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SAMSON Python Scripting

SAMSON Python Scripting

  • Python bindings for SAMSON API

Guide

  • Getting started
  • Running actions
  • Developing scripts
  • Working with documents and nodes
  • Importing and exporting
  • Making operations undoable
  • Selecting nodes
  • Getting nodes
  • Units
    • SBQuantity
      • Mathematical functions
      • SI Unit system
        • unitsSI
        • Convenience constructors
      • Atomic Units Unit System
        • unitsAU
        • Convenience constructors
      • Dalton Unit system
        • unitsDalton
        • Convenience constructors
      • Electronvolt Unit System
        • unitsElectronvolt
        • Convenience constructors
      • KilocaloriePerMole Unit System
        • unitsKilocaloriePerMole
        • Convenience constructors
      • List of defined quantities
      • SBConstant
    • Type
      • SBColor
      • SBDateTime
      • SBRandom
      • SBPhysicalVector3
        • SBAcceleration3
        • SBAngularAcceleration3
        • SBAngularVelocity3
        • SBVector3
        • SBEnergy3
        • SBForce3
        • SBInverseLength3
        • SBInverseMomentum3
        • SBLength3
        • SBMomentum3
        • SBPicometerPerSecond3
        • SBPosition3
        • SBRadian3
        • SBRadianPerSecond3
        • SBSquareLength3
        • SBTorque3
        • SBVelocity3
      • SBPhysicalVector6
        • SBAcceleration6
        • SBVector6
        • SBForce6
        • SBVelocity6
      • SBPhysicalInterval
        • SBAccelerationInterval
        • SBInterval
        • SBEnergyInterval
        • SBForceInterval
        • SBLengthInterval
        • SBMomentumInterval
        • SBPositionInterval
        • SBSquareLengthInterval
        • SBVelocityInterval
      • SBPhysicalIAVector3
        • SBIAAcceleration3
        • SBIAVector3
        • SBIAForce3
        • SBIALength3
        • SBIAMomentum3
        • SBIAPosition3
        • SBIARadian3
        • SBIARadianPerSecond3
        • SBIAVelocity3
      • SBPhysicalMatrix33
        • SBMatrix33
        • SBInverseMass33
        • SBInverseInertiaTensor33
        • SBMass33
        • SBInertiaTensor33
      • SBPhysicalMatrix66
        • SBMatrix66
        • SBInertia66
        • SBInverseInertia66
      • SBSpatialDomain
      • SBSpatialTransform
      • SBUnitCell
  • Colorizing nodes
  • Visualizing
  • Building
  • Presenting and animating
  • Rendering
  • Introspection: using extensions
  • Examples
    • Presentation: play path
    • Create animations and movies without presentations
    • Building a decane molecule
    • Create atoms on a sphere
    • Creation of a carbon nanotube fabric: replication, modification of positions
    • Colorize atoms by position
    • Colorize atoms by velocity along path
    • Visualize coarse-grained systems
    • Colorize connected components by molecular weight
    • Export trajectory frames
    • Compute RMSD between two molecules
    • Compute bond lengths along paths
    • Compute interatomic distances along path
    • Select atoms and bonds by location
    • Select connected components by molecular weight
    • Examples of usage of ASE package
    • Embedded app: a simple GUI with buttons
    • Select connected components by molecular weight

