icolos.utils.execute_external package#

Submodules#

icolos.utils.execute_external.autodockvina module#

class icolos.utils.execute_external.autodockvina.AutoDockVinaExecutor(prefix_execution=None, binary_location=None)[source]#

Bases: ExecutorBase

For the execution of AutoDock Vina 1.2.0.

execute(command: str, arguments: list, check=True, location=None, pipe_input=None)[source]#
is_available()[source]#

icolos.utils.execute_external.cresset_executor module#

class icolos.utils.execute_external.cresset_executor.CressetExecutor(prefix_execution=None, binary_location=None)[source]#

Bases: ExecutorBase

For the execution of Cresset binaries binary.

execute(command: str, arguments: list, check=True, location=None, pipe_input=None)[source]#
is_available()[source]#

icolos.utils.execute_external.crest module#

class icolos.utils.execute_external.crest.CrestExecutor(prefix_execution=None, binary_location=None)[source]#

Bases: ExecutorBase

For the execution of the “crest” binary.

execute(command: str, arguments: list, check=True, location=None, pipe_input=None)[source]#
is_available()[source]#

icolos.utils.execute_external.execute module#

class icolos.utils.execute_external.execute.Executor(prefix_execution=None, binary_location=None)[source]#

Bases: ExecutorBase

For execution of command-line programs that do not have any specific executor themselves.

execute(command: str, arguments: list, check=True, location=None, pipe_input=None)[source]#
is_available()[source]#
class icolos.utils.execute_external.execute.ExecutorBase(prefix_execution=None, binary_location=None)[source]#

Bases: object

Virtual base class for the general and program-specific executors.

abstract execute(command: str, arguments: list, check=True, location=None, pipe_input=None)[source]#
abstract is_available()[source]#
icolos.utils.execute_external.execute.execution_successful(output: str, success_str: str) → bool[source]#

icolos.utils.execute_external.fep_plus module#

class icolos.utils.execute_external.fep_plus.FepPlusExecutor(prefix_execution=None, binary_location=None)[source]#

Bases: ExecutorBase

execute(command: str, arguments: list, check=True, location=None, pipe_input=None)[source]#
is_available()[source]#

icolos.utils.execute_external.glide module#

class icolos.utils.execute_external.glide.GlideExecutor(prefix_execution=None, binary_location=None)[source]#

Bases: ExecutorBase

For the execution of the “glide” binary.

execute(command: str, arguments: list, check=True, location=None, pipe_input=None)[source]#
is_available()[source]#

icolos.utils.execute_external.gold module#

class icolos.utils.execute_external.gold.GoldExecutor(prefix_execution=None, binary_location=None)[source]#

Bases: ExecutorBase

For the execution of CCDC’s GOLD.

execute(command: str, arguments: list, check=True, location=None, pipe_input=None)[source]#
is_available()[source]#

icolos.utils.execute_external.gromacs module#

class icolos.utils.execute_external.gromacs.GromacsExecutor(prefix_execution=None, binary_location=None)[source]#

Bases: ExecutorBase

execute(command: str, arguments: list, check=True, location=None, pipe_input=None)[source]#
is_available()[source]#

icolos.utils.execute_external.ifd_executor module#

icolos.utils.execute_external.jazzy module#

class icolos.utils.execute_external.jazzy.JazzyExecutor(prefix_execution=None, binary_location=None)[source]#

Bases: ExecutorBase

For the execution of the “jazzy” binary.

execute(command: str, arguments: list, check=True, location=None, pipe_input=None)[source]#
is_available()[source]#

icolos.utils.execute_external.kallisto module#

class icolos.utils.execute_external.kallisto.KallistoExecutor(prefix_execution=None, binary_location=None)[source]#

Bases: ExecutorBase

For the execution of the “kallisto” featurizer binary.

execute(command: str, arguments: list, check=True, location=None, pipe_input=None)[source]#
is_available()[source]#

icolos.utils.execute_external.license_token_guard module#

class icolos.utils.execute_external.license_token_guard.SchrodingerLicenseTokenGuard(*, token_guard: TokenGuardParameters)[source]#

Bases: BaseModel

Class that checks, whether enough tokens to execute Schrodinger binaries are available.

class Config[source]#

Bases: object

underscore_attrs_are_private = True#
guard() → bool[source]#
token_guard: TokenGuardParameters#
class icolos.utils.execute_external.license_token_guard.TokenGuardParameters(*, prefix_execution: str = None, binary_location: str = None, token_pools: Dict, wait_interval_seconds: int = 30, wait_limit_seconds: int = 0)[source]#

Bases: BaseModel

binary_location: str#
prefix_execution: str#
token_pools: Dict#
wait_interval_seconds: int#
wait_limit_seconds: int#

icolos.utils.execute_external.ligprep module#

class icolos.utils.execute_external.ligprep.LigprepExecutor(prefix_execution=None, binary_location=None)[source]#

