# SAMSON Python Scripting Guide > Python scripting documentation for SAMSON, including guides, examples, and Python API reference generated from the compiled pybind11 bindings. This file provides a compact LLM-readable index for the SAMSON Python Scripting Guide. For the complete generated text, use `llms-full.txt`. For granular retrieval, use the per-page Markdown exports linked below. ## HTML entry point - [SAMSON Python Scripting Guide](https://documentation.samson-connect.net/scripting/latest/) ## Complete documentation - [Full LLM context](https://documentation.samson-connect.net/scripting/latest/llms-full.txt): Complete resolved Sphinx output, including autodoc-generated Python API documentation from the compiled bindings. ## Important pages - [Python bindings for SAMSON API](https://documentation.samson-connect.net/scripting/latest/index.md): The Python Scripting extension in SAMSON provides Python bindings for SAMSON API and an integrated Python console. It provides you with an access to most of the SAMSON SDK allowing you to access most of SAMSON’s... - [Getting started](https://documentation.samson-connect.net/scripting/latest/docs/GettingStarted.md): The Python Scripting extension in SAMSON provides Python bindings for the SAMSON API and an integrated Python console. - [Running actions](https://documentation.samson-connect.net/scripting/latest/docs/RunningActions.md): The SAMSON interface (SAMSON) provides the SAMSON.runCommand() function to trigger actions and commands by the names you see in the SAMSON interface. - [Developing scripts](https://documentation.samson-connect.net/scripting/latest/docs/DevelopingScripts.md): SAMSON AI is the intelligent assistant for SAMSON. This assistant is designed to help you navigate SAMSON’s functionality and understand its commands, menus, editors, apps, and more. It can explain the platform’s... - [Working with documents and nodes](https://documentation.samson-connect.net/scripting/latest/docs/WorkingWithDocuments.md): SAMSON documents are hierarchies of SAMSON nodes. The hierarchy of the active document is visible in the Document view. - [Importing and exporting](https://documentation.samson-connect.net/scripting/latest/docs/ImportingAndExporting.md): SAMSON provides an extensive set of importers and exporters by default: list of formats supported by default in SAMSON. - [Making operations undoable](https://documentation.samson-connect.net/scripting/latest/docs/MakingOperationsUndoable.md): SAMSON supports Undo and Redo for many operations. Most functions from the SAMSON SDK that modify the data graph can participate in undo/redo. However, simply calling such a function does not automatically make the... - [Selecting nodes](https://documentation.samson-connect.net/scripting/latest/docs/Selecting.md): In SAMSON, to do some operations (inspect, edit, move, simulate, etc) with nodes (atoms, residues, molecules) it is necessary to select them. - [Getting nodes](https://documentation.samson-connect.net/scripting/latest/docs/GettingNodes.md): Often you need to work on specific nodes, pass them to other functions, or perform more precise selections than the built-in actions provide (see Selecting nodes). For that, you can use the getNodes functions, which... - [Units](https://documentation.samson-connect.net/scripting/latest/docs/Units.md): In SAMSON, physical quantities are strongly typed. Every physical quantity has associated Units. - [SBQuantity](https://documentation.samson-connect.net/scripting/latest/docs/api/DataModel/Quantity.md): The samson.SBQuantity sub-module contains Python bindings for SBDQuantity from SAMSON API - it contains all classes related to handling physical units in SAMSON. It allows you to operate with all the possible units... - [Mathematical functions](https://documentation.samson-connect.net/scripting/latest/docs/api/DataModel/Quantity/unitsMathFunctions.md): The SBQuantity module also provides a set of mathematical functions that can be used with quantities:... - [SI Unit system](https://documentation.samson-connect.net/scripting/latest/docs/api/DataModel/Quantity/unitsSI.md): You can check out this unit system’s functions in its base class:... - [unitsSI](https://documentation.samson-connect.net/scripting/latest/docs/api/DataModel/Quantity/unitsSIClass.md): This is the base class for SI units. - [Convenience constructors](https://documentation.samson-connect.net/scripting/latest/docs/api/DataModel/Quantity/unitsSIConvenienceConstructors.md) - [Atomic Units Unit System](https://documentation.samson-connect.net/scripting/latest/docs/api/DataModel/Quantity/unitsAU.md): You can check out this unit system’s functions in its base class:... - [unitsAU](https://documentation.samson-connect.net/scripting/latest/docs/api/DataModel/Quantity/unitsAUClass.md): This is the base class for Atomic Units (AU). - [Convenience constructors](https://documentation.samson-connect.net/scripting/latest/docs/api/DataModel/Quantity/unitsAUConvenienceConstructors.md) - [Dalton Unit system](https://documentation.samson-connect.net/scripting/latest/docs/api/DataModel/Quantity/unitsDalton.md): You can check out this unit system’s functions in its base class:... - [unitsDalton](https://documentation.samson-connect.net/scripting/latest/docs/api/DataModel/Quantity/unitsDaltonClass.md): This is the base class for Dalton Units. - [Convenience constructors](https://documentation.samson-connect.net/scripting/latest/docs/api/DataModel/Quantity/unitsDaltonConvenienceConstructors.md) - [Electronvolt Unit System](https://documentation.samson-connect.net/scripting/latest/docs/api/DataModel/Quantity/unitsElectronvolt.md): You can check out this unit system’s functions in its base class:... - [unitsElectronvolt](https://documentation.samson-connect.net/scripting/latest/docs/api/DataModel/Quantity/unitsElectronvoltClass.md): This is the base class for the Electronvolt Unit. - [Convenience