schrodinger.application.bioluminate.protein_interaction.tasks module

schrodinger.application.bioluminate.protein_interaction.tasks.get_structure_index(st: schrodinger.structure._structure.Structure) → Optional[int]
schrodinger.application.bioluminate.protein_interaction.tasks.set_structure_index(st: schrodinger.structure._structure.Structure, idx: int)
schrodinger.application.bioluminate.protein_interaction.tasks.ensure_value_in_range(min_val: Optional[Union[int, float]] = None, max_val: Optional[Union[int, float]] = None) → type

Return an action class whose __call__ will exit the program if the user-supplied value is outside of the allowed limits. Otherwise, sets the value on the namespace as usual.

class schrodinger.application.bioluminate.protein_interaction.tasks.ProteinInteractionOptions(*args, _param_type=<object object>, **kwargs)

Bases: schrodinger.models.parameters.CompoundParam

neighbor_max_dist: float

A parameter of the class.

ignore_backbone: bool

A parameter of the class.

hbond_min_acceptor_angle: int

A parameter of the class.

hbond_min_donor_angle: int

A parameter of the class.

hbond_max_dist: float

A parameter of the class.

salt_bridge_max_dist: float

A parameter of the class.

max_stack_dist: float

A parameter of the class.

overlap_ratio_cutoff: float

A parameter of the class.

initializeValue()

Override to dynamically set up the default value of the param. Useful for default values that are determined at runtime. This is called any time the param is reset.

classmethod addParserOptions(parser: argparse.ArgumentParser) → None

Add all parameters in this object as arguments to the supplied parser.

hbond_max_distChanged

A pyqtSignal emitted by instances of the class.

hbond_max_distReplaced

A pyqtSignal emitted by instances of the class.

hbond_min_acceptor_angleChanged

A pyqtSignal emitted by instances of the class.

hbond_min_acceptor_angleReplaced

A pyqtSignal emitted by instances of the class.

hbond_min_donor_angleChanged

A pyqtSignal emitted by instances of the class.

hbond_min_donor_angleReplaced

A pyqtSignal emitted by instances of the class.

ignore_backboneChanged

A pyqtSignal emitted by instances of the class.

ignore_backboneReplaced

A pyqtSignal emitted by instances of the class.

max_stack_distChanged

A pyqtSignal emitted by instances of the class.

max_stack_distReplaced

A pyqtSignal emitted by instances of the class.

neighbor_max_distChanged

A pyqtSignal emitted by instances of the class.

neighbor_max_distReplaced

A pyqtSignal emitted by instances of the class.

overlap_ratio_cutoffChanged

A pyqtSignal emitted by instances of the class.

overlap_ratio_cutoffReplaced

A pyqtSignal emitted by instances of the class.

salt_bridge_max_distChanged

A pyqtSignal emitted by instances of the class.

salt_bridge_max_distReplaced

A pyqtSignal emitted by instances of the class.

class schrodinger.application.bioluminate.protein_interaction.tasks.ProteinInteractionInput(*args, _param_type=<object object>, **kwargs)

Bases: schrodinger.models.parameters.CompoundParam

Input for the protein interaction task.

Variables

  • structs – List of protein structures for which the interactions are to be calculated.

  • query_asl_1 – ASL query for residues in the first set.

  • query_asl_2 – ASL query for residues in the first set.

  • options – Interaction calculation options i.e. distance cutoffs, angle constraints etc.

structs: List[schrodinger.structure._structure.Structure]

A parameter of the class.

query_asl_1: str

A parameter of the class.

query_asl_2: str

A parameter of the class.

options: schrodinger.application.bioluminate.protein_interaction.tasks.ProteinInteractionOptions

A parameter of the class.

getEntryIds() → Set[str]
Returns

Return entry IDs of the of input structure.

isIntraChainInteractions() → bool
Returns

Whether the queries encompass intra chain interactions.

getAllResidueStrings() → Set[str]
Returns

String representation of all input structure residues.

getRepresentativeStructure() → Optional[schrodinger.structure._structure.Structure]

self.structs contains poses of the same structure, return the first one as the representative structure if it exists.

optionsChanged

A pyqtSignal emitted by instances of the class.

