Constructor

# new MoorhenMolecule(commandCentre, glRef, storeopt, monomerLibraryPathopt)

Parameters:

Name	Type	Attributes	Default	Description
`commandCentre`	`React.RefObject.<moorhen.CommandCentre>`			A react reference to the command centre instance
`glRef`	`React.RefObject.<webGL.MGWebGL>`			A react reference to the MGWebGL instance
`store`	`ToolkitStore`	<optional>		A Redux store. By default Moorhen Redux store will be used
`monomerLibraryPath`	`string`	<optional>	"./baby-gru/monomers"	A string with the path to the monomer library, relative to the root of the app

Properties:

Name	Type	Description
`name`	`string`	The name assigned to this molecule instance
`molNo`	`number`	The imol assigned to this molecule instance
`atomsDirty`	`boolean`	Whether the cached atoms are outdated
`symmetryOn`	`boolean`	Whether the symmetry is currently being displayed
`sequences`	`object`	List of sequences present in the molecule
`gemmiStructure`	`object`	Object representation of the cached gemmi structure for this molecule
`commandCentre`	`React.RefObject.<moorhen.CommandCentre>`	A react reference to the command centre instance
`glRef`	`React.RefObject.<webGL.MGWebGL>`	A react reference to the MGWebGL instance
`monomerLibraryPath`	`string`	A string with the path to the monomer library, relative to the root of the app

View Source utils/MoorhenMolecule.ts, line 48

Example

import { MoorhenMolecule } from 'moorhen';

// Create a new molecule
const molecule = new MoorhenMolecule(commandCentre, glRef, monomerLibraryPath);

// Set some defaults
molecule.setBackgroundColour(glRef.current.background_colour)

// Load file from a URL
molecule.loadToCootFromURL('/uri/to/file.pdb', 'mol-1');

// Draw coot bond representation and centre on molecule
molecule.fetchIfDirtyAndDraw('CBs');
molecule.centreOn();

// Delete molecule
molecule.delete();

Classes

MoorhenMolecule

Methods

# async SSMSuperpose(movChainId, refMolNo, refChainId, redrawopt) → {Promise.<void>}

Use SSM to superpose this molecule (as the moving structure) with another molecule isntance

Parameters:

Name	Type	Attributes	Default	Description
`movChainId`	`string`			Chain ID for the moving structure
`refMolNo`	`string`			Molecule number for the reference structure
`refChainId`	`string`			Chain ID for the reference structure
`redraw`	`boolean`	<optional>	true	Indicates if the molecule should be redrawn

View Source utils/MoorhenMolecule.ts, line 2955

Returns:

Type: Promise.<void>

# async addDict(fileContent) → {Promise.<void>}

Associate ligand dictionary with this molecule instance

Parameters:

Name	Type	Description
`fileContent`	`string`	The dictionary contents

View Source utils/MoorhenMolecule.ts, line 2810

Returns:

Type: Promise.<void>

# async addLigandOfType(resType, fromMolNoopt) → {Promise.<moorhen.WorkerResponse>}

Add a ligand of a given type to this molecule isntance

Parameters:

Name	Type	Attributes	Default	Description
`resType`	`string`			Three letter code for the ligand of interest
`fromMolNo`	`number`	<optional>	-999999	Indicate the molecule number to which the ligand dictionary was associated (use -999999 for "any")

View Source utils/MoorhenMolecule.ts, line 2788

Returns:

Type: Promise.<moorhen.WorkerResponse>

# async addRepresentation(style, cid, isCustomopt, colourRulesopt, bondOptionsopt, m2tParamsopt)

Add a representation to the molecule

Parameters:

Name	Type	Attributes	Default	Description
`style`	`string`			The style of the new representation
`cid`	`string`			The CID selection for the residues included in the new representation
`isCustom`	`boolean`	<optional>	false	Indicates if the representation is considered "custom"
`colourRules`	`Array.<moorhen.ColourRule>`	<optional>		A list of colour rules that will be applied to the new representation
`bondOptions`	`moorhen.cootBondOptions`	<optional>		An object that describes bond width, atom/bond ratio and other bond settings.
`m2tParams`	`moorhen.m2tParameters`	<optional>		An object that describes ribbon width, nucleotide style and other ribbon settings.

View Source utils/MoorhenMolecule.ts, line 2644

# async animateRefine(n_cyc, n_iteration, final_n_cycopt)

Refine a molecule with animation effect

Parameters:

Name	Type	Attributes	Default	Description
`n_cyc`	`number`			The total number of refinement cycles for each iteration
`n_iteration`	`number`			The number of iterations
`final_n_cyc`	`number`	<optional>	100	Number of refinement cycles in the last iteration

View Source utils/MoorhenMolecule.ts, line 2935

# applyTransform()

Apply cached transformation matrix to molecule

View Source utils/MoorhenMolecule.ts, line 2764

# buffersInclude(bufferIn) → {boolean}

Check whether a particular buffer is included within the representation buffer for this molecule

Parameters:

