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

DuplicateAtoms

class DuplicateAtoms : List<DuplicateAtoms.AtomGroup>

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

PDB files from the Protein Data Bank are usually very high quality files, but rarely a third-party tool will create a malformed PDB file with duplicated atoms. This tool can help correct those errors.

Constructors

DuplicateAtoms

fun DuplicateAtoms(mol: Molecule)

Types

AtomGroup

inner class AtomGroup(name: String, chain: Polymer.Chain?, res: Polymer.Residue?, atoms: List<Atom>)

Functions

contains

open operator override fun contains(element: DuplicateAtoms.AtomGroup): Boolean

containsAll

open override fun containsAll(elements: Collection<DuplicateAtoms.AtomGroup>): Boolean

forEach

open fun forEach(p0: Consumer<in DuplicateAtoms.AtomGroup>)

get

open operator override fun get(index: Int): DuplicateAtoms.AtomGroup

indexOf

open override fun indexOf(element: DuplicateAtoms.AtomGroup): Int

isEmpty

open override fun isEmpty(): Boolean

iterator

open operator override fun iterator(): Iterator<DuplicateAtoms.AtomGroup>

lastIndexOf

open override fun lastIndexOf(element: DuplicateAtoms.AtomGroup): Int

listIterator

open override fun listIterator(): ListIterator<DuplicateAtoms.AtomGroup>

open override fun listIterator(index: Int): ListIterator<DuplicateAtoms.AtomGroup>

parallelStream

open fun parallelStream(): Stream<DuplicateAtoms.AtomGroup>

spliterator

open override fun spliterator(): Spliterator<DuplicateAtoms.AtomGroup>

stream

open fun stream(): Stream<DuplicateAtoms.AtomGroup>

subList

open override fun subList(fromIndex: Int, toIndex: Int): List<DuplicateAtoms.AtomGroup>

toArray

~~open~~ ~~fun~~ <T : Any> ~~toArray~~(p0: IntFunction<Array<T>>): Array<T>

Properties

mol

val mol: Molecule

size

open override val size: Int