constructors](https://documentation.samson-connect.net/scripting/latest/docs/api/DataModel/Quantity/unitsElectronvoltConvenienceConstructors.md) - [KilocaloriePerMole Unit System](https://documentation.samson-connect.net/scripting/latest/docs/api/DataModel/Quantity/unitsKilocaloriePerMole.md): You can check out this unit system’s functions in its base class:... - [unitsKilocaloriePerMole](https://documentation.samson-connect.net/scripting/latest/docs/api/DataModel/Quantity/unitsKilocaloriePerMoleClass.md): This is the base class for the KilocaloriePerMole Unit. - [Convenience constructors](https://documentation.samson-connect.net/scripting/latest/docs/api/DataModel/Quantity/unitsKilocaloriePerMoleConvenienceConstructors.md) - [List of defined quantities](https://documentation.samson-connect.net/scripting/latest/docs/api/DataModel/Quantity/unitsListOfDefinedQuantityTypes.md): SBQuantity.dimensionless - [SBConstant](https://documentation.samson-connect.net/scripting/latest/docs/api/DataModel/Quantity/SBConstant.md): This class provides a set of standard physical constants. You can access them in the following way:... - [Type](https://documentation.samson-connect.net/scripting/latest/docs/api/DataModel/Type.md): The classes below define the basic types used throughout SAMSON, especially for mathematical operations, colors, spatial transformations, random numbers, and date/time values. ## API reference sections - [SBColor](https://documentation.samson-connect.net/scripting/latest/docs/api/DataModel/Type/SBColor.md): This class describes a color and can be used to colorize e.g. atoms individually. - [SBDateTime](https://documentation.samson-connect.net/scripting/latest/docs/api/DataModel/Type/SBDateTime.md): This class implements a date time type. - [SBRandom](https://documentation.samson-connect.net/scripting/latest/docs/api/DataModel/Type/SBRandom.md): This class implements the Mersenne Twister generator from the paper: M. Matsumoto and T. Nishimura, “Mersenne Twister: A 623-dimensionally equidistributed uniform pseudorandom number generator”, ACM Trans. on Modeling... - [SBPhysicalVector3](https://documentation.samson-connect.net/scripting/latest/docs/api/DataModel/Type/SBPhysicalVector3.md): This class represents a three-dimensional physical vector. - [SBAcceleration3](https://documentation.samson-connect.net/scripting/latest/docs/api/DataModel/Type/PhysicalVector3ConvenienceConstructors/acceleration3.md) - [SBAngularAcceleration3](https://documentation.samson-connect.net/scripting/latest/docs/api/DataModel/Type/PhysicalVector3ConvenienceConstructors/angularAcceleration3.md) - [SBAngularVelocity3](https://documentation.samson-connect.net/scripting/latest/docs/api/DataModel/Type/PhysicalVector3ConvenienceConstructors/angularVelocity3.md) - [SBVector3](https://documentation.samson-connect.net/scripting/latest/docs/api/DataModel/Type/PhysicalVector3ConvenienceConstructors/dimensionless3.md) - [SBEnergy3](https://documentation.samson-connect.net/scripting/latest/docs/api/DataModel/Type/PhysicalVector3ConvenienceConstructors/energy3.md) - [SBForce3](https://documentation.samson-connect.net/scripting/latest/docs/api/DataModel/Type/PhysicalVector3ConvenienceConstructors/force3.md) - [SBInverseLength3](https://documentation.samson-connect.net/scripting/latest/docs/api/DataModel/Type/PhysicalVector3ConvenienceConstructors/inverseLength3.md) - [SBInverseMomentum3](https://documentation.samson-connect.net/scripting/latest/docs/api/DataModel/Type/PhysicalVector3ConvenienceConstructors/inverseMomentum3.md) - [SBLength3](https://documentation.samson-connect.net/scripting/latest/docs/api/DataModel/Type/PhysicalVector3ConvenienceConstructors/length3.md) - [SBMomentum3](https://documentation.samson-connect.net/scripting/latest/docs/api/DataModel/Type/PhysicalVector3ConvenienceConstructors/momentum3.md) - [SBPicometerPerSecond3](https://documentation.samson-connect.net/scripting/latest/docs/api/DataModel/Type/PhysicalVector3ConvenienceConstructors/picometerPerSecond3.md) - [SBPosition3](https://documentation.samson-connect.net/scripting/latest/docs/api/DataModel/Type/PhysicalVector3ConvenienceConstructors/position3.md) - [SBRadian3](https://documentation.samson-connect.net/scripting/latest/docs/api/DataModel/Type/PhysicalVector3ConvenienceConstructors/radian3.md) - [SBRadianPerSecond3](https://documentation.samson-connect.net/scripting/latest/docs/api/DataModel/Type/PhysicalVector3ConvenienceConstructors/radianPerSecond3.md) - [SBSquareLength3](https://documentation.samson-connect.net/scripting/latest/docs/api/DataModel/Type/PhysicalVector3ConvenienceConstructors/squareLength3.md) - [SBTorque3](https://documentation.samson-connect.net/scripting/latest/docs/api/DataModel/Type/PhysicalVector3ConvenienceConstructors/torque3.md) - [SBVelocity3](https://documentation.samson-connect.net/scripting/latest/docs/api/DataModel/Type/PhysicalVector3ConvenienceConstructors/velocity3.md) - [SBPhysicalVector6](https://documentation.samson-connect.net/scripting/latest/docs/api/DataModel/Type/SBPhysicalVector6.md): This class represents a physical spatial vector, a six-dimensional vector used to describe rigid-body dynamics and articulated-body dynamics. It has an angular part and a linear part, which may have different units,... - [SBAcceleration6](https://documentation.samson-connect.net/scripting/latest/docs/api/DataModel/Type/PhysicalVector6ConvenienceConstructors/acceleration6.md) - [SBVector6](https://documentation.samson-connect.net/scripting/latest/docs/api/DataModel/Type/PhysicalVector6ConvenienceConstructors/dimensionless6.md) - [SBForce6](https://documentation.samson-connect.net/scripting/latest/docs/api/DataModel/Type/PhysicalVector6ConvenienceConstructors/force6.md) - [SBVelocity6](https://documentation.samson-connect.net/scripting/latest/docs/api/DataModel/Type/PhysicalVector6ConvenienceConstructors/velocity6.md) - [SBPhysicalInterval](https://documentation.samson-connect.net/scripting/latest/docs/api/DataModel/Type/SBPhysicalInterval.md): This