API

  • Core
    • Class
      • SBClass
      • SBAttribute
      • SBFunction
      • SBInterface
      • SBProxy
    • Container
      • SBUUID
      • SBUserPlan
      • SBVersionNumber
    • Meta
      • SBValue
      • SBValueMap
    • Reference
      • SBReferenceIndexer
      • SBReferenceTarget
  • Data Model
    • Asset
      • SBAsset
    • Color Scheme
      • SBColorSchemeConstant
      • SBColorSchemeConstantIllustrate
      • SBColorSchemeCPK
      • SBColorSchemeCPKConstantCarbons
      • SBColorSchemeCPKPerChainCarbons
      • SBColorSchemeCPKPerStructuralModelCarbons
      • SBColorSchemePerChainID
      • SBColorSchemePerChainIllustrate
      • SBColorSchemePerFormalCharge
      • SBColorSchemePerOccupancy
      • SBColorSchemePerPartialCharge
      • SBColorSchemePerResidueHydrophobicity
      • SBColorSchemePerResidueSequenceNumber
      • SBColorSchemePerResidueType
      • SBColorSchemePerSecondaryStructureType
      • SBColorSchemePerSideChainCharge
      • SBColorSchemePerSideChainPolarity
      • SBColorSchemePerStructuralModel
      • SBColorSchemePerStructuralModelIllustrate
      • SBColorSchemePerTemperatureFactor
    • Data Graph
      • SBNode
      • SBNodeColorScheme
      • SBNodeGroup
      • SBNodeIndexer
      • SBNodeMaterial
      • SBNodeMaterialAppearance
      • SBNodeSelector
    • Document
      • SBDocument
      • SBAnimation
      • SBCamera
      • SBFile
      • SBFolder
      • SBLabel
      • SBLight
      • SBNote
      • SBPresentation
      • SBRenderPreset
    • Palette
      • SBPalette
      • SBPaletteDefaultPalette
      • SBPaletteDiscrete
      • SBPaletteDiverging
      • SBPaletteDivergingHCL
      • SBPaletteFlexibleDivergingHCL
      • SBPaletteQualitative
      • SBPaletteQualitativeHCL
      • SBPaletteSequential
      • SBPaletteSequentialHCL
    • SBQuantity
      • Mathematical functions
      • SI Unit system
        • unitsSI
        • Convenience constructors
      • Atomic Units Unit System
        • unitsAU
        • Convenience constructors
      • Dalton Unit system
        • unitsDalton
        • Convenience constructors
      • Electronvolt Unit System
        • unitsElectronvolt
        • Convenience constructors
      • KilocaloriePerMole Unit System
        • unitsKilocaloriePerMole
        • Convenience constructors
      • List of defined quantities
      • SBConstant
    • Type
      • SBColor
      • SBDateTime
      • SBRandom
      • SBPhysicalVector3
        • SBAcceleration3
        • SBAngularAcceleration3
        • SBAngularVelocity3
        • SBVector3
        • SBEnergy3
        • SBForce3
        • SBInverseLength3
        • SBInverseMomentum3
        • SBLength3
        • SBMomentum3
        • SBPicometerPerSecond3
        • SBPosition3
        • SBRadian3
        • SBRadianPerSecond3
        • SBSquareLength3
        • SBTorque3
        • SBVelocity3
      • SBPhysicalVector6
        • SBAcceleration6
        • SBVector6
        • SBForce6
        • SBVelocity6
      • SBPhysicalInterval
        • SBAccelerationInterval
        • SBInterval
        • SBEnergyInterval
        • SBForceInterval
        • SBLengthInterval
        • SBMomentumInterval
        • SBPositionInterval
        • SBSquareLengthInterval
        • SBVelocityInterval
      • SBPhysicalIAVector3
        • SBIAAcceleration3
        • SBIAVector3
        • SBIAForce3
        • SBIALength3
        • SBIAMomentum3
        • SBIAPosition3
        • SBIARadian3
        • SBIARadianPerSecond3
        • SBIAVelocity3
      • SBPhysicalMatrix33
        • SBMatrix33
        • SBInverseMass33
        • SBInverseInertiaTensor33
        • SBMass33
        • SBInertiaTensor33
      • SBPhysicalMatrix66
        • SBMatrix66
        • SBInertia66
        • SBInverseInertia66
      • SBSpatialDomain
      • SBSpatialTransform
      • SBUnitCell
    • Visualization
      • SBVisualPresetStep
      • SBVisualPreset
  • Facade
    • SAMSON
  • GUI
    • Action
      • SBAction
  • Modeling
    • Dynamical Model
      • SBDynamicalModel
      • SBParticleSystem
    • Element
      • SBElement
      • SBElementTable
    • Interaction Model
      • SBInteractionModel
      • SBInteractionModelParticleSystem
    • Model
      • SBModel
      • SBModelNode
    • Property Model
      • SBPropertyModel
    • Structural Model
      • SBStructuralModel
      • SBConformation
      • SBStructuralModelGrid
      • SBStructuralNode
      • SBAtom
      • SBBackbone
      • SBBond
      • SBChain
      • SBStructuralGroup
      • SBHydrogenBond
      • SBHydrogenBondGroup
      • SBMolecule
      • SBResidue
      • SBStructuralRoot
      • SBSegment
      • SBSideChain
      • SBPath
    • Visual Model
      • SBVisualModel
      • SBMesh
      • SBSurface
      • SBTexture
  • Simulation
    • Neighbor Search
      • SBNeighborSearch
      • SBNeighborSearchParticleSystem
      • SBNeighborSearchParticleSystemGrid
      • SBNeighborSearchParticleSystemGridPBC
      • SBNeighborSearchParticleSystemPBC
    • Simulator
      • SBSimulator
      • SBSimulatorParticleSystem
    • State Updater
      • SBStateUpdater
      • SBStateUpdaterParticleSystem
  • Changelog
    • Changelog for 11.x.x
    • Changelog for 10.x.x
    • Changelog for 9.x.x
    • Changelog for 8.x.x
    • Changelog for v.7.x.x
    • Changelog for v.6.0.x
    • Changelog for v.5.0.x
    • Changelog for v.4.0.x
    • Changelog for v.3.0.x
    • Changelog for v.2.0.x
    • Changelog for v.1.0.x
    • Changelog for v.0.12.x
    • Changelog for v.0.11.x
    • Changelog for v.0.10.x
    • Changelog for v.0.9.0
    • Changelog for v.0.8.x
    • Changelog for v.0.7.x
  • Available versions

Additional links

  • SAMSON Connect
  • Documentation Center
  • User Guide
  • Developer Guide
  • Forum
  • SAMSON Extensions
  • Download SAMSON
  • YouTube channel

Simulation

Simulation#

This group contains classes used to run or support simulations, including neighbor searches, simulators, and state updaters.

See also

SAMSON SDK: The Simulation Library Group

  • Neighbor Search
  • Simulator
  • State Updater

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SBTexture

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Neighbor Search

By OneAngstrom

© Copyright OneAngstrom.