Name	Type	Description
`bufferIn`		The buffer with the ID to search for

View Source utils/MoorhenMolecule.ts, line 2685

Returns:

True if the buffer is included in this molecule

Type: boolean

# cacheLigandDict(fileContent) → {void}

Internal function used to store a ligand dictionary in the cache for this molecule instance

Parameters:

Name	Type	Description
`fileContent`	`string`	The dictionary contents

View Source utils/MoorhenMolecule.ts, line 2802

Returns:

Type: void

# async centreAndAlignViewOn(selectionCid, alignWithCBopt, zoomLevelopt) → {Promise.<void>}

Centre the view and align it with the axis of a particular residue

Parameters:

Name	Type	Attributes	Default	Description
`selectionCid`	`string`			CID selection for the residue to centre the view on
`alignWithCB`	`boolean`	<optional>	false	Indicates whether to align with the CB atom for better view of the side chain (when present in the residue)
`zoomLevel`	`number`	<optional>	0.3	Indicates the zoom level to use

View Source utils/MoorhenMolecule.ts, line 2613

Returns:

Type: Promise.<void>

# async centreOn(selectionCid, animateopt) → {Promise.<void>}

Centre the view on a particular residue

Parameters:

Name	Type	Attributes	Default	Description
`selectionCid`	`string`			CID selection for the residue to centre the view on
`animate`	`boolean`	<optional>	true	Indicates whether the change will be animated

View Source utils/MoorhenMolecule.ts, line 2622

Returns:

Type: Promise.<void>

# async changeChainId(oldId, newId, startResNo, endResNo) → {number}

Change the ID of a given chain

Parameters:

Name	Type	Description
`oldId`	`string`	The old chain ID
`newId`	`string`	The new chain ID
`startResNo`	`number`	The start residue number
`endResNo`	`number`	The end residue number

View Source utils/MoorhenMolecule.ts, line 3076

Returns:

- Status code -1 on a conflict, 1 on good, 0 on did nothing

Type: number

# async checkHasGlycans() → {Promise.<boolean>}

Check if the current molecule has glycans

View Source utils/MoorhenMolecule.ts, line 2582

Returns:

- True if the current molecule has glycans

Type: Promise.<boolean>

# checkIsLigand() → {boolean}

Check if the molecule instance consists of a ligand

View Source utils/MoorhenMolecule.ts, line 2439

Returns:

True if the molecule is a ligand

Type: boolean

# clearBuffersOfStyle(style)

Clears the representation buffers for a particular style

Parameters:

Name	Type	Description
`style`	`string`	The style to clear

View Source utils/MoorhenMolecule.ts, line 2672

# clearExtraRestraints() → {Promise.<moorhen.WorkerResponse>}

Clear all additional restraints

View Source utils/MoorhenMolecule.ts, line 2892

Returns:

Type: Promise.<moorhen.WorkerResponse>

# async copyFragmentForRefinement(cid, refinementMap, redraw, redrawFragmentFirst) → {moorhen.Molecule}

Copy a fragment of the current model into a new molecule for refinement

Parameters:

Name	Type	Description
`cid`	`Array.<string>`	The CID selection indicating the residues that will be copied into the new fragment
`refinementMap`	`moorhen.Map`	The map instance used in the refinement
`redraw`	`boolean`	Indicate if the molecules should be redrawn
`redrawFragmentFirst`	`boolean`	Indicate if the fragment should be redrawn first

View Source utils/MoorhenMolecule.ts, line 2492

Returns:

A new molecule instance that can be used for refinement

Type: moorhen.Molecule

# async copyFragmentUsingCid(cid, doRecentreopt, styleopt) → {Promise.<moorhen.Molecule>}

Copy a fragment of the current model into a new molecule using a selection CID

Parameters:

Name	Type	Attributes	Default	Description
`cid`	`string`			The CID selection indicating the residues that will be copied into the new fragment
`doRecentre`	`boolean`	<optional>	true	Indicates whether the view should re-centre on the new copied fragment
`style`	`boolean`	<optional>	"CBs"	Indicates the style used to draw the copied fragment (only takes effect if doRecentre=true)

View Source utils/MoorhenMolecule.ts, line 2481

Returns:

New molecule instance

Type: Promise.<moorhen.Molecule>

# async copyMolecule(doRedraw) → {moorhen.Molecule}

Copy molecule into a new instance

Parameters:

Name	Type	Description
`doRedraw`	`boolean`

View Source utils/MoorhenMolecule.ts, line 2471

Returns:

New molecule instance

Type: moorhen.Molecule

# async delete(popBackImolopt) → {Promise.<moorhen.WorkerResponse>}

Delete this molecule instance

Parameters:

Name	Type	Attributes	Default	Description
`popBackImol`	`boolean`	<optional>	false	Indicates whether the imol for this molecule instance should be popped back (useful for ephemeral molecules)

View Source utils/MoorhenMolecule.ts, line 2447

Returns:

Type: Promise.<moorhen.WorkerResponse>

# async deleteCid(cid, redrawopt) → {object}

Delete residues in a given CID

Parameters:

