BioSimSpace.Process.Amber¶
-
class
BioSimSpace.Process.
Amber
(system, protocol, exe=None, name='amber', work_dir=None, seed=None, property_map={})¶ A class for running simulations using AMBER.
-
__init__
(system, protocol, exe=None, name='amber', work_dir=None, seed=None, property_map={})¶ Constructor.
- Parameters
system (
System
) – The molecular system.protocol (
Protocol
) – The protocol for the AMBER process.exe (str) – The full path to the AMBER executable.
name (str) – The name of the process.
work_dir – The working directory for the process.
seed (int) – A random number seed.
property_map (dict) – A dictionary that maps system “properties” to their user defined values. This allows the user to refer to properties with their own naming scheme, e.g. { “charge” : “my-charge” }
Methods
__init__
(system, protocol[, exe, name, …])Constructor.
addArgs
(args)Append additional command-line arguments.
addToConfig
(config)Add a string to the configuration list.
Clear all of the command-line arguments.
command
()Return the command-line string used to run the process.
deleteArg
(arg)Delete an argument from the dictionary.
exe
()Return the executable.
getAngleEnergy
([time_series, block])Get the angle energy.
Get the command-line arguments string.
Convert the argument dictionary into a list of strings.
getArgs
()Get the dictionary of command-line arguments.
getBondEnergy
([time_series, block])Get the bond energy.
getCentreOfMassKineticEnergy
([time_series, …])Get the kinetic energy of the centre of mass in translation.
Get the list of configuration file strings.
getCurrentAngleEnergy
([time_series])Get the current angle energy.
getCurrentBondEnergy
([time_series])Get the current bond energy.
Get the current kinetic energy of the centre of mass in translation.
getCurrentDensity
([time_series])Get the current density.
getCurrentDihedralEnergy
([time_series])Get the current total dihedral energy (proper + improper).
getCurrentElectrostaticEnergy
([time_series])Get the current dihedral energy.
getCurrentElectrostaticEnergy14
([time_series])Get the current electrostatic energy between atoms 1 and 4.
getCurrentHydrogenBondEnergy
([time_series])Get the current hydrogen bond energy.
getCurrentKineticEnergy
([time_series])Get the current kinetic energy.
getCurrentNonBondedEnergy14
([time_series])Get the current non-bonded energy between atoms 1 and 4.
getCurrentPotentialEnergy
([time_series])Get the current potential energy.
getCurrentPressure
([time_series])Get the current pressure.
getCurrentRecord
(record[, time_series, unit])Get a current record from the stdout dictionary.
Return the current dictionary of stdout time-series records.
getCurrentRestraintEnergy
([time_series])Get the current restraint energy.
getCurrentStep
([time_series])Get the current number of integration steps.
Get the latest molecular system.
getCurrentTemperature
([time_series])Get the current temperature.
getCurrentTime
([time_series])Get the current simulation time.
getCurrentTotalEnergy
([time_series])Get the current total energy.
getCurrentVanDerWaalsEnergy
([time_series])Get the current Van der Vaals energy.
getCurrentVirial
([time_series])Get the current virial.
getCurrentVolume
([time_series])Get the current volume.
getDensity
([time_series, block])Get the density.
getDihedralEnergy
([time_series, block])Get the total dihedral energy (proper + improper).
getElectrostaticEnergy
([time_series, block])Get the electrostatic energy.
getElectrostaticEnergy14
([time_series, block])Get the electrostatic energy between atoms 1 and 4.
getFrame
(index)Return a specific trajectory frame.
getHydrogenBondEnergy
([time_series, block])Get the hydrogen bond energy.
getInput
([name, file_link])Return a link to a zip file containing the input files used by the process.
getKineticEnergy
([time_series, block])Get the kinetic energy.
getName
()Return the process name.
getNonBondedEnergy14
([time_series, block])Get the non-bonded energy between atoms 1 and 4.
getOutput
([name, block, file_link])Return a link to a zip file of the working directory.
Return the package name.
getPotentialEnergy
([time_series, block])Get the potential energy.
getPressure
([time_series, block])Get the pressure.
getRecord
(record[, time_series, unit, block])Get a record from the stdout dictionary.
getRecords
([block])Return the dictionary of stdout time-series records.
getRestraintEnergy
([time_series, block])Get the restraint energy.
getSeed
()Return the random number seed.
getStderr
([block])Return the entire stderr for the process as a list of strings.
getStdout
([block])Return the entire stdout for the process as a list of strings.
getStep
([time_series, block])Get the number of integration steps.
getSystem
([block])Get the latest molecular system.
getTemperature
([time_series, block])Get the temperature.
getTime
([time_series, block])Get the simulation time.
getTotalEnergy
([time_series, block])Get the total energy.
getTrajectory
([block])Return a trajectory object.
getVanDerWaalsEnergy
([time_series, block])Get the Van der Vaals energy.
getVirial
([time_series, block])Get the virial.
getVolume
([time_series, block])Get the volume.
