

soft_core_u0 (int, float, str, Energy) – The softcore u0 value in kcal/mol.

setSoftCoreUmax(soft_core_umax)

Set the soft_core_umax value.

Parameters:

soft_core_umax (int, float, str, Energy) – The softcore Umax value in kcal/mol.

setSteps(steps)

Set the number of minimisation steps.

Parameters:

steps (int) – The number of minimisation steps.