schrodinger.application.livedesign.maestro_data_types module

schrodinger.application.livedesign.maestro_data_types.get_unique_ligands(ct_list)

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

Parameters

ct_list (structure.Structure) – the structures to analyze

Returns

the set of unique ligands

Return type

set of analyze.Ligand

schrodinger.application.livedesign.maestro_data_types.format_numbered_message(base_msg, n, singular_string, plural_string)

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 {n} {variable_string}.’ n = 2 singular_string = egg plural_string = eggs

Example output:

‘I have 2 eggs.’

Parameters

  • base_msg (str) – the message to be formatted. Should contain two new-style formatting replacement points, {n} and {variable_string}, for the number and numbered word that should be added to the message

  • n (int) – the number to be added to the message

  • singular_string (str) – if n = 1, use this string as the numbered word in the message

  • plural_string (str) – if n != 1, use this string as the numbered word in the message

class schrodinger.application.livedesign.maestro_data_types.BaseMaestroData(rl_map, export_mae=False)

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.

Variables

  • _selected_entry_ids – set of entry IDs that were selected in the project prior to the start of a batch iteration. These are held until the end of batch iteration, when the selection state of the project is restored and this value becomes an empty set.

  • BATCHES_INCLUDE_TARGETS (bool) – whether the getBatches() method should return maps that contain receptor structures in addition to ligand structures by default

Vartype

_selected_entry_ids: set(str)

name = ''
description = ''
MIN_NODES = 1
MIN_STRUCTURES = 1
BATCHES_INCLUDE_TARGETS = False
NODE_SINGULAR_STRING = ''
NODE_PLURAL_STRING = ''
TARGET_SINGULAR_STRING = ''
TARGET_PLURAL_STRING = ''
__init__(rl_map, export_mae=False)
Parameters

  • rl_map (data_classes.ReceptorLigandMap) – a receptor-ligand map

  • export_mae (bool) – whether the 3D structure export to LiveDesign will use .mae files (rather than .prjzip files) as 3D data

getAvailableProperties()

Compile all properties of all structures scheduled for export.

Returns

a list of identifying information for the union of all structure properties for each structure scheduled for export

Return type

list(data_classes.LDData)

checkNumEntries(**kwargs)
analyzeStructures()

Compile and cache important ligand and receptor information from the receptor-ligand map. Meant to be called once on initialization.

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

getTargetEntryID(target=None)

Return the entry ID of the target associated with this data class.

Parameters

target (structure.Structure) – a target structure, if applicable

Returns

the target entry ID (if possible), or None

Return type

str or None

getBatches(batch_size, export_3d, include_targets=None)

An generator for receptor-ligand maps containing a subset of the receptor-ligand pairs contained in the rl_map instance variable. If possible, may also modify the open Maestro project to assist with export to LiveDesign.

Parameters

  • batch_size (int) – the largest number of receptor-ligand pairs that will be in the receptor-ligand maps yielded by this method

  • export_3d (bool) – whether to export 3D data

  • include_targets (bool or None) – whether the batches should include targets (e.g. receptors). A value of None (the default) will revert to the class default behavior, which is the correct choice when exporting with LDClient.start_export_assay_and_pose_data().

Returns

an iterator of receptor-ligand maps

Return type

iterator(data_classes.ReceptorLigandMap)

getAlternateBatches(batch_size)

A generator for receptor-alternate ligand maps containing a subset of the receptor-alternate ligand pairs contained in the rl_map instance variable. Alternate ligands are uploaded to LiveDesign as 3D data when the 3D structure does not have the same SMARTS representation as the rest of the structure row.

This method may modify the current Maestro project temporarily in order to export 3D data as a .prjzip file.

Note that this method takes alternate ligands from the rl_map instance variable, but returns ReceptorLigandMap instances in which those alternate ligands are stored as regular ligands. This is so that the LD export infrastructure will function the same when exporting these structures.

Parameters

batch_size (int) – the largest number of receptor-ligand pairs that will be in the receptor-ligand maps yielded by this method

Returns

an iterator of receptor-ligand maps

Return type

iterator(data_classes.ReceptorLigandMap)

exportRLMap(rl_map, export_3d)

Manage the environment for exporting a single receptor-ligand map to LiveDesign by selecting relevant project rows when entering the context environment.