Return the list of input files.
insertArg
(arg, value, index)Insert a command-line argument at a specific index.
isError
()Return whether the process exited with an error.
isQueued
()Return whether the process is queued.
Return whether the process is running.
kill
()Kill the running process.
Reset the command-line arguments.
Reset the configuration parameters.
run
([system, protocol, auto_start, restart])Create and run a new process.
runTime
()Return the running time for the process (in minutes).
setArg
(arg, value)Set a specific command-line argument.
setArgs
(args)Set the dictionary of command-line arguments.
setConfig
(config)Set the list of configuration file strings.
setName
(name)Set the process name.
setSeed
(seed)Set the random number seed.
start
()Start the AMBER process.
stderr
([n])Print the last n lines of the stderr buffer.
stdout
([n])Print the last n lines of the stdout buffer.
wait
([max_time])Wait for the process to finish.
workDir
()Return the working directory.
writeConfig
(file)Write the configuration to file.
-
addArgs
(args)¶ Append additional command-line arguments.
- Parameters
args (dict, collections.OrderedDict) – A dictionary of command line arguments.
-
addToConfig
(config)¶ Add a string to the configuration list.
- Parameters
config (str, [ str ]) – A configuration string, a list of configuration strings, or a path to a configuration file.
-
clearArgs
()¶ Clear all of the command-line arguments.
-
command
()¶ Return the command-line string used to run the process.
- Returns
command – The command string.
- Return type
str
-
deleteArg
(arg)¶ Delete an argument from the dictionary.
- Parameters
arg (str) – The argument to delete.
-
exe
()¶ Return the executable.
- Returns
exe – The path to the executable.
- Return type
str
-
getAngleEnergy
(time_series=False, block='AUTO')¶ Get the angle energy.
- Parameters
time_series (bool) – Whether to return a list of time series records.
block (bool) – Whether to block until the process has finished running.
- Returns
energy – The angle energy.
- Return type
-
getArgString
()¶ Get the command-line arguments string.
- Returns
arg_string – The command-line argument string.
- Return type
str
-
getArgStringList
()¶ Convert the argument dictionary into a list of strings.
- Returns
arg_string_list – The list of command-line arguments.
- Return type
[str]
-
getArgs
()¶ Get the dictionary of command-line arguments.
- Returns
args – The dictionary of command-line arguments.
- Return type
collections.OrderedDict
-
getBondEnergy
(time_series=False, block='AUTO')¶ Get the bond energy.
- Parameters
time_series (bool) – Whether to return a list of time series records.
block (bool) – Whether to block until the process has finished running.
- Returns
energy – The bond energy.
- Return type
-
getCentreOfMassKineticEnergy
(time_series=False, block='AUTO')¶ Get the kinetic energy of the centre of mass in translation.
- Parameters
time_series (bool) – Whether to return a list of time series records.
block (bool) – Whether to block until the process has finished running.
- Returns
energy – The centre of mass kinetic energy.
- Return type
-
getConfig
()¶ Get the list of configuration file strings.
- Returns
config – The list of configuration strings.
- Return type
[str]
-
getCurrentAngleEnergy
(time_series=False)¶ Get the current angle energy.
- Parameters
time_series (bool) – Whether to return a list of time series records.
- Returns
energy – The angle energy.
- Return type
-
getCurrentBondEnergy
(time_series=False)¶ Get the current bond energy.
- Parameters
time_series (bool) – Whether to return a list of time series records.
- Returns
energy – The bond energy.
- Return type
-
getCurrentCentreOfMassKineticEnergy
(time_series=False)¶ Get the current kinetic energy of the centre of mass in translation.
- Parameters
time_series (bool) – Whether to return a list of time series records.
- Returns
energy – The centre of mass kinetic energy.
- Return type
-
getCurrentDensity
(time_series=False)¶ Get the current density.
- Parameters
time_series (bool) – Whether to return a list of time series records.
- Returns
density – The density.
- Return type
float
-
getCurrentDihedralEnergy
(time_series=False)¶ Get the current total dihedral energy (proper + improper).
