edu.duke.cs.osprey/edu.duke.cs.osprey.gui.prep/DesignPosition

DesignPosition

class DesignPosition(name: String, type: String, mol: Molecule)

A position in a molecule that allows removing the existing atoms and aligning and attaching other conformations via an anchor atom system.

Constructors

fun DesignPosition(name: String, type: String, mol: Molecule)

Types

data class AnchorMatch(posAnchors: List<Anchor>, fragAnchors: List<ConfLib.Anchor>)

IllegalAnchorsException

class IllegalAnchorsException(msg: String, pos: DesignPosition) : IllegalStateException

IncompatibleAnchorsException

class IncompatibleAnchorsException(pos: DesignPosition, frag: ConfLib.Fragment) : RuntimeException

Functions

fun anchorDouble(a: Atom, b: Atom, c: Atom, d: Atom): Anchor.Double

fun anchorSingle(a: Atom, b: Atom, c: Atom): Anchor.Single

compatibleFragments

fun compatibleFragments(conflib: ConfLib): List<ConfLib.Fragment>

findAnchorMatch

fun findAnchorMatch(frag: ConfLib.Fragment): DesignPosition.AnchorMatch?

getCurrentAnchorGroups

fun getCurrentAnchorGroups(): List<MutableList<Anchor>>

Looks at the current atoms and the bonding pattern to see which anchor group is currently in use.

isFragmentCompatible

fun isFragmentCompatible(frag: ConfLib.Fragment): Boolean

Returns true iff all the fragment's anchors are compatible with this design position.

fun makeFragment(fragId: String, fragName: String, confId: String = fragId, confName: String = fragName, motions: List<ConfLib.ContinuousMotion> = emptyList()): ConfLib.Fragment

Makes a fragment from the source atoms and coords.

Properties

val anchorGroups: MutableList<MutableList<Anchor>>

Anchor atoms are used to bond and align conformations to the molecule.

val mol: Molecule

var name: String

val sourceAtoms: MutableSet<Atom>

The atoms that will be replaced or re-located by the next conformation. Needs to be initialized when creating a new design position.

var type: String