RenderableMolecule

Inherits Renderable

Used to render a single molecular system, which can be either static or dynamic. The rendering is done using the rendering engine of the ViaMD framework. Many of the parameters are described in greater detail on their Wiki page. It is possible to assign multiple representations to a molecular structure and specify individual settings per representation, including the ability to filter using ViaMD’s powerful filtering scripting language.

The current implementation supports the loading of “PDB”, “Gromacs”, “XYZ”, “XMOL”, and “ARC” files for the molecular structure and “PDB”, “XTC”, “TRR”, “XYZ”, “XMOL”, and “ARC” files for the optional trajectories.

If no trajectory file is provided only the structural information is shown.

Members

Name	Documentation	Type	Description	Optional
MoleculeFile	The path to the file from which the molecular structure is read.	File	Value of type ‘File’	No
AnimationBaseScale	Base scale for the animation. Tune this to sync up its animation with other trajectories.	Double	Value of type ‘Double’	Yes
AnimationRepeatMode	Controls how the animation should be repeated when the end of the animation is reached.	String	In list { PingPong, Wrap, Clamp }	Yes
AnimationSpeed	Playback speed of the animation (in frames per second).	Double	Value of type ‘Double’	Yes
ApplyPbcOnLoad	Applies Periodic Boundary Constraints upon loading trajectory frames.	Boolean	Value of type ‘Boolean’	Yes
ApplyPbcPerFrame	Applies Periodic Boundary Constraints for each interpolated frame (can be CPU-intensive).	Boolean	Value of type ‘Boolean’	Yes
CoarseGrained	Enable if the dataset should be interpreted as coarse grained.	Boolean	Value of type ‘Boolean’	Yes
DimInAtmosphere	Decides if the object should be dimmed (i.e. faded out) when the camera is in the sunny part of an atmosphere.	Boolean	Value of type ‘Boolean’	Yes
Enabled	Determines whether this object will be visible or not.	Boolean	Value of type ‘Boolean’	Yes
Opacity	This value determines the opacity of this renderable. A value of 0 means completely transparent.	Double	In range: ( 0, 1)	Yes
RenderBinMode	A value that specifies if the renderable should be rendered in the Background, Opaque, Pre-/PostDeferredTransparency, Overlay, or Sticker rendering step.	String	In list { Background, Opaque, PreDeferredTransparent, Overlay, PostDeferredTransparent, Sticker }	Yes
Representations	The list of representations that are used to render this molecular dataset. Each representation can consist of a representation type, a coloring method, and and optional filter and scaling that can be applied to each representation individually.	Table	Table parameters	Yes
Tag	A single tag or a list of tags that this renderable will respond to when setting properties.	Table, or String	Value of type ‘Table’, or Value of type ‘String’	Yes
TrajectoryFile	The path to the file from which the trajectory information is read.	File	Value of type ‘File’	Yes
Type	The type of the renderable.	String	Value of type ‘String’	Yes

Inherited members from Renderable

Name	Documentation	Type	Description	Optional
DimInAtmosphere	Decides if the object should be dimmed (i.e. faded out) when the camera is in the sunny part of an atmosphere.	Boolean	Value of type ‘Boolean’	Yes
Enabled	Determines whether this object will be visible or not.	Boolean	Value of type ‘Boolean’	Yes
Opacity	This value determines the opacity of this renderable. A value of 0 means completely transparent.	Double	In range: ( 0, 1)	Yes
RenderBinMode	A value that specifies if the renderable should be rendered in the Background, Opaque, Pre-/PostDeferredTransparency, Overlay, or Sticker rendering step.	String	In list { Background, Opaque, PreDeferredTransparent, Overlay, PostDeferredTransparent, Sticker }	Yes
Tag	A single tag or a list of tags that this renderable will respond to when setting properties.	Table, or String	Value of type ‘Table’, or Value of type ‘String’	Yes
Type	The type of the renderable.	String	Value of type ‘String’	Yes

Table parameters for Representations

The list of representations that are used to render this molecular dataset. Each representation can consist of a representation type, a coloring method, and and optional filter and scaling that can be applied to each representation individually.

• Optional: Yes

Name	Documentation	Type	Description	Optional
*	This is a representation of a molecular dataset. Each representation is rendered independently and can contain different rendering and filtering parameters.	Table	Table parameters	Yes

Table parameters for *

This is a representation of a molecular dataset. Each representation is rendered independently and can contain different rendering and filtering parameters.

