ConfSpace

fun addMutations(pos: DesignPosition, vararg mutations: String)

addPosition

fun addPosition(pos: DesignPosition): DesignPosition

addWildTypeConformation

fun addWildTypeConformation(pos: DesignPosition)

checkPosition

fun checkPosition(pos: DesignPosition)

containsPosition

fun containsPosition(pos: DesignPosition): Boolean

copy

fun copy(vararg mols: Molecule): ConfSpace

fun copy(selMols: List<Molecule> = mols.map { (_, mol) -> mol }): ConfSpace

Makes a copy of the selected molecules along with all their design positions into a new conformation space

countConformations

fun countConformations(): BigInteger

countSequences

fun countSequences(): BigInteger

findMol

fun findMol(name: String): Molecule?

fixedAtoms

fun fixedAtoms(mol: Molecule): List<Atom>

Get all the atoms that aren't part of design positions.

getConformations

fun getConformations(pos: DesignPosition, frag: ConfLib.Fragment): List<ConfSpace.ConfConfSpace>

fun getConformations(pos: DesignPosition, type: String): List<ConfSpace.ConfConfSpace>

getFragments

fun getFragments(pos: DesignPosition): List<ConfLib.Fragment>

fun getFragments(pos: DesignPosition, type: String): List<ConfLib.Fragment>

getMutations

fun getMutations(pos: DesignPosition): MutableSet<String>

libraryFragments

fun libraryFragments(): List<ConfLib.Fragment>

Collect all the unique library (ie non-wild-type) fragments used by the conf space.

positions

fun positions(): List<DesignPosition>

Collect all the positions for all the molecules in a stable order.

wildTypeFragments

fun wildTypeFragments(): List<ConfLib.Fragment>

Collect all the wild-type fragments from the conf space, whether used or not.

conflibs

val conflibs: ConfSpace.ConfLibs

designPositionsByMol

val designPositionsByMol: MutableMap<Molecule, MutableList<DesignPosition>>

molMotions

val molMotions: IdentityHashMap<Molecule, MutableList<MolMotion.Description>>

mols

val mols: List<Pair<MoleculeType, Molecule>>

name

var name: String

positionConfSpaces

val positionConfSpaces: ConfSpace.PositionConfSpaces

assign

fun ConfSpace.assign(assignments: List<PosAssignment>): Assignments

fun ConfSpace.assign(vararg assignments: PosAssignment): Assignments

forEachFragIn

inline fun ConfSpace.forEachFragIn(posInfo1: ConfSpaceIndex.PosInfo, posInfo2: ConfSpaceIndex.PosInfo, block: (Assignments, Assignments.AssignmentInfo, ConfSpaceIndex.ConfInfo, Assignments.AssignmentInfo, ConfSpaceIndex.ConfInfo) -> Unit)

toToml

fun ConfSpace.toToml(): String

ConfSpace

Types

Functions

Properties

Extensions