optionsReplaced

A pyqtSignal emitted by instances of the class.

query_asl_1Changed

A pyqtSignal emitted by instances of the class.

query_asl_1Replaced

A pyqtSignal emitted by instances of the class.

query_asl_2Changed

A pyqtSignal emitted by instances of the class.

query_asl_2Replaced

A pyqtSignal emitted by instances of the class.

structsChanged

A pyqtSignal emitted by instances of the class.

structsReplaced

A pyqtSignal emitted by instances of the class.

class schrodinger.application.bioluminate.protein_interaction.tasks.SingleProteinInteractions(*args, _param_type=<object object>, **kwargs)

Bases: schrodinger.models.parameters.CompoundParam

Stores interaction information between two residues in a single protein pose.

Variables

  • set_1_residue – String representation of the first residue.

  • set_2_residue – String representation of the second residue.

  • struct_idx – Protein structure index.

  • distance – Distance between the two residues.

  • salt_bridges – Number of salt bridges between the two residues.

  • pi_stacking – Number of pi-stacking interactions between the two residues.

  • disulfides – Number of disulfide bonds between the two residues.

  • vdw_clash – Number of van der Waals clashes between the two residues.

  • surface_complementarity – Surface complementarity between the two residues.

  • set_1_buried_sasa – Buried SASA of the first residue.

  • set_2_buried_sasa – Buried SASA of the second residue.

  • hb_ss – Number of hydrogen bonds between side chain - side chain.

  • hb_sb – Number of hydrogen bonds between side chain - backbone.

  • hb_bs – Number of hydrogen bonds between backbone - side chain.

  • hb_bb – Number of hydrogen bonds between backbone - backbone.

set_1_residue: str

A parameter of the class.

set_2_residue: str

A parameter of the class.

struct_idx: int

A parameter of the class.

distance: float

A parameter of the class.

salt_bridges: int

A parameter of the class.

pi_stacking: int

A parameter of the class.

disulfides: int

A parameter of the class.

vdw_clash: int

A parameter of the class.

surface_complementarity: float

A parameter of the class.

set_1_buried_sasa: float

A parameter of the class.

set_2_buried_sasa: float

A parameter of the class.

hb_ss: int

A parameter of the class.

hb_sb: int

A parameter of the class.

hb_bs: int

A parameter of the class.

hb_bb: int

A parameter of the class.

getTotalInteractionCount() → int

Sum of countable interactions between the two residues i.e H-bonds, Salt Bridges, Pi-Stacking, Disulfides, VDW Clashes.

getTotalHydrogenBondCount()
Returns

Total hydrogen bond count.

Return type

int

getSpecificInteractionSummary()
Returns

interaction summary of interactions

Return type

str

distanceChanged

A pyqtSignal emitted by instances of the class.

distanceReplaced

A pyqtSignal emitted by instances of the class.

disulfidesChanged

A pyqtSignal emitted by instances of the class.

disulfidesReplaced

A pyqtSignal emitted by instances of the class.

hb_bbChanged

A pyqtSignal emitted by instances of the class.

hb_bbReplaced

A pyqtSignal emitted by instances of the class.

hb_bsChanged

A pyqtSignal emitted by instances of the class.

hb_bsReplaced

A pyqtSignal emitted by instances of the class.

hb_sbChanged

A pyqtSignal emitted by instances of the class.

hb_sbReplaced

A pyqtSignal emitted by instances of the class.

hb_ssChanged

A pyqtSignal emitted by instances of the class.

hb_ssReplaced

A pyqtSignal emitted by instances of the class.

pi_stackingChanged

A pyqtSignal emitted by instances of the class.

pi_stackingReplaced

A pyqtSignal emitted by instances of the class.

salt_bridgesChanged

A pyqtSignal emitted by instances of the class.

salt_bridgesReplaced

A pyqtSignal emitted by instances of the class.

set_1_buried_sasaChanged

A pyqtSignal emitted by instances of the class.

set_1_buried_sasaReplaced

A pyqtSignal emitted by instances of the class.

set_1_residueChanged

A pyqtSignal emitted by instances of the class.

