icolos.core.step_utils package

Submodules

icolos.core.step_utils.gold_config module

class icolos.core.step_utils.gold_config.ConfigAutomaticSettings(*, autoscale: float = 1.0, autoscale_nops_max: int = 100000, autoscale_nops_min: int = 100)

Bases: BaseModel

autoscale: float

autoscale_nops_max: int

autoscale_nops_min: int

class icolos.core.step_utils.gold_config.ConfigConstraints(*, force_constraints: int = 0)

Bases: BaseModel

force_constraints: int

class icolos.core.step_utils.gold_config.ConfigCovalentBonding(*, covalent: int = 0)

Bases: BaseModel

covalent: int

class icolos.core.step_utils.gold_config.ConfigDataFiles(*, ligand_data_file: List[str] = [], param_file: str = 'DEFAULT', set_ligand_atom_types: int = 1, set_protein_atom_types: int = 0, directory: str = '.', tordist_file: str = 'DEFAULT', make_subdirs: int = 0, save_lone_pairs: int = 1, fit_points_file: str = 'fit_pts.mol2', read_fitpts: str = 0)

Bases: BaseModel

directory: str

fit_points_file: str

ligand_data_file: List[str]

make_subdirs: int

param_file: str

read_fitpts: str

save_lone_pairs: int

set_ligand_atom_types: int

set_protein_atom_types: int

tordist_file: str

class icolos.core.step_utils.gold_config.ConfigFitnessFunctionSettings(*, initial_virtual_pt_match_max: int = 3, relative_ligand_energy: int = 1, gold_fitfunc_path: str = 'goldscore', start_vdw_linear_cutoff: float = 6, score_param_file: str = 'DEFAULT')

Bases: BaseModel

gold_fitfunc_path: str

initial_virtual_pt_match_max: int

relative_ligand_energy: int

score_param_file: str

start_vdw_linear_cutoff: float

class icolos.core.step_utils.gold_config.ConfigFlags(*, internal_ligand_h_bonds: int = 0, flip_free_corners: int = 0, match_ring_templates: int = 0, flip_amide_bonds: int = 0, flip_planar_n: str = '1 flip_ring_NRR flip_ring_NHR', flip_pyramidal_n: str = 0, rotate_carboxylic_oh: str = 'flip', use_tordist: int = 1, postprocess_bonds: int = 1, rotatable_bond_override_file: str = 'DEFAULT', solvate_all: int = 1)

Bases: BaseModel

flip_amide_bonds: int

flip_free_corners: int

flip_planar_n: str

flip_pyramidal_n: str

internal_ligand_h_bonds: int

match_ring_templates: int

postprocess_bonds: int

rotatable_bond_override_file: str

rotate_carboxylic_oh: str

solvate_all: int

use_tordist: int

class icolos.core.step_utils.gold_config.ConfigFloodFill(*, radius: float = 10, origin: str = '0 0 0', do_cavity: int = 1, floodfill_atom_no: int = 0, cavity_file: str, floodfill_center: str = 'cavity_from_ligand 7 atoms')

Bases: BaseModel

cavity_file: str

do_cavity: int

floodfill_atom_no: int

floodfill_center: str

origin: str

radius: float

class icolos.core.step_utils.gold_config.ConfigGeneticOperators(*, pt_crosswt: str = 'auto', allele_mutatewt: str = 'auto', migratewt: str = 'auto')

Bases: BaseModel

allele_mutatewt: str

migratewt: str

pt_crosswt: str

class icolos.core.step_utils.gold_config.ConfigPopulation(*, popsiz: str = 'auto', select_pressure: str = 'auto', n_islands: str = 'auto', maxops: str = 'auto', niche_siz: str = 'auto')

Bases: BaseModel

maxops: str

n_islands: str

niche_siz: str

popsiz: str

select_pressure: str

class icolos.core.step_utils.gold_config.ConfigProteinData(*, protein_datafile: str)

Bases: BaseModel

protein_datafile: str

class icolos.core.step_utils.gold_config.ConfigSaveOptions(*, save_score_in_file: int = 1, save_protein_torsions: int = 1)

Bases: BaseModel

save_protein_torsions: int

save_score_in_file: int

class icolos.core.step_utils.gold_config.ConfigTermination(*, early_termination: int = 1, n_top_solutions: int = 3, rms_tolerance: float = 1.5)

Bases: BaseModel

early_termination: int

n_top_solutions: int

rms_tolerance: float

icolos.core.step_utils.input_merger module

class icolos.core.step_utils.input_merger.InputMerger(config: StepMerge)

