edu.duke.cs.osprey/edu.duke.cs.osprey.molscope.molecule/Atom

Atom

data class Atom(element: Element, name: String, pos: Vector3d)

Constructors

fun Atom(element: Element, name: String, x: Double, y: Double, z: Double)

Types

object Companion

Functions

fun copy(): Atom

fun label(mol: Molecule): String

Make a human-readable label for the atom using information from the molecule

open override fun toString(): String

Properties

val element: Element

val name: String

val pos: Vector3d

Extensions

fun Atom.atomTypeEEF1(mol: Molecule): EEF1.AtomType?

atomTypeEEF1OrThrow

fun Atom.atomTypeEEF1OrThrow(mol: Molecule): EEF1.AtomType

fun Atom.covalentRange(a2: Atom, guesser: BondGuesser = BondGuesser()): ClosedFloatingPointRange<Double>

fun Atom.fixedName(mol: Molecule): String

Generate a unique name for the atom, since atoms can come from multiple molecules.

inCovalentRange

fun Atom.inCovalentRange(a2: Atom, guesser: BondGuesser = BondGuesser()): Boolean

maxCovalentDist

fun Atom.maxCovalentDist(a2: Atom, guesser: BondGuesser = BondGuesser()): Double

minCovalentDist

fun Atom.minCovalentDist(guesser: BondGuesser = BondGuesser()): Double