set_1_residueReplaced

A pyqtSignal emitted by instances of the class.

set_2_buried_sasaChanged

A pyqtSignal emitted by instances of the class.

set_2_buried_sasaReplaced

A pyqtSignal emitted by instances of the class.

set_2_residueChanged

A pyqtSignal emitted by instances of the class.

set_2_residueReplaced

A pyqtSignal emitted by instances of the class.

struct_idxChanged

A pyqtSignal emitted by instances of the class.

struct_idxReplaced

A pyqtSignal emitted by instances of the class.

surface_complementarityChanged

A pyqtSignal emitted by instances of the class.

surface_complementarityReplaced

A pyqtSignal emitted by instances of the class.

vdw_clashChanged

A pyqtSignal emitted by instances of the class.

vdw_clashReplaced

A pyqtSignal emitted by instances of the class.

class schrodinger.application.bioluminate.protein_interaction.tasks.MultipleProteinInteractions(*args, _param_type=<object object>, **kwargs)

Bases: schrodinger.models.parameters.CompoundParam

Stores interaction information between two residues in multiple proteins.

Variables

  • set_1_residue – String representation of the first residue.

  • set_2_residue – String representation of the second residue.

  • input_st_count – Number of input protein structures.

  • interactions – List of interactions between the two residues.

set_1_residue: str

A parameter of the class.

set_2_residue: str

A parameter of the class.

input_st_count: int

A parameter of the class.

interactions: List[schrodinger.application.bioluminate.protein_interaction.tasks.SingleProteinInteractions]

A parameter of the class.

getSpecificInteractionSummary() → str

Return the interaction summary of the first interaction.

getTotalInteractionCount() → float

Average total number of interactions between the two residues.

getNormalisedValue(param)

Normalised value is the average of interactions in each of the protein structure i.e. the sum of the interaction value across all protein structures divided by the total number of protein structures.

Parameters

param – Interaction parameter to normalize. It should be one of the params in SingleProteinInteractions class.

Returns

Average of the interaction count value.

getPercentOfPosesWithInteractions(param)

Percent of poses that contribute to the normalised value of the interaction.

Parameters

param – Interaction to parameter get the percent of poses with interaction.

Returns

Percent of poses with interaction.

hasInteractions(param) → bool

Whether the interaction has a non-default value for the given parameter.

Parameters

param – Interaction parameter to check for interaction.

getPoseIds() → Set[int]

Return the pose ids of proteins that have interactions.

input_st_countChanged

A pyqtSignal emitted by instances of the class.

input_st_countReplaced

A pyqtSignal emitted by instances of the class.

interactionsChanged

A pyqtSignal emitted by instances of the class.

interactionsReplaced

A pyqtSignal emitted by instances of the class.

set_1_residueChanged

A pyqtSignal emitted by instances of the class.

set_1_residueReplaced

A pyqtSignal emitted by instances of the class.

set_2_residueChanged

A pyqtSignal emitted by instances of the class.

set_2_residueReplaced

A pyqtSignal emitted by instances of the class.

class schrodinger.application.bioluminate.protein_interaction.tasks.ProteinInteractionOutput(*args, _param_type=<object object>, **kwargs)

Bases: schrodinger.models.parameters.CompoundParam

Variables

  • residue_interaction_counts – Maps residue string to the number of structures in which it is involved in an interaction. This is different from the input_st_indexes in SingleProteinInteractions since it only counts the structure in which the residue is actively involved in an interaction rather than also counting structures with zero contribution.

  • interactions – List of interactions.

residue_interaction_counts: Dict[str, int]

A parameter of the class.

interactions: List[schrodinger.application.bioluminate.protein_interaction.tasks.MultipleProteinInteractions]

A parameter of the class.

getBuriedSASALimits()

Return buried_sasa limits. :return: Buried SASAs min, max limits. :rtype: tuple(float, float)

getSurfaceComplementarityLimits()

Return surface_complementarity limits. :return: Surface complementarity min, max limits. :rtype: tuple(float, float)

getTotalInteractionCountLimits()

Return total number of interactions limits. :return: Total interaction count min, max limits. :rtype: tuple(int, int)

interactionsChanged

A pyqtSignal emitted by instances of the class.