Bases: object

merge(compounds: List[Compound]) → List[Compound]

unroll_compounds(compounds: list) → List[Compound]

class icolos.core.step_utils.input_merger.StepMerge(*, compounds: bool = True, enumerations: bool = False, merge_compounds_by: str = StepBaseEnum.INPUT_MERGE_BY_NAME, merge_enumerations_by: str = StepBaseEnum.INPUT_MERGE_BY_ID)

Bases: BaseModel

compounds: bool

enumerations: bool

merge_compounds_by: str

merge_enumerations_by: str

icolos.core.step_utils.input_preparator module

class icolos.core.step_utils.input_preparator.InputPreparator(*, workflow: Any = None, logger: BaseLogger = None)

Bases: BaseModel

class Config

Bases: object

arbitrary_types_allowed = True

underscore_attrs_are_private = True

generate_input(step_input: StepInputParameters, step_type)

logger: BaseLogger

workflow: Any

class icolos.core.step_utils.input_preparator.StepCSVInputColumnParameters(*, smiles: str, names: str = None)

Bases: BaseModel

names: str

smiles: str

class icolos.core.step_utils.input_preparator.StepData(*, compounds: ~typing.List[~icolos.core.containers.compound.Compound] = [], generic: ~icolos.core.containers.generic.GenericContainer = <icolos.core.containers.generic.GenericContainer object>, gmx_state: ~icolos.core.containers.gmx_state.GromacsState = Gromacs Topology object: System: [] | Molecules: [] | FF: amber03 | itp files: [] | posre files [])

Bases: BaseModel

class Config

Bases: object

arbitrary_types_allowed = True

compounds: List[Compound]

generic: GenericContainer

gmx_state: GromacsState

class icolos.core.step_utils.input_preparator.StepInputEnforceIDs(*, compound_ids: List = None, enumeration_ids: List = None)

Bases: BaseModel

compound_ids: List

enumeration_ids: List

class icolos.core.step_utils.input_preparator.StepInputParameters(*, compounds: ~typing.List[~icolos.core.step_utils.input_preparator.StepInputSource] = [], generic: ~typing.List[~icolos.core.step_utils.input_preparator.StepInputSource] = [], gmx_state: ~icolos.core.step_utils.input_preparator.StepInputSource = {}, perturbation_map: ~typing.List[~icolos.core.step_utils.input_preparator.StepInputSource] = None, merge: ~icolos.core.step_utils.input_merger.StepMerge = StepMerge(compounds=True, enumerations=False, merge_compounds_by=<StepBaseEnum.INPUT_MERGE_BY_NAME: 'name'>, merge_enumerations_by=<StepBaseEnum.INPUT_MERGE_BY_ID: 'id'>), work_dir: str = None)

Bases: BaseModel

compounds: List[StepInputSource]

generic: List[StepInputSource]

gmx_state: StepInputSource

merge: StepMerge

perturbation_map: List[StepInputSource]

work_dir: str

class icolos.core.step_utils.input_preparator.StepInputSource(*, source: str, source_type: str = None, source_field: str = 'compounds', target_field: str = 'compounds', extension: str = None, format: str = None, delimiter: str = ',', columns: StepCSVInputColumnParameters = None, enforce_ids: StepInputEnforceIDs = None)

Bases: BaseModel

columns: StepCSVInputColumnParameters

delimiter: str

enforce_ids: StepInputEnforceIDs

extension: str

format: str

source: str

source_field: str

source_type: str

target_field: str

class icolos.core.step_utils.input_preparator.StringFile(content)

Bases: str

class icolos.core.step_utils.input_preparator.StringPath(content)

Bases: str

icolos.core.step_utils.obabel_structconvert module

class icolos.core.step_utils.obabel_structconvert.OBabelStructConvert

Bases: object

Utility for converting structure files with Schrodinger’s StructConvert

convert(input_file: str, output_file: str)

execute(arguments: list)

sdf2pdb(sdf_file: str, pdb_file: str)

icolos.core.step_utils.rdkit_utils module

icolos.core.step_utils.rdkit_utils.to_smiles(mol, isomericSmiles=False)

Converts a Mol object into a canonical SMILES string. :param mol: Mol object. :return: A SMILES string.

icolos.core.step_utils.retry module

class icolos.core.step_utils.retry.RetryResult(*, success: bool, tries: int, result: Any = None, exception: Exception = None)

