PV
Getting started with PV
Getting the PV source-code
Installing with bower
Installing from git
Setting up a small website
The index.html file
Running the Example
The Viewer
Initialization and Configuration
Rendering
Camera Positioning/Orientation
Fog and Slab Modes
Viewer Events
Initialization Event (viewerReady)
Mouse Interaction Events (click, doubleClick)
Object Management
Rendered Molecules
Drawing Geometric Shapes
Coloring Molecular Structures
Available color operations
Opacity
Adding a new color operation
Color Notations
Examples
Custom Color Palettes
Example
Molecular Structures
Obtaining and Creating Molecular Structures
Creating Subsets of a Molecular Structure
Loading Molecular Structures
Mol (and MolView)
Chain (and ChainView)
Residue (and ResidueView)
Atom (and AtomView)
Bond
Superposition of structures
PV Usage Code Samples
Display protein together with ligands
Display an NMR ensemble
Highlight atom under mouse cursor
Select atoms/residues using mouse and keyboard
Usage
Displaying a static label on top of the viewer
Displaying a label on an atom
Adding custom geometry to the 3D scene
Measure distance between two atoms
Usage
PV for developers documentation
How to Contribute
Coding conventions
Commits
Before submitting
How to release a new version of PV
Release Testing
Release Publishing
PV
Docs
»
Edit on GitHub
Index
P
P
pv.BaseGeom() (class)
pv.BaseGeom.colorBy() (pv.BaseGeom method)
pv.BaseGeom.eachCentralAtom() (pv.BaseGeom method)
pv.BaseGeom.getColorForAtom() (pv.BaseGeom method)
pv.BaseGeom.selection() (pv.BaseGeom method)
pv.BaseGeom.setOpacity() (pv.BaseGeom method)
pv.BaseGeom.setSelection() (pv.BaseGeom method)
pv.BaseGeom.setShowRelated() (pv.BaseGeom method)
pv.BaseGeom.showRelated() (pv.BaseGeom method)
pv.color.byAtomProp() (pv.color method)
pv.color.byChain() (pv.color method)
pv.color.byElement() (pv.color method)
pv.color.byResidueProp() (pv.color method)
pv.color.bySS() (pv.color method)
pv.color.rainbow() (pv.color method)
pv.color.setColorPalette() (pv.color method)
pv.color.ssSuccession() (pv.color method)
pv.color.uniform() (pv.color method)
pv.CustomMesh() (class)
pv.CustomMesh.addSphere() (pv.CustomMesh method)
pv.CustomMesh.addTube() (pv.CustomMesh method)
pv.io.fetchPdb() (pv.io method)
pv.io.fetchSdf() (pv.io method)
pv.io.pdb() (pv.io method)
pv.io.sdf() (pv.io method)
pv.mol.Atom() (class)
pv.mol.Atom.bonds() (pv.mol.Atom method)
pv.mol.Atom.element() (pv.mol.Atom method)
pv.mol.Atom.isHetatm() (pv.mol.Atom method)
pv.mol.Atom.name() (pv.mol.Atom method)
pv.mol.Atom.occupancy() (pv.mol.Atom method)
pv.mol.Atom.pos() (pv.mol.Atom method)
pv.mol.Atom.tempFactor() (pv.mol.Atom method)
pv.mol.AtomView() (class)
pv.mol.AtomView.bonds() (pv.mol.AtomView method)
pv.mol.AtomView.element() (pv.mol.AtomView method)
pv.mol.AtomView.isHetatm() (pv.mol.AtomView method)
pv.mol.AtomView.name() (pv.mol.AtomView method)
pv.mol.AtomView.occupancy() (pv.mol.AtomView method)
pv.mol.AtomView.pos() (pv.mol.AtomView method)
pv.mol.AtomView.tempFactor() (pv.mol.AtomView method)
pv.mol.Bond() (class)
pv.mol.Chain() (class)
pv.mol.Chain.addResidue() (pv.mol.Chain method)
pv.mol.Chain.backboneTraces() (pv.mol.Chain method)
pv.mol.Chain.eachBackboneTrace() (pv.mol.Chain method)
pv.mol.Chain.name() (pv.mol.Chain method)
pv.mol.Chain.residueByRnum() (pv.mol.Chain method)
pv.mol.Chain.residues() (pv.mol.Chain method)
pv.mol.Chain.residuesInRnumRange() (pv.mol.Chain method)
pv.mol.ChainView() (class)
pv.mol.ChainView.addResidue() (pv.mol.ChainView method)
pv.mol.ChainView.backboneTraces() (pv.mol.ChainView method)
pv.mol.ChainView.eachBackboneTrace() (pv.mol.ChainView method)
pv.mol.ChainView.name() (pv.mol.ChainView method)
pv.mol.ChainView.residueByRnum() (pv.mol.ChainView method)
