Inheritance diagram for UMol.API.APIPython:

Public Member Functions
IEnumerator	waitOf ()

void	setPosScaleRot (Vector3 pos, Vector3 scale, Vector3 rot, Vector3 centerOfRotation)

Static Public Member Functions
static void	ExecuteCommand (string command)
	Allow to call python API commands and record them in the history from C# More...

static UnityMolStructure	load (string filePath, bool readHetm=true)
	Load a local molecular file (pdb/mmcif/gro/mol2/sdf/xyz formats) More...

static UnityMolStructure	fetch (string PDBId, bool usemmCIF=true, bool readHetm=true)
	Fetch a remote molecular file (pdb or mmcif zipped) This function calls showDefault() and centerOnStructure() More...

static void	showHideHydrogensInSelection (string selName, bool? shouldShow=null)
	Show/Hide hydrogens in representations of the provided selection This only works for lines, hyperball and sphere representations More...

static void	showHideSideChainsInSelection (string selName)
	Show/Hide side chains in representations of the current selection This only works for lines, hyperball and sphere representations only More...

static void	showHideBackboneInSelection (string selName)
	Show/Hide backbone in representations of the current selection This only works for lines, hyperball and sphere representations only More...

static void	setModel (string structureName, int modelId)
	Set the current model of the structure This function is used by ModelPlayers.cs to read the models of a structure like a trajectory More...

static void	loadTraj (string structureName, string path)
	Load a trajectory for a loaded structure It creates a XDRFileReader in the corresponding UnityMolStructure and a TrajectoryPlayer More...

static void	unloadTraj (string structureName)
	Unload a trajectory for a specific structure More...

static void	loadDXmap (string structureName, string path)
	Load a density map for a specific structure This function creates a DXReader instance in the UnityMolStructure More...

static void	unloadDXmap (string structureName)
	Unload the density map for the structure More...

static void	readJSONFieldlines (string structureName, string path)
	Read a json file and display fieldLines for the specified structure More...

static void	unloadJSONFieldlines (string structureName)
	Remove the json file for fieldlines stored in the currentModel of the specified structure More...

static int	getStructureGroup (string structureName)
	Utility function to be able to get the group of the structure This group is used to be able to move all the loaded molecules in the same group Groups can be between 0 and 9 included More...

static HashSet< UnityMolStructure >	getStructuresOfGroup (int group)
	Utility function to be able to get the structures of the group This group is used to be able to move all the loaded molecules in the same group Groups can be between 0 and 9 included More...

static void	setStructureGroup (string structureName, int newGroup)
	Utility function to be set the group of a structure This group is used to be able to move all the loaded molecules in the same group Groups can be between 0 and 9 included More...

static void	delete (string structureName)
	Delete a molecule and all its UnityMolSelection and UnityMolRepresentation More...

static void	show (string type)
	Show as 'type' all loaded molecules type can be "cartoon", "c", "surface", "s", "hb", "line", "l", "hbond" More...

static void	showDefault (string selName)
	Create default representations (cartoon for protein + HB for not protein atoms) More...

static void	waitOneFrame ()

static void	showStructureAllRepresentations (string structureName)
	Unhide all representations already created for a specified structure More...

static void	showSelection (string selName, string type, params object[] args)
	Show the selection as 'type' type can be "cartoon", "c", "surface", "s", "hb", "line", "l", "hbond" If the representation is already there, update it if the selection content changed and show it More...

static void	hideSelection (string selName)
	Hide every representations of the specified selection More...

static void	hideSelection (string selName, string type)
	Hide every representation of type 'type' of the specified selection type can be "cartoon", "c", "surface", "s", "hb", "line", "l", "hbond" More...

static void	deleteRepresentationInSelection (string selName, string type)
	Delete every representations of type 'type' of the specified selection type can be "cartoon", "c", "surface", "s", "hb", "line", "l", "hbond" More...

static void	deleteRepresentationsInSelection (string selName)
	Delete every representations of the specified selection More...

static void	hideStructureAllRepresentations (string structureName)
	Hide every representations of the specified structure More...

static bool	areRepresentationsOn (string structureName)
	Utility function to test if a representation is shown for a specified structure More...

static bool	areRepresentationsOn (string selName, string type)
	Utility function to test if a representation of type 'type' is shown for a specified selection type can be "cartoon", "c", "surface", "s", "hb", "line", "l", "hbond" More...

static void	hide (string type)
	Hide all representations of type 'type' type can be "cartoon", "c", "surface", "s", "hb", "line", "l", "hbond" More...

static void	switchSurfaceComputeMethod (string selName)
	Switch between the 2 types of surface computation methods: EDTSurf and MSMS More...

static void	switchCutSurface (string selName, bool isCut)
	Switch between cut surface mode and no-cut surface mode More...

static void	setSolidSurface (string selName)
	Switch all surface representation in selection to a solid surface material More...

static void	setWireframeSurface (string selName)
	Switch all surface representation in selection to a wireframe surface material when available More...

static void	setTransparentSurface (string selName, float alpha=0.8f)
	Switch all surface representation in selection to a transparent surface material More...

static void	setSmoothness (string selName, string type, float val)
	Change hyperball representation parameters in the specified selection to a preset Metaphores can be "Smooth", "Balls&Sticks", "VdW", "Licorice" type can be "cartoon", "c", "surface", "s", "hb", "line", "l", "hbond" More...

