2.1 Find metabolites in the database¶

from marsi.io.db import Metabolite, Reference, Database

Looking for local setup.cfg
Not available [Errno 2] No such file or directory: 'setup.cfg'

/Users/joaca/Documents/repositories/marsi/marsi/chemistry/rdkit.py:25: DeprecationWarning: The rdkit.Chem.MCS module is deprecated; please use rdkit.Chem.rdFMCS instead.
  from rdkit.Chem import AllChem, MACCSkeys, MCS

len(Database.metabolites)

---------------------------------------------------------------------------

TypeError                                 Traceback (most recent call last)

<ipython-input-3-c03391927b54> in <module>()
----> 1 len(Database.metabolites)

TypeError: 'result' object cannot be interpreted as an integer

Metabolites are indexed using InChI key.¶

For example: 1. 2-Deoxy-Glucose: PMMURAAUARKVCB-CERMHHMHSA-N-D 2. Norvaline: SNDPXSYFESPGGJ-SCSAIBSYSA-N

Metabolite.get('PMMURAAUARKVCB-CERMHHMHSA-N')

Formula	C6H12O5
InChi	InChI=1S/C6H12O5/c7-2-4-6(10)3(8)1-5(9)11-4/h3-10H,1-2H2/t3-,4-,5?,6+/m1/s1
InChi Key	PMMURAAUARKVCB-CERMHHMHSA-N
Structure
DBs	drugbank: DB08831
Synonyms	2-Deoxy-D-arabino-hexose

Metabolite.get('SNDPXSYFESPGGJ-SCSAIBSYSA-N')

Formula	C5H11NO2
InChi	InChI=1S/C5H11NO2/c1-2-3-4(6)5(7)8/h4H,2-3,6H2,1H3,(H,7,8)/t4-/m1/s1
InChi Key	SNDPXSYFESPGGJ-SCSAIBSYSA-N
Structure
DBs	zinc: ZINC00391822
Synonyms

The query can also be done using identifiers from databases¶

References are not indexed so this can be very slow.

ref = Reference.get(accession="ZINC00391822", database="zinc")

ref.id

mets = Metabolite.from_references(references=[ref])

mets[0]

Formula	C5H11NO2
InChi	InChI=1S/C5H11NO2/c1-2-3-4(6)5(7)8/h4H,2-3,6H2,1H3,(H,7,8)/t4-/m1/s1
InChi Key	SNDPXSYFESPGGJ-SCSAIBSYSA-N
Structure
DBs	zinc: ZINC00391822
Synonyms