SMILES format using Smiley parser (smy)

The Smiley parser presents an alternative to the standard SMILES parser (SMILES format (smi, smiles)). It was written to be strictly compatible with the OpenSMILES standard (http://opensmiles.org). In comparison, the standard parser is more forgiving to erroneous input, and also supports some extensions such as for radicals.

In addition, the Smiley parser returns detailed error messages when problems arise parsing or validating the SMILES, whereas the standard parser seldom describes the specific problem. For a detailed description of the OpenSMILES semantics, the specification should be consulted. In addition to syntactical and grammatical correctness, the Smiley parser also verifies some basic semantics.

Here are some examples of the errors reported:

SyntaxError: Bracket atom expression contains invalid trailing characters.
F.FB(F)F.[NH2+251][C@@H](CP(c1ccccc1)c1ccccc1)C(C)(C)C 31586112
               ^^
SyntaxError: Unmatched branch opening.
CC(CC
  ^^^
SyntaxError: Unmatched branch closing.
CC)CC
^^^
SemanticsError: Unmatched ring bond.
C1CCC
^
SemanticsError: Conflicing ring bonds.
C-1CCCCC=1

Hydrogen with Hydrogen Count

Hydrogen atoms can not have a hydrogen count. Hydrogen bound to a hydrogen atom should be specified by two bracket atom expressions.

Examples:

[HH]        invalid
[HH1]       invalid (same as [HH]
[HH3]       invalid
[HH0]       valid (same as [H])
[H][H]      valid

Unmatched Ring Bond

Report unmatched ring bonds.

Example:

C1CCC

Conflicting Ring Bonds

When the bond type for ring bonds are explicitly specified at both ends, these should be the same.

Example:

C-1CCCCCC=1

Invalid Ring Bonds

There are two types of invalid ring bonds. The first is when two atoms both have the same two ring bonds. This would mean adding a parallel edge in the graph which is not allowed. The second type is similar but results in a self-loop by having a ring bond number twice.

Examples:

C12CCCC12      parallel bond
C11            self-loop bond

Invalid Chiral Valence

When an atom is specified as being chiral, it should have the correct number of neighboring atoms (possibly including an implicit H inside the bracket.

The valid valences are:

Tetrahedral (TH)          : 4
Allene (AL)               : 4 (*)
Square Planar (SP)        : 4
Trigonal Bypiramidal (TB) : 5
Octahedral(OH)            : 6

(*) The chiral atom has only 2 bonds but the neighbor's neighbors are
    counted: NC(Br)=[C@AL1]=C(F)I

Invalid Chiral Hydrogen Count

Chiral atoms can only have one hydrogen in their bracket since multiple hydrogens would make them not chiral.

Example:

C[C@H2]F

Note

This is a read-only format.