Functional GroupsΒΆ
Below is a list of the functional groups that cocktail-shaker currently supports.
Functional Group |
Class |
SMILES |
Smarts |
Bromine |
Halogens |
Br |
[Br] |
Chlorine |
Halogens |
Cl |
[Cl] |
Fluorine |
Halogens |
F |
[F] |
Acyl Bromide |
Acyl Halides |
C(=O)Br |
[CX3](=[OX1])[Br] |
Acyl Chloride |
Acyl Halides |
C(=O)Cl |
[CX3](=[OX1])[Cl] |
Acyl Fluoride |
Acyl Halides |
C(=O)F |
[CX3](=[OX1])[F] |
Acyl Iodide |
Acyl Halides |
C(=O)I |
[CX3](=[OX1])[I] |
Primary Alcohol |
Alcohols |
O |
[OX2H] |
Ketone |
Ketones |
C(=O)OC |
[CX3]=[OX1] |
Carboxylic Acid |
Acids |
C(=O)O |
[CX3](=O)[OX1H0-,OX2H1] |
Acetic Anhydride |
Anhydrides |
CC(=O)OC(=O)C |
[CX3](=[OX1])[OX2][CX3](=[OX1]) |
Primary Amine |
Amines |
N |
[NX3;H2;!$(NC=[!#6]);!$(NC#[!#6])][#6] |
Secondary Amine |
Amines |
NC |
[NX3;H2,H1;!$(NC=O)] |
Enamine |
Amines |
N |
[NX3][CX3]=[CX3] |
Amide |
Amides |
C(=O)N |
[NX3][CX3](=[OX1])[#6] |
Nitro |
Nitros |
[N+](=O)[O-] |
[$([NX3](=O)=O),$([NX3+](=O)[O-])][!#8] |
Sulfoxide |
Sulfoxides |
S(=O)(=O) |
[$([#16X3](=[OX1])([#6])[#6]),$([#16X3+]([OX1-])([#6])[#6])] |
Ether |
Ethers |
COC |
[OD2]([#6])[#6] |
Azide |
Azides |
C([N-][N+]#N) |
[$(-[NX2-]-[NX2+]#[NX1]),$(-[NX2]=[NX2+]=[NX1-])] |
If you would like to add to this list, the functional group information is stored in the datasource directory under R_Groups.yml.
Each smart pattern recognition is tested thoroughly before moving into the cocktail-shaker package, so please PR your test as well. You can follow the schema outlined in the function test_primary_finding_r_groups.