UMol Namespace Reference

Defines all the functions available from the console More...

Namespaces
namespace	API
namespace	Docking

Classes
class	AllSelection
class	AndOperation
class	AngleAnnotation
class	AnimateAnnotation
class	AnnotationComparer
class	ArcLineAnnotation
class	AroundSelection
class	ArrowAnnotation
class	ArtemisManager
class	ArtemisThreadedClient
class	ArtemisWrapper
class	AtomDuo
class	AtomIdSelection
class	AtomNameSelection
class	AtomRepresentation
class	AtomRepresentationOptihb
class	AtomRepresentationSphere
class	AtomTypeNameSelection
class	BackboneSelection
class	BondRepresentation
class	BondRepresentationHbonds
class	BondRepresentationLine
class	BondRepresentationOptihs
class	ByResSelection
class	CartoonRepresentation
struct	CGAtomITP
class	ChainNameSelection
class	ComputeUnityMolBonds
class	ControllerDrawLine
class	ControllerGrabAndScale
class	CustomRaycast
class	DistanceAnnotation
class	DistanceSelection
class	DNAPlane
class	DockingManager
class	DockingUI
class	DrawAnnotation
class	DSSP
class	DSSP_Bridge
class	DXReader
class	DXSurfaceRepresentation
class	FieldLinesComputation
class	FieldLinesReader
class	FieldLinesRepresentation
class	FieldLinesRepresentationManager
class	GrapplingHookMolecule
class	GROReader
	Creates a UnityMolStructure object from a local GRO file More...
class	HbondDetection
struct	IdDist
class	InputFieldEnter
class	InSphereSelection
class	IonsSelection
class	ISurfaceRepresentation
class	ITPReader
class	KDTree
class	LigandSelection
class	lightAtomComparer
class	LightResidueComparer
class	LineAtomAnnotation
class	LookAtCamera
class	ManipulationManager
class	MDAnalysisSelection
class	MDASelection
class	MetaClass
class	MinimizerManager
class	ModelsPlayer
class	MOL2Reader
	Creates a UnityMolStructure object from a local Mol2 file Format file described here http://chemyang.ccnu.edu.cn/ccb/server/AIMMS/mol2.pdf More...
class	MouseOverSelection
class	NeighborSearchWrapper
class	NothingSelection
class	NotSelection
class	NucleicBackboneSelection
class	NucleicBaseSelection
class	NucleicSelection
class	NucleicSugarSelection
class	ObservedList
class	Operation
class	OptimalView
class	OrOperation
struct	pairString
class	ParsingException
class	PDBReader
	Creates a UnityMolStructure object from a local or remote PDB file More...
class	PDBxReader
	Creates a Molecule object from a local or remote PDBx/mmCIF file file More...
class	PeptidePlane
class	PointerAtomSelection
class	PointerHoverAtom
class	PointerIMD
class	PointerMeasurements
class	PointerMoveUI
class	PrecomputedRepresentationManager
class	PropertySelection
class	ProteinSelection
class	QuickSelectionUI
class	RangeSelection
class	Reader
class	ReadSaveFilesWithBrowser
struct	RepType
class	ResidueNameSelection
class	RibbonMesh
class	RibbonMeshDNA
class	SDFReader
	Creates a UnityMolStructure object from a local SDF file More...
class	SecondaryStructureSelection
class	Segment
class	SelectionParser
class	SelectionSelection
class	SequenceViewerUI
class	SoundAnnotation
class	SphereAnnotation
class	StrideWrapper
class	StringSelection
class	StructureNameSelection
struct	SubRepresentation
class	SurfaceRepresentation
class	SwitchSelectionMode
class	testLoadPDBFiles
class	testMarchingCubes
class	TextAnnotation
class	TorsionAngleAnnotation
class	TrajectoryPlayer
class	UIManager
class	UnarySelection
class	UnityMolAnnotation
class	UnityMolAnnotationManager
class	UnityMolAtom
	Part of the SMCRA data structure, UnityMolAtom stores atom informations of the structure More...
class	UnityMolBondLineManager
class	UnityMolBonds
	Stores the bonds of the model as a dictionary of <UnityMolAtom, UnityMolAtom[]> More...
class	UnityMolCartoonManager
class	UnityMolChain
	Part of the SMCRA data structure, UnityMolChain stores the residues of the structure as a list of UnityMolResidue A reference to the model it belongs is provided More...
class	UnityMolDefaultColors
class	UnityMolGenericRepresentationManager
class	UnityMolHBallMeshManager
class	UnityMolHbondManager
class	UnityMolHighlightManager
class	UnityMolHStickMeshManager
class	UnityMolMain
class	UnityMolModel
	Part of the SMCRA data structure, UnityMolModel stores the chains of the structure as a dictionary <string,UnityMolChain>. It also stores the bonds as UnityMolBonds A list of UnityMolAtom of the model is provided to loop over all atoms quickly More...
class	UnityMolRepresentation
class	UnityMolRepresentationManager
class	UnityMolResidue
	Part of the SMCRA data structure, UnityMolResidue stores the atoms of the structure as a dictionary <string,UnityMolAtom> More...
class	UnityMolSelection
class	UnityMolSelectionManager
class	UnityMolSphereManager
class	UnityMolStructure
	Part of the SMCRA data structure, UnityMolStructure stores the models of the structure More...
class	UnityMolStructureManager
class	UnityMolSurfaceManager
class	UnityMolTopologyDef
class	WaterSelection
class	WrapperCudaSES
class	XDRFileReader
class	XYZReader
	Creates a UnityMolStructure object from a local XYZ file Records several molecules in different models More...

Enumerations
enum	XDRFileReaderStatus {   XDRFileReaderStatus.TRAJECTORYPRESENT = -5, XDRFileReaderStatus.FRAMEDOESNOTEXIST = -4, XDRFileReaderStatus.ENDOFFILE = -3, XDRFileReaderStatus.NUMBEROFATOMSMISMATCH = -2,   XDRFileReaderStatus.FILENOTFOUND = -1, XDRFileReaderStatus.SUCCESS = 0 }
enum	AtomType {   AtomType.sphere = 1, AtomType.optihb = 4, AtomType.cartoon = 5, AtomType.surface = 6,   AtomType.DXSurface = 7, AtomType.FieldLines = 8, AtomType.noatom = -1 }
enum	BondType { BondType.line = 1, BondType.optihs = 4, BondType.hbond = 5, BondType.nobond = -1 }
enum	FFType { FFType.atomic = 0, FFType.HiRERNA = 1 }
enum	SurfMethod { SurfMethod.EDTSurf = 0, SurfMethod.MSMS = 1, SurfMethod.QUICKSES = 2 }

Detailed Description

Defines all the functions available from the console

Only reads ITP files and add them to a dictionary, does NOT create a UnityMolStructure

Grab a molecule (trigger button) or a group of molecules (grip button) Scale using both controllers on the same molecule

Enumeration Type Documentation

AtomType

enum UMol.AtomType

strong

Enumerator
sphere
optihb
cartoon
surface
DXSurface
FieldLines
noatom

BondType

enum UMol.BondType

strong

Enumerator
line
optihs
hbond
nobond

FFType

enum UMol.FFType

strong

Enumerator
atomic
HiRERNA

SurfMethod

enum UMol.SurfMethod

strong

Enumerator
EDTSurf
MSMS
QUICKSES

XDRFileReaderStatus

enum UMol.XDRFileReaderStatus

strong

Enumerator
TRAJECTORYPRESENT
FRAMEDOESNOTEXIST
ENDOFFILE
NUMBEROFATOMSMISMATCH
FILENOTFOUND
SUCCESS