static void	setMetal (string selName, string type, float val)
	Change hyperball representation parameters in the specified selection to a preset Metaphores can be "Smooth", "Balls&Sticks", "VdW", "Licorice" type can be "cartoon", "c", "surface", "s", "hb", "line", "l", "hbond" More...

static void	setHyperBallMetaphore (string selName, string metaphore)
	Change hyperball representation parameters in the specified selection to a preset Metaphores can be "Smooth", "Balls&Sticks", "VdW", "Licorice" More...

static void	setHyperBallShininess (string selName, float shin)
	Set shininess for the hyperball representations of the specified selection More...

static void	setHyperballShrink (string selName, float shrink)
	Set the shrink factor for the hyperball representations of the specified selection More...

static void	setHyperballTexture (string selName, int idTex)
	Change all hyperball representation in the selection with a new texture mapped idTex of the texture is the index in UnityMolMain.atomColors.textures More...

static void	setCartoonColorSS (string selName, string ssType, Color col)
	Set the color of the cartoon representation of the specified selection based on the nature of secondary structure assigned ssType can be "helix", "sheet" or "coil" More...

static void	setRepSize (string selName, string type, float size)
	Change the size of the representation of type 'type' in the selection Mainly used for hyperball representation type can be "cartoon", "c", "surface", "s", "hb", "line", "l", "hbond" More...

static void	colorSelection (string selName, string type, Color col)
	Change the color of all representation of type 'type' in selection type can be "cartoon", "c", "surface", "s", "hb", "line", "l", "hbond" More...

static void	colorSelection (string selName, string type, string colorS)
	Change the color of all representation of type 'type' in selection colorS can be "black", "white", "yellow", "green", "red", "blue", "pink", "gray" type can be "cartoon", "c", "surface", "s", "hb", "line", "l", "hbond" More...

static void	resetColorSelection (string selName, string type)
	Reset the color of all representation of type 'type' in selection to the default value type can be "cartoon", "c", "surface", "s", "hb", "line", "l", "hbond" More...

static void	colorByChain (string selName, string type)
	Use the color palette to color representations of type 'type' in the selection 'selName' by chain type can be "cartoon", "c", "surface", "s", "hb", "line", "l", "hbond" More...

static void	colorByResidue (string selName, string type)
	Use the color palette to color representations of type 'type' in the selection 'selName' by residue type can be "cartoon", "c", "surface", "s", "hb", "line", "l", "hbond" More...

static void	colorByAtom (string selName, string type)
	Color representations of type 'type' in the selection 'selName' by atom More...

static void	colorByCharge (string selName, bool normalizeDensity=false, float minDens=-10.0f, float maxDens=10.0f)
	Use the dx map to color by charge around atoms Only works for surface for now If normalizeDensity is set to true, the density values will be normalized if it is set to true, the default -10\|10 range is used More...

static void	setLineSize (string selName, float val)

static void	centerOnStructure (string structureName, bool lerp=false)
	Offsets all representations to center the structure 'structureName' Instead of moving the camera, move the loaded molecules to center them on the center of the camera More...

static ManipulationManager	getManipulationManager ()

static void	centerOnSelection (string selName, bool lerp=false)
	Offsets all representations to center the selection 'selName' More...

static UnityMolSelection	select (string selMDA, string name="selection", bool createSelection=true, bool addToExisting=false, bool silent=false, bool setAsCurrentSelection=true, bool forceCreate=false)
	Create a UnityMolSelection based on MDAnalysis selection language (https://www.mdanalysis.org/docs/documentation_pages/selections.html) Returns a UnityMolSelection object, adding it to the selection manager if createSelection is true If a selection with the same name already exists and addToExisting is true, add atoms to the already existing selection Set forceCreate to true if the selection is empty but still need to generate the selection More...

static void	addSelectionKeyword (string keyword, string selName)
	Add a keyword to the selection language More...

static void	removeSelectionKeyword (string keyword)
	Remove a keyword from the selection language More...

static void	setCurrentSelection (string selName)
	Set the selection as currentSelection in the UnityMolSelectionManager More...

static void	addToSelection (string selMDA, string name="selection", bool silent=false)
	Look for an existing selection named 'name' and add atoms to it based on MDAnalysis selection language More...

static void	removeFromSelection (string selMDA, string name="selection", bool silent=false)
	Look for an existing selection named 'name' and remove atoms from it based on MDAnalysis selection language More...

static void	deleteSelection (string selName)
	Delete selection 'selName' and all its representations More...

static string	duplicateSelection (string selName)
	Duplicate selection 'selName' and without the representations More...

static bool	renameSelection (string oldSelName, string newSelName)
	Change the 'oldSelName' selection name into 'newSelName' More...

static bool	updateSelectionWithMDA (string selName, string selectionString, bool forceAlteration, bool silent=false)
	Update the atoms of the selection based on a new MDAnalysis language selection The selection only applies to the structures of the selection More...

static UnityMolSelection	selectInSphere (Vector3 position, float radius)
	Select atoms of all loaded molecules inside a sphere defined by a world space position and a radius in Anstrom More...

static void	updateRepresentations (string selName)
	Update representations of the specified selection More...

static void	clearSelections ()
	Clear the currentSelection in UnityMolSelectionManager More...

static bool	isATrajectoryPlaying ()
	Utility function to test if a trajectory is playing for any loaded molecule More...

static void	changeHighlightMaterial (Material newMat)
	Utility function to change the material of highlighted selection More...