Parameters
Returns

the supplied receptor-ligand map

Return type

data_classes.ReceptorLigandMap

exportAlternateRLMap(rl_map)
batchIteration()

Manage the environment for exporting receptor-ligand maps to LiveDesign, e.g. by changing the project selection state after iterating over all receptor-ligand batches.

getNextEntryId()
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.maestro_data_types.IndividualStructureBase(rl_map, export_mae=False)

Bases: schrodinger.application.livedesign.maestro_data_types.BaseMaestroData

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

checkNumNodes(**kwargs)
BATCHES_INCLUDE_TARGETS = False
MIN_NODES = 1
MIN_STRUCTURES = 1
NODE_PLURAL_STRING = ''
NODE_SINGULAR_STRING = ''
TARGET_PLURAL_STRING = ''
TARGET_SINGULAR_STRING = ''
__init__(rl_map, export_mae=False)
Parameters

  • rl_map (data_classes.ReceptorLigandMap) – a receptor-ligand map

  • export_mae (bool) – whether the 3D structure export to LiveDesign will use .mae files (rather than .prjzip files) as 3D data

analyzeStructures()

Compile and cache important ligand and receptor information from the receptor-ligand map. Meant to be called once on initialization.

batchIteration()

Manage the environment for exporting receptor-ligand maps to LiveDesign, e.g. by changing the project selection state after iterating over all receptor-ligand batches.

checkNumEntries(**kwargs)
description = ''
exportAlternateRLMap(rl_map)
exportRLMap(rl_map, export_3d)

Manage the environment for exporting a single receptor-ligand map to LiveDesign by selecting relevant project rows when entering the context environment.

Parameters
Returns

the supplied receptor-ligand map

Return type

data_classes.ReceptorLigandMap

getAlternateBatches(batch_size)

A generator for receptor-alternate ligand maps containing a subset of the receptor-alternate ligand pairs contained in the rl_map instance variable. Alternate ligands are uploaded to LiveDesign as 3D data when the 3D structure does not have the same SMARTS representation as the rest of the structure row.

This method may modify the current Maestro project temporarily in order to export 3D data as a .prjzip file.

Note that this method takes alternate ligands from the rl_map instance variable, but returns ReceptorLigandMap instances in which those alternate ligands are stored as regular ligands. This is so that the LD export infrastructure will function the same when exporting these structures.

Parameters

batch_size (int) – the largest number of receptor-ligand pairs that will be in the receptor-ligand maps yielded by this method

Returns

an iterator of receptor-ligand maps

Return type

iterator(data_classes.ReceptorLigandMap)

getAvailableProperties()

Compile all properties of all structures scheduled for export.

Returns

a list of identifying information for the union of all structure properties for each structure scheduled for export

Return type

list(data_classes.LDData)

getBatches(batch_size, export_3d, include_targets=None)

An generator for receptor-ligand maps containing a subset of the receptor-ligand pairs contained in the rl_map instance variable. If possible, may also modify the open Maestro project to assist with export to LiveDesign.

Parameters

  • batch_size (int) – the largest number of receptor-ligand pairs that will be in the receptor-ligand maps yielded by this method

  • export_3d (bool) – whether to export 3D data

  • include_targets (bool or None) – whether the batches should include targets (e.g. receptors). A value of None (the default) will revert to the class default behavior, which is the correct choice when exporting with LDClient.start_export_assay_and_pose_data().

Returns

an iterator of receptor-ligand maps

Return type

iterator(data_classes.ReceptorLigandMap)

getNextEntryId()
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

getTargetEntryID(target=None)

Return the entry ID of the target associated with this data class.

Parameters

target (structure.Structure) – a target structure, if applicable

Returns

the target entry ID (if possible), or None

Return type

str or None

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 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.maestro_data_types.TargetlessBase(rl_map, export_mae=False)

Bases: schrodinger.application.livedesign.maestro_data_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

dummy_entry_id = None
MAX_NUM_ATOMS = 0
checkNumAtoms(**kwargs)
getTargetEntryID(target=None)

Return the entry ID of the dummy target created during batch export.

See parent class for complete method documentation.