class represents a physical interval. - [SBAccelerationInterval](https://documentation.samson-connect.net/scripting/latest/docs/api/DataModel/Type/PhysicalIntervalConvenienceConstructors/accelerationInterval.md) - [SBInterval](https://documentation.samson-connect.net/scripting/latest/docs/api/DataModel/Type/PhysicalIntervalConvenienceConstructors/dimensionlessInterval.md) - [SBEnergyInterval](https://documentation.samson-connect.net/scripting/latest/docs/api/DataModel/Type/PhysicalIntervalConvenienceConstructors/energyInterval.md) - [SBForceInterval](https://documentation.samson-connect.net/scripting/latest/docs/api/DataModel/Type/PhysicalIntervalConvenienceConstructors/forceInterval.md) - [SBLengthInterval](https://documentation.samson-connect.net/scripting/latest/docs/api/DataModel/Type/PhysicalIntervalConvenienceConstructors/lengthInterval.md) - [SBMomentumInterval](https://documentation.samson-connect.net/scripting/latest/docs/api/DataModel/Type/PhysicalIntervalConvenienceConstructors/momentumInterval.md) - [SBPositionInterval](https://documentation.samson-connect.net/scripting/latest/docs/api/DataModel/Type/PhysicalIntervalConvenienceConstructors/positionInterval.md) - [SBSquareLengthInterval](https://documentation.samson-connect.net/scripting/latest/docs/api/DataModel/Type/PhysicalIntervalConvenienceConstructors/squareLengthInterval.md) - [SBVelocityInterval](https://documentation.samson-connect.net/scripting/latest/docs/api/DataModel/Type/PhysicalIntervalConvenienceConstructors/velocityInterval.md) - [SBPhysicalIAVector3](https://documentation.samson-connect.net/scripting/latest/docs/api/DataModel/Type/SBPhysicalIAVector3.md): This class represents a three-dimensional physical interval vector. - [SBIAAcceleration3](https://documentation.samson-connect.net/scripting/latest/docs/api/DataModel/Type/PhysicalIAVector3ConvenienceConstructors/accelerationInterval3.md) - [SBIAVector3](https://documentation.samson-connect.net/scripting/latest/docs/api/DataModel/Type/PhysicalIAVector3ConvenienceConstructors/dimensionlessInterval3.md) - [SBIAForce3](https://documentation.samson-connect.net/scripting/latest/docs/api/DataModel/Type/PhysicalIAVector3ConvenienceConstructors/forceInterval3.md) - [SBIALength3](https://documentation.samson-connect.net/scripting/latest/docs/api/DataModel/Type/PhysicalIAVector3ConvenienceConstructors/lengthInterval3.md) - [SBIAMomentum3](https://documentation.samson-connect.net/scripting/latest/docs/api/DataModel/Type/PhysicalIAVector3ConvenienceConstructors/momentumInterval3.md) - [SBIAPosition3](https://documentation.samson-connect.net/scripting/latest/docs/api/DataModel/Type/PhysicalIAVector3ConvenienceConstructors/positionInterval3.md) - [SBIARadian3](https://documentation.samson-connect.net/scripting/latest/docs/api/DataModel/Type/PhysicalIAVector3ConvenienceConstructors/radianInterval3.md) - [SBIARadianPerSecond3](https://documentation.samson-connect.net/scripting/latest/docs/api/DataModel/Type/PhysicalIAVector3ConvenienceConstructors/radianPerSecondInterval3.md) - [SBIAVelocity3](https://documentation.samson-connect.net/scripting/latest/docs/api/DataModel/Type/PhysicalIAVector3ConvenienceConstructors/velocityInterval3.md) - [SBPhysicalMatrix33](https://documentation.samson-connect.net/scripting/latest/docs/api/DataModel/Type/SBPhysicalMatrix33.md): This class represents a 3x3 physical matrix. - [SBMatrix33](https://documentation.samson-connect.net/scripting/latest/docs/api/DataModel/Type/PhysicalMatrix33ConvenienceConstructors/dimensionless33.md) - [SBInverseMass33](https://documentation.samson-connect.net/scripting/latest/docs/api/DataModel/Type/PhysicalMatrix33ConvenienceConstructors/inverseMass33.md) - [SBInverseInertiaTensor33](https://documentation.samson-connect.net/scripting/latest/docs/api/DataModel/Type/PhysicalMatrix33ConvenienceConstructors/inverseMomentOfInertia33.md) - [SBMass33](https://documentation.samson-connect.net/scripting/latest/docs/api/DataModel/Type/PhysicalMatrix33ConvenienceConstructors/mass33.md) - [SBInertiaTensor33](https://documentation.samson-connect.net/scripting/latest/docs/api/DataModel/Type/PhysicalMatrix33ConvenienceConstructors/momentOfInertia33.md) - [SBPhysicalMatrix66](https://documentation.samson-connect.net/scripting/latest/docs/api/DataModel/Type/SBPhysicalMatrix66.md): This class represents a spatial matrix, a 6x6 matrix typically used to describe rigid or articulated inertias and inverse inertias. - [SBMatrix66](https://documentation.samson-connect.net/scripting/latest/docs/api/DataModel/Type/PhysicalMatrix66ConvenienceConstructors/dimensionless66.md) - [SBInertia66](https://documentation.samson-connect.net/scripting/latest/docs/api/DataModel/Type/PhysicalMatrix66ConvenienceConstructors/inertia66.md) - [SBInverseInertia66](https://documentation.samson-connect.net/scripting/latest/docs/api/DataModel/Type/PhysicalMatrix66ConvenienceConstructors/inverseInertia66.md) - [SBSpatialDomain](https://documentation.samson-connect.net/scripting/latest/docs/api/DataModel/Type/SBSpatialDomain.md): This class describes a spatial domain. - [SBSpatialTransform](https://documentation.samson-connect.net/scripting/latest/docs/api/DataModel/Type/SBSpatialTransform.md): This class represents a spatial transform. - [SBUnitCell](https://documentation.samson-connect.net/scripting/latest/docs/api/DataModel/Type/SBUnitCell.md): This class represent a unit cell. - [Core](https://documentation.samson-connect.net/scripting/latest/docs/api/Core.md): This group contains the foundational classes used throughout SAMSON, including reflection, generic containers, references, and metadata helpers. - [Class](https://documentation.samson-connect.net/scripting/latest/docs/api/Core/Class.md): The classes below are bindings for SAMSON SDK classes that define fundamental mechanisms used for class introspection in SAMSON. In particular, all exposed classes in SAMSON derive from samson.SBClass, and each