static void	screenshot (string path, int resolutionWidth=1280, int resolutionHeight=720, bool transparentBG=false)
	Take a screenshot of the current viewpoint with a specific resolution More...

static void	startVideo (string filePath, int resolutionWidth=1280, int resolutionHeight=720, int frameRate=30)
	Start to record a video with FFMPEG at a specific resolution and framerate More...

static void	stopVideo ()
	Stop recording More...

static void	undo ()
	Play the opposite function of the lastly called APIPython function recorded in UnityMolMain.pythonUndoCommands More...

static void	saveHistoryScript (string path)
	Save the history of commands executed in a file More...

static void	setRotationCenter (Vector3 newPos)

static void	loadHistoryScript (string path)
	Load a python script of commands (possibly the output of the saveHistoryScript function) More...

static void	setMolParentTransform (Vector3 pos, Vector3 scale, Vector3 rot, Vector3 centerOfRotation)
	Set the position, scale and rotation of the parent of all loaded molecules Linear interpolation between the current state of the camera to the specified values More...

static void	changeGeneralScale (float newVal)
	Change the scale of the parent of the representations of each molecules Try to not move the center of mass More...

static void	addHydrogensReduce (string structureName)
	Use Reduce method to add hydrogens More...

static void	addHydrogensHaad (string structureName)
	Use HAAD method to add hydrogens More...

static void	setAsLigand (string selName, bool isLig=true, bool updateAllSelections=true)
	Set the atoms of the selection named 'selName' to ligand More...

static void	connectIMD (string structureName, string adress, int port)
	Connect to a running simulation using the IMD protocol implemented in Artemis The running simulation is binded to a UnityMolStructure More...

static void	disconnectIMD (string structureName)
	Disconnect from the IMD simulation for the specified structure More...

static string	getSurfaceType (string selName)

static string	getHyperBallMetaphore (string selName)

static void	setCameraNearPlane (float newV)

static void	setCameraFarPlane (float newV)

static List< string >	ls ()
	Print the content of the current directory More...

static void	cd (string newPath)
	Change the current directory More...

static void	pwd ()
	Print the current directory More...

static UnityMolStructure	last ()
	Return the lastly loaded UnityMolStructure More...

static void	bg_color (string colorS)
	Change the background color of the camera More...

static void	switchRotateAxisX ()
	Switch on or off the rotation around the X axis of all loaded molecules More...

static void	switchRotateAxisY ()
	Switch on or off the rotation around the Y axis of all loaded molecules More...

static void	switchRotateAxisZ ()
	Switch on or off the rotation around the Z axis of all loaded molecules More...

static void	changeRotationSpeedX (float val)
	Change the rotation speed around the X axis More...

static void	changeRotationSpeedY (float val)
	Change the rotation speed around the Y axis More...

static void	changeRotationSpeedZ (float val)
	Change the rotation speed around the Z axis More...

static void	setMouseScrollSpeed (float val)
	Change the mouse scroll speed More...

static void	setMouseMoveSpeed (float val)
	Change the speed of mouse rotations and translations More...

static void	stopRotations ()
	Stop rotation around all axis More...

static RepType	getRepType (string type)
	Transform a string of representation type to a RepType object More...

static string	getTypeFromRepType (RepType rept)
	Transform a representation type into a string More...

static void	annotateAtom (string structureName, int atomId)

static void	removeAnnotationAtom (string structureName, int atomId)

static void	annotateAtomText (string structureName, int atomId, string text)

static void	removeAnnotationAtomText (string structureName, int atomId, string text)

static void	annotateLine (string structureName, int atomId, string structureName2, int atomId2)

static void	removeAnnotationLine (string structureName, int atomId, string structureName2, int atomId2)

static void	annotateDistance (string structureName, int atomId, string structureName2, int atomId2)

static void	removeAnnotationDistance (string structureName, int atomId, string structureName2, int atomId2)

static void	annotateAngle (string structureName, int atomId, string structureName2, int atomId2, string structureName3, int atomId3)

static void	removeAnnotationAngle (string structureName, int atomId, string structureName2, int atomId2, string structureName3, int atomId3)

static void	annotateDihedralAngle (string structureName, int atomId, string structureName2, int atomId2, string structureName3, int atomId3, string structureName4, int atomId4)

static void	removeAnnotationDihedralAngle (string structureName, int atomId, string structureName2, int atomId2, string structureName3, int atomId3, string structureName4, int atomId4)

static void	annotateRotatingArrow (string structureName, int atomId, string structureName2, int atomId2)

static void	removeAnnotationRotatingArrow (string structureName, int atomId, string structureName2, int atomId2)

static void	annotateArcLine (string structureName, int atomId, string structureName2, int atomId2, string structureName3, int atomId3)

static void	removeAnnotationArcLine (string structureName, int atomId, string structureName2, int atomId2, string structureName3, int atomId3)

static void	annotateDrawLine (string structureName, List< Vector3 > line, Color col)

static void	removeLastDrawLine (string structureName, int id)

Static Public Attributes
static string	path

Member Function Documentation

◆ addHydrogensHaad()

static void UMol.API.APIPython.addHydrogensHaad ( string structureName )

static

Use HAAD method to add hydrogens

◆ addHydrogensReduce()

static void UMol.API.APIPython.addHydrogensReduce ( string structureName )

static

Use Reduce method to add hydrogens

◆ addSelectionKeyword()

static void UMol.API.APIPython.addSelectionKeyword	(	string	keyword,
		string	selName
	)

static

Add a keyword to the selection language

◆ addToSelection()

static void UMol.API.APIPython.addToSelection	(	string	selMDA,
		string	name = `"selection"`,
		bool	silent = `false`
	)

static

Look for an existing selection named 'name' and add atoms to it based on MDAnalysis selection language