• Optional: Yes

Name	Documentation	Type	Description	Optional
Color	The method by which the selected representation should be colored.	String	In list { Cpk, AtomIndex, ResId, ResIndex, ChainId, ChainIndex, SecondaryStructure, Uniform }	Yes
Filter	The ViaMD filter that can be used to filter atoms, residues, chains, and other primary or secondary structures.	String	Value of type ‘String’	Yes
Scale	A scaling factor that causes a different scaling effect depending on the selected representation type. In general, a larger value will cause the representation to be rendered larger and more prominently.	Double	Value of type ‘Double’	Yes
UniformColor	The uniform color that is used if not coloring method is selected.	Vector4<double>	Value of type ‘Vector4’	Yes

Asset Examples

local moleculeDb = "https://home.thissma.fr/moldata/"



local moleculeO2 = asset.resource({
  Name = "Molecule O2",
  Type = "HttpSynchronization",
  Identifier = "molecule_dynamics_o2",
  Version = 1
})

local moleculeH2O = asset.resource({
  Name = "Molecule H2O",
  Type = "HttpSynchronization",
  Identifier = "molecule_dynamics_h2o",
  Version = 1
})

local moleculeCO2 = asset.resource({
  Name = "Molecule CO2",
  Type = "HttpSynchronization",
  Identifier = "molecule_dynamics_co2",
  Version = 1
})

local moleculeC60 = asset.resource({
  Name = "Molecule C60",
  Type = "HttpSynchronization",
  Identifier = "molecule_dynamics_c60",
  Version = 1
})

local molecule1ala500 = asset.resource({
  Name = "Molecule 1ALA-500",
  Type = "HttpSynchronization",
  Identifier = "molecule_dynamics_1ala-500",
  Version = 1
})

local molecule1bna = asset.resource({
  Name = "Molecule 1BNA",
  Type = "HttpSynchronization",
  Identifier = "molecule_dynamics_1bna",
  Version = 1
})

local iceMelting = asset.resource({
  Name = "Ice Melting Simulation",
  Type = "HttpSynchronization",
  Identifier = "molecule_dynamics_ice-melting",
  Version = 1
})

local aspirin = asset.resource({
  Name = "Molecule Aspirin",
  Type = "HttpSynchronization",
  Identifier = "molecule_dynamics_aspirin",
  Version = 1
})

local amyloid = asset.resource({
  Name = "Molecule Amyloid",
  Type = "HttpSynchronization",
  Identifier = "molecule_dynamics_amyloid",
  Version = 1
})


local MoleculeMisc = {
  Identifier = "MoleculeMisc",
  Tag = { "molecule_visualization" },
  GUI = {
    Name = "Molecule Museum",
    Path = "/Microcosmos/Molecules/Misc",
    Hidden = true
  }
}

local MoleculeO2 = {
  Identifier = "MoleculeMiscO2",
  Parent = MoleculeMisc.Identifier,
  Transform = {
    Translation = {
      Type = "StaticTranslation",
      Position = { 0.0, 0.0, 0.0 }
    }
  },
  Renderable = {
    Type = "RenderableMolecule",
    MoleculeFile = moleculeO2 .. "o2.arc",
    TrajectoryFile = moleculeO2 .. "o2.arc",
    AnimationSpeed = 5.0
  },
  Tag = { "molecule_visualization" },
  GUI = {
    Name = "Dioxygen (O2)",
    Path = "/Microcosmos/Molecules/Misc"
  }
}

local MoleculeH2O = {
  Identifier = "MoleculeMiscH2O",
  Parent = MoleculeMisc.Identifier,
  Transform = {
    Translation = {
      Type = "StaticTranslation",
      Position = { 20.0, 0.0, 0.0 }
    }
  },
  Renderable = {
    Type = "RenderableMolecule",
    MoleculeFile = moleculeH2O .. "h2o.arc"
  },
  Tag = { "molecule_visualization" },
  GUI = {
    Name = "Water (H2O)",
    Path = "/Microcosmos/Molecules/Misc"
  }
}

local MoleculeCO2 = {
  Identifier = "MoleculeMiscCO2",
  Parent = MoleculeMisc.Identifier,
  Transform = {
    Translation = {
      Type = "StaticTranslation",
      Position = { 40.0, 0.0, 0.0 }
    }
  },
  Renderable = {
    Type = "RenderableMolecule",
    MoleculeFile = moleculeCO2 .. "co2.arc",
    Representations = {
      {
        Type = "Licorice"
      }
    }
  },
  Tag = { "molecule_visualization" },
  GUI = {
    Name = "Carbon Dioxyde (CO2)",
    Path = "/Microcosmos/Molecules/Misc"
  }
}

local MoleculeC60 = {
  Identifier = "MoleculeMiscC60",
  Parent = MoleculeMisc.Identifier,
  Transform = {
    Translation = {
      Type = "StaticTranslation",
      Position = { 60.0, 0.0, 0.0 }
    }
  },
  Renderable = {
    Type = "RenderableMolecule",
    MoleculeFile = moleculeC60 .. "c60.arc",
    Representations = {
      {
        Type = "Licorice"
      }
    }
  },
  Tag = { "molecule_visualization" },
  GUI = {
    Name = "C60",
    Path = "/Microcosmos/Molecules/Misc"
  }
}

local MoleculeAlanin = {
  Identifier = "MoleculeMiscAlanin",
  Parent = MoleculeMisc.Identifier,
  Transform = {
    Translation = {
      Type = "StaticTranslation",
      Position = { 110.0, 0.0, 0.0 }
    }
  },
  Renderable = {
    Type = "RenderableMolecule",
    MoleculeFile = molecule1ala500 .. "1ALA-500.pdb",
    TrajectoryFile = molecule1ala500 .. "1ALA-500.pdb",
    AnimationSpeed = 5.0
  },
  Tag = { "molecule_visualization" },
  GUI = {
    Name = "Alanin",
    Path = "/Microcosmos/Molecules/Misc"
  }
}