- Parameters
time_series (bool) – Whether to return a list of time series records.
- Returns
energy – The total dihedral energy.
- Return type
-
getCurrentElectrostaticEnergy
(time_series=False)¶ Get the current dihedral energy.
- Parameters
time_series (bool) – Whether to return a list of time series records.
- Returns
energy – The electrostatic energy.
- Return type
-
getCurrentElectrostaticEnergy14
(time_series=False)¶ Get the current electrostatic energy between atoms 1 and 4.
- Parameters
time_series (bool) – Whether to return a list of time series records.
- Returns
energy – The electrostatic energy between atoms 1 and 4.
- Return type
-
getCurrentHydrogenBondEnergy
(time_series=False)¶ Get the current hydrogen bond energy.
- Parameters
time_series (bool) – Whether to return a list of time series records.
- Returns
energy – The hydrogen bond energy.
- Return type
-
getCurrentKineticEnergy
(time_series=False)¶ Get the current kinetic energy.
- Parameters
time_series (bool) – Whether to return a list of time series records.
- Returns
energy – The kinetic energy.
- Return type
-
getCurrentNonBondedEnergy14
(time_series=False)¶ Get the current non-bonded energy between atoms 1 and 4.
- Parameters
time_series (bool) – Whether to return a list of time series records.
- Returns
energy – The non-bonded energy between atoms 1 and 4.
- Return type
-
getCurrentPotentialEnergy
(time_series=False)¶ Get the current potential energy.
- Parameters
time_series (bool) – Whether to return a list of time series records.
- Returns
energy – The potential energy.
- Return type
-
getCurrentPressure
(time_series=False)¶ Get the current pressure.
- Parameters
time_series (bool) – Whether to return a list of time series records.
- Returns
pressure – The pressure.
- Return type
-
getCurrentRecord
(record, time_series=False, unit=None)¶ Get a current record from the stdout dictionary.
-
getCurrentRecords
()¶ Return the current dictionary of stdout time-series records.
- Returns
records – The dictionary of time-series records.
- Return type
MultiDict
-
getCurrentRestraintEnergy
(time_series=False)¶ Get the current restraint energy.
- Parameters
time_series (bool) – Whether to return a list of time series records.
block (bool) – Whether to block until the process has finished running.
- Returns
energy – The restraint energy.
- Return type
-
getCurrentStep
(time_series=False)¶ Get the current number of integration steps.
- Parameters
time_series (bool) – Whether to return a list of time series records.
- Returns
step – The current number of integration steps.
- Return type
int
-
getCurrentSystem
()¶ Get the latest molecular system.
- Returns
system – The latest molecular system.
- Return type
-
getCurrentTemperature
(time_series=False)¶ Get the current temperature.
- Parameters
time_series (bool) – Whether to return a list of time series records.
- Returns
temperature – The temperature.
- Return type
-
getCurrentTime
(time_series=False)¶ Get the current simulation time.
- Parameters
time_series (bool) – Whether to return a list of time series records.
- Returns
time – The current simulation time in nanoseconds.
- Return type
-
getCurrentTotalEnergy
(time_series=False)¶ Get the current total energy.
- Parameters
time_series (bool) – Whether to return a list of time series records.
- Returns
energy – The total energy.
- Return type
-
getCurrentVanDerWaalsEnergy
(time_series=False)¶ Get the current Van der Vaals energy.
- Parameters
time_series (bool) – Whether to return a list of time series records.
- Returns
energy – The Van der Vaals energy.
- Return type
-
getCurrentVirial
(time_series=False)¶ Get the current virial.
- Parameters
time_series (bool) – Whether to return a list of time series records.
- Returns
virial – The virial.
- Return type
float
-
getCurrentVolume
(time_series=False)¶ Get the current volume.
- Parameters
time_series (bool) – Whether to return a list of time series records.
- Returns
volume – The volume.
- Return type
-
getDensity
(time_series=False, block='AUTO')¶ Get the density.
- Parameters
time_series (bool) – Whether to return a list of time series records.
block (bool) – Whether to block until the process has finished running.
- Returns
density – The density.
- Return type
float
-
getDihedralEnergy
(time_series=False, block='AUTO')¶ Get the total dihedral energy (proper + improper).
- Parameters
time_series (bool) – Whether to return a list of time series records.
block (bool) – Whether to block until the process has finished running.
- Returns
energy – The total dihedral energy.
- Return type
-
getElectrostaticEnergy
(time_series=False, block='AUTO')¶ Get the electrostatic energy.
