A chemical formula is a way of presenting information about the chemical proportions of atoms that constitute a particular chemical compound or molecule, using chemical element symbols, numbers, and sometimes also other symbols, such as parentheses, dashes, brackets, commas and plus (+) and minus (−) signs. These are limited to a single typographic line of symbols, which may include subscripts and superscripts. A chemical formula is not a chemical name, and it contains no words. Although a chemical formula may imply certain simple chemical structures, it is not the same as a full chemical structural formula. Chemical formulas can fully specify the structure of only the simplest of molecules and chemical substances, and are generally more limited in power than are chemical names and structural formulas.
The Object Management Group (OMG) is a computer industry standards consortium. OMG Task Forces develop enterprise integration standards for a range of technologies.
The simplified molecular-input line-entry system (SMILES) is a specification in the form of a line notation for describing the structure of chemical species using short ASCII strings. SMILES strings can be imported by most molecule editors for conversion back into two-dimensional drawings or three-dimensional models of the molecules.
The Z notation is a formal specification language used for describing and modelling computing systems. It is targeted at the clear specification of computer programs and computer-based systems in general.
In computer science, Backus–Naur form or Backus normal form (BNF) is a notation technique for context-free grammars, often used to describe the syntax of languages used in computing, such as computer programming languages, document formats, instruction sets and communication protocols. They are applied wherever exact descriptions of languages are needed: for instance, in official language specifications, in manuals, and in textbooks on programming language theory.
In science and engineering, the parts-per notation is a set of pseudo-units to describe small values of miscellaneous dimensionless quantities, e.g. mole fraction or mass fraction. Since these fractions are quantity-per-quantity measures, they are pure numbers with no associated units of measurement. Commonly used are ppm, ppb, ppt and ppq. This notation is not part of the SI system and its meaning is ambiguous.
The structural formula of a chemical compound is a graphic representation of the molecular structure, showing how the atoms are possibly arranged in the real three-dimensional space. The chemical bonding within the molecule is also shown, either explicitly or implicitly. Unlike chemical formulas, which have a limited number of symbols and are capable of only limited descriptive power, structural formulas provide a more complete geometric representation of the molecular structure. For example, many chemical compounds exist in different isomeric forms, which have different enantiomeric structures but the same chemical formula.
A table is an arrangement of data in rows and columns, or possibly in a more complex structure. Tables are widely used in communication, research, and data analysis. Tables appear in print media, handwritten notes, computer software, architectural ornamentation, traffic signs, and many other places. The precise conventions and terminology for describing tables vary depending on the context. Further, tables differ significantly in variety, structure, flexibility, notation, representation and use. In books and technical articles, tables are typically presented apart from the main text in numbered and captioned floating blocks.
A molecule editor is a computer program for creating and modifying representations of chemical structures.
This article discusses some common molecular file formats, including usage and converting between them.
Chemical table file is a family of text-based chemical file formats that describe molecules and chemical reactions. One format, for example, lists each atom in a molecule, the x-y-z coordinates of that atom, and the bonds among the atoms.
Business Process Model and Notation (BPMN) is a graphical representation for specifying business processes in a business process model.
An object diagram in the Unified Modeling Language (UML), is a diagram that shows a complete or partial view of the structure of a modeled system at a specific time.
The SYBYL line notation or SLN is a specification for unambiguously describing the structure of chemical molecules using short ASCII strings. SLN differs from SMILES in several significant ways. SLN can specify molecules, molecular queries, and reactions in a single line notation whereas SMILES handles these through language extensions. SLN has support for relative stereochemistry, it can distinguish mixtures of enantiomers from pure molecules with pure but unresolved stereochemistry. In SMILES aromaticity is considered to be a property of both atoms and bonds whereas in SLN it is a property of bonds.
Wiswesser line notation (WLN), invented by William J. Wiswesser in 1949, was the first line notation capable of precisely describing complex molecules. It was the basis of ICI Ltd's CROSSBOW database system developed in the late 1960s. WLN allowed for indexing the Chemical Structure Index (CSI) at the Institute for Scientific Information (ISI). It was also the tool used to develop the CAOCI database, the datafile from which Accelrys' ACD file was developed. WLN is still being extensively used by BARK Information Services. Descriptions of how to encode molecules as WLN have been published in several books.
SMILES arbitrary target specification (SMARTS) is a language for specifying substructural patterns in molecules. The SMARTS line notation is expressive and allows extremely precise and transparent substructural specification and atom typing.
The hierarchical editing language for macromolecules (HELM) is a method of describing complex biological molecules. It is a notation that is machine readable to render the composition and structure of peptides, proteins, oligonucleotides, and related small molecule linkers.
