

In [1]:

    
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



In [3]:

    
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:

2-Deoxy-Glucose: PMMURAAUARKVCB-CERMHHMHSA-N-D
Norvaline: SNDPXSYFESPGGJ-SCSAIBSYSA-N



In [2]:

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









    Out[2]:






    
        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



In [3]:

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









    Out[3]:






    
        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.



In [4]:

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



In [5]:

    
ref.id









    Out[5]:





3004454



In [6]:

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



In [7]:

    
mets[0]









    Out[7]:






    
        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



In [ ]:

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

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

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