- Parameters
time_series (bool) – Whether to return a list of time series records.
block (bool) – Whether to block until the process has finished running.
- Returns
energy – The electrostatic energy.
- Return type
-
getElectrostaticEnergy14
(time_series=False, block='AUTO')¶ Get the electrostatic energy between atoms 1 and 4.
- Parameters
time_series (bool) – Whether to return a list of time series records.
block (bool) – Whether to block until the process has finished running.
- Returns
energy – The electrostatic energy between atoms 1 and 4.
- Return type
-
getFrame
(index)¶ Return a specific trajectory frame.
- Parameters
index (int) – The index of the frame.
- Returns
frame – The System object of the corresponding frame.
- Return type
-
getHydrogenBondEnergy
(time_series=False, block='AUTO')¶ Get the hydrogen bond energy.
- Parameters
time_series (bool) – Whether to return a list of time series records.
block (bool) – Whether to block until the process has finished running.
- Returns
energy – The hydrogen bond energy.
- Return type
-
getInput
(name=None, file_link=False)¶ Return a link to a zip file containing the input files used by the process.
- Parameters
name (str) – The name of the zip file.
file_link (bool) – Whether to return a FileLink when working in Jupyter.
- Returns
output – A path, or file link, to an archive of the process input.
- Return type
str, IPython.display.FileLink
-
getKineticEnergy
(time_series=False, block='AUTO')¶ Get the kinetic energy.
- Parameters
time_series (bool) – Whether to return a list of time series records.
block (bool) – Whether to block until the process has finished running.
- Returns
energy – The kinetic energy.
- Return type
-
getName
()¶ Return the process name.
Returns:
- namestr
The name of the process.
-
getNonBondedEnergy14
(time_series=False, block='AUTO')¶ Get the non-bonded energy between atoms 1 and 4.
- Parameters
time_series (bool) – Whether to return a list of time series records.
block (bool) – Whether to block until the process has finished running.
- Returns
energy – The non-bonded energy between atoms 1 and 4.
- Return type
-
getOutput
(name=None, block='AUTO', file_link=False)¶ Return a link to a zip file of the working directory.
- Parameters
name (str) – The name of the zip file.
block (bool) – Whether to block until the process has finished running.
file_link (bool) – Whether to return a FileLink when working in Jupyter.
- Returns
output – A path, or file link, to an archive of the process output.
- Return type
str, IPython.display.FileLink
-
getPackageName
()¶ Return the package name.
- Returns
name – The name of the package.
- Return type
str
-
getPotentialEnergy
(time_series=False, block='AUTO')¶ Get the potential energy.
- Parameters
time_series (bool) – Whether to return a list of time series records.
block (bool) – Whether to block until the process has finished running.
- Returns
energy – The potential energy.
- Return type
-
getPressure
(time_series=False, block='AUTO')¶ Get the pressure.
- Parameters
time_series (bool) – Whether to return a list of time series records.
block (bool) – Whether to block until the process has finished running.
- Returns
pressure – The pressure.
- Return type
-
getRecord
(record, time_series=False, unit=None, block='AUTO')¶ Get a record from the stdout dictionary.
-
getRecords
(block='AUTO')¶ Return the dictionary of stdout time-series records.
- Parameters
block (bool) – Whether to block until the process has finished running.
- Returns
records – The dictionary of time-series records.
- Return type
MultiDict
-
getRestraintEnergy
(time_series=False, block='AUTO')¶ Get the restraint energy.
- Parameters
time_series (bool) – Whether to return a list of time series records.
block (bool) – Whether to block until the process has finished running.
- Returns
energy – The restraint energy.
- Return type
-
getSeed
()¶ Return the random number seed.
- Returns
seed – The random number seed.
- Return type
int
-
getStderr
(block='AUTO')¶ Return the entire stderr for the process as a list of strings.
- Parameters
block (bool) – Whether to block until the process has finished running.
- Returns
error – The list of stderror strings.
- Return type
[str]
-
getStdout
(block='AUTO')¶ Return the entire stdout for the process as a list of strings.
- Parameters
block (bool) – Whether to block until the process has finished running.
- Returns
output – The list of stdout strings.
- Return type
[str]
-
getStep
(time_series=False, block='AUTO')¶ Get the number of integration steps.
- Parameters
time_series (bool) – Whether to return a list of time series records.
block (bool) – Whether to block until the process has finished running.
- Returns
step – The current number of integration steps.
- Return type
int
-
getSystem
(block='AUTO')¶ Get the latest molecular system.
