schrodinger.application.steps.utils module

exception schrodinger.application.steps.utils.StepsError[source]

Bases: RuntimeError

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

args
with_traceback()

Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

schrodinger.application.steps.utils.to_string(obj)[source]

Convert the mol or scored mol to a string representation.

To be used in logging and file writing.

Parameters

obj (Chem.Mol or object) – a step input or output object

Returns

text representation

Return type

str

schrodinger.application.steps.utils.mol_to_structure(mol, step, generate_coordinates=False)[source]

Convert a mol to a structure object catching and reporting exceptions.

Parameters

  • mol (Chem.Mol) – the mol to convert

  • step (stepper._BaseStep) – Step this conversion is being performed for

  • generate_coordinates (bool) – whether coordinates should be generated

Returns

the structure or None if there were issues

Return type

structure.Structure or NoneType

schrodinger.application.steps.utils.structure_to_mol(st, step, input_mol=None)[source]

Convert a structure to a mol object catching and reporting exceptions.

Parameters

  • st (Structure.Structure) – the structure to convert

  • step (stepper._BaseStep) – Step this conversion is being performed for

  • input_mol – the input molecule for this step

Returns

the molecule or None if there were issues

Return type

Chem.Mol or NoneType

schrodinger.application.steps.utils.fragment_to_molecule(fragment)[source]

Create a molecule from a fragment with implicit H.

Parameters

fragment (Chem.Mol) – the fragment

Returns

the molecule version of the fragment

Return type

Chem.Mol

schrodinger.application.steps.utils.validate_core_smarts(step, core_smarts)[source]

Validation of a required core smarts for a step.

Parameters

  • step (stepper.BaseStep) – The step that the validation is for

  • core_smarts (str or NoneType) – the SMARTS to validate

Returns

the list of validation issues

Return type

List[stepper.ValidationIssue]

schrodinger.application.steps.utils.validate_file(step, settings_attr_name)[source]

Validation of an optional file.

Parameters

  • step (stepper.BaseStep) – the step that the validation is for

  • settings_attr_name (str) – the settings attribute name

Returns

the list of validation issues

Return type

List[stepper.ValidationIssues]

schrodinger.application.steps.utils.apply_config_settings_to_step(config_dict, step)[source]

Applies all possible items from settings to the configuration settings of the step.

Parameters

  • config_dict (dict) – the configuration dictionary

  • step (stepper.BaseStep) – the steps to apply the settings to

schrodinger.application.steps.utils.update_params(to_params, from_params)[source]

Update the to_params with the values in from_params.

Parameters
schrodinger.application.steps.utils.validate_smasher_file(smasher_fname)[source]

Validate a Smasher input archive

Parameters

smasher_fname (str) – Filename of the Smasher input to validate

Returns

A string error if issues are encountered, None otherwise.

Return type

str or NoneType

schrodinger.application.steps.utils.need_Hs(mol, sma)[source]

Determine whether the SMARTS of the underlying sma has explicit hydrogens, so that a molecule that has only implicit H’s needs to have hydrogens added in order to be able to have a substructure match.

Parameters

  • mol (Chem.Mol) – the mol to check

  • sma (Chem.Mol) – the smarts mol to check against

Returns

True if addHs is needed, False if it wasn’t needed and None if it can not be determined, i.e., SMARTS never matched

Return type

bool or NoneType