schrodinger.application.livedesign.entry_types module¶
-
class
schrodinger.application.livedesign.entry_types.
BaseEntryData
(structure_map)[source]¶ 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.
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name
= ''¶
-
description
= ''¶
-
min_nodes
= 1¶
-
min_structures
= 1¶
-
node_str
= ''¶
-
target_str
= ''¶
-
__init__
(structure_map)[source]¶ - Parameters
structure_map (dict[str, structure.Structure]) – a dictionary mapping unique strings to structures from some system
-
checkNumEntries
(**kwargs)¶
-
getSummary
()[source]¶ 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
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)[source]¶ 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.
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checkNumNodes
(**kwargs)¶
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__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
-
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
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)[source]¶ 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¶
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checkNumAtoms
(**kwargs)¶
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__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
-
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
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)[source]¶ Bases:
schrodinger.application.livedesign.entry_types.TargetlessBase
-
name
= 'Organometallic Compounds'¶
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description
= 'Upload organometallic compounds. Each compound must be its own entry.'¶
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max_num_atoms
= 700¶
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node_str
= 'organometallic compound'¶
-
getSummary
()[source]¶ 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
-
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
= ''¶
-
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class
schrodinger.application.livedesign.entry_types.
Ligands
(structure_map)[source]¶ Bases:
schrodinger.application.livedesign.entry_types.TargetlessBase
-
name
= 'Ligands'¶
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description
= 'Upload ligands. Each ligand must be in its own entry. Non-ligand structures will be ignored.'¶
-
max_num_atoms
= 130¶
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node_str
= 'ligand'¶
-
getSummary
()[source]¶ 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
-
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)[source]¶ 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.'¶
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node_str
= 'ligand'¶
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target_str
= 'receptor'¶
-
checkNumNodes
(**kwargs)¶
-
checkTargets
(**kwargs)¶
-
getSummary
()[source]¶ 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
-
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)[source]¶ 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'¶
-
checkTargets
(**kwargs)¶
-
checkLigands
(**kwargs)¶
-
getSummary
()[source]¶ 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
-
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)[source]¶ 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
-
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
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)[source]¶ 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)[source]¶ 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)[source]¶ 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, “s” will be appended to
singular_str