◆ annotateAngle()

static void UMol.API.APIPython.annotateAngle	(	string	structureName,
		int	atomId,
		string	structureName2,
		int	atomId2,
		string	structureName3,
		int	atomId3
	)

static

◆ annotateArcLine()

static void UMol.API.APIPython.annotateArcLine	(	string	structureName,
		int	atomId,
		string	structureName2,
		int	atomId2,
		string	structureName3,
		int	atomId3
	)

static

◆ annotateAtom()

static void UMol.API.APIPython.annotateAtom	(	string	structureName,
		int	atomId
	)

static

◆ annotateAtomText()

static void UMol.API.APIPython.annotateAtomText	(	string	structureName,
		int	atomId,
		string	text
	)

static

◆ annotateDihedralAngle()

static void UMol.API.APIPython.annotateDihedralAngle	(	string	structureName,
		int	atomId,
		string	structureName2,
		int	atomId2,
		string	structureName3,
		int	atomId3,
		string	structureName4,
		int	atomId4
	)

static

◆ annotateDistance()

static void UMol.API.APIPython.annotateDistance	(	string	structureName,
		int	atomId,
		string	structureName2,
		int	atomId2
	)

static

◆ annotateDrawLine()

static void UMol.API.APIPython.annotateDrawLine	(	string	structureName,
		List< Vector3 >	line,
		Color	col
	)

static

◆ annotateLine()

static void UMol.API.APIPython.annotateLine	(	string	structureName,
		int	atomId,
		string	structureName2,
		int	atomId2
	)

static

◆ annotateRotatingArrow()

static void UMol.API.APIPython.annotateRotatingArrow	(	string	structureName,
		int	atomId,
		string	structureName2,
		int	atomId2
	)

static

◆ areRepresentationsOn() [1/2]

static bool UMol.API.APIPython.areRepresentationsOn ( string structureName )

static

Utility function to test if a representation is shown for a specified structure

◆ areRepresentationsOn() [2/2]

static bool UMol.API.APIPython.areRepresentationsOn	(	string	selName,
		string	type
	)

static

Utility function to test if a representation of type 'type' is shown for a specified selection type can be "cartoon", "c", "surface", "s", "hb", "line", "l", "hbond"

◆ bg_color()

static void UMol.API.APIPython.bg_color ( string colorS )

static

Change the background color of the camera

◆ cd()

static void UMol.API.APIPython.cd ( string newPath )

static

Change the current directory

◆ centerOnSelection()

static void UMol.API.APIPython.centerOnSelection	(	string	selName,
		bool	lerp = `false`
	)

static

Offsets all representations to center the selection 'selName'

◆ centerOnStructure()

static void UMol.API.APIPython.centerOnStructure	(	string	structureName,
		bool	lerp = `false`
	)

static

Offsets all representations to center the structure 'structureName' Instead of moving the camera, move the loaded molecules to center them on the center of the camera

◆ changeGeneralScale()

static void UMol.API.APIPython.changeGeneralScale ( float newVal )

static

Change the scale of the parent of the representations of each molecules Try to not move the center of mass

◆ changeHighlightMaterial()

static void UMol.API.APIPython.changeHighlightMaterial ( Material newMat )

static

Utility function to change the material of highlighted selection

◆ changeRotationSpeedX()

static void UMol.API.APIPython.changeRotationSpeedX ( float val )

static

Change the rotation speed around the X axis

◆ changeRotationSpeedY()

static void UMol.API.APIPython.changeRotationSpeedY ( float val )

static

Change the rotation speed around the Y axis

◆ changeRotationSpeedZ()

static void UMol.API.APIPython.changeRotationSpeedZ ( float val )

static

Change the rotation speed around the Z axis

◆ clearSelections()

static void UMol.API.APIPython.clearSelections ( )

static

Clear the currentSelection in UnityMolSelectionManager

◆ colorByAtom()

static void UMol.API.APIPython.colorByAtom	(	string	selName,
		string	type
	)

static

Color representations of type 'type' in the selection 'selName' by atom

◆ colorByChain()

static void UMol.API.APIPython.colorByChain	(	string	selName,
		string	type
	)

static

Use the color palette to color representations of type 'type' in the selection 'selName' by chain type can be "cartoon", "c", "surface", "s", "hb", "line", "l", "hbond"

◆ colorByCharge()

static void UMol.API.APIPython.colorByCharge	(	string	selName,
		bool	normalizeDensity = `false`,
		float	minDens = `-10.0f`,
		float	maxDens = `10.0f`
	)

static

Use the dx map to color by charge around atoms Only works for surface for now If normalizeDensity is set to true, the density values will be normalized if it is set to true, the default -10|10 range is used

◆ colorByResidue()

static void UMol.API.APIPython.colorByResidue	(	string	selName,
		string	type
	)

static

Use the color palette to color representations of type 'type' in the selection 'selName' by residue type can be "cartoon", "c", "surface", "s", "hb", "line", "l", "hbond"

