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

ConfSpaceIndex

class ConfSpaceIndex(confSpace: ConfSpace)

Establishes an authritative order for all the positions and conformations in the space. Ignores any design positions that have no position conformation space.

Constructors

ConfSpaceIndex

fun ConfSpaceIndex(confSpace: ConfSpace)

Types

AtomKey

interface AtomKey

ConfInfo

inner class ConfInfo(posInfo: ConfSpaceIndex.PosInfo, fragInfo: ConfSpaceIndex.FragInfo, confConfSpace: ConfSpace.ConfConfSpace, index: Int)

FragInfo

inner class FragInfo(posInfo: ConfSpaceIndex.PosInfo, frag: ConfLib.Fragment, index: Int)

PosInfo

inner class PosInfo(pos: DesignPosition, moli: Int, posConfSpace: ConfSpace.PositionConfSpace, index: Int)

PositionAtomKey

class PositionAtomKey(posi: Int, frag: ConfLib.Fragment?, atomi: Int) : ConfSpaceIndex.AtomKey

WildTypeAtomKey

data class WildTypeAtomKey(moli: Int, atomi: Int) : ConfSpaceIndex.AtomKey

Functions

atomIndexWildType

fun atomIndexWildType(moli: Int): AtomIndex

Get the atom index for the wild type atoms in the given molecule.

findMoli

fun findMoli(mol: Molecule): Int?

findMoliOrThrow

fun findMoliOrThrow(mol: Molecule): Int

findPosi

fun findPosi(pos: DesignPosition): Int?

getPosi

fun getPosi(pos: DesignPosition): Int

matchAtoms

fun matchAtoms(assignments: Assignments): List<AtomIndex>

Build an atom index for assigned molecules.

Properties

confSpace

val confSpace: ConfSpace

fixedAtoms

val fixedAtoms: List<List<Atom>>

Lists of fixed atoms, indexed by molecule index

mols

val mols: List<Molecule>

positions

val positions: List<ConfSpaceIndex.PosInfo>