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import ResidueType from 'ngl/src/store/residue-type.js'
public class | source

ResidueType

Residue type

Constructor Summary

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

Member Summary

Public Members
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Method Summary

Public Methods
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For bonds with order > 1, pick a reference atom

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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

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isCg()

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isDna()

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isIon()

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isRna()

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Public Constructors

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

Params:

NameTypeAttributeDescription
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:

NameTypeAttributeDescription
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