BioSimSpace.Protocol.Minimisation#

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

A class for storing minimisation protocols.

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

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.

Return type:

str, [int]

getSteps()[source]#

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)[source]#

Set the maximum number of steps.

Parameters:

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