◆ colorSelection() [1/2]

static void UMol.API.APIPython.colorSelection	(	string	selName,
		string	type,
		Color	col
	)

static

Change the color of all representation of type 'type' in selection type can be "cartoon", "c", "surface", "s", "hb", "line", "l", "hbond"

◆ colorSelection() [2/2]

static void UMol.API.APIPython.colorSelection	(	string	selName,
		string	type,
		string	colorS
	)

static

Change the color of all representation of type 'type' in selection colorS can be "black", "white", "yellow", "green", "red", "blue", "pink", "gray" type can be "cartoon", "c", "surface", "s", "hb", "line", "l", "hbond"

◆ connectIMD()

static void UMol.API.APIPython.connectIMD	(	string	structureName,
		string	adress,
		int	port
	)

static

Connect to a running simulation using the IMD protocol implemented in Artemis The running simulation is binded to a UnityMolStructure

◆ delete()

static void UMol.API.APIPython.delete ( string structureName )

static

Delete a molecule and all its UnityMolSelection and UnityMolRepresentation

◆ deleteRepresentationInSelection()

static void UMol.API.APIPython.deleteRepresentationInSelection	(	string	selName,
		string	type
	)

static

Delete every representations of type 'type' of the specified selection type can be "cartoon", "c", "surface", "s", "hb", "line", "l", "hbond"

◆ deleteRepresentationsInSelection()

static void UMol.API.APIPython.deleteRepresentationsInSelection ( string selName )

static

Delete every representations of the specified selection

◆ deleteSelection()

static void UMol.API.APIPython.deleteSelection ( string selName )

static

Delete selection 'selName' and all its representations

◆ disconnectIMD()

static void UMol.API.APIPython.disconnectIMD ( string structureName )

static

Disconnect from the IMD simulation for the specified structure

◆ duplicateSelection()

static string UMol.API.APIPython.duplicateSelection ( string selName )

static

Duplicate selection 'selName' and without the representations

◆ ExecuteCommand()

static void UMol.API.APIPython.ExecuteCommand ( string command )

static

Allow to call python API commands and record them in the history from C#

◆ fetch()

static UnityMolStructure UMol.API.APIPython.fetch	(	string	PDBId,
		bool	usemmCIF = `true`,
		bool	readHetm = `true`
	)

static

Fetch a remote molecular file (pdb or mmcif zipped) This function calls showDefault() and centerOnStructure()

◆ getHyperBallMetaphore()

static string UMol.API.APIPython.getHyperBallMetaphore ( string selName )

static

◆ getManipulationManager()

static ManipulationManager UMol.API.APIPython.getManipulationManager ( )

static

◆ getRepType()

static RepType UMol.API.APIPython.getRepType ( string type )

static

Transform a string of representation type to a RepType object

◆ getStructureGroup()

static int UMol.API.APIPython.getStructureGroup ( string structureName )

static

Utility function to be able to get the group of the structure This group is used to be able to move all the loaded molecules in the same group Groups can be between 0 and 9 included

◆ getStructuresOfGroup()

static HashSet<UnityMolStructure> UMol.API.APIPython.getStructuresOfGroup ( int group )

static

Utility function to be able to get the structures of the group This group is used to be able to move all the loaded molecules in the same group Groups can be between 0 and 9 included

◆ getSurfaceType()

static string UMol.API.APIPython.getSurfaceType ( string selName )

static

◆ getTypeFromRepType()

static string UMol.API.APIPython.getTypeFromRepType ( RepType rept )

static

Transform a representation type into a string

◆ hide()

static void UMol.API.APIPython.hide ( string type )

static

Hide all representations of type 'type' type can be "cartoon", "c", "surface", "s", "hb", "line", "l", "hbond"

◆ hideSelection() [1/2]

static void UMol.API.APIPython.hideSelection ( string selName )

static

Hide every representations of the specified selection

◆ hideSelection() [2/2]

static void UMol.API.APIPython.hideSelection	(	string	selName,
		string	type
	)

static

Hide every representation of type 'type' of the specified selection type can be "cartoon", "c", "surface", "s", "hb", "line", "l", "hbond"

◆ hideStructureAllRepresentations()

static void UMol.API.APIPython.hideStructureAllRepresentations ( string structureName )

static

Hide every representations of the specified structure

◆ isATrajectoryPlaying()

static bool UMol.API.APIPython.isATrajectoryPlaying ( )

static

Utility function to test if a trajectory is playing for any loaded molecule

◆ last()

static UnityMolStructure UMol.API.APIPython.last ( )

static

Return the lastly loaded UnityMolStructure

◆ load()

static UnityMolStructure UMol.API.APIPython.load	(	string	filePath,
		bool	readHetm = `true`
	)

static

Load a local molecular file (pdb/mmcif/gro/mol2/sdf/xyz formats)

◆ loadDXmap()

static void UMol.API.APIPython.loadDXmap	(	string	structureName,
		string	path
	)

static

Load a density map for a specific structure This function creates a DXReader instance in the UnityMolStructure

◆ loadHistoryScript()

static void UMol.API.APIPython.loadHistoryScript ( string path )

static

Load a python script of commands (possibly the output of the saveHistoryScript function)

◆ loadTraj()

static void UMol.API.APIPython.loadTraj	(	string	structureName,
		string	path
	)

static

Load a trajectory for a loaded structure It creates a XDRFileReader in the corresponding UnityMolStructure and a TrajectoryPlayer