exposed... - [SBClass](https://documentation.samson-connect.net/scripting/latest/docs/api/Core/Class/SBCClass.md): This class is the root class of numerous classes in SAMSON. In particular, all data graph node classes indirectly derive from SBClass, as well as many SAMSON Extensions classes. - [SBAttribute](https://documentation.samson-connect.net/scripting/latest/docs/api/Core/Class/SBCClassAttribute.md): SAMSON SDK: SBCClassAttribute - [SBFunction](https://documentation.samson-connect.net/scripting/latest/docs/api/Core/Class/SBCClassFunction.md): SAMSON SDK: SBCClassFunction - [SBInterface](https://documentation.samson-connect.net/scripting/latest/docs/api/Core/Class/SBCClassInterface.md): SAMSON SDK: SBCClassInterface - [SBProxy](https://documentation.samson-connect.net/scripting/latest/docs/api/Core/Class/SBCClassProxy.md): This class contains a description of the class factory (its constructors) and the class interface (its functions). It used primarily to call functionality exposed from SAMSON extensions thanks to the introspection... - [Container](https://documentation.samson-connect.net/scripting/latest/docs/api/Core/Container.md): The classes below expose several fundamental container types that are used in SAMSON. - [SBUUID](https://documentation.samson-connect.net/scripting/latest/docs/api/Core/Container/SBCUUID.md): samson.SBUUID objects can hold Universally Unique IDs (UUIDs), which are used to identify classes and SAMSON Extensions. - [SBUserPlan](https://documentation.samson-connect.net/scripting/latest/docs/api/Core/Container/SBCUserPlan.md): samson.SBUserPlan objects holds the user plan. - [SBVersionNumber](https://documentation.samson-connect.net/scripting/latest/docs/api/Core/Container/SBCVersionNumber.md): This class describes a version number in SAMSON, composed of three non-negative integers:... - [Meta](https://documentation.samson-connect.net/scripting/latest/docs/api/Core/Meta.md): Classes below are bindings for SAMSON SDK classes that define fundamental mechanisms used for passing values in the introspection mechanism in SAMSON. In particular, the SAMSON SDK SBValue class encapsulates values to... - [SBValue](https://documentation.samson-connect.net/scripting/latest/docs/api/Core/Meta/SBCMetaValue.md): This class exposes bindings for the SAMSON SDK SBValue class that encapsulates values. It used primarily when calling functionality exposed from SAMSON extensions thanks to the introspection mechanism. - [SBValueMap](https://documentation.samson-connect.net/scripting/latest/docs/api/Core/Meta/SBCMetaValueMap.md): This class exposes bindings for the SAMSON SDK SBValueMap class that describes a value map. This is a convenience class that contains a map from string to samson.SBValue, and can be used, for example, to pass into a... - [Reference](https://documentation.samson-connect.net/scripting/latest/docs/api/Core/Reference.md): The classes below expose key mechanisms for maintaining references to objects in SAMSON. - [SBReferenceIndexer](https://documentation.samson-connect.net/scripting/latest/docs/api/Core/Reference/SBCReferenceIndexer.md): SAMSON SDK: SBCReferenceIndexer - [SBReferenceTarget](https://documentation.samson-connect.net/scripting/latest/docs/api/Core/Reference/SBCReferenceTarget.md): SAMSON SDK: SBCReferenceTarget - [Data Model](https://documentation.samson-connect.net/scripting/latest/docs/api/DataModel.md): This group contains classes for working with the data graph, documents, materials, colors, quantities, and the mathematical types used across the Python API. - [Asset](https://documentation.samson-connect.net/scripting/latest/docs/api/DataModel/Asset.md): This group contains classes related to assets. - [SBAsset](https://documentation.samson-connect.net/scripting/latest/docs/api/DataModel/Asset/SBDAsset.md): SAMSON SDK: SBDAsset - [Color Scheme](https://documentation.samson-connect.net/scripting/latest/docs/api/DataModel/ColorScheme.md): This group contains classes related to color schemes, which define how structural nodes, visual models, and other renderable objects are colorized. - [SBColorSchemeConstant](https://documentation.samson-connect.net/scripting/latest/docs/api/DataModel/ColorScheme/SBDColorSchemeConstant.md): This class describes a constant color scheme. - [SBColorSchemeConstantIllustrate](https://documentation.samson-connect.net/scripting/latest/docs/api/DataModel/ColorScheme/SBDColorSchemeConstantIllustrate.md): This class describes an illustrative constant color scheme. The colorization is done in the way that it resembles the “Molecule of the Month” style by David S. Goodsell. - [SBColorSchemeCPK](https://documentation.samson-connect.net/scripting/latest/docs/api/DataModel/ColorScheme/SBDColorSchemeCPK.md): This class describes the Corey-Pauling-Koltun (CPK) color scheme. - [SBColorSchemeCPKConstantCarbons](https://documentation.samson-connect.net/scripting/latest/docs/api/DataModel/ColorScheme/SBDColorSchemeCPKConstantCarbons.md): This class describes a color scheme that sets a specified color for carbons and colors from the the Corey-Pauling-Koltun (CPK) color scheme for other atom element types. - [SBColorSchemeCPKPerChainCarbons](https://documentation.samson-connect.net/scripting/latest/docs/api/DataModel/ColorScheme/SBDColorSchemeCPKPerChainCarbons.md): This class describes a color scheme that sets colors for carbons based on their chain ID and colors from the the Corey-Pauling-Koltun (CPK) color scheme for other atom element types. - [SBColorSchemeCPKPerStructuralModelCarbons](https://documentation.samson-connect.net/scripting/latest/docs/api/DataModel/ColorScheme/SBDColorSchemeCPKPerStructuralModelCarbons.md): This class describes a color scheme that sets colors for carbons based on their structural model and colors from the the Corey-Pauling-Koltun (CPK) color scheme for other atom element types. - [SBColorSchemePerChainID](https://documentation.samson-connect.net/scripting/latest/docs/api/DataModel/ColorScheme/SBDColorSchemePerChainID.md): This