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 condense_abbreviations condense_abbreviations_from_defs delete draw_to_canvas draw_to_canvas_with_highlights draw_to_canvas_with_offset generate_aligned_coords get_aromatic_form get_as_uint8array get_cxsmarts get_cxsmiles get_descriptors get_inchi get_json get_kekule_form get_molblock get_morgan_fp get_morgan_fp_as_binary_text get_morgan_fp_as_uint8array get_new_coords get_pattern_fp get_pattern_fp_as_binary_text get_pattern_fp_as_uint8array get_pickle get_prop get_prop_list get_smarts get_smiles get_stereo_tags get_substruct_match get_substruct_matches get_svg get_svg_with_highlights get_v3Kmolblock has_coords has_prop is_valid normalize_depiction remove_hs set_new_coords set_prop straighten_depiction

Methods

add_hs

  • Add explicit hydrogens

    Returns string

    V2000 Molfile string with explicit hydrogens

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

  • Delete C++ mol objects manually from memory

    See Emscripten docs for more details

    Returns void

draw_to_canvas

  • Draw the molecule to an HTML5 canvas

    Parameters

    • canvas: HTMLCanvasElement

      canvas ID

    • width: number

      width in pixels

    • height: number

      height in pixels

    Returns void

draw_to_canvas_with_highlights

  • Draw the molecule to an HTML5 canvas, with atom highlights

    Parameters

    Returns void

draw_to_canvas_with_offset

  • 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

generate_aligned_coords

  • Aligns molecule with the template. you can also specify the following options (passed as a stringified JSON object)

    Parameters

    • templateMol: JSMol
    • options: string

    Returns string

get_aromatic_form

  • Returns the V2000 Molfile representation of the aromatic form of the molecule

    Returns string

get_as_uint8array

  • Returns an unsigned integer array representation

    Returns Uint8Array

get_cxsmarts

  • Returns the Chemaxon Extended SMARTS string

    Returns string

get_cxsmiles

  • Returns the Chemaxon Extended SMILES string

    Returns string

get_descriptors

  • Returns a stringified JSON object of molecular descriptors

    Returns string

get_inchi

  • Return the InChI string

    Returns string

get_json

  • Returns the JSON representation

    Returns string

get_kekule_form

  • Returns the V2000 Molfile representation of the kekule form of the molecule

    Returns string

get_molblock

  • Returns the V2000 Molfile string

    Returns string

get_morgan_fp

  • Returns the Morgan fingerprint as string

    Returns string

  • Returns the Morgan fingerprint as string.

    You can also specify the following options (passed as a stringified JSON object)

    Parameters

    • options: string

    Returns string

get_morgan_fp_as_binary_text

  • get_morgan_fp_as_binary_text(): string

  • Returns the Morgan fingerprint as binary

    Returns string

  • get_morgan_fp_as_binary_text(radius, len): string

  • Returns the Morgan fingerprint as binary

    Parameters

    • radius: number

      fingerprint radius

    • len: number

      fingerprint length

    Returns string

get_morgan_fp_as_uint8array

  • Returns the Morgan fingerprint as an unsigned integer array

    Returns Uint8Array

  • Returns the Morgan fingerprint as an unsigned integer array

    You can also specify the following options (passed as a stringified JSON object)

    Parameters

    • options: string

    Returns Uint8Array

get_new_coords

  • Return a V2000 Molfile string with newly generated coordinates

    Returns string

  • Return a V2000 Molfile string with newly generated coordinates

    Parameters

    • useCoordGen: boolean

      use the CoordGen algorithm

    Returns string

get_pattern_fp

  • Returns the pattern fingerprint as string

    Returns string

  • Returns the pattern fingerprint as string

    you can also specify the following options (passed as a stringified JSON object)

    Parameters

    • options: string

    Returns string

get_pattern_fp_as_binary_text

  • get_pattern_fp_as_binary_text(): string

  • Returns the pattern fingerprint as binary

    Returns string

  • get_pattern_fp_as_binary_text(len): string

  • Returns the pattern fingerprint as binary

    Parameters

    • len: number

      fingerprint length

    Returns string

get_pattern_fp_as_uint8array

  • Returns the pattern fingerprint as an unsigned integer array

    Returns Uint8Array

  • Returns the pattern fingerprint as an unsigned integer array

    you can also specify the following options (passed as a stringified JSON object)

    Parameters

    • options: string

    Returns Uint8Array

get_pickle

  • Returns the pickled string representation of the molecule

    Returns string

get_prop

  • Get a property on the molecule

    Parameters

    • key: string

      property name

    Returns string

get_prop_list

  • Returns the list of property names

    Returns string[]

  • Returns the list of property names

    Parameters

    • includePrivate: boolean

      set to true to include private properties

    Returns 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[]

get_smarts

  • Returns the SMARTS string

    Returns string

get_smiles

  • Returns the SMILES string

    Returns string

get_stereo_tags

  • Returns a stringified JSON object containing the atoms and bonds of stereo centers

    Returns string

get_substruct_match

  • Returns a substructure match string

    Parameters

    • q: JSMol

      query molecule

    Returns string

    A stringified JSON object containing the matched atoms and bonds of the parent molecule

get_substruct_matches

  • Returns all substructure matches

    Parameters

    • q: JSMol

      query molecule

    Returns string

    A stringified JSON object containing the matched atoms and bonds of the parent molecule

get_svg

  • Returns an SVG of the molecule

    Returns string

  • Returns an SVG of the molecule

    Parameters

    • width: number

      Width in pixels

    • height: number

      Height in pixels

    Returns string

get_svg_with_highlights

  • Returns an SVG of the molcule, with atoms highlighted

    Parameters

    Returns string

get_v3Kmolblock

  • Returns the V3000 Molfile string

    Returns string

has_coords

  • Check is the molecule has any 2D coordinates generated

    Returns boolean

has_prop

  • Check whether the molecule has a certain property

    Parameters

    • key: string

      property name

    Returns boolean

is_valid

  • Returns true if the molecule's structure is valid

    Returns boolean

normalize_depiction

  • Returns number

  • Parameters

    • canonicalize: number

    Returns number

  • Parameters

    • canonicalize: number
    • scaleFactor: number

    Returns number

remove_hs

  • Remove explicit hydrogens

    Returns string

    V2000 Molfile string without explicit hydrogens

set_new_coords

  • Generate new 2D coordinates

    Returns boolean

  • Generate new 2D coordinates

    Parameters

    • useCoordGen: boolean

      use the CoordGen algorithm

    Returns boolean

set_prop

  • Sets a property on the molecule

    Parameters

    • key: string

      property name

    • val: string

      property value

    Returns 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

straighten_depiction

  • Returns void

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