BioSimSpace.Process.Somd¶

class BioSimSpace.Process.Somd(system, protocol, exe=None, name='somd', platform='CPU', work_dir=None, seed=None, extra_options={}, extra_lines=[], extra_args={}, property_map={}, **kwargs)[source]¶

A class for running simulations using SOMD.

__init__(system, protocol, exe=None, name='somd', platform='CPU', work_dir=None, seed=None, extra_options={}, extra_lines=[], extra_args={}, property_map={}, **kwargs)[source]¶

Constructor.

Parameters:

system (System) – The molecular system.
protocol (Protocol) – The protocol for the SOMD process.
exe (str) – The full path to the SOMD executable.
name (str) – The name of the process.
platform (str) – The platform for the simulation: “CPU”, “CUDA”, or “OPENCL”.
work_dir – The working directory for the process.
seed (int) – A random number seed. Note that SOMD only uses a seed for FreeEnergy protocols. The seed should only be used for debugging purposes since SOMD uses the same seed for each Monte Carlo cycle.
extra_options (dict) – A dictionary containing extra options. Overrides the defaults generated by the protocol.
extra_lines ([str]) – A list of extra lines to put at the end of the configuration file.
extra_args (dict) – A dictionary of extra command-line arguments to pass to the SOMD executable.
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” }
kwargs (dict) – Additional keyword arguments.

Methods

`__init__`(system, protocol[, exe, name, ...])	Constructor.
`addArgs`(args)	Append additional command-line arguments.
`addToConfig`(config)	Add a string to the configuration list.
`clearArgs`()	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.
`getArgString`()	Get the command-line arguments string.
`getArgStringList`()	Convert the argument dictionary into a list of strings.
`getArgs`()	Get the dictionary of command-line arguments.
`getConfig`()	Get the list of configuration file strings.
`getCurrentGradient`([time_series])	Get the current free energy gradient.
`getCurrentSystem`()	Get the latest molecular system.
`getCurrentTime`([time_series])	Get the current time (in nanoseconds).
`getFrame`(index)	Return a specific trajectory frame.
`getGradient`([time_series, block])	Get the free energy gradient.
`getInput`([name, file_link])	Return a link to a zip file containing the input files used by the process.
`getName`()	Return the process name.
`getOutput`([name, block, file_link])	Return a link to a zip file of the working directory.
`getPackageName`()	Return the package name.
`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.
`getSystem`([block])	Get the latest molecular system.
`getTime`([time_series, block])	Get the time (in nanoseconds).
`getTrajectory`([backend, block])	Return a trajectory object.
`inputFiles`()	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.
`isRunning`()	Return whether the process is running.
`kill`()	Kill the running process.
`resetArgs`()	Reset the command-line arguments.
`resetConfig`()	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 SOMD 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

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

getConfig()¶

Get the list of configuration file strings.

Returns:: config – The list of configuration strings.
Return type:: [str]

getCurrentGradient(time_series=False)[source]¶

Get the current free energy gradient.

Parameters:: time_series (bool) – Whether to return a list of time series records.
Returns:: gradient – The current free energy gradient.
Return type:: float

getCurrentSystem()[source]¶

Get the latest molecular system.

Returns:: system – The latest molecular system.
Return type:: System

getCurrentTime(time_series=False)[source]¶

Get the current time (in nanoseconds).

Parameters:: time_series (bool) – Whether to return a list of time series records.
Returns:: time – The current simulation time in nanoseconds.
Return type:: Time

getFrame(index)[source]¶

Return a specific trajectory frame.

Parameters:: index (int) – The index of the frame.
Returns:: frame – The System object of the corresponding frame.
Return type:: System

getGradient(time_series=False, block='AUTO')[source]¶

Get the free energy gradient.

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:

gradient – The free energy gradient.

Return type:

float

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

getName()¶

Return the process name.

Returns:

namestr: The name of the process.

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

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]

getSystem(block='AUTO')[source]¶

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:: System

getTime(time_series=False, block='AUTO')[source]¶

Get the time (in nanoseconds).

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:

Time

getTrajectory(backend='AUTO', block='AUTO')[source]¶

Return a trajectory object.

Parameters:

backend (str) – The backend to use for trajectory parsing. To see supported backends, run BioSimSpace.Trajectory.backends(). Using “AUTO” will try each in sequence.
block (bool) – Whether to block until the process has finished running.

Returns:

trajectory – The latest trajectory object.

Return type:

Trajectory

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:

system (System) – The molecular system.
protocol (Protocol) – The simulation protocol.
auto_start (bool) – Whether to start the process automatically.
restart (bool) – Whether to restart the simulation, i.e. use the original system.

Returns:

process – The new process object.

Return type:

Procees

runTime()¶

Return the running time for the process (in minutes).

Returns:: runtime – The runtime in minutes.
Return type:: Time

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()[source]¶

Start the SOMD process.

Returns:: process – A handle to the running process.
Return type:: Process.Somd

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.