The following is a working list of chemical notations used in chemistry. It does not contain most commercial formats (SDF, MOL, Gaussian, XYZ, etc...) but instead focuses on formats which more linear and human-readable (i.e. not heavily based on coordinates).
Human readable nomenclature
Empirical formula
Chemical formula
Chemical formula with functional group notation
Chemical formula with bond-structural notation
Chemical formula with bond graphics
Chemical formula with molecular obrital
Chemical formula with electron flow arrows
Skeletal formula*
IUPAC name
Zeolite nomenclature
Metal-organic framework (MOF) nomenclature
Crystallographic nomenclatures, http://www.iucr.org/resources/commissions/crystallographic-nomenclature
Quasi-crystal nomenclature
IUPAC Polymer nomenclature
polymer notations based on monomer, repeating groups or blocks
Human & machine readable
SMILES
SMARTS
SMIRKS
Canonical SMILES
CHORTLES - http://pubs.acs.org/doi/abs/10.1021/ci00028a012
InChI
InChI Key
Sybyl line notation (SLN) - http://pubs.acs.org/doi/abs/10.1021/ci7004687; http://pubs.acs.org/doi/abs/10.1021/ci960109j
FASTA
PLN (protein line notation) - http://www.biochemfusion.com/doc/Biochemfusion_PLN_1.4_spec.pdf
PLN binary format - http://www.biochemfusion.com/doc/Biochemfusion_BinaryMoleculeFormat_1.0_spec.pdf
Protein primary structure - full amino acid name
Protein primary structure - 3 letter amino acid
Protein primary structure - single letter amino acid
WizePairZ - http://pubs.acs.org/doi/abs/10.1021/ci100084s
CHEMO - http://pubs.acs.org/doi/abs/10.1021/ci9501094
Line notation for Markush structures - http://pubs.acs.org/doi/abs/10.1021/c160030a011
Line system for coordination compounds - http://pubs.acs.org/doi/abs/10.1021/c160016a010
Reaction-MQL - http://pubs.acs.org/doi/abs/10.1021/ci800215t
Organic compounds - http://pubs.acs.org/doi/abs/10.1021/c160011a003
RInChI - http://www.jcheminf.com/content/5/1/45
Topology and graph theory
Wiswesser line notation (WLN)
Wiswesser lines notation for polyhexes
N-tuple code
Boundary representation
Binary boundary representation
Weighted ID (WID)
QSAR based
QSPR based
Descriptor spaces
Diagram based notations
Kekulé structures
Dewar structures
Rumer diagrams
Slater determinant (matrix representation)
Molecular orbitals
Bond line notation
Valence bond
Dash and wedge bond stereochemistry notation
Resonance structures
Molecular orbital** - Varying degrees of molecular orbitals can be superimposed on line structures
Symmetry classifications (point group, space group)
Database representation
Hash code
Binary hash code
Industry specific
Cement chemist notation (CCN)
Mineral naming
Mineralogical nomenclature of silicas
Indexing pesticides - http://pubs.acs.org/doi/abs/10.1021/c160015a007
International nomenclature of cosmetic ingredients (INCI)
CRC compound classification scheme
CAS number
IRAC MoA classification scheme (insecticides; mode of action) - http://www.irac-online.org/documents/moa-classification/?ext=pdf
IARC PAH (polyaromatic hydrocarbon) classification - http://www.crios.be/PAHs/specific_classification/IARC.htm
Pesticides
http://www.pesticideinfo.org/Docs/ref_general2.html
California DPR chemical code
US EPA PC Code
FICTS
FICuS
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