BioSimSpace.Protocol.ATMAnnealing¶

class BioSimSpace.Protocol.ATMAnnealing(system=None, data=None, timestep=2.0000 fs, runtime=0.2000 ns, temperature=300.0000 K, pressure=1.0000 atm, thermostat_time_constant=1.0000 ps, report_interval=100, restart_interval=100, core_alignment=True, com_distance_restraint=True, com_k=25 kcal mol-1 Å-2, com_restraint_width=5.0000 A, 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, direction=1, lambda1=0.0, lambda2=0.0, alpha=0.0, uh=0.0, W0=0.0, anneal_values='default', anneal_numcycles=100)[source]¶

Annealing protocol for ATM simulations.

__init__(system=None, data=None, timestep=2.0000 fs, runtime=0.2000 ns, temperature=300.0000 K, pressure=1.0000 atm, thermostat_time_constant=1.0000 ps, report_interval=100, restart_interval=100, core_alignment=True, com_distance_restraint=True, com_k=25 kcal mol-1 Å-2, com_restraint_width=5.0000 A, 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, direction=1, lambda1=0.0, lambda2=0.0, alpha=0.0, uh=0.0, W0=0.0, anneal_values='default', anneal_numcycles=100)[source]¶

Create a new annealing protocol.

Parameters:

system (System) – A prepared ATM system.
data (dict) – The ATM data dictionary.
timestep (str, Time) – The integration timestep.
runtime (str, Time) – The running time.
temperature (str, Temperature) – The temperature.
pressure (str, Pressure) – The pressure. Pass pressure=None to use the NVT ensemble.
thermostat_time_constant (str, Time) – Time constant for thermostat coupling.
report_interval (int) – The frequency at which statistics are recorded. (In integration steps.)
restart_interval (int) – The frequency at which restart configurations and trajectory
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 (float, GeneralUnit) – 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 (float, Length) – The width of the flat-bottom potential used for coordinate restraint in Angstroms.
pos_restrained_atoms ([int]) – The atoms to be restrained.
soft_core_umax (int, float, str, Energy) – The Umax value for the ATM softcore potential (kcal/mol).
soft_core_u0 (int, float, str, Energy) – The uh value for the ATM softcore potential (kcal/mol).
soft_core_a (int, float, str, Energy) – The a value for the ATM softcore potential.
direction (str) – The direction of the Annealing.
lambda1 (float) – The lambda1 value for the ATM force. Superceded by any values defined in anneal_values.
lambda2 (float) – The lambda2 value for the ATM force. Superceded by any values defined in anneal_values.
alpha (int, float, str, Energy) – The alpha value for the ATM force. Value in kcal/mol. Superceded by any values defined in anneal_values.
uh (int, float, str, Energy) – The uh value for the ATM force. Value in kcal/mol. Superceded by any values defined in anneal_values.
W0 (int, float, str, Energy) – The W0 value for the ATM force. Value in kcal/mol. Superceded by any values defined in anneal_values.
anneal_values (dict, None, "default") –
If None, then no annealing will be performed. If “default”, then lambda values will be annealed from 0 to 0.5. If more complex annealing is required, then a dictionary with some or all of the following keys should be given:

”lambda1_start”float
The starting value for lambda1.

”lambda1_end”float
The ending value for lambda1.

”lambda2_start”float
The starting value for lambda2.

”lambda2_end”float
The ending value for lambda2.

”alpha_start”float
The starting value for alpha.

”alpha_end”float
The ending value for alpha.

”uh_start”float
The starting value for uh.

”uh_end”float
The ending value for uh.

”W0_start”float
The starting value for W0.

”W0_end”float
The ending value for W0

Any unspecified values will use their default lambda=0 value.
anneal_numcycles (int) – The number of annealing cycles to perform, defines the rate at which values are incremented. Default 100.

