Interface JSMol

Represents a molecule object generated by RDKit.js

Remarks

JSMol's are created using the RDKitModule.get_mol() methods.

Hierarchy

JSMol

Methods

add_hs

add_hs(): string
Add explicit hydrogens

Returns
V2000 Molfile string with explicit hydrogens

Returns string
- Defined in index.d.ts:337

condense_abbreviations

condense_abbreviations(): string
Returns string
- Defined in index.d.ts:182
condense_abbreviations(maxCoverage: number, useLinkers: boolean): string
Parameters
- maxCoverage: number
- useLinkers: boolean
Returns string
- Defined in index.d.ts:183

condense_abbreviations_from_defs

condense_abbreviations_from_defs(definitions: string, maxCoverage: number, useLinkers: boolean): string
Parameters
- definitions: string
- maxCoverage: number
- useLinkers: boolean
Returns string
- Defined in index.d.ts:184

delete

delete(): void
Delete C++ mol objects manually from memory

See Emscripten docs for more details

Returns void
- Defined in index.d.ts:18

draw_to_canvas

draw_to_canvas(canvas: HTMLCanvasElement, width: number, height: number): void
Draw the molecule to an HTML5 canvas
Parameters
- canvas: HTMLCanvasElement
  
  canvas ID
- width: number
  
  width in pixels
- height: number
  
  height in pixels
Returns void
- Defined in index.d.ts:357

draw_to_canvas_with_highlights

draw_to_canvas_with_highlights(canvas: HTMLCanvasElement, details: string): void
Draw the molecule to an HTML5 canvas, with atom highlights
Parameters
- canvas: HTMLCanvasElement
  
  canvas ID
- details: string
  
  A stringified JSON object containing any of the following options https://www.rdkitjs.com/#drawing-molecules-all-options
Returns void
- Defined in index.d.ts:369

draw_to_canvas_with_offset

draw_to_canvas_with_offset(canvas: HTMLCanvasElement, offsetx: number, offsety: number, width: number, height: number): void
Draw the molecule to an HTML5 canvas with an offset
Parameters
- canvas: HTMLCanvasElement
  
  canvas ID
- offsetx: number
  
  offset X in pixels
- offsety: number
  
  offset Y in pixels
- width: number
  
  width in pixels
- height: number
  
  height in pixels
Returns void
- Defined in index.d.ts:383

generate_aligned_coords

generate_aligned_coords(templateMol: JSMol): string
Aligns molecule with the template
Parameters
- templateMol: JSMol
  
  template molecule
Returns string
- Defined in index.d.ts:197
generate_aligned_coords(templateMol: JSMol, useCoordGen: boolean): string
Aligns molecule with the template
Parameters
- templateMol: JSMol
  
  template molecule
- useCoordGen: boolean
  
  use CoordGen algorithm
Returns string
- Defined in index.d.ts:205
generate_aligned_coords(templateMol: JSMol, useCoordGen: boolean, allowOptionalAttachements: boolean): string
Aligns molecule with the template
Parameters
- templateMol: JSMol
  
  template molecule
- useCoordGen: boolean
  
  use CoordGen algorithm
- allowOptionalAttachements: boolean
Returns string
- Defined in index.d.ts:214
generate_aligned_coords(templateMol: JSMol, useCoordGen: boolean, allowOptionalAttachements: boolean, acceptFailure: boolean): string
Aligns molecule with the template
Parameters
- templateMol: JSMol
  
  template molecule
- useCoordGen: boolean
  
  use CoordGen algorithm
- allowOptionalAttachements: boolean
- acceptFailure: boolean
Returns string
- Defined in index.d.ts:228

get_aromatic_form

get_aromatic_form(): string
Returns the V2000 Molfile representation of the aromatic form of the molecule

Returns string
- Defined in index.d.ts:245

get_as_uint8array

get_as_uint8array(): Uint8Array
Returns an unsigned integer array representation

Returns Uint8Array
- Defined in index.d.ts:53

get_cxsmarts

get_cxsmarts(): string
Returns the Chemaxon Extended SMARTS string

Returns string
- Defined in index.d.ts:32

get_cxsmiles

get_cxsmiles(): string
Returns the Chemaxon Extended SMILES string

Returns string
- Defined in index.d.ts:26

get_descriptors

get_descriptors(): string
Returns a stringified JSON object of molecular descriptors

Returns string
- Defined in index.d.ts:99

get_inchi

get_inchi(): string
Return the InChI string

Returns string
- Defined in index.d.ts:44

get_json

get_json(): string
Returns the JSON representation

Returns string
- Defined in index.d.ts:47

get_kekule_form

get_kekule_form(): string
Returns the V2000 Molfile representation of the kekule form of the molecule