class describes a color scheme based on the chain ID. - [SBColorSchemePerChainIllustrate](https://documentation.samson-connect.net/scripting/latest/docs/api/DataModel/ColorScheme/SBDColorSchemePerChainIllustrate.md): This class describes an illustrative color scheme based on chain ID. The colorization is done in the way that it resembles the “Molecule of the Month” style by David S. Goodsell. - [SBColorSchemePerFormalCharge](https://documentation.samson-connect.net/scripting/latest/docs/api/DataModel/ColorScheme/SBDColorSchemePerFormalCharge.md): This class describes a color scheme based on the formal charge of atoms. - [SBColorSchemePerOccupancy](https://documentation.samson-connect.net/scripting/latest/docs/api/DataModel/ColorScheme/SBDColorSchemePerOccupancy.md): This class describes a color scheme based on atoms’ occupancy. - [SBColorSchemePerPartialCharge](https://documentation.samson-connect.net/scripting/latest/docs/api/DataModel/ColorScheme/SBDColorSchemePerPartialCharge.md): This class describes a color scheme based on the partial charge of atoms. - [SBColorSchemePerResidueHydrophobicity](https://documentation.samson-connect.net/scripting/latest/docs/api/DataModel/ColorScheme/SBDColorSchemePerResidueHydrophobicity.md): This class describes a per residue hydrophobicity color scheme. Several scales are available via the Inspector or via SBResidue functionality. - [SBColorSchemePerResidueSequenceNumber](https://documentation.samson-connect.net/scripting/latest/docs/api/DataModel/ColorScheme/SBDColorSchemePerResidueSequenceNumber.md): This class describes a color scheme based on the residue sequence number. - [SBColorSchemePerResidueType](https://documentation.samson-connect.net/scripting/latest/docs/api/DataModel/ColorScheme/SBDColorSchemePerResidueType.md): This class describes a color scheme based on the residue type (ALA, GLY, HIS, etc.). - [SBColorSchemePerSecondaryStructureType](https://documentation.samson-connect.net/scripting/latest/docs/api/DataModel/ColorScheme/SBDColorSchemePerSecondaryStructureType.md): This class describes a color scheme based on the secondary structure (alpha-helices, beta-sheets, and loops). - [SBColorSchemePerSideChainCharge](https://documentation.samson-connect.net/scripting/latest/docs/api/DataModel/ColorScheme/SBDColorSchemePerSideChainCharge.md): This class describes a per side chain charge color scheme for amino acid residues. - [SBColorSchemePerSideChainPolarity](https://documentation.samson-connect.net/scripting/latest/docs/api/DataModel/ColorScheme/SBDColorSchemePerSideChainPolarity.md): This class describes a per side chain polarity color scheme for amino acid residues. - [SBColorSchemePerStructuralModel](https://documentation.samson-connect.net/scripting/latest/docs/api/DataModel/ColorScheme/SBDColorSchemePerStructuralModel.md): This class describes a color scheme based on the structural model. - [SBColorSchemePerStructuralModelIllustrate](https://documentation.samson-connect.net/scripting/latest/docs/api/DataModel/ColorScheme/SBDColorSchemePerStructuralModelIllustrate.md): This class describes an illustrative color scheme based on structural model. The colorization is done in the way that it resembles the “Molecule of the Month” style by David S. Goodsell. - [SBColorSchemePerTemperatureFactor](https://documentation.samson-connect.net/scripting/latest/docs/api/DataModel/ColorScheme/SBDColorSchemePerTemperatureFactor.md): This class describes a color scheme based on the temperature factor of atoms. - [Data Graph](https://documentation.samson-connect.net/scripting/latest/docs/api/DataModel/DataGraph.md): This group contains the core data-graph classes used to organize nodes and their properties in SAMSON, including base nodes, indexers, selectors, and material-related classes. - [SBNode](https://documentation.samson-connect.net/scripting/latest/docs/api/DataModel/DataGraph/SBDNode.md): The data graph contains everything directly or indirectly added by the user through SAMSON’s user interface, plugins, etc. A data graph node has basic pre-defined data and functionalities to manage the data (models,... - [SBNodeColorScheme](https://documentation.samson-connect.net/scripting/latest/docs/api/DataModel/DataGraph/SBDNodeColorScheme.md): This is a base class that describes a color scheme in SAMSON. - [SBNodeGroup](https://documentation.samson-connect.net/scripting/latest/docs/api/DataModel/DataGraph/SBDNodeGroup.md): This class describes a group of nodes. In SAMSON, you can group selected nodes to perform various operations using them, e.g. to select the nodes in the group, intersect the current selection with the nodes in the... - [SBNodeIndexer](https://documentation.samson-connect.net/scripting/latest/docs/api/DataModel/DataGraph/SBDNodeIndexer.md): This class describes a node indexer (a list of nodes). - [SBNodeMaterial](https://documentation.samson-connect.net/scripting/latest/docs/api/DataModel/DataGraph/SBDNodeMaterial.md): Data graph nodes in SAMSON may have materials that apply to themselves and their descendants (if the descendants do not have their own materials). Materials are used to modify the visual appearance of data graph nodes.... - [SBNodeMaterialAppearance](https://documentation.samson-connect.net/scripting/latest/docs/api/DataModel/DataGraph/SBDNodeMaterialAppearance.md): This class describes a material appearance used in SBNodeMaterial. - [SBNodeSelector](https://documentation.samson-connect.net/scripting/latest/docs/api/DataModel/DataGraph/SBDNodeSelector.md): This class describes a node selector. - [Document](https://documentation.samson-connect.net/scripting/latest/docs/api/DataModel/Document.md): This group contains classes related to SAMSON documents and the document-level nodes they can contain, such as folders, cameras, labels, notes, lights, presentations, and render presets. - [SBDocument](https://documentation.samson-connect.net/scripting/latest/docs/api/DataModel/Document/SBDDocument.md): This