◆ ls()

static List<string> UMol.API.APIPython.ls ( )

static

Print the content of the current directory

◆ pwd()

static void UMol.API.APIPython.pwd ( )

static

Print the current directory

◆ readJSONFieldlines()

static void UMol.API.APIPython.readJSONFieldlines	(	string	structureName,
		string	path
	)

static

Read a json file and display fieldLines for the specified structure

◆ removeAnnotationAngle()

static void UMol.API.APIPython.removeAnnotationAngle	(	string	structureName,
		int	atomId,
		string	structureName2,
		int	atomId2,
		string	structureName3,
		int	atomId3
	)

static

◆ removeAnnotationArcLine()

static void UMol.API.APIPython.removeAnnotationArcLine	(	string	structureName,
		int	atomId,
		string	structureName2,
		int	atomId2,
		string	structureName3,
		int	atomId3
	)

static

◆ removeAnnotationAtom()

static void UMol.API.APIPython.removeAnnotationAtom	(	string	structureName,
		int	atomId
	)

static

◆ removeAnnotationAtomText()

static void UMol.API.APIPython.removeAnnotationAtomText	(	string	structureName,
		int	atomId,
		string	text
	)

static

◆ removeAnnotationDihedralAngle()

static void UMol.API.APIPython.removeAnnotationDihedralAngle	(	string	structureName,
		int	atomId,
		string	structureName2,
		int	atomId2,
		string	structureName3,
		int	atomId3,
		string	structureName4,
		int	atomId4
	)

static

◆ removeAnnotationDistance()

static void UMol.API.APIPython.removeAnnotationDistance	(	string	structureName,
		int	atomId,
		string	structureName2,
		int	atomId2
	)

static

◆ removeAnnotationLine()

static void UMol.API.APIPython.removeAnnotationLine	(	string	structureName,
		int	atomId,
		string	structureName2,
		int	atomId2
	)

static

◆ removeAnnotationRotatingArrow()

static void UMol.API.APIPython.removeAnnotationRotatingArrow	(	string	structureName,
		int	atomId,
		string	structureName2,
		int	atomId2
	)

static

◆ removeFromSelection()

static void UMol.API.APIPython.removeFromSelection	(	string	selMDA,
		string	name = `"selection"`,
		bool	silent = `false`
	)

static

Look for an existing selection named 'name' and remove atoms from it based on MDAnalysis selection language

◆ removeLastDrawLine()

static void UMol.API.APIPython.removeLastDrawLine	(	string	structureName,
		int	id
	)

static

◆ removeSelectionKeyword()

static void UMol.API.APIPython.removeSelectionKeyword ( string keyword )

static

Remove a keyword from the selection language

◆ renameSelection()

static bool UMol.API.APIPython.renameSelection	(	string	oldSelName,
		string	newSelName
	)

static

Change the 'oldSelName' selection name into 'newSelName'

◆ resetColorSelection()

static void UMol.API.APIPython.resetColorSelection	(	string	selName,
		string	type
	)

static

Reset the color of all representation of type 'type' in selection to the default value type can be "cartoon", "c", "surface", "s", "hb", "line", "l", "hbond"

◆ saveHistoryScript()

static void UMol.API.APIPython.saveHistoryScript ( string path )

static

Save the history of commands executed in a file

◆ screenshot()

static void UMol.API.APIPython.screenshot	(	string	path,
		int	resolutionWidth = `1280`,
		int	resolutionHeight = `720`,
		bool	transparentBG = `false`
	)

static

Take a screenshot of the current viewpoint with a specific resolution

◆ select()

static UnityMolSelection UMol.API.APIPython.select	(	string	selMDA,
		string	name = `"selection"`,
		bool	createSelection = `true`,
		bool	addToExisting = `false`,
		bool	silent = `false`,
		bool	setAsCurrentSelection = `true`,
		bool	forceCreate = `false`
	)

static

Create a UnityMolSelection based on MDAnalysis selection language (https://www.mdanalysis.org/docs/documentation_pages/selections.html) Returns a UnityMolSelection object, adding it to the selection manager if createSelection is true If a selection with the same name already exists and addToExisting is true, add atoms to the already existing selection Set forceCreate to true if the selection is empty but still need to generate the selection

◆ selectInSphere()

static UnityMolSelection UMol.API.APIPython.selectInSphere	(	Vector3	position,
		float	radius
	)

static

Select atoms of all loaded molecules inside a sphere defined by a world space position and a radius in Anstrom

◆ setAsLigand()

static void UMol.API.APIPython.setAsLigand	(	string	selName,
		bool	isLig = `true`,
		bool	updateAllSelections = `true`
	)

static

Set the atoms of the selection named 'selName' to ligand

◆ setCameraFarPlane()

static void UMol.API.APIPython.setCameraFarPlane ( float newV )

static

◆ setCameraNearPlane()

static void UMol.API.APIPython.setCameraNearPlane ( float newV )

static

◆ setCartoonColorSS()

static void UMol.API.APIPython.setCartoonColorSS	(	string	selName,
		string	ssType,
		Color	col
	)

static

Set the color of the cartoon representation of the specified selection based on the nature of secondary structure assigned ssType can be "helix", "sheet" or "coil"

◆ setCurrentSelection()

static void UMol.API.APIPython.setCurrentSelection ( string selName )

static

Set the selection as currentSelection in the UnityMolSelectionManager

◆ setHyperBallMetaphore()

static void UMol.API.APIPython.setHyperBallMetaphore	(	string	selName,
		string	metaphore
	)

static

Change hyperball representation parameters in the specified selection to a preset Metaphores can be "Smooth", "Balls&Sticks", "VdW", "Licorice"