BATCHES_INCLUDE_TARGETS = False
MIN_NODES = 1
MIN_STRUCTURES = 1
NODE_PLURAL_STRING = ''
NODE_SINGULAR_STRING = ''
TARGET_PLURAL_STRING = ''
TARGET_SINGULAR_STRING = ''
__init__(rl_map, export_mae=False)
Parameters

  • rl_map (data_classes.ReceptorLigandMap) – a receptor-ligand map

  • export_mae (bool) – whether the 3D structure export to LiveDesign will use .mae files (rather than .prjzip files) as 3D data

analyzeStructures()

Compile and cache important ligand and receptor information from the receptor-ligand map. Meant to be called once on initialization.

batchIteration()

Manage the environment for exporting receptor-ligand maps to LiveDesign, e.g. by changing the project selection state after iterating over all receptor-ligand batches.

checkNumEntries(**kwargs)
checkNumNodes(**kwargs)
description = ''
exportAlternateRLMap(rl_map)
exportRLMap(rl_map, export_3d)

Manage the environment for exporting a single receptor-ligand map to LiveDesign by selecting relevant project rows when entering the context environment.

Parameters
Returns

the supplied receptor-ligand map

Return type

data_classes.ReceptorLigandMap

getAlternateBatches(batch_size)

A generator for receptor-alternate ligand maps containing a subset of the receptor-alternate ligand pairs contained in the rl_map instance variable. Alternate ligands are uploaded to LiveDesign as 3D data when the 3D structure does not have the same SMARTS representation as the rest of the structure row.

This method may modify the current Maestro project temporarily in order to export 3D data as a .prjzip file.

Note that this method takes alternate ligands from the rl_map instance variable, but returns ReceptorLigandMap instances in which those alternate ligands are stored as regular ligands. This is so that the LD export infrastructure will function the same when exporting these structures.

Parameters

batch_size (int) – the largest number of receptor-ligand pairs that will be in the receptor-ligand maps yielded by this method

Returns

an iterator of receptor-ligand maps

Return type

iterator(data_classes.ReceptorLigandMap)

getAvailableProperties()

Compile all properties of all structures scheduled for export.

Returns

a list of identifying information for the union of all structure properties for each structure scheduled for export

Return type

list(data_classes.LDData)

getBatches(batch_size, export_3d, include_targets=None)

An generator for receptor-ligand maps containing a subset of the receptor-ligand pairs contained in the rl_map instance variable. If possible, may also modify the open Maestro project to assist with export to LiveDesign.

Parameters

  • batch_size (int) – the largest number of receptor-ligand pairs that will be in the receptor-ligand maps yielded by this method

  • export_3d (bool) – whether to export 3D data

  • include_targets (bool or None) – whether the batches should include targets (e.g. receptors). A value of None (the default) will revert to the class default behavior, which is the correct choice when exporting with LDClient.start_export_assay_and_pose_data().

Returns

an iterator of receptor-ligand maps

Return type

iterator(data_classes.ReceptorLigandMap)

getNextEntryId()
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

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 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.maestro_data_types.OrganometallicCompounds(rl_map, export_mae=False)

Bases: schrodinger.application.livedesign.maestro_data_types.TargetlessBase

name = 'Organometallic Compounds'
description = 'Upload organometallic compounds. Each compound must be its own entry.'
MAX_NUM_ATOMS = 700
NODE_SINGULAR_STRING = 'organometallic compound'
NODE_PLURAL_STRING = 'organometallic compounds'
analyzeStructures()

Record the total number of compounds.

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

BATCHES_INCLUDE_TARGETS = False
MIN_NODES = 1
MIN_STRUCTURES = 1
TARGET_PLURAL_STRING = ''
TARGET_SINGULAR_STRING = ''
__init__(rl_map, export_mae=False)
Parameters

  • rl_map (data_classes.ReceptorLigandMap) – a receptor-ligand map

  • export_mae (bool) – whether the 3D structure export to LiveDesign will use .mae files (rather than .prjzip files) as 3D data

batchIteration()

Manage the environment for exporting receptor-ligand maps to LiveDesign, e.g. by changing the project selection state after iterating over all receptor-ligand batches.

checkNumAtoms(**kwargs)
checkNumEntries(**kwargs)
checkNumNodes(**kwargs)
dummy_entry_id = None
exportAlternateRLMap(rl_map)
exportRLMap(rl_map, export_3d)

Manage the environment for exporting a single receptor-ligand map to LiveDesign by selecting relevant project rows when entering the context environment.

Parameters
Returns

the supplied receptor-ligand map

Return type

data_classes.ReceptorLigandMap

getAlternateBatches(batch_size)

A generator for receptor-alternate ligand maps containing a subset of the receptor-alternate ligand pairs contained in the rl_map instance variable. Alternate ligands are uploaded to LiveDesign as 3D data when the 3D structure does not have the same SMARTS representation as the rest of the structure row.

