schrodinger.application.livedesign.entry_types module¶

class schrodinger.application.livedesign.entry_types.BaseEntryData(structure_map)¶

Bases: schrodinger.ui.qt.appframework2.validation.ValidationMixin

Abstract class for storing and validating data for various formats of ligand-based systems in anticipation of export to LiveDesign.

name = ''¶

description = ''¶

min_nodes = 1¶

min_structures = 1¶

node_str = ''¶

target_str = ''¶

entry_singular = 'entry'¶

__init__(structure_map)¶

Parameters: structure_map (dict[str, structure.Structure]) – a dictionary mapping unique strings to structures from some system

getNumTargets()¶

Returns: the number of unique targets in the system
Return type: int

getRLMap()¶

Returns: a copy of the stored receptor ligand map
Return type: data_classes.ReceptorLigandMap

checkNumEntries(**kwargs)¶

getSummary()¶

Return a summary of the receptor and ligand data stored in this object.

Returns: a summary of the data stored on this object
Return type: str

formatSummaryMessage(*msgs)¶

Returns a formatted summary string. Takes the form of ‘msg1 (msg2, msg3…)’

Parameters: msgs (str) – messages to separate
Returns: Formatted string
Return type: str

reportValidation(results)¶

Present validation messages to the user. This is an implmentation of the ValidationMixin interface and does not need to be called directly.

This method assumes that error and question methods have been defined in the subclass, as in e.g. widget_mixins.MessageBoxMixin.

Parameters: results (validation.ValidationResults) – Set of validation results generated by validate
Returns: if True, there were no validation errors and the user decided to continue despite any warnings. If False, there was at least one validation error or the user decided to abort when faced with a warning.

runValidation(silent=False, validate_children=True, stop_on_fail=True)¶

Runs validation and reports the results (unless run silently).

Parameters

silent (bool) – run without any reporting (i.e. error messages to the user). This is useful if we want to programmatically test validity. Changes return value of this method from ValidationResults to a boolean.
validate_children (bool) – run validation on all child objects. See _validateChildren for documentation on what this entails.
stop_on_fail (bool) – stop validation when first failure is encountered

Returns

if silent is False, returns the validation results. If silent is True, returns a boolean generated by reportValidation.

Return type

ValidationResults or bool

class schrodinger.application.livedesign.entry_types.IndividualStructureBase(structure_map)¶

Bases: schrodinger.application.livedesign.entry_types.BaseEntryData

Class representing data types for which each structure in the input receptor-ligand map is either a single target or a single node structure.

getNumNodes()¶

Returns: the number of unique nodes in this system
Return type: int

checkNumNodes(**kwargs)¶

__init__(structure_map)¶

Parameters: structure_map (dict[str, structure.Structure]) – a dictionary mapping unique strings to structures from some system

checkNumEntries(**kwargs)¶

description = ''¶

entry_singular = 'entry'¶

formatSummaryMessage(*msgs)¶

Returns a formatted summary string. Takes the form of ‘msg1 (msg2, msg3…)’

Parameters: msgs (str) – messages to separate
Returns: Formatted string
Return type: str

getNumTargets()¶

Returns: the number of unique targets in the system
Return type: int

getRLMap()¶

Returns: a copy of the stored receptor ligand map
Return type: data_classes.ReceptorLigandMap

getSummary()¶

Return a summary of the receptor and ligand data stored in this object.

Returns: a summary of the data stored on this object
Return type: str

min_nodes = 1¶

min_structures = 1¶

name = ''¶

node_str = ''¶

reportValidation(results)¶

Present validation messages to the user. This is an implmentation of the ValidationMixin interface and does not need to be called directly.

This method assumes that error and question methods have been defined in the subclass, as in e.g. widget_mixins.MessageBoxMixin.

Parameters: results (validation.ValidationResults) – Set of validation results generated by validate
Returns: if True, there were no validation errors and the user decided to continue despite any warnings. If False, there was at least one validation error or the user decided to abort when faced with a warning.

runValidation(silent=False, validate_children=True, stop_on_fail=True)¶

Runs validation and reports the results (unless run silently).

