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

Package edu.duke.cs.osprey.molscope.molecule

Types

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

class AtomMap : Bijection<Atom>

A bijection between two sets of atoms.

class AtomPair(a: Atom, b: Atom)

A pair of atoms that defines equality by atom identity (ie ===), and is insensitive to atom order.

interface ChainGenerator

Generates chains for non-polymer molecules when combining with polymers.

ChainIdGenerator

interface ChainIdGenerator

Creates unique chain ids to solve chain id conflicts when combining molecules into Polymers.

class ChainMap : Bijection<Polymer.Chain>

ContentAtomPair

class ContentAtomPair(a: Atom, b: Atom)

A pair of atoms that defines equality by atom equality (ie ==), and is insensitive to atom order.

enum Element : Enum<Element>

open class Molecule(name: String, type: String?, netCharge: Int?)

A collection of atoms (possibly) connected together by covalent bonds.

class MoleculeMap : Bijection<Molecule>

open class MoleculeMaps(mols: MoleculeMap, atoms: AtomMap)

MoleculeSelector

typealias MoleculeSelector = (Molecule) -> List<Atom>

A function that returns a subset of atoms in a molecule

MoleculeSelectors

object MoleculeSelectors

class Polymer(name: String) : Molecule

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

class PolymerMaps(maps: MoleculeMaps, chains: ChainMap, residues: ResidueMap) : MoleculeMaps

class ResidueMap : Bijection<Polymer.Residue>

Functions

fun Collection<Atom>.allPairs(other: Collection<Atom>): List<AtomPair>

fun Collection<Molecule>.combine(name: String, chainIdGenerator: ChainIdGenerator? = null, chainGenerator: ChainGenerator? = null): Pair<Molecule, AtomMap>

Combine multiple Molecules into a single Molecule (by making copies of the input molecules) and returns a map between the input atoms (A side) and the atoms in the combined molecule (B side).

fun MoleculeSelector.filter(mol: Molecule): Molecule

Applies the selector and returns a new molecule containing only the selected atoms. Polymer structure is preserved where possible

fun Iterable<Set<Atom>>.intersection(): MutableSet<Atom>

fun Set<Atom>.intersection(other: Set<Atom>): MutableSet<Atom>

fun Collection<Atom>.toIdentitySet(): MutableSet<Atom>

fun Iterable<Set<Atom>>.union(): MutableSet<Atom>

fun Set<Atom>.union(other: Set<Atom>): MutableSet<Atom>