This method may modify the current Maestro project temporarily in order to export 3D data as a .prjzip file.

Note that this method takes alternate ligands from the rl_map instance variable, but returns ReceptorLigandMap instances in which those alternate ligands are stored as regular ligands. This is so that the LD export infrastructure will function the same when exporting these structures.

Parameters

batch_size (int) – the largest number of receptor-ligand pairs that will be in the receptor-ligand maps yielded by this method

Returns

an iterator of receptor-ligand maps

Return type

iterator(data_classes.ReceptorLigandMap)

getAvailableProperties()

Compile all properties of all structures scheduled for export.

Returns

a list of identifying information for the union of all structure properties for each structure scheduled for export

Return type

list(data_classes.LDData)

getBatches(batch_size, export_3d, include_targets=None)

An generator for receptor-ligand maps containing a subset of the receptor-ligand pairs contained in the rl_map instance variable. If possible, may also modify the open Maestro project to assist with export to LiveDesign.

Parameters

  • batch_size (int) – the largest number of receptor-ligand pairs that will be in the receptor-ligand maps yielded by this method

  • export_3d (bool) – whether to export 3D data

  • include_targets (bool or None) – whether the batches should include targets (e.g. receptors). A value of None (the default) will revert to the class default behavior, which is the correct choice when exporting with LDClient.start_export_assay_and_pose_data().

Returns

an iterator of receptor-ligand maps

Return type

iterator(data_classes.ReceptorLigandMap)

getNextEntryId()
getTargetEntryID(target=None)

Return the entry ID of the dummy target created during batch export.

See parent class for complete method documentation.

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.maestro_data_types.Ligands(rl_map, export_mae=False)

Bases: schrodinger.application.livedesign.maestro_data_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_SINGULAR_STRING = 'ligand'
NODE_PLURAL_STRING = 'ligands'
analyzeStructures()

Only record the number of unique ligands.

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

BATCHES_INCLUDE_TARGETS = False
MIN_NODES = 1
MIN_STRUCTURES = 1
TARGET_PLURAL_STRING = ''
TARGET_SINGULAR_STRING = ''
__init__(rl_map, export_mae=False)
Parameters

  • rl_map (data_classes.ReceptorLigandMap) – a receptor-ligand map

  • export_mae (bool) – whether the 3D structure export to LiveDesign will use .mae files (rather than .prjzip files) as 3D data

batchIteration()

Manage the environment for exporting receptor-ligand maps to LiveDesign, e.g. by changing the project selection state after iterating over all receptor-ligand batches.

checkNumAtoms(**kwargs)
checkNumEntries(**kwargs)
checkNumNodes(**kwargs)
dummy_entry_id = None
exportAlternateRLMap(rl_map)
exportRLMap(rl_map, export_3d)

Manage the environment for exporting a single receptor-ligand map to LiveDesign by selecting relevant project rows when entering the context environment.

Parameters
Returns

the supplied receptor-ligand map

Return type

data_classes.ReceptorLigandMap

getAlternateBatches(batch_size)

A generator for receptor-alternate ligand maps containing a subset of the receptor-alternate ligand pairs contained in the rl_map instance variable. Alternate ligands are uploaded to LiveDesign as 3D data when the 3D structure does not have the same SMARTS representation as the rest of the structure row.

This method may modify the current Maestro project temporarily in order to export 3D data as a .prjzip file.

Note that this method takes alternate ligands from the rl_map instance variable, but returns ReceptorLigandMap instances in which those alternate ligands are stored as regular ligands. This is so that the LD export infrastructure will function the same when exporting these structures.

Parameters

batch_size (int) – the largest number of receptor-ligand pairs that will be in the receptor-ligand maps yielded by this method

Returns

an iterator of receptor-ligand maps

Return type

iterator(data_classes.ReceptorLigandMap)

getAvailableProperties()

Compile all properties of all structures scheduled for export.

Returns

a list of identifying information for the union of all structure properties for each structure scheduled for export

Return type

list(data_classes.LDData)

getBatches(batch_size, export_3d, include_targets=None)

An generator for receptor-ligand maps containing a subset of the receptor-ligand pairs contained in the rl_map instance variable. If possible, may also modify the open Maestro project to assist with export to LiveDesign.