Parameters

silent (bool) – run without any reporting (i.e. error messages to the user). This is useful if we want to programmatically test validity. Changes return value of this method from ValidationResults to a boolean.
validate_children (bool) – run validation on all child objects. See _validateChildren for documentation on what this entails.
stop_on_fail (bool) – stop validation when first failure is encountered

Returns

if silent is False, returns the validation results. If silent is True, returns a boolean generated by reportValidation.

Return type

ValidationResults or bool

target_str = ''¶

class schrodinger.application.livedesign.entry_types.TargetlessBase(structure_map)¶

Bases: schrodinger.application.livedesign.entry_types.IndividualStructureBase

Base class for data types that do not have a target structure. Subclasses must redefine max_num_atoms.

Variables: max_num_atoms (int) – the maximum number of atoms per structure

max_num_atoms = 0¶

checkNumAtoms(**kwargs)¶

__init__(structure_map)¶

Parameters: structure_map (dict[str, structure.Structure]) – a dictionary mapping unique strings to structures from some system

checkNumEntries(**kwargs)¶

checkNumNodes(**kwargs)¶

description = ''¶

entry_singular = 'entry'¶

formatSummaryMessage(*msgs)¶

Returns a formatted summary string. Takes the form of ‘msg1 (msg2, msg3…)’

Parameters: msgs (str) – messages to separate
Returns: Formatted string
Return type: str

getNumNodes()¶

Returns: the number of unique nodes in this system
Return type: int

getNumTargets()¶

Returns: the number of unique targets in the system
Return type: int

getRLMap()¶

Returns: a copy of the stored receptor ligand map
Return type: data_classes.ReceptorLigandMap

getSummary()¶

Return a summary of the receptor and ligand data stored in this object.

Returns: a summary of the data stored on this object
Return type: str

min_nodes = 1¶

min_structures = 1¶

name = ''¶

node_str = ''¶

reportValidation(results)¶

Present validation messages to the user. This is an implmentation of the ValidationMixin interface and does not need to be called directly.

This method assumes that error and question methods have been defined in the subclass, as in e.g. widget_mixins.MessageBoxMixin.

Parameters: results (validation.ValidationResults) – Set of validation results generated by validate
Returns: if True, there were no validation errors and the user decided to continue despite any warnings. If False, there was at least one validation error or the user decided to abort when faced with a warning.

runValidation(silent=False, validate_children=True, stop_on_fail=True)¶

Runs validation and reports the results (unless run silently).

Parameters

silent (bool) – run without any reporting (i.e. error messages to the user). This is useful if we want to programmatically test validity. Changes return value of this method from ValidationResults to a boolean.
validate_children (bool) – run validation on all child objects. See _validateChildren for documentation on what this entails.
stop_on_fail (bool) – stop validation when first failure is encountered

Returns

if silent is False, returns the validation results. If silent is True, returns a boolean generated by reportValidation.

Return type

ValidationResults or bool

target_str = ''¶

class schrodinger.application.livedesign.entry_types.OrganometallicCompounds(structure_map)¶

Bases: schrodinger.application.livedesign.entry_types.TargetlessBase

name = 'Organometallic Compounds'¶

description = 'Upload organometallic compounds. Each compound must be its own entry.'¶

max_num_atoms = 700¶

node_str = 'organometallic compound'¶

getNumNodes()¶

Returns: the number of unique nodes in this system
Return type: int

__init__(structure_map)¶

Parameters: structure_map (dict[str, structure.Structure]) – a dictionary mapping unique strings to structures from some system

checkNumAtoms(**kwargs)¶

checkNumEntries(**kwargs)¶

checkNumNodes(**kwargs)¶

entry_singular = 'entry'¶

formatSummaryMessage(*msgs)¶

Returns a formatted summary string. Takes the form of ‘msg1 (msg2, msg3…)’

Parameters: msgs (str) – messages to separate
Returns: Formatted string
Return type: str

getNumTargets()¶

Returns: the number of unique targets in the system
Return type: int

getRLMap()¶

Returns: a copy of the stored receptor ligand map
Return type: data_classes.ReceptorLigandMap

getSummary()¶

Return a summary of the receptor and ligand data stored in this object.

