edu.duke.cs.osprey/edu.duke.cs.osprey.gui.compiler/CompiledConfSpace

CompiledConfSpace

class CompiledConfSpace(name: String, forcefields: List<CompiledConfSpace.ForcefieldInfo>, molInfos: List<CompiledConfSpace.MolInfo>, resInfos: List<CompiledConfSpace.ResInfo>, staticAtoms: List<CompiledConfSpace.AtomInfo>, staticEnergies: List<Double>, positions: List<CompiledConfSpace.PosInfo>, atomPairs: List<AtomPairs>)

Types

data class AtomInfo(name: String, pos: Vector3d, molIndex: Int, resIndex: Int)

data class ConfInfo(id: String, type: String, atoms: List<CompiledConfSpace.AtomInfo>, motions: List<CompiledConfSpace.MotionInfo>, fragIndex: Int, internalEnergies: List<Double>)

data class ForcefieldInfo(name: String, ospreyImplementation: String, settings: List<Pair<String, Any>>)

data class FragInfo(name: String, atomNames: List<String>)

data class MolInfo(name: String, type: String?)

sealed class MotionInfo

data class PosInfo(name: String, wildType: String, fragments: List<CompiledConfSpace.FragInfo>, confs: List<CompiledConfSpace.ConfInfo>)

data class ResInfo(chainId: String, id: String, type: String, indexInChain: Int)

Properties

val atomPairs: List<AtomPairs>

in the same order as the forcefields

val forcefields: List<CompiledConfSpace.ForcefieldInfo>

val molInfos: List<CompiledConfSpace.MolInfo>

val name: String

val positions: List<CompiledConfSpace.PosInfo>

val resInfos: List<CompiledConfSpace.ResInfo>

val staticAtoms: List<CompiledConfSpace.AtomInfo>

val staticEnergies: List<Double>

in the same order as the forcefields

Extensions

fun CompiledConfSpace.toBytes(): ByteArray

Compiled conf spaces are actually big enough that parsing the TOML file can run the JVM out of heap space! So, we need a more efficient format...