◆ setHyperBallShininess()

static void UMol.API.APIPython.setHyperBallShininess	(	string	selName,
		float	shin
	)

static

Set shininess for the hyperball representations of the specified selection

◆ setHyperballShrink()

static void UMol.API.APIPython.setHyperballShrink	(	string	selName,
		float	shrink
	)

static

Set the shrink factor for the hyperball representations of the specified selection

◆ setHyperballTexture()

static void UMol.API.APIPython.setHyperballTexture	(	string	selName,
		int	idTex
	)

static

Change all hyperball representation in the selection with a new texture mapped idTex of the texture is the index in UnityMolMain.atomColors.textures

◆ setLineSize()

static void UMol.API.APIPython.setLineSize	(	string	selName,
		float	val
	)

static

◆ setMetal()

static void UMol.API.APIPython.setMetal	(	string	selName,
		string	type,
		float	val
	)

static

Change hyperball representation parameters in the specified selection to a preset Metaphores can be "Smooth", "Balls&Sticks", "VdW", "Licorice" type can be "cartoon", "c", "surface", "s", "hb", "line", "l", "hbond"

◆ setModel()

static void UMol.API.APIPython.setModel	(	string	structureName,
		int	modelId
	)

static

Set the current model of the structure This function is used by ModelPlayers.cs to read the models of a structure like a trajectory

◆ setMolParentTransform()

static void UMol.API.APIPython.setMolParentTransform	(	Vector3	pos,
		Vector3	scale,
		Vector3	rot,
		Vector3	centerOfRotation
	)

static

Set the position, scale and rotation of the parent of all loaded molecules Linear interpolation between the current state of the camera to the specified values

◆ setMouseMoveSpeed()

static void UMol.API.APIPython.setMouseMoveSpeed ( float val )

static

Change the speed of mouse rotations and translations

◆ setMouseScrollSpeed()

static void UMol.API.APIPython.setMouseScrollSpeed ( float val )

static

Change the mouse scroll speed

◆ setPosScaleRot()

void UMol.API.APIPython.setPosScaleRot	(	Vector3	pos,
		Vector3	scale,
		Vector3	rot,
		Vector3	centerOfRotation
	)

◆ setRepSize()

static void UMol.API.APIPython.setRepSize	(	string	selName,
		string	type,
		float	size
	)

static

Change the size of the representation of type 'type' in the selection Mainly used for hyperball representation type can be "cartoon", "c", "surface", "s", "hb", "line", "l", "hbond"

◆ setRotationCenter()

static void UMol.API.APIPython.setRotationCenter ( Vector3 newPos )

static

◆ setSmoothness()

static void UMol.API.APIPython.setSmoothness	(	string	selName,
		string	type,
		float	val
	)

static

Change hyperball representation parameters in the specified selection to a preset Metaphores can be "Smooth", "Balls&Sticks", "VdW", "Licorice" type can be "cartoon", "c", "surface", "s", "hb", "line", "l", "hbond"

◆ setSolidSurface()

static void UMol.API.APIPython.setSolidSurface ( string selName )

static

Switch all surface representation in selection to a solid surface material

◆ setStructureGroup()

static void UMol.API.APIPython.setStructureGroup	(	string	structureName,
		int	newGroup
	)

static

Utility function to be set the group of a structure This group is used to be able to move all the loaded molecules in the same group Groups can be between 0 and 9 included

◆ setTransparentSurface()

static void UMol.API.APIPython.setTransparentSurface	(	string	selName,
		float	alpha = `0.8f`
	)

static

Switch all surface representation in selection to a transparent surface material

◆ setWireframeSurface()

static void UMol.API.APIPython.setWireframeSurface ( string selName )

static

Switch all surface representation in selection to a wireframe surface material when available

◆ show()

static void UMol.API.APIPython.show ( string type )

static

Show as 'type' all loaded molecules type can be "cartoon", "c", "surface", "s", "hb", "line", "l", "hbond"

◆ showDefault()

static void UMol.API.APIPython.showDefault ( string selName )

static

Create default representations (cartoon for protein + HB for not protein atoms)

◆ showHideBackboneInSelection()

static void UMol.API.APIPython.showHideBackboneInSelection ( string selName )

static

Show/Hide backbone in representations of the current selection This only works for lines, hyperball and sphere representations only

◆ showHideHydrogensInSelection()

static void UMol.API.APIPython.showHideHydrogensInSelection	(	string	selName,
		bool?	shouldShow = `null`
	)

static

Show/Hide hydrogens in representations of the provided selection This only works for lines, hyperball and sphere representations

◆ showHideSideChainsInSelection()

static void UMol.API.APIPython.showHideSideChainsInSelection ( string selName )

static

Show/Hide side chains in representations of the current selection This only works for lines, hyperball and sphere representations only

◆ showSelection()

static void UMol.API.APIPython.showSelection	(	string	selName,
		string	type,
		params object []	args
	)

static

Show the selection as 'type' type can be "cartoon", "c", "surface", "s", "hb", "line", "l", "hbond" If the representation is already there, update it if the selection content changed and show it