Parameters

  • batch_size (int) – the largest number of receptor-ligand pairs that will be in the receptor-ligand maps yielded by this method

  • export_3d (bool) – whether to export 3D data

  • include_targets (bool or None) – whether the batches should include targets (e.g. receptors). A value of None (the default) will revert to the class default behavior, which is the correct choice when exporting with LDClient.start_export_assay_and_pose_data().

Returns

an iterator of receptor-ligand maps

Return type

iterator(data_classes.ReceptorLigandMap)

getNextEntryId()
getTargetEntryID(target=None)

Return the entry ID of the dummy target created during batch export.

See parent class for complete method documentation.

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.maestro_data_types.DockedPoses(rl_map, export_mae=False)

Bases: schrodinger.application.livedesign.maestro_data_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.'
BATCHES_INCLUDE_TARGETS = True
NODE_SINGULAR_STRING = 'ligand'
NODE_PLURAL_STRING = 'ligands'
TARGET_SINGULAR_STRING = 'receptor'
TARGET_PLURAL_STRING = 'receptors'
getTargetEntryID(target=None)

Because all receptor-ligand pairs in the receptor-ligand map should have the same receptor, return the entry ID associated with any of them.

See parent class for complete method documentation.

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

analyzeStructures()

Calculate and store receptor data in addition to the ligand data calculated by the superclass method.

MIN_NODES = 1
MIN_STRUCTURES = 1
__init__(rl_map, export_mae=False)
Parameters

  • rl_map (data_classes.ReceptorLigandMap) – a receptor-ligand map

  • export_mae (bool) – whether the 3D structure export to LiveDesign will use .mae files (rather than .prjzip files) as 3D data

batchIteration()

Manage the environment for exporting receptor-ligand maps to LiveDesign, e.g. by changing the project selection state after iterating over all receptor-ligand batches.

checkNumEntries(**kwargs)
exportAlternateRLMap(rl_map)
exportRLMap(rl_map, export_3d)

Manage the environment for exporting a single receptor-ligand map to LiveDesign by selecting relevant project rows when entering the context environment.

Parameters
Returns

the supplied receptor-ligand map

Return type

data_classes.ReceptorLigandMap

getAlternateBatches(batch_size)

A generator for receptor-alternate ligand maps containing a subset of the receptor-alternate ligand pairs contained in the rl_map instance variable. Alternate ligands are uploaded to LiveDesign as 3D data when the 3D structure does not have the same SMARTS representation as the rest of the structure row.

This method may modify the current Maestro project temporarily in order to export 3D data as a .prjzip file.

Note that this method takes alternate ligands from the rl_map instance variable, but returns ReceptorLigandMap instances in which those alternate ligands are stored as regular ligands. This is so that the LD export infrastructure will function the same when exporting these structures.

Parameters

batch_size (int) – the largest number of receptor-ligand pairs that will be in the receptor-ligand maps yielded by this method

Returns

an iterator of receptor-ligand maps

Return type

iterator(data_classes.ReceptorLigandMap)

getAvailableProperties()

Compile all properties of all structures scheduled for export.

Returns

a list of identifying information for the union of all structure properties for each structure scheduled for export

Return type

list(data_classes.LDData)

getBatches(batch_size, export_3d, include_targets=None)

An generator for receptor-ligand maps containing a subset of the receptor-ligand pairs contained in the rl_map instance variable. If possible, may also modify the open Maestro project to assist with export to LiveDesign.

Parameters

  • batch_size (int) – the largest number of receptor-ligand pairs that will be in the receptor-ligand maps yielded by this method

  • export_3d (bool) – whether to export 3D data

  • include_targets (bool or None) – whether the batches should include targets (e.g. receptors). A value of None (the default) will revert to the class default behavior, which is the correct choice when exporting with LDClient.start_export_assay_and_pose_data().

Returns

an iterator of receptor-ligand maps

Return type

iterator(data_classes.ReceptorLigandMap)

getNextEntryId()
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.maestro_data_types.Complexes(rl_map, export_mae=False)

Bases: schrodinger.application.livedesign.maestro_data_types.BaseMaestroData

BATCHES_INCLUDE_TARGETS = True
name = 'Receptor-Ligand Complexes'
description = 'Upload receptor-ligand complexes. Selection should include n entries, where each entry includes a receptor and at least one ligand.'
NODE_SINGULAR_STRING = 'ligand'
NODE_PLURAL_STRING = 'ligands'
TARGET_SINGULAR_STRING = 'receptors'
checkTargets(**kwargs)
checkLigands(**kwargs)
getTargetEntryID(target=None)

Return the entry ID of the provided receptor structure.

