edu.duke.cs.osprey/edu.duke.cs.osprey.gui.io

Package edu.duke.cs.osprey.gui.io

Types

Link copied to clipboard
class ChainGeneratorBondedGroup(idGenerator: ChainIdGenerator) : ChainGenerator
Content copied to clipboard

Generates a chain with one residue for each group of bonded atoms in the molecule. Useful for small molecules and solvents, as long as we have bonds.

Link copied to clipboard
class ChainGeneratorByMolType(idGenerator: ChainIdGenerator) : ChainGenerator
Content copied to clipboard
Link copied to clipboard
class ChainGeneratorSingleResidue(idGenerator: ChainIdGenerator) : ChainGenerator
Content copied to clipboard

Generates single-residue chains for non-polymer molecules. Useful for small molecules.

Link copied to clipboard
open class ChainIdGeneratorAZ : ChainIdGenerator
Content copied to clipboard

Generates chain ids in the range A-Z.

Link copied to clipboard
class ConfLib(id: String, name: String, fragments: Map<String, ConfLib.Fragment>, description: String?, citation: String?)
Content copied to clipboard

Conformation Library

Link copied to clipboard
data class FragmentsTOML(toml: String, idsByFrag: Map<ConfLib.Fragment, String>)
Content copied to clipboard
Link copied to clipboard
class LaunchLimits(maxInFlight: Int)
Content copied to clipboard
Link copied to clipboard
class Mol2Metadata
Content copied to clipboard
Link copied to clipboard
class Mol2ParseException(line: String, msg: String) : RuntimeException
Content copied to clipboard
Link copied to clipboard
data class OMOLMapped(toml: String, indicesByAtom: Map<Atom, Int>)
Content copied to clipboard
Link copied to clipboard
object OspreyService
Content copied to clipboard
Link copied to clipboard
class ProcessStreamer(processBuilder: ProcessBuilder)
Content copied to clipboard

Reads stdout and stderr from a process and sends the lines back in a ConcurrentLinkedQueue instance.

Link copied to clipboard
class TomlParseException(msg: String, pos: TomlPosition?) : RuntimeException
Content copied to clipboard
Link copied to clipboard
object UserSettings
Content copied to clipboard

Functions

Link copied to clipboard
fun Collection<Molecule>.combineForPDB(name: String): Pair<Molecule, AtomMap>
Content copied to clipboard

A wrapper for Molecule.combine() that tries to intelligently generate polymer chains for non-polymer molecules to satisfy the limitations of the PDB file format.

Link copied to clipboard
fun Molecule.Companion.fromMol2(mol2: String, isPolymer: Boolean? = null): Molecule
Content copied to clipboard

Read a molecule in MOL2 format.

Link copied to clipboard
fun Molecule.Companion.fromMol2WithMetadata(mol2: String, isPolymer: Boolean? = null): Pair<Molecule, Mol2Metadata>
Content copied to clipboard
Link copied to clipboard
fun Molecule.Companion.fromOMOL(toml: String, throwOnMissingAtoms: Boolean = DefaultThrowOnMissingAtoms): List<Molecule>
Content copied to clipboard

Read molecules from the OMOL (OSPREY molecule) format.

fun Molecule.Companion.fromOMOL(doc: TomlParseResult, throwOnMissingAtoms: Boolean = DefaultThrowOnMissingAtoms): List<Molecule>
Content copied to clipboard
Link copied to clipboard
fun Molecule.Companion.fromOMOLWithAtoms(doc: TomlParseResult, throwOnMissingAtoms: Boolean = DefaultThrowOnMissingAtoms): List<Pair<Molecule, Map<Int, Atom>>>
Content copied to clipboard
Link copied to clipboard
fun Molecule.Companion.fromPDB(pdb: String): Molecule
Content copied to clipboard

Read a molecule in PDB format.