Name	Type	Attributes	Default	Description
`cid`	`string`			The CID to delete
`redraw`	`boolean`	<optional>	true	Indicates if the molecule should be redrawn

View Source utils/MoorhenMolecule.ts, line 2944

Returns:

- A pair where first is the return status and second is the atom count of the molecule after deletion

Type: object

# async downloadAtoms(formatopt)

Download the PDB file contents of the molecule in its current state

Parameters:

Name	Type	Attributes	Default	Description
`format`	`string`	<optional>	'pdb'	File format will match the one of the original file unless specified here

View Source utils/MoorhenMolecule.ts, line 2575

# drawBiomolecule(fetchSymMatrixopt) → {void}

Draw symmetry mates for the current molecule

Parameters:

Name	Type	Attributes	Default	Description
`fetchSymMatrix`	`boolean`	<optional>	true	Indicates whether a new symmetry matrix must be fetched from libcoot api

View Source utils/MoorhenMolecule.ts, line 2388

Returns:

Type: void

# async drawEnvironment(selectionCid) → {Promise.<void>}

Draw enviroment distances for a given residue

Parameters:

Name	Type	Description
`selectionCid`	`string`	The CID selection to draw the environment

View Source utils/MoorhenMolecule.ts, line 2737

Returns:

Type: Promise.<void>

# async drawHover(selectionString) → {Promise.<void>}

Draw a hover effect over a selected residue

Parameters:

Name	Type	Description
`selectionString`	`string`	The CID selection for the residue that will be highlighted

View Source utils/MoorhenMolecule.ts, line 2699

Returns:

Type: Promise.<void>

# async drawResidueSelection(selectionString) → {Promise.<void>}

Highlight residues in a selected CID range

Parameters:

Name	Type	Description
`selectionString`	`string`	The CID selection for the residues that will be highlighted

View Source utils/MoorhenMolecule.ts, line 2707

Returns:

Type: Promise.<void>

# async drawSymmetry(fetchSymMatrixopt) → {Promise.<void>}

Draw symmetry mates for the current molecule

Parameters:

Name	Type	Attributes	Default	Description
`fetchSymMatrix`	`boolean`	<optional>	true	Indicates whether a new symmetry matrix must be fetched from libcoot api

View Source utils/MoorhenMolecule.ts, line 2396

Returns:

Type: Promise.<void>

# async drawUnitCell()

Draw the unit cell of this molecule

View Source utils/MoorhenMolecule.ts, line 2691

# async drawWithStyleFromMesh(style, meshObjects, cidopt) → {Promise.<void>}

Draw molecule from a given mesh

Parameters:

Name	Type	Attributes	Description
`style`	`string`		Indicate the style to be drawn
`meshObjects`	`Array.<any>`		The mesh obects that will be drawn
`cid`	`string`	<optional>	The new buffer CID selection

View Source utils/MoorhenMolecule.ts, line 2632

Returns:

Type: Promise.<void>

# async exportAsGltf(representationId) → {ArrayBuffer}

Export the current molecule as a gltf file in binary format

Parameters:

Name	Type	Description
`representationId`	`string`	The id of the representation to export

View Source utils/MoorhenMolecule.ts, line 3048

Returns:

- The contents of the gltf file in binary format

Type: ArrayBuffer

# fetchBiomoleculeMatrix() → {void}

Fetch the matrices representing the biomolecule of the current model from gemmi

View Source utils/MoorhenMolecule.ts, line 2374

Returns:

Type: void

# async fetchDefaultColourRules()

Set the default colour rules for this molecule from libcoot API

View Source utils/MoorhenMolecule.ts, line 2852

# async fetchHeaderInfo(useCache) → {Promise.<libcootApi.headerInfoJS>}

Fetch header information for this molecule instance

Parameters:

Name	Type	Description
`useCache`	`boolean`	Whether to use the cached results or not

View Source utils/MoorhenMolecule.ts, line 3105

Returns:

Object containing header information

Type: Promise.<libcootApi.headerInfoJS>

# async fetchIfDirtyAndDraw(style) → {Promise.<void>}

Draw the molecule with a particular style. If the molecule atoms are marked as "dirty" then fetch new atoms.

Parameters:

Name	Type	Description
`style`	`string`	The style that will be drawn

View Source utils/MoorhenMolecule.ts, line 2603

Returns:

Type: Promise.<void>

# async fetchSymmetryMatrix() → {Promise.<void>}

Fetch the symmetry matrix for the current model from libcoot api

View Source utils/MoorhenMolecule.ts, line 2381

Returns:

Type: Promise.<void>

# async fitLigand(mapMolNo, ligandMolNo, fitRightHereopt, redrawopt, useConformersopt, conformerCountopt) → {Promise.<Array.<moorhen.Molecule>>}

A function to fit a given ligand

Parameters:

Name	Type	Attributes	Default	Description
`mapMolNo`	`number`			The map iMol that will be used for ligand fitting
`ligandMolNo`	`number`			The ligand iMol that will be fitted
`fitRightHere`	`boolean`	<optional>	true	Indicates if the ligand should be fitted at the current origin
`redraw`	`boolean`	<optional>	false	Indicates if the fitted ligands should be drawn
`useConformers`	`boolean`	<optional>	false	Indicates if there is need to test multiple conformers
`conformerCount`	`number`	<optional>	0	Conformer count

View Source utils/MoorhenMolecule.ts, line 2979

Returns:

- A list of fitted ligands

Type: Promise.<Array.<moorhen.Molecule>>

# async gemmiAtomsForCid(cid) → {Promise.<Array.<moorhen.AtomInfo>>}

Get atom information for a given CID selection

Parameters:

Name	Type	Description
`cid`	`string`	The CID selection

View Source utils/MoorhenMolecule.ts, line 2839

Returns:

JS objects containing atom information

Type: Promise.<Array.<moorhen.AtomInfo>>

# async generateSelfRestraints(cidopt, maxRadiusopt) → {Promise.<void>}

Generate self restraints

Parameters:

Name	Type	Attributes	Default	Description
`cid`	`string`	<optional>	"//"	The CID for local restraints
`maxRadius`	`number`	<optional>	4.2	The maximum radius for the restraints

View Source utils/MoorhenMolecule.ts, line 2886

Returns:

Type: Promise.<void>

# async getActiveAtom() → {string}

Get the active atom for this molecule

View Source utils/MoorhenMolecule.ts, line 2714

Returns:

The active atom CID

Type: string

# async getAtoms(formatopt) → {string}

Get a string with the PDB file contents of the molecule in its current state

Parameters:

Name	Type	Attributes	Default	Description
`format`	`string`	<optional>	'pdb'	File format will match the one of the original file unless specified here

View Source utils/MoorhenMolecule.ts, line 2568

Returns:

A string representation file contents

Type: string

# getChainNames() → {Array.<string>}

Get a list with the names of the chains in the current model

View Source utils/MoorhenMolecule.ts, line 2770

Returns:

- A list of chain names in the current structure

Type: Array.<string>

# getDict(comp_id) → {string}

Get dictionary for a ligand associated with this molecule

Parameters:

Name	Type	Description
`comp_id`	`string`	Three letter code for the ligand of interest

View Source utils/MoorhenMolecule.ts, line 2795

Returns:

The ligand dictionary

Type: string

# async getLigandSVG(resName, useCache) → {Promise.<Array.<string>>}

Get SVG descriptions for the ligands in this molecule instance

Parameters:

Name	Type	Description
`resName`	`string`	The name of the ligand to get SVG descriptions for
`useCache`	`boolean`	Whether to use the cached results or not

View Source utils/MoorhenMolecule.ts, line 3065

Returns:

A list of SVG descriptions for the ligands in this molecule instance

Type: Promise.<Array.<string>>

# async getMoleculeDiameter() → {number}

Get the diameter of this molecule

View Source utils/MoorhenMolecule.ts, line 2589

Returns:

The molecule diameter

Type: number

# async getNcsRelatedChains() → {Array.<Array.<string>>}

Get chain IDs that are related by NCS or molecular symmetry

View Source utils/MoorhenMolecule.ts, line 2992

Returns:

An array of arrays where chain IDs are grouped together

Type: Array.<Array.<string>>

# async getNeighborResiduesCids(selectionCid, radius, minDist, maxDist) → {Promise.<Array.<string>>}

Get the CIDs for all residues wihtin a distance threshold of a set of residues

Parameters:

Name	Type	Description
`selectionCid`	`string`	The CID indicating the selection of residues used for the search
`radius`	`number`	The radius used in the search
`minDist`	`number`	Minimum distance for the serch
`maxDist`	`number`	Maximum distance for the search

View Source utils/MoorhenMolecule.ts, line 2427

Returns:

List of CIDs with the residues found within the radius of search

Type: Promise.<Array.<string>>

# getNonSelectedCids(cid) → {Array.<string>}

Get the CIDs of residues not included in the input CID

Parameters:

Name	Type	Description
`cid`	`string`	The input CID selection

View Source utils/MoorhenMolecule.ts, line 3032

Returns:

An array of CIDs for the residue ranges not included in the input CID

Type: Array.<string>

# async getNumberOfAtoms() → {Promise.<number>}

A function to get the number of atoms in the current molecule

View Source utils/MoorhenMolecule.ts, line 2999

Returns:

The number of atoms in the molecule

Type: Promise.<number>

# async getPrivateerValidation(useCache) → {Promise.<Array.<privateer.ResultsEntry>>}

Get results of privateer validation for this molecule instance

Parameters:

Name	Type	Description
`useCache`	`boolean`	Whether to use the cached results or not

View Source utils/MoorhenMolecule.ts, line 3056

Returns:

A list of results from privateer validation

Type: Promise.<Array.<privateer.ResultsEntry>>

# getResidueBFactors() → {Array.<object>}

Get information about the residue B-factors

View Source utils/MoorhenMolecule.ts, line 2985

Returns:

An array of objects indicating the residue CID and B-factor

Type: Array.<object>

# async getSecondaryStructInfo(modelNumber) → {Array.<object>}

Get the secondary structure information for the residues in the current molecule

Parameters:

Name	Type	Description
`modelNumber`	`number`	The model number to extract secondary structure information from

View Source utils/MoorhenMolecule.ts, line 3040

Returns:

An array of objects containing the secondary structure information for each residue

Type: Array.<object>

# getUnitCellParams()

Get the unit cell parameters for the molecule

View Source utils/MoorhenMolecule.ts, line 2416

Returns:

An object with the unit cell parameters

# hide(style, cidopt)

Hide a type of representation for the molecule

Parameters:

Name	Type	Attributes	Description
`style`	`string`		The representation style to hide
`cid`	`string`	<optional>	The CID selection for the representation

View Source utils/MoorhenMolecule.ts, line 2666

# async hideCid(cid, redrawopt) → {Promise.<void>}

Hide representations for a given CID selection

Parameters:

Name	Type	Attributes	Default	Description
`cid`	`string`			The CID selection
`redraw`	`boolean`	<optional>	true	Indicates if the molecule should be redrawn

View Source utils/MoorhenMolecule.ts, line 2861

Returns:

Type: Promise.<void>

# async isValidSelection(cid) → {boolean}

Test whether an atom selection is valid

Parameters:

Name	Type	Description
`cid`	`string`	The CID selection

View Source utils/MoorhenMolecule.ts, line 3025

Returns:

Whether the selection is valid

Type: boolean

# isVisible(excludeStyles) → {boolean}

Determine whether this molecule instance has any visible buffers

Parameters:

Name	Type	Description
`excludeStyles`	`Array.<string>`	A list of representation styles that should be excluded from this check

View Source utils/MoorhenMolecule.ts, line 2846

Returns:

True if the molecule has any visible buffers

Type: boolean

# async loadMissingMonomer(newTlc, attachToMolecule) → {Promise.<string>}

Load a the missing dictionary for a monomer. First attempts to load it from the monomer library, if it fails it will load from the EBI.

Parameters:

Name	Type	Description
`newTlc`	`string`	Three letter code for the monomer
`attachToMolecule`	`number`	Molecule number for which the dicitonary will be associated

View Source utils/MoorhenMolecule.ts, line 2545

Returns:

Type: Promise.<string>

# async loadMissingMonomers() → {Promise.<moorhen.Molecule>}

Attempt to load dictionaries for all missing monomers present in the molecule

View Source utils/MoorhenMolecule.ts, line 2552

Returns:

This molecule instance

Type: Promise.<moorhen.Molecule>

# async loadToCootFromFile(source) → {Promise.<moorhen.Molecule>}

Load a new molecule from the contents of a file

Parameters:

Name	Type	Description
`source`	`File`	The input file

View Source utils/MoorhenMolecule.ts, line 2520

Returns:

The new molecule

Type: Promise.<moorhen.Molecule>

# async loadToCootFromString(coordData, name) → {Promise.<moorhen.Molecule>}

Load a new molecule from a string

Parameters:

Name	Type	Description
`coordData`	`string`	The molecule data
`name`	`string`	The new molecule name

View Source utils/MoorhenMolecule.ts, line 2536

Returns:

The new molecule

Type: Promise.<moorhen.Molecule>

# async loadToCootFromURL(url, molName, optionsopt) → {Promise.<moorhen.Molecule>}

Load a new molecule from a file URL

Parameters:

Name	Type	Attributes	Description
`url`	`string`		The url to the path with the data for the new molecule
`molName`	`string`		The new molecule name
`options`	`object`	<optional>	Options passed to fetch API

View Source utils/MoorhenMolecule.ts, line 2512

Returns:

The new molecule

Type: Promise.<moorhen.Molecule>

# async lsqkbSuperpose(refMolNo, residueMatches, matchTypeopt, redrawopt) → {Promise.<void>}

Use LSQKB to superpose this molecule (as the moving structure) with another molecule isntance

Parameters:

Name	Type	Attributes	Default	Description
`refMolNo`	`string`			Molecule number for the reference structure
`residueMatches`	`Array.<moorhen.lskqbResidueRangeMatch>`			A list of objects describing the residue matches for LSQKB
`matchType`	`number`	<optional>	1	The match type for LSQKB: 0 - all \| 1 - main \| 2 - CAs
`redraw`	`boolean`	<optional>	true	Indicates if the molecule should be redrawn

View Source utils/MoorhenMolecule.ts, line 2966

Returns:

Type: Promise.<void>

# async mergeFragmentFromRefinement(cid, fragmentMolecule, acceptTransformopt, refineAfterMergeopt)

Merge a fragment that was used for refinement into the current molecule

Parameters:

Name	Type	Attributes	Default	Description
`cid`	`Array.<string>`			The CID selection used to create the fragment
`fragmentMolecule`	`moorhen.Molecule`			The fragment molecule
`acceptTransform`	`boolean`	<optional>	true	Indicates whether the transformation should be accepted
`refineAfterMerge`	`boolean`	<optional>	false	Indicates whether another cycle of refinement should be run after merging the fragment

