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()¶

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: List[structure.Structure]

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

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: data_classes.ReceptorLigandMap

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()¶

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()¶

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()¶

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

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

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'¶

__init__(structure_map)¶

Parameters: structure_map (dict[str, structure.Structure]) – a dictionary mapping unique strings to structures from some system

checkNumNodes()¶: Override this method to catch case where a single protein-ligand complex is supplied but the “Docked Poses” option is selected. Produces a helpful error in this case. Make sure this code is called before the superclass checkNumNodes() so that this error is produced rather than a less specific error.

checkTargets()¶

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()¶

checkLigands()¶

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.'¶

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 message
number (int) – the number to be added to the message
singular_str (str) – the singular word for the object being described
plural_str (str or NoneType) – optionally, the plural word for the object being described; by default, inflect will be used to pluralize