See parent class for complete method documentation.

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
TARGET_PLURAL_STRING = ''
__init__(rl_map, export_mae=False)
Parameters

  • rl_map (data_classes.ReceptorLigandMap) – a receptor-ligand map

  • export_mae (bool) – whether the 3D structure export to LiveDesign will use .mae files (rather than .prjzip files) as 3D data

analyzeStructures()

Compile and cache important ligand and receptor information from the receptor-ligand map. Meant to be called once on initialization.

batchIteration()

Manage the environment for exporting receptor-ligand maps to LiveDesign, e.g. by changing the project selection state after iterating over all receptor-ligand batches.

checkNumEntries(**kwargs)
exportAlternateRLMap(rl_map)
exportRLMap(rl_map, export_3d)

Manage the environment for exporting a single receptor-ligand map to LiveDesign by selecting relevant project rows when entering the context environment.

Parameters
Returns

the supplied receptor-ligand map

Return type

data_classes.ReceptorLigandMap

getAlternateBatches(batch_size)

A generator for receptor-alternate ligand maps containing a subset of the receptor-alternate ligand pairs contained in the rl_map instance variable. Alternate ligands are uploaded to LiveDesign as 3D data when the 3D structure does not have the same SMARTS representation as the rest of the structure row.

This method may modify the current Maestro project temporarily in order to export 3D data as a .prjzip file.

Note that this method takes alternate ligands from the rl_map instance variable, but returns ReceptorLigandMap instances in which those alternate ligands are stored as regular ligands. This is so that the LD export infrastructure will function the same when exporting these structures.

Parameters

batch_size (int) – the largest number of receptor-ligand pairs that will be in the receptor-ligand maps yielded by this method

Returns

an iterator of receptor-ligand maps

Return type

iterator(data_classes.ReceptorLigandMap)

getAvailableProperties()

Compile all properties of all structures scheduled for export.

Returns

a list of identifying information for the union of all structure properties for each structure scheduled for export

Return type

list(data_classes.LDData)

getBatches(batch_size, export_3d, include_targets=None)

An generator for receptor-ligand maps containing a subset of the receptor-ligand pairs contained in the rl_map instance variable. If possible, may also modify the open Maestro project to assist with export to LiveDesign.

Parameters

  • batch_size (int) – the largest number of receptor-ligand pairs that will be in the receptor-ligand maps yielded by this method

  • export_3d (bool) – whether to export 3D data

  • include_targets (bool or None) – whether the batches should include targets (e.g. receptors). A value of None (the default) will revert to the class default behavior, which is the correct choice when exporting with LDClient.start_export_assay_and_pose_data().

Returns

an iterator of receptor-ligand maps

Return type

iterator(data_classes.ReceptorLigandMap)

getNextEntryId()
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.maestro_data_types.CovalentDockingComplexes(rl_map, export_mae=False)

Bases: schrodinger.application.livedesign.maestro_data_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.'
BATCHES_INCLUDE_TARGETS = True
MIN_NODES = 1
MIN_STRUCTURES = 1
NODE_PLURAL_STRING = 'ligands'
NODE_SINGULAR_STRING = 'ligand'
TARGET_PLURAL_STRING = ''
TARGET_SINGULAR_STRING = 'receptors'
__init__(rl_map, export_mae=False)
Parameters

  • rl_map (data_classes.ReceptorLigandMap) – a receptor-ligand map

  • export_mae (bool) – whether the 3D structure export to LiveDesign will use .mae files (rather than .prjzip files) as 3D data

analyzeStructures()

Compile and cache important ligand and receptor information from the receptor-ligand map. Meant to be called once on initialization.

batchIteration()

Manage the environment for exporting receptor-ligand maps to LiveDesign, e.g. by changing the project selection state after iterating over all receptor-ligand batches.

checkLigands(**kwargs)
checkNumEntries(**kwargs)
checkTargets(**kwargs)
exportAlternateRLMap(rl_map)
exportRLMap(rl_map, export_3d)

Manage the environment for exporting a single receptor-ligand map to LiveDesign by selecting relevant project rows when entering the context environment.

