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

Polymer

class Polymer(name: String) : Molecule

An extension to Molecule that supports residues in a chain topology, and separates mainchain from sidechain

Constructors

Polymer

fun Polymer(name: String)

Types

Chain

class Chain(id: String)

Residue

class Residue(id: String, type: String)

Functions

bfs

fun bfs(source: Atom, visitSource: Boolean = false, shouldVisit: (fromAtom: Atom, toAtom: Atom, dist: Int) -> Boolean = { _, _, _ -> true }): Iterable<Molecule.Searched>

Crawl the bond network in breadth-first order starting at the source atom.

copy

open override fun copy(): Polymer

copyTo

fun copyTo(dst: Molecule): MoleculeMaps

fun copyTo(dst: Polymer): PolymerMaps

copyWithMaps

open override fun copyWithMaps(): Pair<Polymer, MoleculeMaps>

Copies the molecule and returns a map between the copied atoms, where A is this molecule and B is the copy.

dfs

fun dfs(source: Atom, visitSource: Boolean = false, shouldVisit: (fromAtom: Atom, toAtom: Atom, dist: Int) -> Boolean = { _, _, _ -> true }): Iterable<Molecule.Searched>

Crawl the bond network in depth-first order starting at the source atom.

equals

open operator override fun equals(other: Any?): Boolean

findChainAndResidue

fun findChainAndResidue(atom: Atom): Pair<Polymer.Chain, Polymer.Residue>?

findChainOrThrow

fun findChainOrThrow(id: String): Polymer.Chain

findResidue

fun findResidue(atom: Atom): Polymer.Residue?

findResidueOrThrow

fun findResidueOrThrow(atom: Atom): Polymer.Residue

fun findResidueOrThrow(chainId: String, resId: String): Polymer.Residue

hashCode

open override fun hashCode(): Int

mapAtomsByNameTo

fun mapAtomsByNameTo(other: Molecule): AtomMap

Creates an atom map from this molecule to another molecule, assuming each atom name is unique. If the molecules are polymers, atom names need only be unique within a single residue.

mapAtomsByValueTo

fun mapAtomsByValueTo(other: Molecule): AtomMap

Creates an atom map from this molecule to another molecule, for only the atoms with identical values (ie, name, element, coordinates). Non-matching atoms will not be mapped.

toString