Bases: BaseModel

class Config

Bases: object

arbitrary_types_allowed = True

exception: Exception

result: Any

success: bool

tries: int

icolos.core.step_utils.retry.retry(n_tries, retry_wait_seconds, allowed_exceptions=())

icolos.core.step_utils.run_variables_resolver module

class icolos.core.step_utils.run_variables_resolver.RunVariablesResolver

Bases: object

resolve(input_str: str, input_object) → str

resolve_compound_level(input_str: str, comp: Compound) → str

resolve_conformer_level(input_str: str, conf: Conformer) → str

resolve_enumeration_level(input_str: str, enum: Enumeration) → str

icolos.core.step_utils.sdconvert_util module

class icolos.core.step_utils.sdconvert_util.SDConvertUtil(prefix_execution: Optional[str] = None, binary_location: Optional[str] = None)

Bases: object

execute(arguments: list)

mae2sdf(mae_file: str, sdf_file: str)

sdf2mae(sdf_file: str, mae_file: str)

sdf2pdb(sdf_file: str, pdb_file: str)

icolos.core.step_utils.step_writeout module

class icolos.core.step_utils.step_writeout.StepWriteoutCompoundAggregationParameters(*, mode: StepBaseEnum = StepBaseEnum.WRITEOUT_COMP_AGGREGATION_MODE_ALL, highest_is_best: bool = True, key: str = None)

Bases: BaseModel

highest_is_best: bool

key: str

mode: StepBaseEnum

class icolos.core.step_utils.step_writeout.StepWriteoutCompoundParameters(*, category: ~icolos.utils.enums.step_enums.StepBaseEnum, aggregation: ~icolos.core.step_utils.step_writeout.StepWriteoutCompoundAggregationParameters = StepWriteoutCompoundAggregationParameters(mode=<StepBaseEnum.WRITEOUT_COMP_AGGREGATION_MODE_ALL: 'all'>, highest_is_best=True, key=None), key: str = None, selected_tags: ~typing.List[str] = None)

Bases: BaseModel

aggregation: StepWriteoutCompoundAggregationParameters

category: StepBaseEnum

key: str

selected_tags: List[str]

class icolos.core.step_utils.step_writeout.StepWriteoutDestinationParameters(*, resource: str = None, type: StepBaseEnum = StepBaseEnum.INPUT_SOURCE_TYPE_FILE, format: StepBaseEnum = StepBaseEnum.FORMAT_TXT, merge: bool = True, mode: StepBaseEnum = StepBaseEnum.WRITEOUT_DESTINATION_BASE_NAME)

Bases: BaseModel

format: StepBaseEnum

merge: bool

mode: StepBaseEnum

resource: str

type: StepBaseEnum

class icolos.core.step_utils.step_writeout.StepWriteoutGenericParameters(*, key: str)

Bases: BaseModel

key: str

class icolos.core.step_utils.step_writeout.StepWriteoutGromacsParameters(*, key: str)

Bases: BaseModel

key: str

class icolos.core.step_utils.step_writeout.StepWriteoutParameters(*, compounds: StepWriteoutCompoundParameters = None, generic: StepWriteoutGenericParameters = None, gmx_state: StepWriteoutGromacsParameters = None, destination: StepWriteoutDestinationParameters = None)

Bases: BaseModel

compounds: StepWriteoutCompoundParameters

destination: StepWriteoutDestinationParameters

generic: StepWriteoutGenericParameters

gmx_state: StepWriteoutGromacsParameters

class icolos.core.step_utils.step_writeout.WriteOutHandler(*, config: StepWriteoutParameters, data: StepData = None, workflow_data: BaseModel = None)

Bases: BaseModel

class Config

Bases: object

underscore_attrs_are_private = True

config: StepWriteoutParameters

data: StepData

get_data() → StepData

set_data(data: StepData)

set_workflow_data(data)

workflow_data: BaseModel

write()

icolos.core.step_utils.structcat_util module

class icolos.core.step_utils.structcat_util.StructcatUtil(prefix_execution: Optional[str] = None, binary_location: Optional[str] = None, backend: str = 'obabel')

Bases: object

concatenate(input_files: List[str], output_file: str, location: Optional[str] = None)

icolos.core.step_utils.structconvert module

class icolos.core.step_utils.structconvert.StructConvert(prefix_execution: str, binary_location: Optional[str] = None)

Bases: object

Utility for converting structure files with Schrodinger’s StructConvert

convert(input_file: str, output_file: str)

execute(arguments: list)

mae2pdb(mae_file: str, pdb_file: str)

pdb2mae(pdb_file: str, mae_file: str)

sdf2pdb(sdf_file: str, pdb_file: str)

Module contents