BioSimSpace.Protocol.Minimisation

class BioSimSpace.Protocol.Minimisation(steps=10000, restraint=None, force_constant=10 kcal mol-1 Å-2)

A class for storing minimisation protocols.

__init__(steps=10000, restraint=None, force_constant=10 kcal mol-1 Å-2)

Constructor.

Parameters:

• steps (int) – The maximum number of steps to perform.

• 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.

Methods

__init__([steps, restraint, force_constant])	Constructor.
getForceConstant()	Return the force constant for the restraint.
getRestraint()	Return the type of restraint.
getSteps()	Return the maximum number of steps.
restraints()	Return a list of the supported restraint keywords.
setForceConstant(force_constant)	Set the force constant for the restraint.
setRestraint(restraint)	Set the type of restraint.
setSteps(steps)	Set the maximum number of steps.

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

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]

getSteps()

Return the maximum number of steps.

Returns:

steps – The maximum 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]

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.

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.

setSteps(steps)

Set the maximum number of steps.

Parameters:

steps (int) – The maximum number of minimisation steps.