class AmberTopology(pointers: List<Int>, atomNames: List<String>, atomicNumbers: List<Int>, residuePointers: List<Int>, residueLabels: List<String>, bondsIncHydrogen: List<Int>, bondsWithoutHydrogen: List<Int>, dihedralsIncHydrogen: List<Int>, dihedralsWithoutHydrogen: List<Int>, charges: List<Double>, atomTypeIndices: List<Int>, nonbondedParmIndices: List<Int>, esScaleFactors: List<Double>, vdwScaleFactors: List<Double>, lennardJonesACoeff: List<Double>, lennardJonesBCoeff: List<Double>, atomTypes: List<String>)

A representation of the parts of the AMBER topology file format that we care about in OSPREY.

AmberTypes

data class AmberTypes(ffname: ForcefieldName, atomTypes: Map<Int, String>, bondTypes: Map<IntPair, String>, atomCharges: Map<Int, String>)

Architecture

enum Architecture : Enum<Architecture>

CrdIO

object CrdIO

ForcefieldName

data class ForcefieldName(name: String, atomTypes: AmberAtomTypes?)

Hybridization

enum Hybridization : Enum<Hybridization>

MappingException

class MappingException(msg: String) : RuntimeException

MinimizerInfo

class MinimizerInfo(mol: Molecule, restrainedAtoms: List<Atom>)

MissingAtom

data class MissingAtom(mol: Molecule, chain: Polymer.Chain?, res: Polymer.Residue?, atom: Atom)

MoleculeMapper

class MoleculeMapper(src: Molecule, dst: Molecule)

Maps from a Antechamber/LEaP-generated mol2 molecule to a Molscope molecule.

MoleculeType

enum MoleculeType : Enum<MoleculeType>

OperatingSystem

enum OperatingSystem : Enum<OperatingSystem>

ParseException

class ParseException(msg: String) : RuntimeException

Platform

class Platform(os: OperatingSystem, arch: Architecture)

ProtonatedAtom

data class ProtonatedAtom(mol: Molecule, chain: Polymer.Chain?, res: Polymer.Residue?, heavy: Atom, light: Atom)

Protonation

data class Protonation(element: Element, numHeavy: Int, numH: Int, hybridization: Hybridization)

TopIO

object TopIO

Functions

calcModsAmber

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

calcParamsAmber

suspend fun AmberMolParams.calcParamsAmber(): AmberParams

suspend fun List<AmberMolParams>.calcParamsAmber(): AmberParams

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()

Removes all hydrogen atoms from the molecule.

fun Molecule.deprotonate(atom: Atom)

Removes all bonded hydrogen atoms from the atom.

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.

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

minimize

suspend fun List<MinimizerInfo>.minimize(numSteps: Int)

Minimize the selected molecules with molecule-associated information using sander from AmberTools

minimizeBlocking

fun List<MinimizerInfo>.minimizeBlocking(numSteps: Int)

partition

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

fun Collection<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.

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

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.