- Parameters
block (bool) – Whether to block until the process has finished running.
- Returns
system – The latest molecular system.
- Return type
-
getTemperature
(time_series=False, block='AUTO')¶ Get the temperature.
- Parameters
time_series (bool) – Whether to return a list of time series records.
block (bool) – Whether to block until the process has finished running.
- Returns
temperature – The temperature.
- Return type
-
getTime
(time_series=False, block='AUTO')¶ Get the simulation time.
- Parameters
time_series (bool) – Whether to return a list of time series records.
block (bool) – Whether to block until the process has finished running.
- Returns
time – The current simulation time in nanoseconds.
- Return type
-
getTotalEnergy
(time_series=False, block='AUTO')¶ Get the total energy.
- Parameters
time_series (bool) – Whether to return a list of time series records.
block (bool) – Whether to block until the process has finished running.
- Returns
energy – The total energy.
- Return type
-
getTrajectory
(block='AUTO')¶ Return a trajectory object.
- Parameters
block (bool) – Whether to block until the process has finished running.
- Returns
trajectory – The latest trajectory object.
- Return type
-
getVanDerWaalsEnergy
(time_series=False, block='AUTO')¶ Get the Van der Vaals energy.
- Parameters
time_series (bool) – Whether to return a list of time series records.
block (bool) – Whether to block until the process has finished running.
- Returns
energy – The Van der Vaals energy.
- Return type
-
getVirial
(time_series=False, block='AUTO')¶ Get the virial.
- Parameters
time_series (bool) – Whether to return a list of time series records.
block (bool) – Whether to block until the process has finished running.
- Returns
virial – The virial.
- Return type
float
-
getVolume
(time_series=False, block='AUTO')¶ Get the volume.
- Parameters
time_series (bool) – Whether to return a list of time series records.
block (bool) – Whether to block until the process has finished running.
- Returns
volume – The volume.
- Return type
-
inputFiles
()¶ Return the list of input files.
- Returns
input_files – The list of autogenerated input files.
- Return type
[str]
-
insertArg
(arg, value, index)¶ Insert a command-line argument at a specific index.
- Parameters
arg (str) – The argument to set.
value – The value of the argument.
index (int) – The index in the dictionary.
-
isError
()¶ Return whether the process exited with an error.
- Returns
is_error – Whether the process exited with an error.
- Return type
bool
-
isQueued
()¶ Return whether the process is queued.
- Returns
is_queued – Whether the process is queued.
- Return type
bool
-
isRunning
()¶ Return whether the process is running.
- Returns
is_running – Whether the process is running.
- Return type
bool
-
kill
()¶ Kill the running process.
-
resetArgs
()¶ Reset the command-line arguments.
-
resetConfig
()¶ Reset the configuration parameters.
-
run
(system=None, protocol=None, auto_start=True, restart=False)¶ Create and run a new process.
- Parameters
- Returns
process – The new process object.
- Return type
-
runTime
()¶ Return the running time for the process (in minutes).
- Returns
runtime – The runtime in minutes.
- Return type
-
setArg
(arg, value)¶ Set a specific command-line argument.
For command-line flags, i.e. boolean arguments, the key should specify whether the flag is enabled (True) or not (False).
- Parameters
arg (str) – The argument to set.
value (bool, str) – The value of the argument.
-
setArgs
(args)¶ Set the dictionary of command-line arguments.
- Parameters
args (dict, collections.OrderedDict) – A dictionary of command-line arguments.
-
setConfig
(config)¶ Set the list of configuration file strings.
- Parameters
config (str, [str]) – The list of configuration strings, or a path to a configuration file.
-
setName
(name)¶ Set the process name.
- Parameters
name (str) – The process name.
-
setSeed
(seed)¶ Set the random number seed.
- Parameters
seed (int) – The random number seed.
-
start
()¶ Start the AMBER process.
- Returns
process – The process object.
- Return type
-
stderr
(n=10)¶ Print the last n lines of the stderr buffer.
- Parameters
n (int) – The number of lines to print.
-
stdout
(n=10)¶ Print the last n lines of the stdout buffer.
- Parameters
n (int) – The number of lines to print.
-
wait
(max_time=None)¶ Wait for the process to finish.
- Parameters
max_time (
Time
, int, float) – The maximum time to wait (in minutes).
-
workDir
()¶ Return the working directory.
- Returns
work_dir – The path of the working directory.
- Return type
str
-
writeConfig
(file)¶ Write the configuration to file.
- Parameters
file (str) – The path to a file.
-