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Surge: Isomers generation

Introduction​

Surge is a tool to generate isomers from a molecular formula. It is based on the paper Surge: a fast open-source chemical graph generator.

Isomers generation​

This tool provides a list of options for the generation of isomers. The list of options is given in the panel shown below.

Surge Options

The options are as follows:

  • Molecular Fromula: The molecular formula for which the isomers are to be generated.
  • Limit: The maximum number of isomers to be generated.
  • Timeout: The maximum time in seconds to generate isomers (maximum 30s).
  • Calculate IdCode: Whether to calculate the idCode for each isomer.
  • Disallow triple bonds: Whether to disallow triple bonds in the isomers.
  • Require Planarity: Whether to require planarity in the isomers.
  • Limit 3 rings: Limit the number of rings of length 3, with the format max or min:max.
  • Limit 3 rings: Limit the number of rings of length 5, with the format max or min:max.
  • No small ring triple bonds: Whether to disallow triple bonds in rings of size up to 7.
  • Bredt's rule one: Whether to apply Bredt's rule for two rings ijij with one bond in common (33, 34, 35, 36, 44, 45).
  • Bredt's rule two: Whether to apply Bredt's rule for two rings ijij with two bonds in common (ijij up to 56).
  • Bredt's rule three: Whether to apply Bredt's rule for two rings of size 6 sharing three bonds.
  • No K33 K24: Whether to disallow K33 and K24 subgraphs.
  • No cone: None of cone of P4, K4 with 3-ear.
  • No allene: Whether to disallow allenes (A=A=A) in a ring or not.
  • No allene in small rings: Whether to disallow allenes in rings of size up to 8.
  • No small rings common atoms: No atom in more than one ring of length 3 or 4.

After setting all the options, click on the Search strucural isomers button to generate the isomers. The results are shown in a table as shown below.

Surge Results

A list of SMILES and idCodes are shown on the right panel and can easily be copied.

Using the chemical structure editor, you can draw a structure and search for the substructure in the generated isomers. While the substructure is being drawn, the search is performed in real-time and the results are shown in the table.

substructure search