Returns: a summary of the data stored on this object
Return type: str

min_nodes = 1¶

min_structures = 1¶

reportValidation(results)¶

Present validation messages to the user. This is an implmentation of the ValidationMixin interface and does not need to be called directly.

This method assumes that error and question methods have been defined in the subclass, as in e.g. widget_mixins.MessageBoxMixin.

Parameters: results (validation.ValidationResults) – Set of validation results generated by validate
Returns: if True, there were no validation errors and the user decided to continue despite any warnings. If False, there was at least one validation error or the user decided to abort when faced with a warning.

runValidation(silent=False, validate_children=True, stop_on_fail=True)¶

Runs validation and reports the results (unless run silently).

Parameters

silent (bool) – run without any reporting (i.e. error messages to the user). This is useful if we want to programmatically test validity. Changes return value of this method from ValidationResults to a boolean.
validate_children (bool) – run validation on all child objects. See _validateChildren for documentation on what this entails.
stop_on_fail (bool) – stop validation when first failure is encountered

Returns

if silent is False, returns the validation results. If silent is True, returns a boolean generated by reportValidation.

Return type

ValidationResults or bool

target_str = ''¶

class schrodinger.application.livedesign.entry_types.Ligands(structure_map)¶

Bases: schrodinger.application.livedesign.entry_types.TargetlessBase

name = 'Ligands'¶

description = 'Upload ligands. Each ligand must be in its own entry. Non-ligand structures will be ignored.'¶

max_num_atoms = 100¶

node_str = 'ligand'¶

__init__(structure_map)¶

Parameters: structure_map (dict[str, structure.Structure]) – a dictionary mapping unique strings to structures from some system

checkNumAtoms(**kwargs)¶

checkNumEntries(**kwargs)¶

checkNumNodes(**kwargs)¶

entry_singular = 'entry'¶

formatSummaryMessage(*msgs)¶

Returns a formatted summary string. Takes the form of ‘msg1 (msg2, msg3…)’

Parameters: msgs (str) – messages to separate
Returns: Formatted string
Return type: str

getNumNodes()¶

Returns: the number of unique nodes in this system
Return type: int

getNumTargets()¶

Returns: the number of unique targets in the system
Return type: int

getRLMap()¶

Returns: a copy of the stored receptor ligand map
Return type: data_classes.ReceptorLigandMap

getSummary()¶

Return a summary of the receptor and ligand data stored in this object.

Returns: a summary of the data stored on this object
Return type: str

min_nodes = 1¶

min_structures = 1¶

reportValidation(results)¶

Present validation messages to the user. This is an implmentation of the ValidationMixin interface and does not need to be called directly.

This method assumes that error and question methods have been defined in the subclass, as in e.g. widget_mixins.MessageBoxMixin.

Parameters: results (validation.ValidationResults) – Set of validation results generated by validate
Returns: if True, there were no validation errors and the user decided to continue despite any warnings. If False, there was at least one validation error or the user decided to abort when faced with a warning.

runValidation(silent=False, validate_children=True, stop_on_fail=True)¶

Runs validation and reports the results (unless run silently).

Parameters

silent (bool) – run without any reporting (i.e. error messages to the user). This is useful if we want to programmatically test validity. Changes return value of this method from ValidationResults to a boolean.
validate_children (bool) – run validation on all child objects. See _validateChildren for documentation on what this entails.
stop_on_fail (bool) – stop validation when first failure is encountered

Returns

if silent is False, returns the validation results. If silent is True, returns a boolean generated by reportValidation.

