Molecule Class

Construct a blank Molecule object.

Construct a Molecule object and initialize it with atoms and bonds from src.

The collection contains all atoms.

The collection contains all bonds.

Canonical Code of the structure

Returns element composition

Returns the molecular exact mass

Extended SMILES string

The fingerprints of the structure. (documents)

The string version of the fingerprints of the structure. (link)

Formula in plain-text

Formula in HTML

Normalized searchable formula

Compute the topological hash code of molecule. Each identical chemical structure has its own hash code.

Compute the topological hash code of molecule, but ignore stereochemistry.

Returns the InChI (The IUPAC International Chemical Identifier). InChI extension has to be installed to call this function. If not installed, it always return null.

InChIKey is hashed InChI, which is more efficient to be used as structure key.

Test if the Molecule is empty.

Returns the molecular weight

Get ordered atom list.

Returns the molecule t-PSA (Topological Polar Surface Area), which is invented by Peter Ertl etc.

The collection contains all atoms and bonds.

SMILES string

Returns Smallest Set of Smallest Rings (SSSR) from the molecule topological graph.

A higher level of structure characterization (link)

The string version of StructureKeys

Find all connected bonds of a given atom

Break metal bonds

Change atoms' position to make the structure looks nicer. If no coordinates, new 2D coordinates will be assigned. If it is a reaction, it also re-layout the reaction components.

Change atoms's position to make the structure looks nicers

Clear all contained objects, including atoms and bonds.

Clear Atom/Bond colors

Clone the molecule.

Generate 3D coordinates. ForceField extension has to be installed.

Copy all objects, including atoms and bonds, to another molecule.

Count atoms

Count atoms

Count atoms

Convert rings to aromatic

Dump all contents to console for debugging purpose

Determines whether the specified Object is equal to the current Object.

Test if this molecule is topologically identical to the query molecule

Allows an object to try to free resources and perform other cleanup operations before it is reclaimed by garbage collection.

Compute the neat formal charges of the molecule, which actually add all atom formal charges together.

Returns Atom stereochemistry CIP

Get the 3D bounds of this molecule.

Create the canonical code

Serves as a hash function for a particular type.

Draw a radar chart to visualize druglikeness of the molecular using MW, CLogP, NoHA, NoHD, NoRB, tPSA

Return the image bytes of the radar chart

Find all R groups.

Gets the Type of the current instance.

Test if the molecule contains any R group. R group defines a structure variable.

Test if the atoms have Z coordaintes

Highlight scaffold with a given color

Convert aromatic rings into kekule form

Creates a shallow copy of the current Object.

Merge from all contents of a molecule

Neutrialize atom charges

Neutralize ionic bonds

Normalize the molecular formula

Compute the total number of hydrogen bond acceptors.

Compute the total number of hydrogen bond donors.

Compute the total number of rotable bonds. Rotatable bond is defined as any single non-ring bond, bounded to nonterminal heavy (i.e., non-hydrogen) atom

Try to open a binary data, which could be a binary file, for a compress file

Read from a stream, which can be any chemical file format

Try to parse a generic chemical string, which could be SMILES, InChI, MolFile or other chemical string

Try to open a known binary data

Try to open a binary data, which could be a binary file, for a compress file

Read from a stream, and the file format is known

Read from a stream, which can be any chemical file format

Parse a known chemical string

Try to parse a chemical string

Try to open a file

Parse a InChI string

Parse a chemical name string

Parse a SMILES string

Remove all explicit hydrogen atoms

Reset atom ID, starting from 1

Reset atom ID, starting from a given number

Strip salts and solvates

Generate an image for the structure

Generate an image for the structure

Generate structure image

Generate structure image

Mark this molecule modified, so cached topological data, such as SSSR, will be invalidated.

Split fragments to different Molecule

Split fragments to different atom-bond set

Test if the molecule is a substructure of the input query

Test if the molecule is a super structure of the input query

Compute the Tanimoto Coefficient of two fingerprints.

Generate an image of the structure

Generate an image of the structure

Generate an image of the structure

Generate a vector image, which is resizable

Generate a vector image, which is resizable

Serialize the object to a string

Translate the whole structure

Write object into a file

Store the object into a stream

Store the object into a stream

Compute XLogP of the molcule. ForceField extension has to be installed. It returns NaN if not installed.