Namespace: chem

dg.chem

Cheminformatics-related routines

Enumerations

• Notation
• SKETCHER_MODE

Classes

• Sketcher
• SketcherBase

Variables

CHEM_FILTER_ALIGN

• Const CHEM_FILTER_ALIGN: "align"

Defined in

src/chem.ts:47

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CHEM_FILTER_HIGHLIGHT

• Const CHEM_FILTER_HIGHLIGHT: "highlight"

Defined in

src/chem.ts:48

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FILTER_KEY

• Const FILTER_KEY: "chem-filter"

Defined in

src/chem.ts:46

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KEY

• Const KEY: "selected"

Defined in

src/chem.ts:45

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SKETCHER_LOCAL_STORAGE

• SKETCHER_LOCAL_STORAGE: string = 'sketcher'

Defined in

src/chem.ts:43

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STORAGE_NAME

• Const STORAGE_NAME: "sketcher"

Defined in

src/chem.ts:44

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currentSketcherType

• currentSketcherType: string = DEFAULT_SKETCHER

Defined in

src/chem.ts:63

Functions

canvasMol

▸ canvasMol(x, y, w, h, canvas, molString, scaffoldMolString?, options?): Promise<void>

Renders a molecule to canvas (using RdKit) TODO: should NOT be async See example: chem

Parameters

Name	Type	Default value
x	number	undefined
y	number	undefined
w	number	undefined
h	number	undefined
canvas	Object	undefined
molString	string	undefined
scaffoldMolString	null | string	null
options	Object	undefined
options.normalizeDepiction	boolean	true
options.straightenDepiction	boolean	true

Returns

Promise<void>

Defined in

src/chem.ts:835

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checkSmiles

▸ checkSmiles(s): boolean

Parameters

Name	Type
s	string

Returns

boolean

Defined in

src/chem.ts:875

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convert

▸ convert(s, sourceFormat, targetFormat): string

Parameters

Name	Type
s	string
sourceFormat	Notation
targetFormat	Notation

Returns

string

Defined in

src/chem.ts:867

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descriptors

▸ descriptors(table, column, descriptors): Promise<DataFrame>

Calculates specified descriptors for the molecular column. See example: https://public.datagrok.ai/js/samples/domains/chem/descriptors

Async

Parameters

Name	Type	Description
table	DataFrame	Table.
column	string	Column name with SMILES to calculate descriptors for.
descriptors	string[]	RDKit descriptors to calculate.

Returns

Promise<DataFrame>

Defined in

src/chem.ts:795

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descriptorsTree

▸ descriptorsTree(): Promise<object>

Returns available descriptors tree. See example: https://public.datagrok.ai/js/samples/domains/chem/descriptors

Returns

Promise<object>

Defined in

src/chem.ts:804

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diversitySearch

▸ diversitySearch(column, settings?): Promise<DataFrame>

Returns the specified number of most diverse molecules in the column. See example: https://datagrok.ai/help/datagrok/solutions/domains/chem/#similarity-and-diversity-search

Async

Parameters

Name	Type	Default value	Description
column	Column<any>	undefined	Column with molecules to search in
settings	Object	undefined	Settings
settings.limit	number	Number.MAX_VALUE	Would return top limit molecules

Returns

Promise<DataFrame>

• DataFrame with 1 column:
  • molecule: set of diverse structures

Defined in

src/chem.ts:724

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drawMolecule

▸ drawMolecule(molString, w?, h?, popupMenu?): HTMLDivElement

Parameters

Name	Type	Default value
molString	string	undefined
w?	number	undefined
h?	number	undefined
popupMenu	boolean	false

Returns

HTMLDivElement

Defined in

src/chem.ts:847

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findSimilar

▸ findSimilar(column, molecule?, settings?): Promise<DataFrame | null>

Computes similarity scores for molecules in the input vector based on a preferred similarity score. See example: https://public.datagrok.ai/js/samples/domains/chem/similarity-scoring-sorted