Returns string
- Defined in index.d.ts:248

get_molblock

get_molblock(): string
Returns the V2000 Molfile string

Returns string
- Defined in index.d.ts:35

get_morgan_fp

get_morgan_fp(): string
Returns the Morgan fingerprint as string

Returns string
- Defined in index.d.ts:107
get_morgan_fp(radius: number, len: number): string
Returns the Morgan fingerprint as string
Parameters
- radius: number
  
  fingerprint radius
- len: number
  
  fingerprint length
Returns string
- Defined in index.d.ts:115

get_morgan_fp_as_binary_text

get_morgan_fp_as_binary_text(): string
Returns the Morgan fingerprint as binary

Returns string
- Defined in index.d.ts:120
get_morgan_fp_as_binary_text(radius: number, len: number): string
Returns the Morgan fingerprint as binary
Parameters
- radius: number
  
  fingerprint radius
- len: number
  
  fingerprint length
Returns string
- Defined in index.d.ts:128

get_morgan_fp_as_uint8array

get_morgan_fp_as_uint8array(): Uint8Array
Returns the Morgan fingerprint as an unsigned integer array

Returns Uint8Array
- Defined in index.d.ts:133
get_morgan_fp_as_uint8array(radius: number, fplen: number): Uint8Array
Returns the Morgan fingerprint as an unsigned integer array
Parameters
- radius: number
  
  fingerprint radius
- fplen: number
  
  fingerprint length
Returns Uint8Array
- Defined in index.d.ts:141

get_new_coords

get_new_coords(): string
Return a V2000 Molfile string with newly generated coordinates

Returns string
- Defined in index.d.ts:261
get_new_coords(useCoordGen: boolean): string
Return a V2000 Molfile string with newly generated coordinates
Parameters
- useCoordGen: boolean
  
  use the CoordGen algorithm
Returns string
- Defined in index.d.ts:268

get_pattern_fp

get_pattern_fp(): string
Returns the pattern fingerprint as string

Returns string
- Defined in index.d.ts:146
get_pattern_fp(len: number): string
Returns the pattern fingerprint as string
Parameters
- len: number
  
  fingerprint length
Returns string
- Defined in index.d.ts:153

get_pattern_fp_as_binary_text

get_pattern_fp_as_binary_text(): string
Returns the pattern fingerprint as binary

Returns string
- Defined in index.d.ts:158
get_pattern_fp_as_binary_text(len: number): string
Returns the pattern fingerprint as binary
Parameters
- len: number
  
  fingerprint length
Returns string
- Defined in index.d.ts:165

get_pattern_fp_as_uint8array

get_pattern_fp_as_uint8array(): Uint8Array
Returns the pattern fingerprint as an unsigned integer array

Returns Uint8Array
- Defined in index.d.ts:170
get_pattern_fp_as_uint8array(fplen: number): Uint8Array
Returns the pattern fingerprint as an unsigned integer array
Parameters
- fplen: number
  
  fingerprint length
Returns Uint8Array
- Defined in index.d.ts:177

get_pickle

get_pickle(): string
Returns the pickled string representation of the molecule

Returns string
- Defined in index.d.ts:41

get_prop

get_prop(key: string): string
Get a property on the molecule
Parameters
- key: string
  
  property name
Returns string
- Defined in index.d.ts:320

get_prop_list

get_prop_list(): string[]
Returns the list of property names

Returns string[]
- Defined in index.d.ts:281
get_prop_list(includePrivate: boolean): string[]
Returns the list of property names
Parameters
- includePrivate: boolean
  
  set to true to include private properties
Returns string[]
- Defined in index.d.ts:288
get_prop_list(includePrivate: boolean, includeComputed: boolean): string[]
Returns the list of property names
Parameters
- includePrivate: boolean
  
  set to true to include private properties
- includeComputed: boolean
  
  set to true to include computed properties
Returns string[]
- Defined in index.d.ts:296

get_smarts

get_smarts(): string
Returns the SMARTS string

Returns string
- Defined in index.d.ts:29

get_smiles

get_smiles(): string
Returns the SMILES string

Returns string
- Defined in index.d.ts:23

get_stereo_tags

get_stereo_tags(): string
Returns a stringified JSON object containing the atoms and bonds of stereo centers