interactionsReplaced

A pyqtSignal emitted by instances of the class.

residue_interaction_countsChanged

A pyqtSignal emitted by instances of the class.

residue_interaction_countsReplaced

A pyqtSignal emitted by instances of the class.

class schrodinger.application.bioluminate.protein_interaction.tasks.ProteinInteractionSubTask(*args, _param_type=<object object>, **kwargs)

Bases: schrodinger.tasks.tasks.ComboSubprocessTask

Task to calculate interactions between residues in multiple proteins. Each input structure should have a unique integer value set as the structure index (see set_structure_index() and get_structure_index()). This is used to identify the structure in the output.

input: schrodinger.application.bioluminate.protein_interaction.tasks.ProteinInteractionInput

A parameter of the class.

output: schrodinger.application.bioluminate.protein_interaction.tasks.ProteinInteractionOutput

A parameter of the class.

mainFunction()
onProgressChanged(progress)
calling_contextChanged

A pyqtSignal emitted by instances of the class.

calling_contextReplaced

A pyqtSignal emitted by instances of the class.

failure_infoChanged

A pyqtSignal emitted by instances of the class.

failure_infoReplaced

A pyqtSignal emitted by instances of the class.

inputChanged

A pyqtSignal emitted by instances of the class.

inputReplaced

A pyqtSignal emitted by instances of the class.

max_progressChanged

A pyqtSignal emitted by instances of the class.

max_progressReplaced

A pyqtSignal emitted by instances of the class.

nameChanged

A pyqtSignal emitted by instances of the class.

nameReplaced

A pyqtSignal emitted by instances of the class.

outputChanged

A pyqtSignal emitted by instances of the class.

outputReplaced

A pyqtSignal emitted by instances of the class.

progressChanged

A pyqtSignal emitted by instances of the class.

progressReplaced

A pyqtSignal emitted by instances of the class.

progress_stringChanged

A pyqtSignal emitted by instances of the class.

progress_stringReplaced

A pyqtSignal emitted by instances of the class.

statusChanged

A pyqtSignal emitted by instances of the class.

statusReplaced

A pyqtSignal emitted by instances of the class.

class schrodinger.application.bioluminate.protein_interaction.tasks.ProteinInteractionTask(*args, _param_type=<object object>, **kwargs)

Bases: schrodinger.tasks.tasks.ComboSubprocessTask

Protein Interaction Analysis driver task that can run multiple ProteinInteractionSubTask in parallel for a batch of protein structures.

Variables

MAX_SUBTASKS – Maximum number of subtasks to run in parallel.

input: schrodinger.application.bioluminate.protein_interaction.tasks.ProteinInteractionInput

A parameter of the class.

output: schrodinger.application.bioluminate.protein_interaction.tasks.ProteinInteractionOutput

A parameter of the class.

MAX_SUBTASKS = 4
DEFAULT_TASKDIR_SETTING = 2
mainFunction()
calling_contextChanged

A pyqtSignal emitted by instances of the class.

calling_contextReplaced

A pyqtSignal emitted by instances of the class.

failure_infoChanged

A pyqtSignal emitted by instances of the class.

failure_infoReplaced

A pyqtSignal emitted by instances of the class.

inputChanged

A pyqtSignal emitted by instances of the class.

inputReplaced

A pyqtSignal emitted by instances of the class.

max_progressChanged

A pyqtSignal emitted by instances of the class.

max_progressReplaced

A pyqtSignal emitted by instances of the class.

nameChanged

A pyqtSignal emitted by instances of the class.

nameReplaced

A pyqtSignal emitted by instances of the class.

outputChanged

A pyqtSignal emitted by instances of the class.

outputReplaced

A pyqtSignal emitted by instances of the class.

progressChanged

A pyqtSignal emitted by instances of the class.

progressReplaced

A pyqtSignal emitted by instances of the class.

progress_stringChanged

A pyqtSignal emitted by instances of the class.

progress_stringReplaced

A pyqtSignal emitted by instances of the class.

statusChanged

A pyqtSignal emitted by instances of the class.

statusReplaced

A pyqtSignal emitted by instances of the class.