◆ showStructureAllRepresentations()

static void UMol.API.APIPython.showStructureAllRepresentations ( string structureName )

static

Unhide all representations already created for a specified structure

◆ startVideo()

static void UMol.API.APIPython.startVideo	(	string	filePath,
		int	resolutionWidth = `1280`,
		int	resolutionHeight = `720`,
		int	frameRate = `30`
	)

static

Start to record a video with FFMPEG at a specific resolution and framerate

◆ stopRotations()

static void UMol.API.APIPython.stopRotations ( )

static

Stop rotation around all axis

◆ stopVideo()

static void UMol.API.APIPython.stopVideo ( )

static

Stop recording

◆ switchCutSurface()

static void UMol.API.APIPython.switchCutSurface	(	string	selName,
		bool	isCut
	)

static

Switch between cut surface mode and no-cut surface mode

◆ switchRotateAxisX()

static void UMol.API.APIPython.switchRotateAxisX ( )

static

Switch on or off the rotation around the X axis of all loaded molecules

◆ switchRotateAxisY()

static void UMol.API.APIPython.switchRotateAxisY ( )

static

Switch on or off the rotation around the Y axis of all loaded molecules

◆ switchRotateAxisZ()

static void UMol.API.APIPython.switchRotateAxisZ ( )

static

Switch on or off the rotation around the Z axis of all loaded molecules

◆ switchSurfaceComputeMethod()

static void UMol.API.APIPython.switchSurfaceComputeMethod ( string selName )

static

Switch between the 2 types of surface computation methods: EDTSurf and MSMS

◆ undo()

static void UMol.API.APIPython.undo ( )

static

Play the opposite function of the lastly called APIPython function recorded in UnityMolMain.pythonUndoCommands

◆ unloadDXmap()

static void UMol.API.APIPython.unloadDXmap ( string structureName )

static

Unload the density map for the structure

◆ unloadJSONFieldlines()

static void UMol.API.APIPython.unloadJSONFieldlines ( string structureName )

static

Remove the json file for fieldlines stored in the currentModel of the specified structure

◆ unloadTraj()

static void UMol.API.APIPython.unloadTraj ( string structureName )

static

Unload a trajectory for a specific structure

◆ updateRepresentations()

static void UMol.API.APIPython.updateRepresentations ( string selName )

static

Update representations of the specified selection

◆ updateSelectionWithMDA()

static bool UMol.API.APIPython.updateSelectionWithMDA	(	string	selName,
		string	selectionString,
		bool	forceAlteration,
		bool	silent = `false`
	)

static

Update the atoms of the selection based on a new MDAnalysis language selection The selection only applies to the structures of the selection

◆ waitOf()

IEnumerator UMol.API.APIPython.waitOf ( )

◆ waitOneFrame()

static void UMol.API.APIPython.waitOneFrame ( )

static

Member Data Documentation

◆ path

string UMol.API.APIPython.path

static

The documentation for this class was generated from the following file:

C:/Users/Xavier/Dev/UnityMolX/Assets/Scripts/API/APIPython.cs

Public Member Functions

Static Public Member Functions

Static Public Attributes

Member Function Documentation

◆ addHydrogensHaad()

◆ addHydrogensReduce()

◆ addSelectionKeyword()

◆ addToSelection()

◆ annotateAngle()

◆ annotateArcLine()

◆ annotateAtom()

◆ annotateAtomText()

◆ annotateDihedralAngle()

◆ annotateDistance()

◆ annotateDrawLine()

◆ annotateLine()

◆ annotateRotatingArrow()

◆ areRepresentationsOn() [1/2]

◆ areRepresentationsOn() [2/2]

◆ bg_color()

◆ cd()

◆ centerOnSelection()

◆ centerOnStructure()

◆ changeGeneralScale()

◆ changeHighlightMaterial()

◆ changeRotationSpeedX()

◆ changeRotationSpeedY()

◆ changeRotationSpeedZ()

◆ clearSelections()

◆ colorByAtom()

◆ colorByChain()

◆ colorByCharge()

◆ colorByResidue()

◆ colorSelection() [1/2]

◆ colorSelection() [2/2]

◆ connectIMD()

◆ delete()

◆ deleteRepresentationInSelection()

◆ deleteRepresentationsInSelection()

◆ deleteSelection()

◆ disconnectIMD()

◆ duplicateSelection()

◆ ExecuteCommand()

◆ fetch()

◆ getHyperBallMetaphore()

◆ getManipulationManager()

◆ getRepType()

◆ getStructureGroup()

◆ getStructuresOfGroup()

◆ getSurfaceType()

◆ getTypeFromRepType()

◆ hide()

◆ hideSelection() [1/2]

◆ hideSelection() [2/2]

◆ hideStructureAllRepresentations()

◆ isATrajectoryPlaying()

◆ last()

◆ load()

◆ loadDXmap()

◆ loadHistoryScript()

◆ loadTraj()

◆ ls()

◆ pwd()

◆ readJSONFieldlines()

◆ removeAnnotationAngle()

◆ removeAnnotationArcLine()

◆ removeAnnotationAtom()

◆ removeAnnotationAtomText()

◆ removeAnnotationDihedralAngle()

◆ removeAnnotationDistance()

◆ removeAnnotationLine()

◆ removeAnnotationRotatingArrow()

◆ removeFromSelection()

◆ removeLastDrawLine()

◆ removeSelectionKeyword()

◆ renameSelection()

◆ resetColorSelection()

◆ saveHistoryScript()

◆ screenshot()

◆ select()