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

Package edu.duke.cs.osprey.gui.prep

Types

Anchor

sealed class Anchor

Assignments

class Assignments(confSpace: ConfSpace, assignments: List<PosAssignment>)

Copies the molecules from the conformation space, and set the conformations at each specified design position.

AtomTree

class AtomTree(atoms: List<Atom>)

Builds a k-d tree that allows effecient nearest neighbor queries

BondGuesser

class BondGuesser(tolerance: Double, minDist: Double, elementProps: EnumMap<Element, BondGuesser.ElementProps>)

ConfSpace

class ConfSpace(mols: List<Pair<MoleculeType, Molecule>>)

ConfSpacePrep

class ConfSpacePrep(win: WindowCommands, confSpace: ConfSpace)

ConfSwitcher

class ConfSwitcher(pos: DesignPosition, molInfo: Assignments.MolInfo)

Sets conformations on a molecule at a design position.

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.

DuplicateAtoms

class DuplicateAtoms : List<DuplicateAtoms.AtomGroup>

Detects atom duplications in a molecule, and provides tools for removing one of the duplicated atoms.

ForcefieldAnalyzer

class ForcefieldAnalyzer(mols: List<Molecule>)

IllegalAlignmentException

class IllegalAlignmentException(msg: String) : IllegalArgumentException

MoleculePrep

class MoleculePrep(win: WindowCommands, mols: List<Molecule>)

NotAProteinException

class NotAProteinException(msg: String) : RuntimeException

PosAssignment

class PosAssignment(pos: DesignPosition, frag: ConfLib.Fragment, conf: ConfLib.Conf)

Proteins

object Proteins

Functions

assign

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

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

covalentRange

fun Atom.covalentRange(a2: Atom, guesser: BondGuesser = BondGuesser()): ClosedFloatingPointRange<Double>

guessBonds

fun Molecule.guessBonds(guesser: BondGuesser = BondGuesser(), searchDist: Double = 5.0): List<BondGuesser.Bond>

Attempts to guess where the bonds should be based on known elemental valences and covalent bond lengths.

inCovalentRange

fun Atom.inCovalentRange(a2: Atom, guesser: BondGuesser = BondGuesser()): Boolean

maxCovalentDist

fun Atom.maxCovalentDist(a2: Atom, guesser: BondGuesser = BondGuesser()): Double

minCovalentDist

fun Atom.minCovalentDist(guesser: BondGuesser = BondGuesser()): Double

toTree

fun List<Atom>.toTree(): AtomTree