Link copied to clipboard
fun ConfSpace.Companion.fromToml(toml: String): ConfSpace
Content copied to clipboard
Link copied to clipboard
fun TomlTable.getArrayOrThrow(key: String, pos: TomlPosition? = null): TomlArray
Content copied to clipboard
Link copied to clipboard
fun TomlTable.getBooleanOrThrow(key: String, pos: TomlPosition? = null): Boolean
Content copied to clipboard
Link copied to clipboard
fun TomlTable.getDoubleOrThrow(key: String, pos: TomlPosition? = null): Double
Content copied to clipboard
Link copied to clipboard
fun TomlArray.getInt(index: Int): Int
Content copied to clipboard
fun TomlTable.getInt(key: String): Int?
Content copied to clipboard
Link copied to clipboard
fun TomlTable.getIntOrThrow(key: String, pos: TomlPosition? = null): Int
Content copied to clipboard
Link copied to clipboard
fun TomlTable.getStringOrThrow(key: String, pos: TomlPosition? = null): String
Content copied to clipboard
Link copied to clipboard
fun TomlTable.getTableOrThrow(key: String, pos: TomlPosition? = null): TomlTable
Content copied to clipboard
Link copied to clipboard
fun Path.read(): String
Content copied to clipboard
Link copied to clipboard
fun Path.readBytes(): ByteArray
Content copied to clipboard
Link copied to clipboard
fun ProcessBuilder.stream(): ProcessStreamer
Content copied to clipboard
Link copied to clipboard
inline fun <R> tempFolder(name: String, block: (Path) -> R): R
Content copied to clipboard
Link copied to clipboard
fun CompiledConfSpace.toBytes(): ByteArray
Content copied to clipboard

Compiled conf spaces are actually big enough that parsing the TOML file can run the JVM out of heap space! So, we need a more efficient format...

Link copied to clipboard
fun Molecule.toMol2(metadata: Mol2Metadata? = null): String
Content copied to clipboard

Save the molecule to the Mol2 format.

Link copied to clipboard
fun <ERROR CLASS>.toMolecule(name: String? = null): Molecule
Content copied to clipboard

Convert an OSPREY molecule to a Molscope molecule.

Link copied to clipboard
fun Molecule.toOMOL(): String
Content copied to clipboard

fun List<Molecule>.toOMOL(): String
Content copied to clipboard

Save the molecules to the OMOL (OSPREY molecule) format.

Link copied to clipboard
fun List<Molecule>.toOMOLMapped(flattenAtomIndices: Boolean = false): OMOLMapped
Content copied to clipboard
Link copied to clipboard
fun Molecule.toOspreyMol(throwOnNonChainPolymerAtoms: Boolean = false, translateSSasCYX: Boolean = false, translateHIStoEDP: Boolean = false): <ERROR CLASS>
Content copied to clipboard

Convert a Molscope molecule to an OSPREY molecule.

Link copied to clipboard
fun Molecule.toPDB(throwOnNonChainPolymerAtoms: Boolean = false, translateSSasCYX: Boolean = false, comment: String? = null, energy: Double? = null, includeTer: Boolean = false, includeSSBondConect: Boolean = false, translateHIStoEDP: Boolean = false): String
Content copied to clipboard

Save the molecule to PDB format.

Link copied to clipboard
fun ConfSpace.toToml(): String
Content copied to clipboard
fun ConfLib.toToml(table: String? = null): String
Content copied to clipboard

fun List<ConfLib.Fragment>.toToml(resolveIdCollisions: Boolean = false, table: String? = null): FragmentsTOML
Content copied to clipboard

Writes out a list of fragments to TOML

Link copied to clipboard
fun String.toTomlKey(): String
Content copied to clipboard

see: https://github.com/toml-lang/toml#keys

Link copied to clipboard
fun Point3d.toVector3d(): Vector3d
Content copied to clipboard
Link copied to clipboard
fun ByteArray.write(path: Path)
Content copied to clipboard
fun String.write(path: Path)
Content copied to clipboard

Properties

Link copied to clipboard
val Path.exists: Boolean
Content copied to clipboard