Methods

`__init__`([system, data, timestep, runtime, ...])	Create a new annealing protocol.
`getAlignKDistance`()	Return the align_k_distance value.
`getAlignKPsi`()	Return the align_k_psi value.
`getAlignKTheta`()	Return the align_k_theta value.
`getAlpha`()	Return the alpha value for the ATM force.
`getAnnealNumCycles`()	Return the number of annealing cycles.
`getAnnealValues`()	Return the anneal protocol.
`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.
`getDirection`()	Return the direction of the equilibration.
`getForceConstant`()	Return the force constant for the restraint.
`getLambda1`()	Return the lambda1 value for the ATM force.
`getLambda2`()	Return the lambda2 value for the ATM force.
`getPosRestWidth`()	Return the width of the position restraint.
`getPressure`()	Return the pressure.
`getReportInterval`()	Return the interval between reporting statistics.
`getRestartInterval`()	Return the interval between saving restart confiugrations, and/or trajectory frames.
`getRestraint`()	Return the type of restraint.
`getRunTime`()	Return the running time.
`getSoftCoreA`()	Return the soft_core_a value.
`getSoftCoreU0`()	Return the soft_core_u0 value.
`getSoftCoreUmax`()	Return the soft_core_umax value.
`getTemperature`()	Return temperature.
`getThermostatTimeConstant`()	Return the time constant for the thermostat.
`getTimeStep`()	Return the time step.
`getUh`()	Return the uh value for the ATM force.
`getW0`()	Return the W0 value for the ATM force.
`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.
`setAlpha`(alpha)	Set the alpha value for the ATM force.
`setAnnealNumCycles`(anneal_numcycles)	Set the number of annealing cycles.
`setAnnealValues`(anneal_values)	Set the anneal protocol.
`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.
`setDirection`(direction)	Set the direction of the equilibration.
`setForceConstant`(force_constant)	Set the force constant for the restraint.
`setLambda1`(lambda1)	Set the lambda1 value for the ATM force.
`setLambda2`(lambda2)	Set the lambda2 value for the ATM force.
`setPosRestWidth`(positional_restraint_width)	Set the width of the position restraint.
`setPressure`(pressure)	Set the pressure.
`setReportInterval`(report_interval)	Set the interval at which statistics are reported.
`setRestartInterval`(restart_interval)	Set the interval between saving restart confiugrations, and/or trajectory frames.
`setRestraint`(restraint)	Set the type of restraint.
`setRuntime`(runtime)	Set the running time.
`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.
`setTemperature`(temperature)	Set the temperature.
`setThermostatTimeConstant`(...)	Set the time constant for the thermostat.
`setTimestep`(timestep)	Set the time step.
`setUh`(uh)	Set the uh value for the ATM force.
`setW0`(W0)	Set the W0 value for the ATM force.

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

getAlpha()[source]¶

Return the alpha value for the ATM force.

Returns:: alpha – The alpha value for the ATM force in kcal/mol. Ignored if use_atm_force is False.
Return type:: Energy

getAnnealNumCycles()[source]¶

Return the number of annealing cycles.

Returns:: anneal_numcycles – The number of annealing cycles.
Return type:: int

getAnnealValues()[source]¶

Return the anneal protocol.

Returns:: anneal_protocol – The anneal protocol.
Return type:: dict

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

getDirection()[source]¶

Return the direction of the equilibration.

Returns:: direction – The direction of the equilibration. Ignored if use_atm_force is False.
Return type:: str

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

getLambda1()[source]¶

Return the lambda1 value for the ATM force.

Returns:: lambda1 – The lambda1 value for the ATM force. Ignored if use_atm_force is False.
Return type:: float

getLambda2()[source]¶

Return the lambda2 value for the ATM force.

Returns:: lambda2 – The lambda2 value for the ATM force. Ignored if use_atm_force is False.
Return type:: float

getPosRestWidth()¶

Return the width of the position restraint.

Returns:: positional_restraint_width – The width of the position restraint.
Return type:: Length

getPressure()[source]¶

Return the pressure.