pv.mol.ChainView.residues() (pv.mol.ChainView method)
pv.mol.ChainView.residuesInRnumRange() (pv.mol.ChainView method)
pv.mol.matchResiduesByIndex() (pv.mol method)
pv.mol.matchResiduesByNum() (pv.mol method)
pv.mol.Mol() (class)
pv.mol.Mol.addChain() (pv.mol.Mol method)
pv.mol.Mol.addResidues() (pv.mol.Mol method)
pv.mol.Mol.atomCount() (pv.mol.Mol method)
pv.mol.Mol.atomSelect() (pv.mol.Mol method)
pv.mol.Mol.center() (pv.mol.Mol method)
pv.mol.Mol.chain() (pv.mol.Mol method)
pv.mol.Mol.chainByName() (pv.mol.Mol method)
pv.mol.Mol.chains() (pv.mol.Mol method)
pv.mol.Mol.chainsByName() (pv.mol.Mol method)
pv.mol.Mol.eachAtom() (pv.mol.Mol method)
pv.mol.Mol.eachResidue() (pv.mol.Mol method)
pv.mol.Mol.full() (pv.mol.Mol method)
pv.mol.Mol.residueSelect() (pv.mol.Mol method)
pv.mol.Mol.select() (pv.mol.Mol method)
pv.mol.Mol.selectWithin() (pv.mol.Mol method)
pv.mol.MolView() (class)
pv.mol.MolView.addAtom() (pv.mol.MolView method)
pv.mol.MolView.addChain() (pv.mol.MolView method)
pv.mol.MolView.atomCount() (pv.mol.MolView method)
pv.mol.MolView.atomSelect() (pv.mol.MolView method)
pv.mol.MolView.center() (pv.mol.MolView method)
pv.mol.MolView.chain() (pv.mol.MolView method)
pv.mol.MolView.chainByName() (pv.mol.MolView method)
pv.mol.MolView.chains() (pv.mol.MolView method)
pv.mol.MolView.chainsByName() (pv.mol.MolView method)
pv.mol.MolView.eachAtom() (pv.mol.MolView method)
pv.mol.MolView.eachResidue() (pv.mol.MolView method)
pv.mol.MolView.full() (pv.mol.MolView method)
pv.mol.MolView.removeAtom() (pv.mol.MolView method)
pv.mol.MolView.residueSelect() (pv.mol.MolView method)
pv.mol.MolView.select() (pv.mol.MolView method)
pv.mol.MolView.selectWithin() (pv.mol.MolView method)
pv.mol.Residue() (class)
pv.mol.Residue.addAtom() (pv.mol.Residue method)
pv.mol.Residue.atom() (pv.mol.Residue method)
pv.mol.Residue.atoms() (pv.mol.Residue method)
pv.mol.Residue.index() (pv.mol.Residue method)
pv.mol.Residue.isAminoAcid() (pv.mol.Residue method)
pv.mol.Residue.isWater() (pv.mol.Residue method)
pv.mol.Residue.name() (pv.mol.Residue method)
pv.mol.Residue.num() (pv.mol.Residue method)
pv.mol.ResidueView() (class)
pv.mol.ResidueView.addAtom() (pv.mol.ResidueView method)
pv.mol.ResidueView.atom() (pv.mol.ResidueView method)
pv.mol.ResidueView.atoms() (pv.mol.ResidueView method)
pv.mol.ResidueView.index() (pv.mol.ResidueView method)
pv.mol.ResidueView.isAminoAcid() (pv.mol.ResidueView method)
pv.mol.ResidueView.isWater() (pv.mol.ResidueView method)
pv.mol.ResidueView.name() (pv.mol.ResidueView method)
pv.mol.ResidueView.num() (pv.mol.ResidueView method)
pv.mol.superpose() (pv.mol method)
pv.Viewer() (class)
pv.Viewer.add() (pv.Viewer method)
pv.Viewer.addListener() (pv.Viewer method)
pv.Viewer.autoZoom() (pv.Viewer method)
pv.Viewer.cartoon() (pv.Viewer method)
pv.Viewer.centerOn() (pv.Viewer method)
pv.Viewer.customMesh() (pv.Viewer method)
pv.Viewer.fitTo() (pv.Viewer method)
pv.Viewer.get() (pv.Viewer method)
pv.Viewer.hide() (pv.Viewer method)
pv.Viewer.label() (pv.Viewer method)
pv.Viewer.lines() (pv.Viewer method)
pv.Viewer.lineTrace() (pv.Viewer method)
pv.Viewer.on() (pv.Viewer method)
pv.Viewer.points() (pv.Viewer method)
pv.Viewer.quality() (pv.Viewer method)
pv.Viewer.renderAs() (pv.Viewer method)
pv.Viewer.rm() (pv.Viewer method)
pv.Viewer.setCamera() (pv.Viewer method)
pv.Viewer.setCenter() (pv.Viewer method)
pv.Viewer.setRotation() (pv.Viewer method)
pv.Viewer.setZoom() (pv.Viewer method)
pv.Viewer.show() (pv.Viewer method)
pv.Viewer.slabMode() (pv.Viewer method)
pv.Viewer.sline() (pv.Viewer method)
pv.Viewer.spheres() (pv.Viewer method)
pv.Viewer.spin() (pv.Viewer method)
pv.Viewer.trace() (pv.Viewer method)
pv.Viewer.tube() (pv.Viewer method)