View Source utils/MoorhenMolecule.ts, line 2502

# async mergeMolecules(otherMolecules, doHideopt) → {Promise.<void>}

Merge a set of molecules in this molecule instance

Parameters:

Name	Type	Attributes	Default	Description
`otherMolecules`	`moorhen.Molecule`			A list of other molecules to merge into this instance
`doHide`	`boolean`	<optional>	false	Indicates whether the source molecules should be hidden when finish

View Source utils/MoorhenMolecule.ts, line 2779

Returns:

Type: Promise.<void>

# async minimizeEnergyUsingCidAnimated(cid, ncyc, nIterations, useRamaRestraints, ramaWeight, useTorsionRestraints, torsionWeight)

Minimize the energy of a given set of residues (usually a ligand)

Parameters:

Name	Type	Description
`cid`		The CID for the input residues
`ncyc`		The number of cycles
`nIterations`		The number of iterations
`useRamaRestraints`		Indicates whether ramachandran restraints should be used
`ramaWeight`		Indicates the weight assigned to ramachandran restraints
`useTorsionRestraints`		Indicates whether torsion restraints should be used
`torsionWeight`		Indicates the weight assigned to torsion restraints

View Source utils/MoorhenMolecule.ts, line 3097

# async moveMoleculeHere(x, y, z) → {Promise.<void>}

Move the molecule to a new position

Parameters:

Name	Type	Description
`x`	`number`	Coordinate X
`y`	`number`	Coordinate Y
`z`	`number`	Coordinate Z

View Source utils/MoorhenMolecule.ts, line 3009

Returns:

Type: Promise.<void>

# async parseCidIntoSelection(cid) → {object}

Parse a CID selection into a residue selection object

Parameters:

Name	Type	Description
`cid`	`string`	The CID selection

View Source utils/MoorhenMolecule.ts, line 3017

Returns:

An object for the residue selection

Type: object

# parseSequences() → {void}

Parse the sequences in the molecule

View Source utils/MoorhenMolecule.ts, line 2433

Returns:

Type: void

# async redo() → {Promise.<void>}

Redo last action performed on this molecule

View Source utils/MoorhenMolecule.ts, line 2824

Returns:

Type: Promise.<void>

# async redraw() → {Promise.<void>}

Redraw the molecule representations

View Source utils/MoorhenMolecule.ts, line 2744

Returns:

Type: Promise.<void>

# async redrawAdaptativeBonds(selectionString) → {Promise.<void>}

Draw bonds for a given glRef origin

Parameters:

Name	Type	Description
`selectionString`	`string`	The CID selection for the residues that will be highlighted

View Source utils/MoorhenMolecule.ts, line 2729

Returns:

Type: Promise.<void>

# async redrawRepresentation(id)

Redraw a molecule representation

Parameters:

Name	Type	Description
`id`	`string`	Unique identifier for the representation of interest

View Source utils/MoorhenMolecule.ts, line 2651

# async refineResidueRange(chainId, start, stop, ncycopt, redrawopt) → {Promise.<void>}

Refine a residue range

Parameters:

Name	Type	Attributes	Default	Description
`chainId`	`string`			The chain ID for the residue range
`start`	`string`			First residue number in the range
`stop`	`string`			Last residue number in the range
`ncyc`	`number`	<optional>	4000	Number of refinement cycles
`redraw`	`boolean`	<optional>	true	Indicates if the molecule should be redrawn

View Source utils/MoorhenMolecule.ts, line 2915

Returns:

Type: Promise.<void>

# async refineResiduesUsingAtomCid(cid, mode, ncycopt, redrawopt) → {Promise.<void>}

Refine a set of residues

Parameters:

Name	Type	Attributes	Default	Description
`cid`	`string`			The CID selection with the atoms that should be refined
`mode`	`string`			Refinement mode (SINGLE, TRIPLE ...etc.)
`ncyc`	`number`	<optional>	4000	Number of refinement cycles
`redraw`	`boolean`	<optional>	true	Indicates if the molecule should be redrawn

View Source utils/MoorhenMolecule.ts, line 2903

Returns:

Type: Promise.<void>

# async refineResiduesUsingAtomCidAnimated(cid, activeMap, dist, redraw, redrawFragmentFirst)

Refine a residue CID with animation

Parameters:

Name	Type	Description
`cid`	`Array.<string>`	The CID selection used to create the fragment
`activeMap`	`moorhen.Map`	The map instance used in the refinement
`dist`	`number`	The maximum distance used to get neighboring residues for the refinement. Use -1 for literal CID instead of neighbours.
`redraw`	`boolean`	Indicate if the molecules should be redrawn
`redrawFragmentFirst`	`boolean`	Indicate if the fragment should be redrawn first

View Source utils/MoorhenMolecule.ts, line 2926

# removeRepresentation(representationId)

Remove a representation for this molecule instance

Parameters:

Name	Type	Description
`representationId`	`string`	The unique identifier for the representation