Returns:: pressure – The pressure.
Return type:: Pressure

getReportInterval()[source]¶: Return the interval between reporting statistics. (In integration steps.). :returns: report_interval – The number of integration steps between reporting statistics. :rtype: int

getRestartInterval()[source]¶

Return the interval between saving restart confiugrations, and/or trajectory frames. (In integration steps.).

Returns:: restart_interval – The number of integration steps between saving restart configurations and/or trajectory frames.
Return type:: int

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]

getRunTime()[source]¶

Return the running time.

Returns:: runtime – The simulation run time.
Return type:: Time

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

getTemperature()[source]¶

Return temperature.

Returns:: temperature – The simulation temperature.
Return type:: Temperature

getThermostatTimeConstant()[source]¶

Return the time constant for the thermostat.

Returns:: runtime – The time constant for the thermostat.
Return type:: Time

getTimeStep()[source]¶

Return the time step.

Returns:: time – The integration time step.
Return type:: Time

getUh()[source]¶

Return the uh value for the ATM force.

Returns:: uh – The uh value for the ATM force in kcal/mol. Ignored if use_atm_force is False.
Return type:: Energy

getW0()[source]¶

Return the W0 value for the ATM force.

Returns:: W0 – The W0 value for the ATM force in kcal/mol. Ignored if use_atm_force is False.
Return type:: Energy

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.

setAlpha(alpha)[source]¶

Set the alpha value for the ATM force.

Parameters:: alpha (int, float, str, Energy) – The alpha value for the ATM force in kcal/mol. Ignored if use_atm_force is False.

setAnnealNumCycles(anneal_numcycles)[source]¶

Set the number of annealing cycles.

Parameters:: anneal_numcycles (int) – The number of annealing cycles.

setAnnealValues(anneal_values)[source]¶

Set the anneal protocol.

Parameters:: anneal_values (dict) – The anneal values.

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.

setDirection(direction)[source]¶

Set the direction of the equilibration.

Parameters:: direction (str) – The direction of the equilibration. Ignored if use_atm_force is False.

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.

setLambda1(lambda1)[source]¶

Set the lambda1 value for the ATM force.

Parameters:: lambda1 (float) – The lambda1 value for the ATM force. Ignored if use_atm_force is False.

setLambda2(lambda2)[source]¶

Set the lambda2 value for the ATM force.

Parameters:: lambda2 (float) – The lambda2 value for the ATM force. Ignored if use_atm_force is False.

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.

setPressure(pressure)[source]¶

Set the pressure.

Parameters:: pressure (str, Pressure) – The pressure.

setReportInterval(report_interval)[source]¶

Set the interval at which statistics are reported. (In integration steps.).

Parameters:: report_interval (int) – The number of integration steps between reporting statistics.

setRestartInterval(restart_interval)[source]¶

Set the interval between saving restart confiugrations, and/or trajectory frames. (In integration steps.).

Parameters:: restart_interval (int) – The number of integration steps between saving restart configurations and/or trajectory frames.

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.

setRuntime(runtime)[source]¶

Set the running time.

Parameters:: runtime (str, Time) – The simulation run time.

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.

setTemperature(temperature)[source]¶

Set the temperature.

Parameters:: temperature (str, Temperature) – The simulation temperature.

setThermostatTimeConstant(thermostat_time_constant)[source]¶

Set the time constant for the thermostat.

Parameters:: thermostat_time_constant (str, Time) – The time constant for the thermostat.

setTimestep(timestep)[source]¶

Set the time step.

Parameters:: time (str, Time) – The integration time step.

setUh(uh)[source]¶

Set the uh value for the ATM force.

Parameters:: uh (int, float, str, Energy) – The uh value for the ATM force in kcal/mol. Ignored if use_atm_force is False.

setW0(W0)[source]¶

Set the W0 value for the ATM force.

Parameters:: W0 (int, float, str, Energy) – The W0 value for the ATM force in kcal/mol. Ignored if use_atm_force is False.