Discussion Section

[rapodaca]

Scope, limitations, observations. Maybe some more context.

• benefits
  • compact
  • examples with byte counts
    • compare with molfile
    • use in REPLs
    • Jupyter
    • hand-codable
  • easy to learn
  • designed for lossless (de)serialization
  • c.f. InChI
  • handles most of organic chemistry
• tradeoffs
  • non-representable entities
  • non-VB examples
    • organometallics, homotropylium cation, dative bonding
  • non-tetrahedral stereochemistry
    • e.g., TB, OH, lone-pair tetrahedral
  • conformational restriction other than (E)/(Z) double bonds
  • PPBs are error-prone
• compatibility
  • SMILES itself is not well-defined
  • gather public documentation on syntax/semantics (just the docs)
  • Daylight, OpenSMILES, CDK, OpenBabel, RDKit, Jchem, OE, etc.
  • in case of conflict among tools, choose ease of implementation
  • unsupported
  • some selections (e.g. [se])
  • the "aromatic" bond (:)
  • extreme charges (< -9, > 9)
  • arbitrary element symbols
• extensions
  • extension field
  • can be used to encode application-specific information as integer
    • limited range (0-9999)
    • can be used together with metadata
  • versioning
  • breaks compatibility, but maybe metadata format
  • metaformats - maybe
  • in-line vs out-of-line
  • leverage extension
  • expanding range of selectable atoms
  • additional configuration classes (OH, TB, etc)
  • canonicalization
  • "preferred format"
  • atomic numbering
• outlook
  • detailed spec opens new paths
  • reference implementation
  • to be reported
  • validation suites
  • improve data quality by detecting syntax/semantics differences
  • writing better implementations
  • reading/writing sections
  • performance benchmarks
  • apples/apples comparisons using the same protocols
  • faster processing
  • standardization efforts
  • more detailed, structured source material to draw from
  • select, rather than develop elements of standard
  • better line notations
  • clearly-delineated scope and limitations
  • lots of room for improvement
  • may or may not happen through dialect extensions