edu.duke.cs.osprey/edu.duke.cs.osprey.gui.forcefield.eef1/EEF1ForcefieldParams

EEF1ForcefieldParams

class EEF1ForcefieldParams : ForcefieldParams

Types

inner class AtomPairParams(vdwRadiusa: Double, lambdaa: Double, vdwRadiusb: Double, lambdab: Double, alpha1: Double, alpha2: Double) : ForcefieldParams.AtomPairParams

AtomPairsParams

inner class AtomPairsParams(molsParams: Map<Int, EEF1ForcefieldParams.AtomsParams>) : ForcefieldParams.AtomPairsParams

AtomParams

inner class AtomParams(type: EEF1.AtomType) : ForcefieldParams.AtomParams

AtomsParams

class AtomsParams : ForcefieldParams.AtomsParams

Companion

object Companion

Functions

combineAtomsParams

open override fun combineAtomsParams(info1: ForcefieldParams.AtomsInfo, info2: ForcefieldParams.AtomsInfo): ForcefieldParams.AtomsParams

Combines together atoms params from two variations of the same molecule. Useful for eg applying two mutations to the same molecule. If the two atoms parameters disagree on params for an atom, the tie should be broken by picking the atom params from the atoms params whose given atom indices contain the disagreeable atom's index. The two given sets of atom indices should not overlap. If a tie can't be broken with the preferred atom indices, the implementation should throw an exception.

parameterizeAtomPairs

open suspend override fun parameterizeAtomPairs(infos: List<ForcefieldParams.MolInfo>): EEF1ForcefieldParams.AtomPairsParams

Compute the forcefield parameters for a list of molecules.

parameterizeAtoms

open suspend override fun parameterizeAtoms(mol: Molecule, atomIndex: AtomIndex, netCharge: Int?): EEF1ForcefieldParams.AtomsParams

Compute the forcefield parameters for a molecule.

settings

open fun settings(): Map<String, Any>

Any settings needed by the Osprey runtime to calculate this forcefield.

Properties

forcefield

open override val forcefield: Forcefield.EEF1

scale

var scale: Double = 0.5

Scaling to apply to the solvent forcefield energy.

unconnectedDistance

open override val unconnectedDistance: Int = 4

What's the smallest bond distance where two atoms are treated the same as two totally unconnected atoms? eg. 1-4 bonds should use 4, 1-5 bonds should use 5