Parameters
Returns

the supplied receptor-ligand map

Return type

data_classes.ReceptorLigandMap

getAlternateBatches(batch_size)

A generator for receptor-alternate ligand maps containing a subset of the receptor-alternate ligand pairs contained in the rl_map instance variable. Alternate ligands are uploaded to LiveDesign as 3D data when the 3D structure does not have the same SMARTS representation as the rest of the structure row.

This method may modify the current Maestro project temporarily in order to export 3D data as a .prjzip file.

Note that this method takes alternate ligands from the rl_map instance variable, but returns ReceptorLigandMap instances in which those alternate ligands are stored as regular ligands. This is so that the LD export infrastructure will function the same when exporting these structures.

Parameters

batch_size (int) – the largest number of receptor-ligand pairs that will be in the receptor-ligand maps yielded by this method

Returns

an iterator of receptor-ligand maps

Return type

iterator(data_classes.ReceptorLigandMap)

getAvailableProperties()

Compile all properties of all structures scheduled for export.

Returns

a list of identifying information for the union of all structure properties for each structure scheduled for export

Return type

list(data_classes.LDData)

getBatches(batch_size, export_3d, include_targets=None)

An generator for receptor-ligand maps containing a subset of the receptor-ligand pairs contained in the rl_map instance variable. If possible, may also modify the open Maestro project to assist with export to LiveDesign.

Parameters

  • batch_size (int) – the largest number of receptor-ligand pairs that will be in the receptor-ligand maps yielded by this method

  • export_3d (bool) – whether to export 3D data

  • include_targets (bool or None) – whether the batches should include targets (e.g. receptors). A value of None (the default) will revert to the class default behavior, which is the correct choice when exporting with LDClient.start_export_assay_and_pose_data().

Returns

an iterator of receptor-ligand maps

Return type

iterator(data_classes.ReceptorLigandMap)

getNextEntryId()
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

getTargetEntryID(target=None)

Return the entry ID of the provided receptor structure.

See parent class for complete method documentation.

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

schrodinger.application.livedesign.maestro_data_types.import_and_copy_rl_map(rl_map)

Import the receptor and ligand structures in rl_map into the current Maestro project, then create and return a new ReceptorLigandMap instance using the structures just imported into the project.

Parameters

rl_map (data_classes.ReceptorLigandMap) – a receptor-ligand map

Returns

a receptor-ligand map similar to rl_map, but which exclusively contains structures copied from the Maestro project

Return type

data_classes.ReceptorLigandMap

schrodinger.application.livedesign.maestro_data_types.remove_rl_map_from_pt(rl_map)

Remove all rows in the Maestro project that have entry IDs corresponding to the entry IDs in the structures contained in a receptor-ligand map.

Parameters

rl_map (data_classes.ReceptorLigandMap) – a receptor-ligand map

schrodinger.application.livedesign.maestro_data_types.get_ld_data_from_data_names(data_names)

Given a list of structure data names (e.g. “s_m_title”), return a list of corresponding LD Data instances.

Parameters

data_names (list(str)) – a list of structure data names

Returns

a list of LD Data objects corresponding to each structure data name

Return type

list(data_classes.LDData)

schrodinger.application.livedesign.maestro_data_types.get_structure_data_names(structures)
Parameters

structures (list(structure.Structure)) – a list of structures

Returns

set of data names for every property on each structure

Return type

set(str)

schrodinger.application.livedesign.maestro_data_types.get_structure_entry_IDs(structures)
Parameters

structures (list(structure.Structure)) – a list of structures

Returns

a set of the entry IDs stored in each structure

Return type

set(str)

schrodinger.application.livedesign.maestro_data_types.maestro_select_rl_map(rl_map)

Context manager that selects project rows associated with a receptor-ligand map on entrance, and restores the original project selection on exit.

Parameters

rl_map (data_classes.ReceptorLigandMap) – a receptor-ligand map

schrodinger.application.livedesign.maestro_data_types.maestro_select_only(entry_ids)

Select the specified entry IDs in the project and deselect all others.

Parameters

entry_ids (list(str)) – the entry IDs corresponding to entries currently in the project

schrodinger.application.livedesign.maestro_data_types.import_and_get_structure(st)

Import the supplied structure into the project table, then retrieve the structure from the newly-created project entry. If None is supplied rather than a structure, return None.

Parameters

st (structure.Structure or NoneType) – a structure (or None)

Returns

the structure retrieved from the entry row created by importing st into the project table, or None if no structure is provided

Return type

structure.Structure or None