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 = ''
__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_classes2.ReceptorLigandMap
checkNumEntries(**kwargs)
getSummary()

Return a summary of the receptor and ligand data stored in this object. Meant to be overridden by a subclass.

Returns:a summary of the data stored on this object
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 = ''
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_classes2.ReceptorLigandMap
getSummary()

Return a summary of the receptor and ligand data stored in this object. Meant to be overridden by a subclass.

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 = ''
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_classes2.ReceptorLigandMap
getSummary()

Return a summary of the receptor and ligand data stored in this object. Meant to be overridden by a subclass.

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
getSummary()

Return a summary of the receptor and ligand data stored in this object. Meant to be overridden by a subclass.

Returns:a summary of the data stored on this object
Return type:str
__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)
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_classes2.ReceptorLigandMap
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 = 130
node_str = 'ligand'
getSummary()

Return a summary of the receptor and ligand data stored in this object. Meant to be overridden by a subclass.

Returns:a summary of the data stored on this object
Return type:str
__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)
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_classes2.ReceptorLigandMap
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)
getSummary()

Return a summary of the receptor and ligand data stored in this object. Meant to be overridden by a subclass.

Returns:a summary of the data stored on this object
Return type:str
__init__(structure_map)
Parameters:structure_map (dict[str, structure.Structure]) – a dictionary mapping unique strings to structures from some system
checkNumEntries(**kwargs)
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_classes2.ReceptorLigandMap
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)
getSummary()

Return a summary of the receptor and ligand data stored in this object. Meant to be overridden by a subclass.

Returns:a summary of the data stored on this object
Return type:str
__init__(structure_map)
Parameters:structure_map (dict[str, structure.Structure]) – a dictionary mapping unique strings to structures from some system
checkNumEntries(**kwargs)
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_classes2.ReceptorLigandMap
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)
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_classes2.ReceptorLigandMap
getSummary()

Return a summary of the receptor and ligand data stored in this object. Meant to be overridden by a subclass.

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_unique_ligands(sts)

Return the set of ligands in a list of cts that is unique by SMILES.

Parameters:sts (structure.Structure) – the structures to analyze
Returns:the set of unique ligands
Return type:set of analyze.Ligand
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, “s” will be appended to singular_str