In place of a detailed outline of the strategy for creating SMARTS patterns for classification (which doesn't exist), the following at least lists common features that we have used in constructing the patterns that constitute the core of yaccl.
This page can be considered an extension of such introductory pages by Daylight as:
- https://www.daylight.com/dayhtml_tutorials/languages/smarts/smarts_examples.html
- https://www.daylight.com/dayhtml_tutorials/languages/smarts/
- https://www.daylight.com/dayhtml/doc/theory/theory.smarts.html
The patterns are all working in rdkit.
| SMILES | comment |
|---|---|
C |
aliphatic C |
c |
aromatic C |
[#6] |
any C |
[CR0] |
aliphatic C not in ring |
[CR1] |
aliphatic C in exactly one ring |
[cr5] |
aromatic C in 5-member ring |
[Cr;!r3;!r4;!r5;!r6;!r7] |
aliphatic C in macrocycle (>7) |
[CX4H1] |
C bound to 4 atoms, of which one is H |
| --- | --- |
[$(C);$(CO)] |
C bound to O---this only describes and matches the C! |
[$(C);$([CX4H1](C)(C)O),$([CX4H2](C)C)] |
C bound either to C,C,O,H or to C,C,H,H |
[$(C);!$(C(~C)(~C)(~C)~C)] |
C not bound to 4 other C |
[CR0][$([CR0]);$([CX3H0](=O)),$([CX4H1](C)(C)O),$([CX4H2](C)C)][CR0] |
C-CH2-C or C-CHOH-C or C-C(=O)-C outside of any ring |
[$(C);$([CX4H1](C)(C)O),$([CX4H2](C)C),$([CX3H0](C)(C)O),$([CX3H1](C)C)]~[$(C);$([CX4H1](C)(C)O),$([CX4H2](C)C),$([CX3H0](C)(C)O),$([CX3H1](C)C)] |
C-C or C=C as part of a C-chain, with possible O being bound |
| --- | --- |
[#6R1]1~[#7R1]~[#6R1]~[#6R1]~[#6R1]~[#6R1]~1 |
pyridine ring in any state of hydrogenization (e.g. piperidine), with no second ring fused |
[$([#6]);$([CX4r5]N),$([CX4r5]CN),$([CX4r6]N),$([CX4r6]CN), $([CX4r6]CCN),$([cX3r6]n),$([cX3r6]cn),$([cX3r6]ccn)] |
C inside a 5- or 6-ring with N being in 1- or 2-position (5-ring), or in 1,2,3-position (aliphatic/aromatic). Reader task: this can be shortened |
[$([cR1]);!$(c(c)(n)[CR0][CR0](~[CR0](O))[NR0]) ;!$(c(c)(n)[CR0][CR0][NR0]~[CR0](O)) ;!$(c(c)(n)CC[NR1;!r5,!r6,!r7,!r8]~C(O))] |
aromatic C, part of a single ring, without attached ringless CC(CC=O)N moiety, without attached ringless CCNC(=O) moiety (as well as its tautomer CCN=C(O) ), without attached CCNC(=O) (or tautomer) in a ring bigger than 8. This atom is part of the SMARTS for imidazole alkaloid; if we wouldn't exlude all the moieties we would taint our alkaloids with peptides or cyclopeptides containing His |