schrodinger.application.desmond.test_utils module¶
- schrodinger.application.desmond.test_utils.unzip_and_get_membrane_test_files(fep_type: str) Tuple[str, str, str] ¶
Unzip test files for the membrane launcher workflow into cwd and return filenames. The first file is the expected .fmp input file for the membrane launcher stage, the second file is the expected .cms output file from the multisim job and the third file is the expected .fmp output file from the stage.
- exception schrodinger.application.desmond.test_utils.InvalidTagError¶
Bases:
Exception
Custom exception so invalid tags can be specifically captured.
- exception schrodinger.application.desmond.test_utils.UnregisteredFileError¶
Bases:
Exception
Exception raised when attempting to access an unregistered file.
- class schrodinger.application.desmond.test_utils.FileRegistrationTag(value)¶
Bases:
enum.Enum
- FEP_PLUS = 'fep_plus'¶
- MXMD = 'mxmd'¶
- SOLUBILITY = 'solubility'¶
- LAMBDA_DYNAMICS = 'lambda_dynamics'¶
- LIGAND = 'ligand'¶
- RECEPTOR = 'receptor'¶
- MEMBRANE = 'membrane'¶
- SOLVENT = 'solvent'¶
- COMPLEX = 'complex'¶
- FRAGMENT = 'fragment'¶
- ION = 'ion'¶
- COSOLVENT = 'cosolvent'¶
- CRYSTAL_WATER = 'crystal water'¶
- POSITIVE_SALT = 'positive salt'¶
- NEGATIVE_SALT = 'negative salt'¶
- ALCHEMICAL_WATER = 'alchemical_water'¶
- PRM_PROTEIN_BINDING = 'prm_protein_binding'¶
- PRM_LIGAND_BINDING = 'prm_ligand_binding'¶
- PROTEIN_STABILITY = 'prm_stability'¶
- PRM_THERMOSTABILITY = 'prm_thermostability'¶
- PROTEIN_SELECTIVITY = 'protein_selectivity'¶
- COVALENT_LIGAND = 'covalent_ligand'¶
- SMALL_MOLECULE = 'small_molecule'¶
- METALLOPROTEIN = 'metalloprotein'¶
- LIGAND_SELECTIVITY = 'ligand_selectivity'¶
- ABSOLUTE_BINDING = 'absolute_binding'¶
- DEFAULT = 'default_protocol'¶
- CHARGED = 'charge_protocol'¶
- FORMALCHARGED = 'charge0'¶
- COREHOPPING = 'core-hopping'¶
- MACROCYCLE_COREHOPPING = 'macrocycle-core-hopping'¶
- FRAGMENT_LINKING = 'fragment-linking'¶
- STAR_TOPOLOGY = 'star_topology'¶
- WINDMILL_TOPOLOGY = 'windmill_topology'¶
- NORMAL_TOPOLOGY = 'normal_topology'¶
- FRAGMENT_HYDRATION = ('solvent_fragment_hydration',)¶
- RESTRAINED_FRAGMENT_HYDRATION = 'solvent_restrained_fragment_hydration'¶
- SOLVATION = 'solvation'¶
- FEP_GROUPS = 'fep_groups'¶
- PH_DEPENDENCE = 'ph_dependence'¶
- CONSTANT_PH = 'constant_ph'¶
- COMPRESSED = 'compressed'¶
- ENE = 'ene'¶
- PROTEIN_PREP = 'protein_prep'¶
- CSP = 'csp'¶
- CONFORMER_GENERATION = 'conformer_generation'¶
- exception schrodinger.application.desmond.test_utils.InvalidFileRegistrationError¶
Bases:
Exception
Custom exception so file registration errors can be specifically captured.
- class schrodinger.application.desmond.test_utils.FileRegistration(path: pathlib.Path, tickets: List[str], description: str, tags: List[str])¶
Bases:
object
Metadata container for a file that is registered in a
FileRegistry
.- Variables
path – Path to the file relative to the location of the registry.
tickets – Ticket(s) associated with the creation or modification of the test file.
description – A brief statement describing the contents and use of the test file.
tags – Key words that tag a particular file for ease of searching.
- path: pathlib.Path¶
- description: str¶
- __init__(path: pathlib.Path, tickets: List[str], description: str, tags: List[str]) None ¶
- class schrodinger.application.desmond.test_utils.UnregisteredFile(filename: str, error_message: str)¶
Bases:
object
Class to represent a file that is not registered in the registry.
- filename: str¶
- error_message: str¶
- __init__(filename: str, error_message: str) None ¶
- class schrodinger.application.desmond.test_utils.FileRegistry(path: pathlib.Path, registry: mappingproxy)¶
Bases:
object
Container for registered files used to access the absolute path of files during, e.g., a pytest session.
- Variables
path – Path to the file registry data.
registry – Map between the filename and the file’s metadata.
- path: pathlib.Path¶
- registry: mappingproxy¶
- classmethod load(registry_filename: pathlib.Path) schrodinger.application.desmond.test_utils.FileRegistryType ¶
Load file registry and instantiate
FileRegistry
object.- Parameters
registry_filename – path to the file registry.
- Returns
the loaded file registry
- get_file_registration(filename: str) schrodinger.application.desmond.test_utils.FileRegistration ¶
Return the
FileRegistration
for a particularfilename
.- Parameters
filename – the name of the file in the registry
- Raises
UnregisteredFileError – If
filename
is not registered.
- get_file_path(filename: str) pathlib.Path ¶
Return the path to the registered file.
- Parameters
filename – the name of the file in the registry
- Returns
the absolute path to the file
- __init__(path: pathlib.Path, registry: mappingproxy) None ¶