Returns string
- Defined in index.d.ts:242

get_substruct_match

get_substruct_match(q: JSMol): string
Returns a substructure match string

Returns
A stringified JSON object containing the matched atoms and bonds of the parent molecule
Parameters
- q: JSMol
  
  query molecule
Returns string
- Defined in index.d.ts:85

get_substruct_matches

get_substruct_matches(q: JSMol): string
Returns all substructure matches

Returns
A stringified JSON object containing the matched atoms and bonds of the parent molecule
Parameters
- q: JSMol
  
  query molecule
Returns string
- Defined in index.d.ts:93

get_svg

get_svg(): string
Returns an SVG of the molecule

Returns string
- Defined in index.d.ts:59
get_svg(width: number, height: number): string
Returns an SVG of the molecule
Parameters
- width: number
  
  Width in pixels
- height: number
  
  Height in pixels
Returns string
- Defined in index.d.ts:67

get_svg_with_highlights

get_svg_with_highlights(details: string): string
Returns an SVG of the molcule, with atoms highlighted
Parameters
- details: string
  
  A stringified JSON object containing any of the following options https://www.rdkitjs.com/#drawing-molecules-all-options
Returns string
- Defined in index.d.ts:74

get_v3Kmolblock

get_v3Kmolblock(): string
Returns the V3000 Molfile string

Returns string
- Defined in index.d.ts:38

has_coords

has_coords(): boolean
Check is the molecule has any 2D coordinates generated

Returns boolean
- Defined in index.d.ts:239

has_prop

has_prop(key: string): boolean
Check whether the molecule has a certain property
Parameters
- key: string
  
  property name
Returns boolean
- Defined in index.d.ts:278

is_valid

is_valid(): boolean
Returns true if the molecule's structure is valid

Returns boolean
- Defined in index.d.ts:236

normalize_depiction

normalize_depiction(): number
Returns number
- Defined in index.d.ts:342
normalize_depiction(canonicalize: number): number
Parameters
- canonicalize: number
Returns number
- Defined in index.d.ts:343
normalize_depiction(canonicalize: number, scaleFactor: number): number
Parameters
- canonicalize: number
- scaleFactor: number
Returns number
- Defined in index.d.ts:344

remove_hs

remove_hs(): string
Remove explicit hydrogens

Returns
V2000 Molfile string without explicit hydrogens

Returns string
- Defined in index.d.ts:330

set_new_coords

set_new_coords(): boolean
Generate new 2D coordinates

Returns boolean
- Defined in index.d.ts:251
set_new_coords(useCoordGen: boolean): boolean
Generate new 2D coordinates
Parameters
- useCoordGen: boolean
  
  use the CoordGen algorithm
Returns boolean
- Defined in index.d.ts:258

set_prop

set_prop(key: string, val: string): boolean
Sets a property on the molecule
Parameters
- key: string
  
  property name
- val: string
  
  property value
Returns boolean
- Defined in index.d.ts:304
set_prop(key: string, val: string, computed: boolean): boolean
Sets a property on the molecule
Parameters
- key: string
  
  property name
- val: string
  
  property value
- computed: boolean
  
  set true to flag the value as computed
Returns boolean
- Defined in index.d.ts:313

straighten_depiction

straighten_depiction(): void
Returns void
- Defined in index.d.ts:345

Interface JSMol

Remarks

Hierarchy

Index

Methods

Methods

add_hs

Returns

Returns string

condense_abbreviations

Returns string

Parameters

maxCoverage: number

useLinkers: boolean

Returns string

condense_abbreviations_from_defs

Parameters

definitions: string

maxCoverage: number

useLinkers: boolean

Returns string

delete

Returns void

draw_to_canvas

Parameters

canvas: HTMLCanvasElement

width: number

height: number

Returns void

draw_to_canvas_with_highlights

Parameters

canvas: HTMLCanvasElement

details: string

Returns void

draw_to_canvas_with_offset

Parameters

canvas: HTMLCanvasElement

offsetx: number

offsety: number

width: number

height: number

Returns void

generate_aligned_coords

Parameters

templateMol: JSMol

Returns string

Parameters

templateMol: JSMol

useCoordGen: boolean

Returns string

Parameters

templateMol: JSMol

useCoordGen: boolean

allowOptionalAttachements: boolean

Returns string

Parameters

templateMol: JSMol

useCoordGen: boolean

allowOptionalAttachements: boolean

acceptFailure: boolean

Returns string

get_aromatic_form

Returns string

get_as_uint8array

Returns Uint8Array

get_cxsmarts

Returns string

get_cxsmiles

Returns string

get_descriptors

Returns string

get_inchi

Returns string

get_json

Returns string

get_kekule_form

Returns string

get_molblock

Returns string

get_morgan_fp