import ResidueType from 'ngl/src/store/residue-type.js'

public class | source

ResidueType

Residue type

Constructor Summary

Public Constructor
public	constructor(structure: Structure, resname: String, atomTypeIdList: Array, hetero: Boolean, chemCompType: String, bonds: Object)

Member Summary

Public Members
public	atomCount
public	atomTypeIdList
public	backboneEndAtomIndex
public	backboneEndType
public	backboneIndexList
public	backboneStartAtomIndex
public	backboneStartType
public	backboneType
public	bondReferenceAtomIndices
public	bonds
public	chemCompType
public	direction1AtomIndex
public	direction2AtomIndex
public	hetero
public	moleculeType
public	resname
public	rings
public	rungEndAtomIndex
public	structure
public	traceAtomIndex

Method Summary

Public Methods
public	assignBondReferenceAtomIndices(): undefined For bonds with order > 1, pick a reference atom
public	calculateBondGraph(): Object
public	calculateRings(r: ResidueProxy): undefined Calculates ring atoms within a residue Adaptation of RDKit's fastFindRings method by G. Landrum: https://github.com/rdkit/rdkit/blob/master/Code/GraphMol/FindRings.cpp
public	getAtomIndexByName()
public	getBackboneIndexList()
public	getBackboneType()
public	getBondGraph()
public	getBondIndex()
public	getBondReferenceAtomIndex()
public	getBonds()
public	getMoleculeType()
public	getRings()
public	hasAtomWithName()
public	hasBackbone()
public	hasBackboneAtoms()
public	hasCgDnaBackbone()
public	hasCgProteinBackbone()
public	hasCgRnaBackbone()
public	hasDnaBackbone()
public	hasProteinBackbone()
public	hasRnaBackbone()
public	isCg()
public	isDna()
public	isHetero()
public	isIon()
public	isNucleic()
public	isProtein()
public	isRna()
public	isSaccharide()
public	isWater()

Public Constructors

public constructor(structure: Structure, resname: String, atomTypeIdList: Array, hetero: Boolean, chemCompType: String, bonds: Object) source

Params:

Name	Type	Attribute	Description
structure	Structure		the structure object
resname	String		name of the residue
atomTypeIdList	Array		list of IDs of AtomTypes corresponding to the atoms of the residue
hetero	Boolean		hetero flag
chemCompType	String		chemical component type
bonds	Object	optional	TODO

Public Members

public atomCount source

public atomTypeIdList source

public backboneEndAtomIndex source

public backboneEndType source

public backboneIndexList source

public backboneStartAtomIndex source

public backboneStartType source

public backboneType source

public bondReferenceAtomIndices source

public bonds source

public chemCompType source

public direction1AtomIndex source

public direction2AtomIndex source

public hetero source

public moleculeType source

public resname source

public rings source

public rungEndAtomIndex source

public structure source

public traceAtomIndex source

Public Methods

public assignBondReferenceAtomIndices(): undefined source

For bonds with order > 1, pick a reference atom

Return:

undefined

public calculateBondGraph(): Object source

Return:

Object

bondGraph - represents the bonding in this residue: { ai1: [ ai2, ai3, ...], ...}

public calculateRings(r: ResidueProxy): undefined source

Calculates ring atoms within a residue Adaptation of RDKit's fastFindRings method by G. Landrum: https://github.com/rdkit/rdkit/blob/master/Code/GraphMol/FindRings.cpp

Params:

Name	Type	Attribute	Description
r	ResidueProxy		The residue for which we are to find rings

Return:

undefined

public getAtomIndexByName() source

public getBackboneIndexList() source

public getBackboneType() source

public getBondGraph() source

public getBondIndex() source

public getBondReferenceAtomIndex() source

public getBonds() source

public getMoleculeType() source

public getRings() source

public hasAtomWithName() source

public hasBackbone() source

public hasBackboneAtoms() source

public hasCgDnaBackbone() source

public hasCgProteinBackbone() source

public hasCgRnaBackbone() source

public hasDnaBackbone() source

public hasProteinBackbone() source

public hasRnaBackbone() source

public isCg() source

public isDna() source

public isHetero() source

public isIon() source

public isNucleic() source

public isProtein() source

public isRna() source

public isSaccharide() source

public isWater() source