View Source utils/MoorhenMolecule.ts, line 2678

# async replaceModelWithCoordData(coordData) → {Promise.<void>}

Replace the current molecule some file contents

Parameters:

Name	Type	Description
`coordData`	`string`	The coord data for new model

View Source utils/MoorhenMolecule.ts, line 2349

Returns:

Type: Promise.<void>

# async replaceModelWithFile(fileUrl) → {Promise.<void>}

Replace the current molecule with the model in a file

Parameters:

Name	Type	Description
`fileUrl`	`string`	The uri to the file with the new model

View Source utils/MoorhenMolecule.ts, line 2341

Returns:

Type: Promise.<void>

# async rigidBodyFit(cidsString, mapNo) → {Promise.<void>}

Run rigid body fitting

Parameters:

Name	Type	Description
`cidsString`	`string`	Residue CID selection
`mapNo`	`number`	Map number that should be used

View Source utils/MoorhenMolecule.ts, line 2877

Returns:

Type: Promise.<void>

# setAtomsDirty(state) → {void}

Set the cached molecule atoms as "dirty". This means new bond representations need to be fetched next time the molecule is redrawn.

Parameters:

Name	Type	Description
`state`	`boolean`	Indicate whether the current atom representation is dirty

View Source utils/MoorhenMolecule.ts, line 2560

Returns:

Type: void

# setBackgroundColour(backgroundColour)

Set the background colour where the molecule is being drawn. Used to detect whether the background is dark and molecule needs to be rendered using lighter colours.

Parameters:

Name	Type	Description
`backgroundColour`	`Array.<number>`	The rgba indicating the background colour

View Source utils/MoorhenMolecule.ts, line 2402

# async setDrawAdaptativeBonds(newValue)

Value setter for MoorhenMolecule.adaptativeBondsEnabled

Parameters:

Name	Type	Description
`newValue`	`boolean`	The new value

View Source utils/MoorhenMolecule.ts, line 2721

# setSymmetryRadius(radius) → {Promise.<void>}

Set the radius to draw symmetry mates

Parameters:

Name	Type	Description
`radius`	`number`	Symmetry mates with an atom within this radius will be drawn

View Source utils/MoorhenMolecule.ts, line 2368

Returns:

Type: Promise.<void>

# show(style, cidopt) → {void}

Show the representation for the molecule

Parameters:

Name	Type	Attributes	Description
`style`	`string`		The representation style to show
`cid`	`string`	<optional>	The CID selection for the representation

View Source utils/MoorhenMolecule.ts, line 2659

Returns:

Type: void

# async splitMultiModels(drawopt) → {Array.<moorhen.Molecule>}

Split a molecule with multiple models into separate molecules (one for each model)

Parameters:

Name	Type	Attributes	Default	Description
`draw`	`boolean`	<optional>	false	Indicates whether the new molecules should be drawn

View Source utils/MoorhenMolecule.ts, line 3084

Returns:

- A list with the new molecules

Type: Array.<moorhen.Molecule>

# toggleBiomolecule() → {void}

Turn on/off molecule symmetry

View Source utils/MoorhenMolecule.ts, line 2355

Returns:

Type: void

# toggleSymmetry() → {Promise.<void>}

Turn on/off molecule symmetry

View Source utils/MoorhenMolecule.ts, line 2361

Returns:

Type: Promise.<void>

# async transferLigandDicts(toMolecule, overrideopt)

Transfer ligand dictionaries stored in this molecule instance to other molecule

Parameters:

Name	Type	Attributes	Default	Description
`toMolecule`	`morhen.Molecule`			The molecule where the metadata will be transferred
`override`	`boolean`	<optional>	false	Override ligand dictionaries already stored under the same ligand name in the other molecule instance

View Source utils/MoorhenMolecule.ts, line 2463

# async transferMetaData(otherMolecule, transferDictsopt)

Transfer metadata stored in this molecule instance to other molecule

Parameters:

Name	Type	Attributes	Default	Description
`otherMolecule`	`morhen.Molecule`			The molecule where the metadata will be transferred
`transferDicts`	`boolean`	<optional>	true	Indicates whether ligand dictionaries should also be transferred

View Source utils/MoorhenMolecule.ts, line 2455

# transformedCachedAtomsAsMovedAtoms(selectionCid) → {Array.<Array.<moorhen.AtomInfo>>}

Move residues by applying a series of cached matrix transformations

Parameters:

Name	Type	Description
`selectionCid`	`string`	The CID selection for the set of residues that will be moved

View Source utils/MoorhenMolecule.ts, line 2751

Returns:

New atom information for the moved residues

Type: Array.<Array.<moorhen.AtomInfo>>

# async undo() → {Promise.<void>}

Undo last action performed on this molecule

View Source utils/MoorhenMolecule.ts, line 2817

Returns:

Type: Promise.<void>

# async unhideAll(redrawopt)

Unhide all the molecule representations

Parameters:

Name	Type	Attributes	Default	Description
`redraw`	`boolean`	<optional>	true	Indicates if the molecule should be redrawn