Return type

ValidationResults or bool

target_str = ''¶

class schrodinger.application.livedesign.entry_types.DockedPoses(structure_map)¶

Bases: schrodinger.application.livedesign.entry_types.IndividualStructureBase

name = 'Docked Poses'¶

description = 'Upload docked poses based on the PV format. Selection should include one receptor, in its own entry, and docked ligands, each in a separate entry.'¶

node_str = 'ligand'¶

target_str = 'receptor'¶

checkNumNodes(**kwargs)¶

checkTargets(**kwargs)¶

__init__(structure_map)¶

Parameters: structure_map (dict[str, structure.Structure]) – a dictionary mapping unique strings to structures from some system

checkNumEntries(**kwargs)¶

entry_singular = 'entry'¶

formatSummaryMessage(*msgs)¶

Returns a formatted summary string. Takes the form of ‘msg1 (msg2, msg3…)’

Parameters: msgs (str) – messages to separate
Returns: Formatted string
Return type: str

getNumNodes()¶

Returns: the number of unique nodes in this system
Return type: int

getNumTargets()¶

Returns: the number of unique targets in the system
Return type: int

getRLMap()¶

Returns: a copy of the stored receptor ligand map
Return type: data_classes.ReceptorLigandMap

getSummary()¶

Return a summary of the receptor and ligand data stored in this object.

Returns: a summary of the data stored on this object
Return type: str

min_nodes = 1¶

min_structures = 1¶

reportValidation(results)¶

Present validation messages to the user. This is an implmentation of the ValidationMixin interface and does not need to be called directly.

This method assumes that error and question methods have been defined in the subclass, as in e.g. widget_mixins.MessageBoxMixin.

Parameters: results (validation.ValidationResults) – Set of validation results generated by validate
Returns: if True, there were no validation errors and the user decided to continue despite any warnings. If False, there was at least one validation error or the user decided to abort when faced with a warning.

runValidation(silent=False, validate_children=True, stop_on_fail=True)¶

Runs validation and reports the results (unless run silently).

Parameters

silent (bool) – run without any reporting (i.e. error messages to the user). This is useful if we want to programmatically test validity. Changes return value of this method from ValidationResults to a boolean.
validate_children (bool) – run validation on all child objects. See _validateChildren for documentation on what this entails.
stop_on_fail (bool) – stop validation when first failure is encountered

Returns

if silent is False, returns the validation results. If silent is True, returns a boolean generated by reportValidation.

Return type

ValidationResults or bool

class schrodinger.application.livedesign.entry_types.Complexes(structure_map)¶

Bases: schrodinger.application.livedesign.entry_types.BaseEntryData

name = 'Receptor-Ligand Complexes'¶

description = 'Upload receptor-ligand complexes. Selection should include at least one entry, where each entry includes a receptor and at least one ligand.'¶

node_str = 'ligand'¶

target_str = 'receptor'¶

getNumNodes()¶

Returns: the number of unique nodes in this system
Return type: int

checkTargets(**kwargs)¶

checkLigands(**kwargs)¶

__init__(structure_map)¶

Parameters: structure_map (dict[str, structure.Structure]) – a dictionary mapping unique strings to structures from some system

checkNumEntries(**kwargs)¶

entry_singular = 'entry'¶

formatSummaryMessage(*msgs)¶

Returns a formatted summary string. Takes the form of ‘msg1 (msg2, msg3…)’

Parameters: msgs (str) – messages to separate
Returns: Formatted string
Return type: str

getNumTargets()¶

Returns: the number of unique targets in the system
Return type: int

getRLMap()¶

Returns: a copy of the stored receptor ligand map
Return type: data_classes.ReceptorLigandMap

getSummary()¶

Return a summary of the receptor and ligand data stored in this object.

Returns: a summary of the data stored on this object
Return type: str

min_nodes = 1¶

min_structures = 1¶

reportValidation(results)¶

Present validation messages to the user. This is an implmentation of the ValidationMixin interface and does not need to be called directly.

This method assumes that error and question methods have been defined in the subclass, as in e.g. widget_mixins.MessageBoxMixin.

Parameters: results (validation.ValidationResults) – Set of validation results generated by validate
Returns: if True, there were no validation errors and the user decided to continue despite any warnings. If False, there was at least one validation error or the user decided to abort when faced with a warning.

runValidation(silent=False, validate_children=True, stop_on_fail=True)¶

Runs validation and reports the results (unless run silently).

Parameters

silent (bool) – run without any reporting (i.e. error messages to the user). This is useful if we want to programmatically test validity. Changes return value of this method from ValidationResults to a boolean.
validate_children (bool) – run validation on all child objects. See _validateChildren for documentation on what this entails.
stop_on_fail (bool) – stop validation when first failure is encountered

Returns

if silent is False, returns the validation results. If silent is True, returns a boolean generated by reportValidation.