Bases: ExecutorBase

For the execution of the “ligprep” binary.

execute(command: str, arguments: list, check=True, location=None, pipe_input=None)[source]#
is_available()[source]#

icolos.utils.execute_external.macromodel module#

class icolos.utils.execute_external.macromodel.MacromodelExecutor(prefix_execution=None, binary_location=None)[source]#

Bases: ExecutorBase

For the execution of the “macromodel” binary.

execute(command: str, arguments: list, check=True, location=None, pipe_input=None)[source]#
is_available()[source]#

icolos.utils.execute_external.omega module#

class icolos.utils.execute_external.omega.OMEGAExecutor(prefix_execution=None, binary_location=None)[source]#

Bases: ExecutorBase

For the execution of the “oeomega” binary.

execute(command: str, arguments: list, check=True, location=None, pipe_input=None)[source]#
is_available()[source]#

icolos.utils.execute_external.openbabel module#

class icolos.utils.execute_external.openbabel.OpenBabelExecutor[source]#

Bases: ExecutorBase

For the execution of the “obabel” binary.

execute(command: str, arguments: list, check=True, location=None, pipe_input=None)[source]#
is_available()[source]#

icolos.utils.execute_external.pmx module#

class icolos.utils.execute_external.pmx.PMXExecutor(prefix_execution=None, binary_location=None)[source]#

Bases: ExecutorBase

execute(command: str, arguments: list, check=True, location=None, pipe_input=None)[source]#
is_available()[source]#

icolos.utils.execute_external.prime module#

class icolos.utils.execute_external.prime.PrimeExecutor(prefix_execution=None, binary_location=None)[source]#

Bases: ExecutorBase

For the execution of the “prime_mmgbsa” binary.

execute(command: str, arguments: list, check=True, location=None, pipe_input=None)[source]#
is_available()[source]#

icolos.utils.execute_external.schrodinger module#

class icolos.utils.execute_external.schrodinger.SchrodingerExecutor(prefix_execution=None, binary_location=None)[source]#

Bases: ExecutorBase

For the execution of Schrodinger’s support entry points

execute(command: str, arguments: list, check=True, location=None, pipe_input=None)[source]#
is_available()[source]#

icolos.utils.execute_external.sdconvert module#

class icolos.utils.execute_external.sdconvert.SDConvertExecutor(prefix_execution=None, binary_location=None)[source]#

Bases: ExecutorBase

For the execution of the “sdconvert” binary.

execute(command: str, arguments: list, check=True, location=None, pipe_input=None)[source]#
is_available()[source]#

icolos.utils.execute_external.slurm_executor module#

class icolos.utils.execute_external.slurm_executor.SlurmExecutor(cores: int, partition: str, time: str, mem: str, tasks: str, modules: List, other_args: dict, gres: str, additional_lines: List, prefix_execution=None, binary_location=None)[source]#

Bases: ExecutorBase

For execution of batch jobs to a Slurm cluster.

execute(command: Optional[str] = None, arguments: Optional[list] = None, check: bool = True, location=None, pipe_input=None, tmpfile: Optional[str] = None, wait: bool = True)[source]#

Creates and executes the batch script using the provided resource requirements If a path to an existing batch script has not been passed via tmpfile, it is created Attempts to sbatch the jobscript, falling back on bash to provide compatibility with workstations (in this case #SLURM lines are ignored, and the execution becomes blocking)

is_available()[source]#
prepare_batch_script(command: str, arguments: List, pipe_input: Optional[str] = None, location: Optional[str] = None) → str[source]#

Generate the batch script for a specific job and write to disk :param str command: command to be executed :param List arguments: List of arguments to be appended to the command :param str pipe_input: string to be piped to the program being executed, defaults to None :param str location: directory where batch script will be written, defaults to None :return str : path to the batch script

icolos.utils.execute_external.structcat module#

class icolos.utils.execute_external.structcat.StructcatExecutor(prefix_execution=None, binary_location=None)[source]#

Bases: ExecutorBase

For the execution of the “structcat” binary.

execute(command: str, arguments: list, check=True, location=None, pipe_input=None)[source]#
is_available()[source]#

icolos.utils.execute_external.turbomole module#

class icolos.utils.execute_external.turbomole.TurbomoleExecutor(prefix_execution=None, binary_location=None)[source]#

Bases: ExecutorBase

For the execution of the “turbomole” binary.

execute(command: str, arguments: list, check=True, location=None, pipe_input=None)[source]#
is_available()[source]#

icolos.utils.execute_external.xtb module#

class icolos.utils.execute_external.xtb.XTBExecutor(prefix_execution=None, binary_location=None)[source]#

Bases: ExecutorBase

For the execution of the “xtb” binary.

execute(command: str, arguments: list, check=True, location=None, pipe_input=None)[source]#
is_available()[source]#

Module contents#