class describes a document. A document may contain various types of nodes: cameras, structural nodes, dynamical models, simulators, visual models, notes, labels, folders, etc. - [SBAnimation](https://documentation.samson-connect.net/scripting/latest/docs/api/DataModel/Document/SBDDocumentAnimation.md): See Presenting and animating section to learn how to create animations. - [SBCamera](https://documentation.samson-connect.net/scripting/latest/docs/api/DataModel/Document/SBDDocumentCamera.md): The SBCamera class implements all mechanisms related to cameras in SAMSON. A camera provides a 3D view of visualizable objects in SAMSON’s data graph, and can be easily controlled to point to a specific location, zoom... - [SBFile](https://documentation.samson-connect.net/scripting/latest/docs/api/DataModel/Document/SBDDocumentFile.md): SAMSON SDK: SBDDocumentFile - [SBFolder](https://documentation.samson-connect.net/scripting/latest/docs/api/DataModel/Document/SBDDocumentFolder.md): This class describes a document folder. A document folder may contain various types of nodes: structural nodes, dynamical models, simulators, visual models, notes, labels, other folders, etc. - [SBLabel](https://documentation.samson-connect.net/scripting/latest/docs/api/DataModel/Document/SBDDocumentLabel.md): SAMSON SDK: SBDDocumentLabel - [SBLight](https://documentation.samson-connect.net/scripting/latest/docs/api/DataModel/Document/SBDDocumentLight.md): This class implements all mechanisms related to lights in SAMSON which are used in rendering (path tracing). Lights have the following properties:... - [SBNote](https://documentation.samson-connect.net/scripting/latest/docs/api/DataModel/Document/SBDDocumentNote.md): You can add notes in documents. They can be used, for example, to store experiment notebooks, descriptions, code snippets, etc. This notes can be accessed and modified from Python and in SAMSON using the Inspector. - [SBPresentation](https://documentation.samson-connect.net/scripting/latest/docs/api/DataModel/Document/SBDDocumentPresentation.md): Presenting and animating - [SBRenderPreset](https://documentation.samson-connect.net/scripting/latest/docs/api/DataModel/Document/SBDDocumentRenderPreset.md): This class describes a render preset that contains various rendering settings. You can add multiple render preset nodes in a document, copy them, and apply them to set the global rendering settings accordingly. - [Palette](https://documentation.samson-connect.net/scripting/latest/docs/api/DataModel/Palette.md): This group contains classes related to color palettes. Palettes are especially useful when you want to map numeric values or categories to colors in a consistent way. - [SBPalette](https://documentation.samson-connect.net/scripting/latest/docs/api/DataModel/Palette/SBDPalette.md): This class is a base class for color palettes. - [SBPaletteDefaultPalette](https://documentation.samson-connect.net/scripting/latest/docs/api/DataModel/Palette/SBDPaletteDefaultPalette.md): This class contains pre-defined default palettes. Currently, it contains only HCL palettes. - [SBPaletteDiscrete](https://documentation.samson-connect.net/scripting/latest/docs/api/DataModel/Palette/SBDPaletteDiscrete.md): This class is a base class for discrete color palettes. - [SBPaletteDiverging](https://documentation.samson-connect.net/scripting/latest/docs/api/DataModel/Palette/SBDPaletteDiverging.md): This class is a base class for diverging color palettes. - [SBPaletteDivergingHCL](https://documentation.samson-connect.net/scripting/latest/docs/api/DataModel/Palette/SBDPaletteDivergingHCL.md): This class is a base class for diverging HCL (Hue-Chroma-Luminance) color palettes. - [SBPaletteFlexibleDivergingHCL](https://documentation.samson-connect.net/scripting/latest/docs/api/DataModel/Palette/SBDPaletteFlexibleDivergingHCL.md): This class is a base class for flexible diverging HCL (Hue-Chroma-Luminance) color palette - [SBPaletteQualitative](https://documentation.samson-connect.net/scripting/latest/docs/api/DataModel/Palette/SBDPaletteQualitative.md): This class is a base class for qualitative color palettes. - [SBPaletteQualitativeHCL](https://documentation.samson-connect.net/scripting/latest/docs/api/DataModel/Palette/SBDPaletteQualitativeHCL.md): This class is a base class for qualitative HCL (Hue-Chroma-Luminance) color palettes. - [SBPaletteSequential](https://documentation.samson-connect.net/scripting/latest/docs/api/DataModel/Palette/SBDPaletteSequential.md): This class is a base class for sequential color palettes. - [SBPaletteSequentialHCL](https://documentation.samson-connect.net/scripting/latest/docs/api/DataModel/Palette/SBDPaletteSequentialHCL.md): This class is a base class for sequential HCL color palettes. - [Visualization](https://documentation.samson-connect.net/scripting/latest/docs/api/DataModel/Visualization.md): This group contains classes related to visualization management, in particular visual presets and their individual steps. - [SBVisualPresetStep](https://documentation.samson-connect.net/scripting/latest/docs/api/DataModel/Visualization/SBDVisualPresetStep.md): This class is a base class for visual presets. - [SBVisualPreset](https://documentation.samson-connect.net/scripting/latest/docs/api/DataModel/Visualization/SBDVisualPreset.md): This class is a base class for visual presets. - [Facade](https://documentation.samson-connect.net/scripting/latest/docs/api/Facade.md): This group contains the high-level interfaces that gather frequently used functionality from across SAMSON into a few convenient entry points. - [SAMSON](https://documentation.samson-connect.net/scripting/latest/docs/api/Facade/SAMSON.md): This sub-module is the main interface to SAMSON API. You can access some of SAMSON functionality directly from this sub-module, for example:... - [GUI](https://documentation.samson-connect.net/scripting/latest/docs/api/GUI.md): This group contains GUI-related classes that