Async

Parameters

Name	Type	Default value	Description
column	Column<any>	undefined	Column with molecules to search in
molecule	string	''	Reference molecule in one of formats supported by RDKit: smiles, cxsmiles, molblock, v3Kmolblock, and inchi
settings	Object	undefined	Properties for the similarity function
settings.cutoff	number	0.0	Would drop molecules which score is lower than cutoff
settings.limit	number	Number.MAX_VALUE	Would return top limit molecules based on the score

Returns

Promise<DataFrame | null>

• DataFrame with 3 columns:
  • molecule: original molecules string representation from the input column
  • score: similarity scores within the range from 0.0 to 1.0; DataFrame is sorted descending by this column
  • index: indices of the molecules in the original input column

Defined in

src/chem.ts:700

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getSimilarities

▸ getSimilarities(column, molecule?, settings?): Promise<Column | null>

Computes similarity scores for molecules in the input vector based on a preferred similarity score. See example: https://public.datagrok.ai/js/samples/domains/chem/similarity-scoring-scores

Async

Parameters

Name	Type	Default value	Description
column	Column<any>	undefined	Column with molecules to search in
molecule	string	''	Reference molecule in one of formats supported by RDKit: smiles, cxsmiles, molblock, v3Kmolblock, and inchi
settings	object	{}	Properties for the similarity function (type, parameters, etc.)

Returns

Promise<Column | null>

• Column of corresponding similarity scores

Defined in

src/chem.ts:673

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isMolBlock

▸ isMolBlock(s): boolean

Parameters

Name	Type
s	null | string

Returns

boolean

Defined in

src/chem.ts:65

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isSmarts

▸ isSmarts(s): boolean

Parameters

Name	Type
s	string

Returns

boolean

Defined in

src/chem.ts:883

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mcs

▸ mcs(table, column, returnSmarts?, exactAtomSearch?, exactBondSearch?): Promise<string>

Finds Most Common Substructure in the specified column. See example: https://public.datagrok.ai/js/samples/domains/chem/mcs

Async

Parameters

Name	Type	Default value	Description
table	DataFrame	undefined	-
column	string	undefined	Column with SMILES to analyze.
returnSmarts	boolean	false	-
exactAtomSearch	boolean	true	-
exactBondSearch	boolean	true	-

Returns

Promise<string>

Defined in

src/chem.ts:774

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rGroup

▸ rGroup(table, column, core): Promise<DataFrame>

Performs R-group analysis. See example: https://public.datagrok.ai/js/samples/domains/chem/descriptors

Async

Parameters

Name	Type	Description
table	DataFrame	Table.
column	string	Column name with molecules to analyze.
core	string	Core molecule.

Returns

Promise<DataFrame>

Defined in

src/chem.ts:761

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searchSubstructure

▸ searchSubstructure(column, pattern?, settings?): Promise<BitSet>

Searches for a molecular pattern in a given column, returning a bitset with hits. See example: https://public.datagrok.ai/js/samples/domains/chem/substructure-search-library

Async

Parameters

Name	Type	Default value	Description
column	Column<any>	undefined	Column with molecules to search
pattern	string	''	Pattern, either one of which RDKit supports
settings	Object	{}
settings.molBlockFailover?	string	undefined	-

Returns

Promise<BitSet>

Defined in

src/chem.ts:741

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sketcher

▸ sketcher(onChangedCallback, smiles?): HTMLElement

Sketches Molecule sketcher.

Parameters

Name	Type	Default value	Description
onChangedCallback	Function	undefined	a function that accepts (smiles, molfile)
smiles	string	''	Initial molecule

Returns

HTMLElement

Defined in

src/chem.ts:862

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smilesFromSmartsWarning

▸ smilesFromSmartsWarning(): string

Returns

string

Defined in

src/chem.ts:894

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svgMol

▸ svgMol(smiles, width?, height?, options?): HTMLDivElement

Renders a molecule to SVG See example: https://public.datagrok.ai/js/samples/domains/chem/mol-rendering

Parameters

Name	Type	Default value	Description
smiles	string	undefined	accepts smiles/molfile format
width	number	300
height	number	200
options?	Object	undefined	OCL.IMoleculeToSVGOptions

Returns

HTMLDivElement

Defined in

src/chem.ts:817