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 common data for all types of systems in anticipation of export to LiveDesign.
- name = ''¶
- description = ''¶
- min_structures = 1¶
- __init__(structure_map)¶
- Parameters
structure_map (dict[str, structure.Structure]) – a dictionary mapping unique strings to structures from some system
- 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
- getProperties()¶
- Returns
a set of structure property names
- Return type
set[str]
- getSamplePropertyValue(prop_name: Optional[str]) Optional[str] ¶
Get a sample property value if one is available
- Parameters
prop_name – Property name
- Returns
Property value
- checkNumEntries(**kwargs)¶
- 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
andquestion
methods have been defined in the subclass, as in e.g.widget_mixins.MessageBoxMixin
.- Parameters
results (
validation.ValidationResults
) – Set of validation results generated byvalidate
- 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.GenericEntities(structure_map)¶
Bases:
schrodinger.application.livedesign.entry_types.BaseEntryData
Class representing data type of Generic Entities, stores all data related to Generic Entities export.
- name = 'Generic Entities'¶
- __init__(structure_map)¶
- Parameters
structure_map (dict[str, structure.Structure]) – a dictionary mapping unique strings to structures from some system
- getStructures()¶
Return the structures.
- Returns
structures
- Return type
- getProperties() Set[str] ¶
Get a set of property names for all the structures
- Returns
a set of structure property names
- getSamplePropertyValue(prop_name: Optional[str]) Optional[str] ¶
Get a sample property value if one is available
- Parameters
prop_name – Property name
- Returns
Property value
- checkNumEntries(**kwargs)¶
- description = ''¶
- 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
- 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_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
andquestion
methods have been defined in the subclass, as in e.g.widget_mixins.MessageBoxMixin
.- Parameters
results (
validation.ValidationResults
) – Set of validation results generated byvalidate
- 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.BaseReceptorLigandData(structure_map)¶
Bases:
schrodinger.application.livedesign.entry_types.BaseEntryData
Abstract class for storing and validating data for various formats of ligand-based systems in anticipation of export to LiveDesign.
- min_nodes = 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
- getProperties() Set[str] ¶
Get a set of property names for all ligands in rl_map
- Returns
a set of structure property names
- getSamplePropertyValue(prop_name: Optional[str]) Optional[str] ¶
Get a sample property value if one is available
- Parameters
prop_name – Property name
- Returns
Property value
- checkNumEntries(**kwargs)¶
- description = ''¶
- 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
- 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_structures = 1¶
- name = ''¶
- 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
andquestion
methods have been defined in the subclass, as in e.g.widget_mixins.MessageBoxMixin
.- Parameters
results (
validation.ValidationResults
) – Set of validation results generated byvalidate
- 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.BaseReceptorLigandData
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
- getProperties() Set[str] ¶
Get a set of property names for all ligands in rl_map
- Returns
a set of structure property names
- getRLMap()¶
- Returns
a copy of the stored receptor ligand map
- Return type
- getSamplePropertyValue(prop_name: Optional[str]) Optional[str] ¶
Get a sample property value if one is available
- Parameters
prop_name – Property name
- Returns
Property value
- 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
andquestion
methods have been defined in the subclass, as in e.g.widget_mixins.MessageBoxMixin
.- Parameters
results (
validation.ValidationResults
) – Set of validation results generated byvalidate
- 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
- getProperties() Set[str] ¶
Get a set of property names for all ligands in rl_map
- Returns
a set of structure property names
- getRLMap()¶
- Returns
a copy of the stored receptor ligand map
- Return type
- getSamplePropertyValue(prop_name: Optional[str]) Optional[str] ¶
Get a sample property value if one is available
- Parameters
prop_name – Property name
- Returns
Property value
- 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
andquestion
methods have been defined in the subclass, as in e.g.widget_mixins.MessageBoxMixin
.- Parameters
results (
validation.ValidationResults
) – Set of validation results generated byvalidate
- 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
- getProperties() Set[str] ¶
Get a set of property names for all ligands in rl_map
- Returns
a set of structure property names
- getRLMap()¶
- Returns
a copy of the stored receptor ligand map
- Return type
- getSamplePropertyValue(prop_name: Optional[str]) Optional[str] ¶
Get a sample property value if one is available
- Parameters
prop_name – Property name
- Returns
Property value
- 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
andquestion
methods have been defined in the subclass, as in e.g.widget_mixins.MessageBoxMixin
.- Parameters
results (
validation.ValidationResults
) – Set of validation results generated byvalidate
- 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.'¶
- node_str = 'ligand'¶
- __init__(structure_map)¶
- Parameters
structure_map (dict[str, structure.Structure]) – a dictionary mapping unique strings to structures from some system
- max_num_atoms = 0¶
- 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
- getProperties() Set[str] ¶
Get a set of property names for all ligands in rl_map
- Returns
a set of structure property names
- getRLMap()¶
- Returns
a copy of the stored receptor ligand map
- Return type
- getSamplePropertyValue(prop_name: Optional[str]) Optional[str] ¶
Get a sample property value if one is available
- Parameters
prop_name – Property name
- Returns
Property value
- 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
andquestion
methods have been defined in the subclass, as in e.g.widget_mixins.MessageBoxMixin
.- Parameters
results (
validation.ValidationResults
) – Set of validation results generated byvalidate
- 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
- getProperties() Set[str] ¶
Get a set of property names for all ligands in rl_map
- Returns
a set of structure property names
- getRLMap()¶
- Returns
a copy of the stored receptor ligand map
- Return type
- getSamplePropertyValue(prop_name: Optional[str]) Optional[str] ¶
Get a sample property value if one is available
- Parameters
prop_name – Property name
- Returns
Property value
- 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
andquestion
methods have been defined in the subclass, as in e.g.widget_mixins.MessageBoxMixin
.- Parameters
results (
validation.ValidationResults
) – Set of validation results generated byvalidate
- 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.BaseReceptorLigandData
- 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
- getProperties() Set[str] ¶
Get a set of property names for all ligands in rl_map
- Returns
a set of structure property names
- getRLMap()¶
- Returns
a copy of the stored receptor ligand map
- Return type
- getSamplePropertyValue(prop_name: Optional[str]) Optional[str] ¶
Get a sample property value if one is available
- Parameters
prop_name – Property name
- Returns
Property value
- 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
andquestion
methods have been defined in the subclass, as in e.g.widget_mixins.MessageBoxMixin
.- Parameters
results (
validation.ValidationResults
) – Set of validation results generated byvalidate
- 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
- getProperties() Set[str] ¶
Get a set of property names for all ligands in rl_map
- Returns
a set of structure property names
- getRLMap()¶
- Returns
a copy of the stored receptor ligand map
- Return type
- getSamplePropertyValue(prop_name: Optional[str]) Optional[str] ¶
Get a sample property value if one is available
- Parameters
prop_name – Property name
- Returns
Property value
- 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
andquestion
methods have been defined in the subclass, as in e.g.widget_mixins.MessageBoxMixin
.- Parameters
results (
validation.ValidationResults
) – Set of validation results generated byvalidate
- 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 messagenumber (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