are directly exposed to Python. In everyday scripts, most UI-facing functionality is typically accessed through SAMSON, while this section documents the explicit GUI objects... - [Action](https://documentation.samson-connect.net/scripting/latest/docs/api/GUI/Action.md): This group contains classes related to SAMSON actions, which are the command objects that can be triggered from menus, toolbars, shortcuts, or Python. - [SBAction](https://documentation.samson-connect.net/scripting/latest/docs/api/GUI/Action/SBGAction.md): Running actions - [Modeling](https://documentation.samson-connect.net/scripting/latest/docs/api/Modeling.md): This group contains classes related to structural, visual, dynamical, interaction, and property models in SAMSON. - [Dynamical Model](https://documentation.samson-connect.net/scripting/latest/docs/api/Modeling/DynamicalModel.md): This group defines dynamical models, which store the simulated state associated with a system. The pages listed below correspond to the dynamical model classes that are currently exposed in Python. - [SBDynamicalModel](https://documentation.samson-connect.net/scripting/latest/docs/api/Modeling/DynamicalModel/SBMDynamicalModel.md): This class describes the base class for dynamical models. - [SBParticleSystem](https://documentation.samson-connect.net/scripting/latest/docs/api/Modeling/DynamicalModel/SBMDynamicalModelParticleSystem.md): This class describes a particle system in SAMSON, i.e. a dynamical system composed of particles. A particle system has two buffers - a position buffer and a momentum buffer - which may be used to write adaptive... - [Element](https://documentation.samson-connect.net/scripting/latest/docs/api/Modeling/Element.md): This group defines classes related to the periodic table and element information used by structural nodes such as atoms. - [SBElement](https://documentation.samson-connect.net/scripting/latest/docs/api/Modeling/Element/SBMElement.md): This class is used to describe the periodic table in SAMSON. - [SBElementTable](https://documentation.samson-connect.net/scripting/latest/docs/api/Modeling/Element/SBMElementTable.md): This class is used to describe the periodic table in SAMSON. - [Interaction Model](https://documentation.samson-connect.net/scripting/latest/docs/api/Modeling/InteractionModel.md): This group defines interaction models, which compute interactions such as forces for a dynamical model. The particle-system interaction model is the main specialization currently exposed in Python. - [SBInteractionModel](https://documentation.samson-connect.net/scripting/latest/docs/api/Modeling/InteractionModel/SBMInteractionModel.md): This class describes the base class for interaction models. - [SBInteractionModelParticleSystem](https://documentation.samson-connect.net/scripting/latest/docs/api/Modeling/InteractionModel/SBMInteractionModelParticleSystem.md): This class describes a particle system interaction model in SAMSON. A particle system interaction model has one buffer - a force buffer which may be used to write adaptive simulation algorithms. - [Model](https://documentation.samson-connect.net/scripting/latest/docs/api/Modeling/Model.md): This group defines the common base classes for models in SAMSON. Structural, visual, dynamical, interaction, and property models all build on these abstractions. - [SBModel](https://documentation.samson-connect.net/scripting/latest/docs/api/Modeling/Model/SBMModel.md): This class describes the common base class for models in SAMSON. - [SBModelNode](https://documentation.samson-connect.net/scripting/latest/docs/api/Modeling/Model/SBMModelNode.md): SAMSON SDK: SBMModelNode - [Property Model](https://documentation.samson-connect.net/scripting/latest/docs/api/Modeling/PropertyModel.md): This group defines property models, which are used to represent computed or derived properties associated with a system. - [SBPropertyModel](https://documentation.samson-connect.net/scripting/latest/docs/api/Modeling/PropertyModel/SBMPropertyModel.md): This class describes the base class for property models. - [Structural Model](https://documentation.samson-connect.net/scripting/latest/docs/api/Modeling/StructuralModel.md): This group defines structural model nodes such as structural models, conformations, molecules, residues, atoms, bonds, and other nodes that describe molecular structure and hierarchy. - [SBStructuralModel](https://documentation.samson-connect.net/scripting/latest/docs/api/Modeling/StructuralModel/SBMStructuralModel.md): SAMSON SDK: SBMStructuralModel - [SBConformation](https://documentation.samson-connect.net/scripting/latest/docs/api/Modeling/StructuralModel/SBMStructuralModelConformation.md): This class describes a structural conformation, i.e. a set of positions of atoms (samson.SBAtom). - [SBStructuralModelGrid](https://documentation.samson-connect.net/scripting/latest/docs/api/Modeling/StructuralModel/SBMStructuralModelGrid.md): This class is a base class to perform neighbor search between atoms. Internally, the neighbor search algorithm uses a grid to efficiently determine neighbors. - [SBStructuralNode](https://documentation.samson-connect.net/scripting/latest/docs/api/Modeling/StructuralModel/SBMStructuralModelNode.md): This is a base class for structural model nodes. - [SBAtom](https://documentation.samson-connect.net/scripting/latest/docs/api/Modeling/StructuralModel/SBMStructuralModelNodeAtom.md): This class describes an atom in a structural model. - [SBBackbone](https://documentation.samson-connect.net/scripting/latest/docs/api/Modeling/StructuralModel/SBMStructuralModelNodeBackbone.md): SAMSON SDK: SBMStructuralModelNodeBackbone - [SBBond](https://documentation.samson-connect.net/scripting/latest/docs/api/Modeling/StructuralModel/SBMStructuralModelNodeBond.md): This class describes a bond in a structural model. - [SBChain](https://documentation.samson-connect.net/scripting/latest/docs/api/Modeling/StructuralModel/SBMStructuralModelNodeChain.md): SAMSON