Return type

ValidationResults or bool

class schrodinger.application.livedesign.entry_types.CovalentDockingComplexes(structure_map)¶

Bases: schrodinger.application.livedesign.entry_types.Complexes

name = 'Covalent Docking Complexes'¶

description = 'Upload covalent docking structures. Selection should include outputs from the covalent docking panel. Uploaded ligands will be the original (input) structures prior to covalent docking processing.'¶

__init__(structure_map)¶

Parameters: structure_map (dict[str, structure.Structure]) – a dictionary mapping unique strings to structures from some system

checkLigands(**kwargs)¶

checkNumEntries(**kwargs)¶

checkTargets(**kwargs)¶

entry_singular = 'entry'¶

formatSummaryMessage(*msgs)¶

Returns a formatted summary string. Takes the form of ‘msg1 (msg2, msg3…)’

Parameters: msgs (str) – messages to separate
Returns: Formatted string
Return type: str

getNumNodes()¶

Returns: the number of unique nodes in this system
Return type: int

getNumTargets()¶

Returns: the number of unique targets in the system
Return type: int

getRLMap()¶

Returns: a copy of the stored receptor ligand map
Return type: data_classes.ReceptorLigandMap

getSummary()¶

Return a summary of the receptor and ligand data stored in this object.

Returns: a summary of the data stored on this object
Return type: str

min_nodes = 1¶

min_structures = 1¶

node_str = 'ligand'¶

reportValidation(results)¶

Present validation messages to the user. This is an implmentation of the ValidationMixin interface and does not need to be called directly.

This method assumes that error and question methods have been defined in the subclass, as in e.g. widget_mixins.MessageBoxMixin.

Parameters: results (validation.ValidationResults) – Set of validation results generated by validate
Returns: if True, there were no validation errors and the user decided to continue despite any warnings. If False, there was at least one validation error or the user decided to abort when faced with a warning.

runValidation(silent=False, validate_children=True, stop_on_fail=True)¶

Runs validation and reports the results (unless run silently).

Parameters

silent (bool) – run without any reporting (i.e. error messages to the user). This is useful if we want to programmatically test validity. Changes return value of this method from ValidationResults to a boolean.
validate_children (bool) – run validation on all child objects. See _validateChildren for documentation on what this entails.
stop_on_fail (bool) – stop validation when first failure is encountered

Returns

if silent is False, returns the validation results. If silent is True, returns a boolean generated by reportValidation.

Return type

ValidationResults or bool

target_str = 'receptor'¶

schrodinger.application.livedesign.entry_types.separate_complex(complex_st)¶

Given a receptor-ligand complex structure, separate the ligands from the receptors. Return a list of ‘receptor’ structures and a corresponding list of ligand structures. The receptors are the rest of the complex once the ligand has been removed.

Parameters: complex_st (structure.Structure) – a ligand-receptor complex
Returns: a receptor list and corresponding ligand list
Return type: tuple(list(structure.Structure), list(structure.Structure))

schrodinger.application.livedesign.entry_types.get_ligands(sts, unique_smiles=False)¶

Get a list of ligand smiles represented in sts

Parameters

sts (list(structure.Structure)) – the structures to analyze
unique_smiles (bool) – whether to only count sts with unique SMILES

Returns

list of smiles

Return type

list(str)

schrodinger.application.livedesign.entry_types.format_numbered_message(base_msg, number, singular_str, plural_str=None)¶

Given a specially-formatted message containing a numbered word, return the proper human-readable translation using the correct form of that word.

Example input:
base_msg = ‘I have {number} {variable_str}.’ n = 2 singular_str = egg

Example output:
‘I have 2 eggs.’

Parameters

base_msg (str) – the message to be formatted. Should contain two new-style formatting replacement points, {number} and {variable_str}, for the number and numbered word that should be added to the message
number (int) – the number to be added to the message
singular_str (str) – the singular word for the object being described
plural_str (str or NoneType) – optionally, the plural word for the object being described; by default, inflect will be used to pluralize