edu.duke.cs.osprey/edu.duke.cs.osprey.gui.prep/Anchor/Double

Double

class Double(mol: Molecule, a: Atom, b: Atom, c: Atom, d: Atom) : Anchor

Functions

open override fun align(atoms: Set<Atom>, anchorCoords: ConfLib.AnchorCoords)

Aligns the attached atoms such that: anchors line segments a->b are in the same direction and have midpoints coincident at m. anchor wedges c<-m->d are rotated about the a-b axis so their center directions are parallel. Since the different anchors can have different lengths of the a-b line segments, and different dihedral angles c->a->b->d, this method is an approximate method for aligning the two coordinate systems that tries to keep the error from accumulating all in one linear or angular distance.

open override fun bondToAnchors(anchor: ConfLib.Anchor, bondFunc: (List<ConfLib.AtomInfo>, Atom) -> Unit)

connectedAtomsIsSingleComponent

open override fun connectedAtomsIsSingleComponent(atoms: Set<Atom>): Boolean

fun copy(mol: Molecule = this.mol, a: Atom = this.a, b: Atom = this.b, c: Atom = this.c, d: Atom = this.d): Anchor.Double

open override fun copyToMol(mol: Molecule, oldToNew: AtomMap): Anchor.Double

fun findResidue(): Polymer.Residue?

Returns the residue of the first anchor atom, if any

getConnectedAtoms

open override fun getConnectedAtoms(atoms: Set<Atom>): MutableSet<Atom>

Filters the given atoms down to just the ones connected to the anchor atoms.

isAnchorCompatible

open override fun isAnchorCompatible(anchor: ConfLib.Anchor): Boolean

makeLibraryAnchor

open override fun makeLibraryAnchor(atoms: Set<Atom>, id: Int, getAtomInfo: (Atom) -> ConfLib.AtomInfo): ConfLib.Anchor.Double

Translate the molecule anchor atoms into a ConfLib anchor definition

makeLibraryCoords

open override fun makeLibraryCoords(): ConfLib.AnchorCoords.Double

Properties

val a: Atom

open override val anchorAtoms: List<Atom>

val b: Atom

val c: Atom

val d: Atom

val mol: Molecule