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.