The modelcif.protocol Python module

Classes for handling modeling protocols.

class modelcif.protocol.Step(input_data, output_data, name=None, details=None, software=None)

A single step in a Protocol.

This class describes a generic step in a modeling protocol. In most cases, a more specific subclass should be used, such as TemplateSearchStep, ModelingStep, or ModelSelectionStep.

Parameters:

• input_data (modelcif.data.DataGroup or modelcif.data.Data) – Any objects that this step takes as input. Any individual modelcif.data.Data object (such as a template structure, target sequence, alignment, or model coordinates) can be given here, or a group of such objects (as a modelcif.data.DataGroup object) can be passed.

• output_data (modelcif.data.DataGroup or modelcif.data.Data) – Any objects that this step creates as output, similarly to input_data.

• name (str) – A short name for this step.

• details (str) – Longer description of this step.

• software (modelcif.Software or modelcif.SoftwareGroup) – The software that was employed in this modeling step.

class modelcif.protocol.TemplateSearchStep(input_data, output_data, name=None, details=None, software=None)

A modeling protocol step that searches for templates. See Step for more details.

class modelcif.protocol.TemplateSelectionStep(input_data, output_data, name=None, details=None, software=None)

A modeling protocol step that selects one or more templates. See Step for more details.

class modelcif.protocol.TargetTemplateAlignmentStep(input_data, output_data, name=None, details=None, software=None)

A modeling protocol step that creates a target-template alignment. See Step for more details.

class modelcif.protocol.CoevolutionMSAStep(input_data, output_data, name=None, details=None, software=None)

A modeling protocol step that creates a coevolution multiple sequence alignment. See Step for more details.

class modelcif.protocol.ContactPredictionStep(input_data, output_data, name=None, details=None, software=None)

A modeling protocol step that predicts contacts. See Step for more details.

class modelcif.protocol.ModelingStep(input_data, output_data, name=None, details=None, software=None)

A modeling protocol step that generates model coordinates. See Step for more details.

class modelcif.protocol.ModelSelectionStep(input_data, output_data, name=None, details=None, software=None)

A modeling protocol step that filters candidates to select models. See Step for more details.

class modelcif.protocol.ModelRefinementStep(input_data, output_data, name=None, details=None, software=None)

A modeling protocol step that refines models. See Step for more details.

class modelcif.protocol.ModelAssessmentStep(input_data, output_data, name=None, details=None, software=None)

A modeling protocol step that performs model quality assessment. See Step for more details.

class modelcif.protocol.BackboneGenerationStep(input_data, output_data, name=None, details=None, software=None)

A modeling protocol step that generates backbone coordinates for protein design. See Step for more details.

class modelcif.protocol.SequenceDesignStep(input_data, output_data, name=None, details=None, software=None)

A modeling protocol step that generates sequences for protein design. This includes inverse folding. See Step for more details.

class modelcif.protocol.StructureValidationStep(input_data, output_data, name=None, details=None, software=None)

A modeling protocol step that assesses designed sequences with their modeled structures. See Step for more details.

class modelcif.protocol.EnergyEstimateStep(input_data, output_data, name=None, details=None, software=None)

A modeling protocol step that performs an energy estimate. See Step for more details.

class modelcif.protocol.ExperimentalValidationStep(input_data, output_data, name=None, details=None, software=None)

A modeling protocol step that conducts experimental validation. See Step for more details.

class modelcif.protocol.Protocol

A modeling protocol. Each protocol consists of a number of protocol steps.

steps

All modeling steps (Step objects)