View Source utils/MoorhenMolecule.ts, line 2868

# async updateAtoms()

Update the cached atoms with the latest information from the libcoot api

View Source utils/MoorhenMolecule.ts, line 2595

# async updateGemmiStructure(coordString) → {Promise.<void>}

Update the cached gemmi structure for this molecule

Parameters:

Name	Type	Description
`coordString`	`string`

View Source utils/MoorhenMolecule.ts, line 2410

Returns:

Type: Promise.<void>

# async updateLigands() → {Promise.<void>}

Update the ligand dictionaries for this molecule instance

View Source utils/MoorhenMolecule.ts, line 2831

Returns:

Type: Promise.<void>

# async updateWithMovedAtoms(movedResidues) → {Promise.<void>}

Update the molecule with a set of moved residues

Parameters:

Name	Type	Description
`movedResidues`	`Array.<Array.<moorhen.AtomInfo>>`	Set of moved residues

View Source utils/MoorhenMolecule.ts, line 2759

Returns:

Type: Promise.<void>

# static guessCoordFormat(coordDataString) → {string}

Guess the coordinate format from the file contents

Parameters:

Name	Type	Description
`coordDataString`	`string`	The file contents

View Source utils/MoorhenMolecule.ts, line 2527

Returns:

- The file format

Type: string

Moorhen Developer Documentation

# new MoorhenMolecule(commandCentre, glRef, storeopt, monomerLibraryPathopt)

Parameters:

Properties:

Example

Classes

Methods

# async SSMSuperpose(movChainId, refMolNo, refChainId, redrawopt) → {Promise.<void>}

Parameters:

# async addDict(fileContent) → {Promise.<void>}

Parameters:

# async addLigandOfType(resType, fromMolNoopt) → {Promise.<moorhen.WorkerResponse>}

Parameters:

# async addRepresentation(style, cid, isCustomopt, colourRulesopt, bondOptionsopt, m2tParamsopt)

Parameters:

# async animateRefine(n_cyc, n_iteration, final_n_cycopt)

Parameters:

# applyTransform()

# buffersInclude(bufferIn) → {boolean}

Parameters:

# cacheLigandDict(fileContent) → {void}

Parameters:

# async centreAndAlignViewOn(selectionCid, alignWithCBopt, zoomLevelopt) → {Promise.<void>}

Parameters:

# async centreOn(selectionCid, animateopt) → {Promise.<void>}

Parameters:

# async changeChainId(oldId, newId, startResNo, endResNo) → {number}

Parameters:

# async checkHasGlycans() → {Promise.<boolean>}

# checkIsLigand() → {boolean}

# clearBuffersOfStyle(style)

Parameters:

# clearExtraRestraints() → {Promise.<moorhen.WorkerResponse>}

# async copyFragmentForRefinement(cid, refinementMap, redraw, redrawFragmentFirst) → {moorhen.Molecule}

Parameters:

# async copyFragmentUsingCid(cid, doRecentreopt, styleopt) → {Promise.<moorhen.Molecule>}

Parameters:

# async copyMolecule(doRedraw) → {moorhen.Molecule}

Parameters:

# async delete(popBackImolopt) → {Promise.<moorhen.WorkerResponse>}

Parameters:

# async deleteCid(cid, redrawopt) → {object}

Parameters:

# async downloadAtoms(formatopt)

Parameters:

# drawBiomolecule(fetchSymMatrixopt) → {void}

Parameters:

# async drawEnvironment(selectionCid) → {Promise.<void>}

Parameters:

# async drawHover(selectionString) → {Promise.<void>}

Parameters:

# async drawResidueSelection(selectionString) → {Promise.<void>}

Parameters:

# async drawSymmetry(fetchSymMatrixopt) → {Promise.<void>}

Parameters:

# async drawUnitCell()

# async drawWithStyleFromMesh(style, meshObjects, cidopt) → {Promise.<void>}

Parameters:

# async exportAsGltf(representationId) → {ArrayBuffer}

Parameters:

# fetchBiomoleculeMatrix() → {void}

# async fetchDefaultColourRules()

# async fetchHeaderInfo(useCache) → {Promise.<libcootApi.headerInfoJS>}

Parameters:

# async fetchIfDirtyAndDraw(style) → {Promise.<void>}

Parameters:

# async fetchSymmetryMatrix() → {Promise.<void>}

# async fitLigand(mapMolNo, ligandMolNo, fitRightHereopt, redrawopt, useConformersopt, conformerCountopt) → {Promise.<Array.<moorhen.Molecule>>}

Parameters:

# async gemmiAtomsForCid(cid) → {Promise.<Array.<moorhen.AtomInfo>>}

Parameters:

# async generateSelfRestraints(cidopt, maxRadiusopt) → {Promise.<void>}

Parameters:

# async getActiveAtom() → {string}

# async getAtoms(formatopt) → {string}

Parameters:

# getChainNames() → {Array.<string>}

# getDict(comp_id) → {string}

Parameters:

# async getLigandSVG(resName, useCache) → {Promise.<Array.<string>>}