schrodinger.application.livedesign.maestro_data_types module¶

class schrodinger.application.livedesign.maestro_data_types.Export3D¶

Bases: enum.Enum

An enumeration.

Optional = 3¶

Required = 1¶

Unavailable = 2¶

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.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.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)¶

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

name = ''¶

description = ''¶

export_3d = 3¶

MIN_NODES = 1¶

MIN_STRUCTURES = 1¶

BATCHES_INCLUDE_TARGETS = False¶

NODE_SINGULAR_STRING = ''¶

NODE_PLURAL_STRING = ''¶

TARGET_SINGULAR_STRING = ''¶

TARGET_PLURAL_STRING = ''¶

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)¶

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
Returns:	an iterator of receptor-ligand maps
Return type:	iterator(data_classes.ReceptorLigandMap)

getRLEntryIDs(rl_map=None)¶

Return all available entry IDs for structures found in the supplied receptor-ligand map. If no receptor-ligand map is specified, the rl_map instance variable will be used.

Parameters:	rl_map (`data_classes.ReceptorLigandMap` or `None`) – a receptor-ligand map, or `None`
Returns:	a list of entry IDs
Return type:	list()

exportRLMap(rl_map)¶

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

Parameters:	rl_map (data_classes.ReceptorLigandMap) – the receptor-ligand map for export
Returns:	the supplied receptor-ligand map
Return type:	data_classes.ReceptorLigandMap

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()¶

class schrodinger.application.livedesign.maestro_data_types.IndividualStructureBase(rl_map)¶

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)¶

class schrodinger.application.livedesign.maestro_data_types.TargetlessBase(rl_map)¶

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.

class schrodinger.application.livedesign.maestro_data_types.OrganometallicCompounds(rl_map)¶

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

class schrodinger.application.livedesign.maestro_data_types.Ligands(rl_map)¶

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

class schrodinger.application.livedesign.maestro_data_types.DockedPoses(rl_map)¶

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.'¶

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.

class schrodinger.application.livedesign.maestro_data_types.Complexes(rl_map)¶

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

class schrodinger.application.livedesign.maestro_data_types.CovalentDockingComplexes(rl_map)¶

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.'¶

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)