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 fun copy(): Molecule

copyTo

fun copyTo(dst: Molecule): MoleculeMaps

copyWithMaps

open fun copyWithMaps(): Pair<Molecule, 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

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

open override fun toString(): String

Properties

atoms

val atoms: Molecule.Atoms

bonds

val bonds: Molecule.Bonds

name

var name: String

A human-readable description for the molecule.

netCharge

var netCharge: Int? = null

a formal net charge for the molecule, used by some forcefields to parameterize small molecules

type

var type: String? = null

A machine-readable descrition for the molecule, often 3 characters long.

Inheritors

Polymer

Extensions

calcModsAmber

suspend fun Molecule.calcModsAmber(types: AmberTypes, atomIndex: AtomIndex): String?

calcTypesAmber

suspend fun Molecule.calcTypesAmber(molType: MoleculeType, atomIndex: AtomIndex, ffname: ForcefieldName = molType.defaultForcefieldNameOrThrow, generateCharges: AmberChargeGeneration? = null): AmberTypes

Calculate Amber types for atoms and bonds. Pass values to chargeMethod and netCharge to calculate partial charges for small molecules as well.

deprotonate

fun Molecule.deprotonate(atom: Atom)

Removes all bonded hydrogen atoms from the atom.

fun Molecule.deprotonate()

Removes all hydrogen atoms from the molecule.

findProtonation

fun Molecule.findProtonation(atom: Atom, numH: Int, hybridization: Hybridization): Protonation?

findTypeOrThrow

fun Molecule.findTypeOrThrow(): MoleculeType

Returns the type of the molecule based on AMBER rules for residue classification, or throws an exception.

findTypes

fun Molecule.findTypes(): Set<MoleculeType>

Returns the types of the molecules in the Molecule instance based on AMBER rules for residue classification.

guessBonds

fun Molecule.guessBonds(guesser: BondGuesser = BondGuesser(), searchDist: Double = 5.0): List<BondGuesser.Bond>

Attempts to guess where the bonds should be based on known elemental valences and covalent bond lengths.

inferBondsAmber

suspend fun Molecule.inferBondsAmber(): List<AtomPair>

Uses Amber forcefields to infer atom connectivity, but not bond order.

inferBondsAmberBlocking

fun Molecule.inferBondsAmberBlocking(): List<AtomPair>

inferMissingAtomsAmber

suspend fun Molecule.inferMissingAtomsAmber(): List<MissingAtom>

Uses Amber forcefields to infer missing heavy atoms and their positions.

inferMissingAtomsAmberBlocking

fun Molecule.inferMissingAtomsAmberBlocking(): List<MissingAtom>

inferProtonation

suspend fun Molecule.inferProtonation(): List<ProtonatedAtom>

Returns a list of heavy-hydrogen atom pairs based on inferred forcefield atom and bond types.

inferProtonationBlocking

fun Molecule.inferProtonationBlocking(): List<ProtonatedAtom>

mapTo

fun Molecule.mapTo(dst: Molecule): MoleculeMapper

partition

fun Molecule.partition(combineSolvent: Boolean = true): List<Pair<MoleculeType, Molecule>>

partitionAndAtomMap

fun Molecule.partitionAndAtomMap(combineSolvent: Boolean = true): Pair<List<Pair<MoleculeType, Molecule>>, AtomMap>

Partition a single Molecule into a list of Molecules based on AMBER rules for residue classification.

protonate

suspend fun Molecule.protonate(atom: Atom, protonation: Protonation)

Adds hydrogens atoms to the atom in the supplied protonation state.

protonateBlocking

fun Molecule.protonateBlocking(atom: Atom, protonation: Protonation)

protonations

fun Molecule.protonations(atom: Atom): List<Protonation>

Get all the supported protonation states for the specified atom.

show

fun Molecule.show(focusAtom: Atom? = null, wait: Boolean = false)

toMol2

fun Molecule.toMol2(metadata: Mol2Metadata? = null): String

Save the molecule to the Mol2 format.

toOMOL

fun Molecule.toOMOL(): String

toOspreyMol

fun Molecule.toOspreyMol(throwOnNonChainPolymerAtoms: Boolean = false, translateSSasCYX: Boolean = false, translateHIStoEDP: Boolean = false): <ERROR CLASS>

Convert a Molscope molecule to an OSPREY molecule.

toPDB

fun Molecule.toPDB(throwOnNonChainPolymerAtoms: Boolean = false, translateSSasCYX: Boolean = false, comment: String? = null, energy: Double? = null, includeTer: Boolean = false, includeSSBondConect: Boolean = false, translateHIStoEDP: Boolean = false): String

Save the molecule to PDB format.