Mapped

inner class Mapped

Functions

fun addMissingAtoms(coords: List<Vector3d>, filter: (Atom, Polymer.Residue?) -> Boolean = { atom: Atom, residue: Polymer.Residue? -> true }): Int

Adds all the extra atoms defined by AMBER.

fun atom(i: Int): Atom?

Returns the electrostatic scaling divisor for the atom pair. Assumes the atoms are already 1-4 bonded!

fun nonbondIndex(atoma: Atom, atomb: Atom): Int

fun nonbondIndex(indexa: Int, indexb: Int): Int

Reset all bonds in the molecule to only those defined by the AMBER topology.

fun vdw(atoma: Atom, atomb: Atom): Pair<Double, Double>

fun vdw(indexa: Int, indexb: Int): Pair<Double, Double>

fun vdwDivisor14(indexa: Int, indexb: Int): Double

Returns the van der Waals scaling divisor for the atom pair. Assumes the atoms are already 1-4 bonded!