Applications - Design and Use of Relational Databases in Chemistry - page 168

structure

property

name
cansmiles
coords

TEXT

TEXT
tvalue TEXT
nvalue NUMERIC
INTEGER

name

TEXT

NUMERIC[]
INTEGER
INTEGER[]

PK id *

FK id *

atoms
isosmiles
fp

TEXT

BIT VARYING

sdf
molfile TEXT
PF id * INTEGER

Figure 13.3 Entity relationship diagram for table created by sdfloader.

script defines the following commands: molgrep, molcat, molview,
molarb, molrandom, molnear, and molsame. These are described
individually below.

13.5.1 molgrep
The molgrep utility takes two arguments: the name of the schema con-
taining structures previously loaded, and a SMILES or SMARTS string.
The result is a list of SMILES and names from structure table, which
match the SMARTS string or which contain the SMILES as a substructure.
For example:

molgrep drugs 'c1ccccc1C(=O)NC'

prints the following subset from the drugs.structure table.

OC(=O)c1ccccc1Nc1cccc(c1)C(F)(F)F|flufenamic
Fc1ccc(cc1)C(=O)CCCN1CCC(O)(CC1)c1ccc(Cl)cc1|haloperidol
CCN(CC)CCNC(=O)c1ccc(N)cc1|procainamide
CCCCNc1ccc(cc1)C(=O)OCCN(C)C|tetracaine

13.5.2 molcat
The molcat utility takes one argument: the name of the schema into
which structures were loaded using the smiloader or sdfloader util-
ity. It prints the SMILES and names of all the structures in the structure
table in that schema. For example:

molcat vla4