Names and identifiers

IUPAC name

A systematic chemical name that describes a structure according to naming rules. AtomLens can experimentally translate supported IUPAC names into structure input.

OPSIN

The name-to-structure parser used by AtomLens for IUPAC name translation.

SMILES

A compact text line that encodes atoms, bonds, branches, rings, charges, and sometimes stereochemistry for a molecule.

ISO SMILES

AtomLens' label for isomeric SMILES, which keeps stereochemistry and isotope information when that information is available.

CXSMILES

An extended SMILES notation that can carry extra annotations such as coordinates, atom labels, highlights, Markush features, and query information.

InChI

The IUPAC International Chemical Identifier, a standard text identifier for a chemical structure.

InChIKey

A fixed-length hash derived from an InChI. It is easier to search and compare than the full InChI, but it is not a complete structure description.

RInChI

The Reaction InChI, a standard identifier that describes a chemical reaction by combining the InChI identifiers for its participants.

RInChIKey

A hash identifier derived from an RInChI. AtomLens shows long, short, and web variants when it can generate them.

Long RInChIKey

The most information-rich RInChIKey variant. It is longer but gives the lowest practical collision risk among the displayed RInChIKey forms.

Short RInChIKey

A shorter RInChIKey variant that AtomLens also uses when naming extracted reaction files.

Web RInChIKey

The shortest RInChIKey variant, intended for compact web search and linking rather than as the strongest unique identifier.

RInChI Status

The generation result for a reaction identifier. Success means the identifier was produced; warning or error means AtomLens received diagnostic messages.

RInChI Messages

Diagnostic text from the RInChI generator explaining warnings or errors.

Molecular formula

A count of the elements in a molecule, such as C2H6O for ethanol.

Structure properties

Atom

An individual element center in the structure, such as carbon, oxygen, nitrogen, or chlorine.

Bond

A connection between atoms. Bond order describes whether it is single, double, triple, aromatic, or another supported type.

Heavy atom

An atom other than hydrogen. Heavy atom count is often a quick measure of structure size.

Molecular weight

The calculated mass of one molecule, displayed in daltons (Da).

Molar mass

The mass of one mole of the substance, displayed in grams per mole (g/mol).

Monoisotopic mass

The mass calculated from the most common isotope of each element, useful for mass spectrometry work.

Dalton (Da)

A unit used for molecular-scale mass. One dalton is close to the mass of one proton or neutron.

H-Bond Donor

A group that can donate a hydrogen bond, commonly involving hydrogens attached to oxygen or nitrogen.

H-Bond Acceptor

An atom or group that can accept a hydrogen bond, commonly involving oxygen, nitrogen, or sulfur lone pairs.

TPSA

Topological polar surface area. It estimates exposed polar surface from the 2D structure and is often used to reason about permeability.

Van der Waals Volume

An approximate volume occupied by the atoms in a molecule based on their van der Waals radii.

Rotatable Bond

A bond that can usually rotate freely. Higher counts often mean a more flexible molecule.

Ring Count

The number of ring systems detected in the molecule.

Rule of Five

Lipinski's quick guideline for drug-like small molecules, based on molecular weight, hydrogen bonding, and related properties.

Aromaticity

A bonding pattern common in benzene-like rings. AtomLens can draw aromatic systems with inner lines or aromatic circles.

Stereochemistry

Information about three-dimensional arrangement, such as wedge bonds, double-bond geometry, or chiral centers.

Isotope

An atom of the same element with a different mass number. Isotopes can be preserved in identifiers and isomeric SMILES.

Charge

A positive or negative formal charge assigned to an atom or group.

Valency

The expected number or pattern of bonds around an atom. Unusual valency can indicate a real special case or a malformed structure.

Query atom

An atom placeholder used in search or query formats. It can represent a class of possible atoms instead of one exact element.

Query bond

A bond placeholder used in search or query formats. It can represent several possible bond types.

Highlight

Visual annotation that marks atoms, bonds, or regions of interest without changing the underlying chemistry.

Reaction terms

Reaction

A chemical transformation with input substances and output substances, sometimes with agents or conditions.

Reactant

A starting substance consumed or transformed by the reaction.

Agent

A reagent, catalyst, solvent, or condition involved in the reaction but not treated as a main reactant or product.

Product

A substance produced by the reaction.

Reaction participant

Any reactant, agent, or product displayed as part of the reaction.

Stoichiometry

The relative amount or coefficient of a participant in a reaction.

Direction

The meaning of the reaction arrow, such as forward, backward, bidirectional, no-go, retrosynthetic, resonance, or undirected.

Forward

A reaction direction where reactants are transformed into products in the displayed left-to-right direction.

Backward

A reaction direction where the displayed arrow points from products back toward reactants.

Bidirectional

A reaction direction indicating that both forward and reverse transformations are relevant.

No Go

A reaction direction used to indicate that the transformation is not expected or did not proceed.

Retrosynthetic

A planning direction that works backward from a target product to possible starting materials.

Resonance

A relationship between alternative drawings of the same electronic structure, rather than a normal chemical conversion.

Undirected

A reaction record without a specific reaction direction.

Atom-map number

A number that links corresponding atoms across reactants and products so changes can be followed through a reaction.

Reaction SMILES

A SMILES-based text format for reactions, usually separating reactants, agents, and products with arrow-like delimiters.

Formats and notation

CML

Chemical Markup Language, an XML format for molecules and reactions.

MDL Molfile

A common structure file format for one molecule, usually using the .mol extension.

MDL SDFile

A multi-record structure format, usually using .sdf or .sd , that can store molecules plus named data fields.

SDF Attribute

A named data field stored with an SDF record, such as a supplier ID, activity value, or annotation.

V2000

The older and widely supported MDL Molfile/RXN syntax.

V3000

A newer MDL Molfile/RXN syntax that can represent larger and more complex structures.

MDL RXN

An MDL reaction file format, usually using the .rxn extension.

MDL RDF

An MDL reaction data file format that can contain reaction records plus associated data.

Tripos MOL2

A text structure format often used for molecular modeling and atom-type information.

PDB

Protein Data Bank format, commonly used for macromolecular 3D structures.

XYZ

A simple coordinate format listing atoms and 3D positions.

CSV

Comma-separated values. AtomLens uses CSV for extracted SDF attribute tables.

SVG

Scalable Vector Graphics. AtomLens can export or share structure drawings as resolution-independent artwork.

PNG

A raster image format useful for snapshots and sharing into apps that expect images.

PDF

A page-based document format useful for printing, review, and vector-preserving sharing.

Markush structure

A generic structure with variable groups, often used to describe a family of related compounds.

R-group

A variable substituent in a Markush or query structure.

Scaffold

The main shared core of a structure or structure family.

Repeat unit

A structural unit that repeats in a polymer or repeating notation.

Link node

A notation feature that represents repeated attachment through a link in certain query or polymer-like structures.