SDK: SBMStructuralModelNodeChain - [SBStructuralGroup](https://documentation.samson-connect.net/scripting/latest/docs/api/Modeling/StructuralModel/SBMStructuralModelNodeGroup.md): SAMSON SDK: SBMStructuralModelNodeGroup - [SBHydrogenBond](https://documentation.samson-connect.net/scripting/latest/docs/api/Modeling/StructuralModel/SBMStructuralModelNodeHydrogenBond.md): SAMSON SDK: SBMStructuralModelNodeHydrogenBond - [SBHydrogenBondGroup](https://documentation.samson-connect.net/scripting/latest/docs/api/Modeling/StructuralModel/SBMStructuralModelNodeHydrogenBondGroup.md): SAMSON SDK: SBMStructuralModelNodeHydrogenBondGroup - [SBMolecule](https://documentation.samson-connect.net/scripting/latest/docs/api/Modeling/StructuralModel/SBMStructuralModelNodeMolecule.md): SAMSON SDK: SBMStructuralModelNodeMolecule - [SBResidue](https://documentation.samson-connect.net/scripting/latest/docs/api/Modeling/StructuralModel/SBMStructuralModelNodeResidue.md): SAMSON SDK: SBMStructuralModelNodeResidue - [SBStructuralRoot](https://documentation.samson-connect.net/scripting/latest/docs/api/Modeling/StructuralModel/SBMStructuralModelNodeRoot.md): This is an internal structural root node of the structural model node. It is created and used internally. - [SBSegment](https://documentation.samson-connect.net/scripting/latest/docs/api/Modeling/StructuralModel/SBMStructuralModelNodeSegment.md): SAMSON SDK: SBMStructuralModelNodeSegment - [SBSideChain](https://documentation.samson-connect.net/scripting/latest/docs/api/Modeling/StructuralModel/SBMStructuralModelNodeSideChain.md): SAMSON SDK: SBMStructuralModelNodeSideChain - [SBPath](https://documentation.samson-connect.net/scripting/latest/docs/api/Modeling/StructuralModel/SBMStructuralModelPath.md): This class describes a structural path, i.e. a trajectory of atoms (samson.SBAtom). - [Visual Model](https://documentation.samson-connect.net/scripting/latest/docs/api/Modeling/VisualModel.md): This group defines visual models and the geometry objects they use for rendering. In practice, a visual model is the document node you apply to a system, while meshes, surfaces, and textures describe the rendered... - [SBVisualModel](https://documentation.samson-connect.net/scripting/latest/docs/api/Modeling/VisualModel/SBMVisualModel.md): Visual models in SAMSON are document nodes that control how molecular systems are rendered in the viewport. - [SBMesh](https://documentation.samson-connect.net/scripting/latest/docs/api/Modeling/VisualModel/SBMVisualModelMesh.md): This class describes a mesh, that is, a collection of one or more surfaces belonging to a visual model. - [SBSurface](https://documentation.samson-connect.net/scripting/latest/docs/api/Modeling/VisualModel/SBMVisualModelSurface.md): This class describes a renderable surface that stores the triangle geometry of a mesh. - [SBTexture](https://documentation.samson-connect.net/scripting/latest/docs/api/Modeling/VisualModel/SBMVisualModelTexture.md): This class describes a texture that can be attached to a surface for rendering. - [Simulation](https://documentation.samson-connect.net/scripting/latest/docs/api/Simulation.md): This group contains classes used to run or support simulations, including neighbor searches, simulators, and state updaters. - [Neighbor Search](https://documentation.samson-connect.net/scripting/latest/docs/api/Simulation/NeighborSearch.md): The classes below define neighbor-search algorithms that efficiently query nearby atoms or particles, which is especially useful in simulation and analysis workflows. - [SBNeighborSearch](https://documentation.samson-connect.net/scripting/latest/docs/api/Simulation/NeighborSearch/SBSNeighborSearch.md): This class describes the base interface for neighbor-search algorithms in SAMSON. - [SBNeighborSearchParticleSystem](https://documentation.samson-connect.net/scripting/latest/docs/api/Simulation/NeighborSearch/SBSNeighborSearchParticleSystem.md): SAMSON SDK: SBSNeighborSearchParticleSystem - [SBNeighborSearchParticleSystemGrid](https://documentation.samson-connect.net/scripting/latest/docs/api/Simulation/NeighborSearch/SBSNeighborSearchParticleSystemGrid.md): SAMSON SDK: SBSNeighborSearchParticleSystemGrid - [SBNeighborSearchParticleSystemGridPBC](https://documentation.samson-connect.net/scripting/latest/docs/api/Simulation/NeighborSearch/SBSNeighborSearchParticleSystemGridPBC.md): SAMSON SDK: SBSNeighborSearchParticleSystemGridPBC - [SBNeighborSearchParticleSystemPBC](https://documentation.samson-connect.net/scripting/latest/docs/api/Simulation/NeighborSearch/SBSNeighborSearchParticleSystemPBC.md): SAMSON SDK: SBSNeighborSearchParticleSystemPBC - [Simulator](https://documentation.samson-connect.net/scripting/latest/docs/api/Simulation/Simulator.md): The classes below define simulators, which coordinate a dynamical model, an interaction model, and a state updater to run a simulation. - [SBSimulator](https://documentation.samson-connect.net/scripting/latest/docs/api/Simulation/Simulator/SBSSimulator.md): This class describes a simulator, which combines a dynamical model, an interaction model, and a state updater into a runnable simulation workflow. - [SBSimulatorParticleSystem](https://documentation.samson-connect.net/scripting/latest/docs/api/Simulation/Simulator/SBSSimulatorParticleSystem.md): SAMSON SDK: SBSSimulatorParticleSystem - [State Updater](https://documentation.samson-connect.net/scripting/latest/docs/api/Simulation/StateUpdater.md): The classes below define state updaters, which advance or relax the simulated state during a simulation. - [SBStateUpdater](https://documentation.samson-connect.net/scripting/latest/docs/api/Simulation/StateUpdater/SBSStateUpdater.md): This class describes the base class for state updaters. - [SBStateUpdaterParticleSystem](https://documentation.samson-connect.net/scripting/latest/docs/api/Simulation/StateUpdater/SBSStateUpdaterParticleSystem.md): SAMSON SDK: SBSStateUpdaterParticleSystem