local MoleculeDNA = {
  Identifier = "MoleculeMiscDNA",
  Parent = MoleculeMisc.Identifier,
  Transform = {
    Translation = {
      Type = "StaticTranslation",
      Position = { 160.0, 0.0, 0.0 }
    }
  },
  Renderable = {
    Type = "RenderableMolecule",
    MoleculeFile = molecule1bna .. "1bna.pdb",
    Representations = {
      {
        Type = "Licorice"
      }
    }
  },
  Tag = { "molecule_visualization" },
  GUI = {
    Name = "DNA",
    Path = "/Microcosmos/Molecules/Misc"
  }
}

local MoleculeIce = {
  Identifier = "MoleculeMiscIce",
  Parent = MoleculeMisc.Identifier,
  Transform = {
    Translation = {
      Type = "StaticTranslation",
      Position = { 210.0, 0.0, 0.0 }
    }
  },
  Renderable = {
    Type = "RenderableMolecule",
    MoleculeFile = iceMelting .. "ice.gro",
    TrajectoryFile = iceMelting .. "ice.xtc",
    AnimationSpeed = 10.0
  },
  Tag = { "molecule_visualization" },
  GUI = {
    Name = "Ice Melting",
    Path = "/Microcosmos/Molecules/Misc"
  }
}

local MoleculeAspirin = {
  Identifier = "MoleculeMiscAspirin",
  Parent = MoleculeMisc.Identifier,
  Transform = {
    Translation = {
      Type = "StaticTranslation",
      Position = { 310.0, 0.0, 0.0 }
    }
  },
  Renderable = {
    Type = "RenderableMolecule",
    MoleculeFile = aspirin .. "aspirin.gro",
    TrajectoryFile = aspirin .. "aspirin.xtc",
    AnimationSpeed = 5.0,
    Representations = {
      {
        Type = "Licorice",
        Filter = "not water"
      }
    }
  },
  Tag = { "molecule_visualization" },
  GUI = {
    Name = "Aspirin",
    Path = "/Microcosmos/Molecules/Misc"
  }
}

local MoleculeAmyloidMarker = {
  Identifier = "MoleculeMiscAmyloidMarker",
  Parent = MoleculeMisc.Identifier,
  Transform = {
    Translation = {
      Type = "StaticTranslation",
      Position = { 510.0, 0.0, 0.0 }
    }
  },
  Renderable = {
    Type = "RenderableMolecule",
    MoleculeFile = amyloid .. "60pft_in_tau.gro",
    TrajectoryFile = amyloid .. "60pft_in_tau-traj-96-106ns.xtc",
    AnimationSpeed = 0.1
  },
  Tag = { "molecule_visualization" },
  GUI = {
    Name = "Amyloid Marker",
    Path = "/Microcosmos/Molecules/Misc"
  }
}


asset.onInitialize(function()
  openspace.addSceneGraphNode(MoleculeMisc)
  openspace.addSceneGraphNode(MoleculeO2)
  openspace.addSceneGraphNode(MoleculeH2O)
  openspace.addSceneGraphNode(MoleculeCO2)
  openspace.addSceneGraphNode(MoleculeC60)
  openspace.addSceneGraphNode(MoleculeAlanin)
  openspace.addSceneGraphNode(MoleculeDNA)
  openspace.addSceneGraphNode(MoleculeIce)
  openspace.addSceneGraphNode(MoleculeAspirin)
  openspace.addSceneGraphNode(MoleculeAmyloidMarker)
end)

asset.onDeinitialize(function()
  openspace.removeSceneGraphNode(MoleculeAmyloidMarker)
  openspace.removeSceneGraphNode(MoleculeAspirin)
  openspace.removeSceneGraphNode(MoleculeIce)
  openspace.removeSceneGraphNode(MoleculeDNA)
  openspace.removeSceneGraphNode(MoleculeAlanin)
  openspace.removeSceneGraphNode(MoleculeC60)
  openspace.removeSceneGraphNode(MoleculeCO2)
  openspace.removeSceneGraphNode(MoleculeH2O)
  openspace.removeSceneGraphNode(MoleculeO2)
  openspace.removeSceneGraphNode(MoleculeMisc)
end)

asset.export(MoleculeMisc)
asset.export(MoleculeO2)
asset.export(MoleculeH2O)
asset.export(MoleculeCO2)
asset.export(MoleculeC60)
asset.export(MoleculeAlanin)
asset.export(MoleculeDNA)
asset.export(MoleculeIce)
asset.export(MoleculeAspirin)
asset.export(MoleculeAmyloidMarker)



asset.meta = {
  Name = "Various Molecules",
  Description = [[Visualizes a selection of different molecules to represent the
    functionality of the MolVis rendering framework.]],
  Author = "OpenSpace Team",
  URL = "https://openspaceproject.com",
  License = "MIT license"
}