In [1]:

    

from marsi.nearest_neighbors import search_closest_compounds


    

    




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.

In [2]:

    

from marsi.chemistry.common import dynamic_fingerprint_cut


    

In [3]:

    

glucose_inchi = "InChI=1/C6H12O6/c7-1-2-3(8)4(9)5(10)6(11)12-2/h2-11H,1H2/t2-,3-,4+,5-,6+/m1/s1"


    

In [4]:

    

from marsi.chemistry.molecule import Molecule


    

In [5]:

    

glucose_molecule = Molecule.from_inchi(glucose_inchi)


    

In [6]:

    

glucose_molecule


    

    
Out[6]:

In [7]:

    

cutoff = dynamic_fingerprint_cut(glucose_molecule.num_atoms); cutoff


    

    
Out[7]:





0.439615

In [8]:

    

hits = search_closest_compounds(molecule=glucose_molecule, fp_cut=cutoff)


    

    




/usr/local/miniconda3/envs/marsi/lib/python3.5/site-packages/sklearn/utils/validation.py:475 DataConversionWarning: Data with input dtype int32 was converted to bool by check_pairwise_arrays.






    






 
 










    




/Users/joaca/Documents/repositories/marsi/marsi/chemistry/rdkit.py:258 DeprecationWarning: The rdkit.Chem.MCS module is deprecated; please use rdkit.Chem.rdFMCS instead.

In [9]:

    

hits.sort_values('structural_score', ascending=False).head(15)


    

    
Out[9]:







  

    

      

      
formula
      
atoms
      
bonds
      
tanimoto_similarity
      
structural_score
    
  
  

    

      
BQCCAEOLPYCBAE-UKFBFLRUSA-N
      
C6H13NO5
      
25
      
25
      
0.777778
      
0.96
    
    

      
MSWZFWKMSRAUBD-RDQKPOQOSA-N
      
C6H13NO5
      
25
      
25
      
0.777778
      
0.96
    
    

      
MSWZFWKMSRAUBD-UKFBFLRUSA-N
      
C6H13NO5
      
25
      
25
      
0.777778
      
0.96
    
    

      
WCWOEQFAYSXBRK-GKFJPSPNSA-N
      
C6H13NO5
      
25
      
25
      
0.692308
      
0.96
    
    

      
WCWOEQFAYSXBRK-FPRJBGLDSA-N
      
C6H13NO5
      
25
      
25
      
0.692308
      
0.96
    
    

      
WCWOEQFAYSXBRK-FQJSGBEDSA-N
      
C6H13NO5
      
25
      
25
      
0.692308
      
0.96
    
    

      
MSWZFWKMSRAUBD-FQJSGBEDSA-N
      
C6H13NO5
      
25
      
25
      
0.777778
      
0.96
    
    

      
WCWOEQFAYSXBRK-QBFJYBIGSA-N
      
C6H13NO5
      
25
      
25
      
0.692308
      
0.96
    
    

      
WCWOEQFAYSXBRK-DVKNGEFBSA-N
      
C6H13NO5
      
25
      
25
      
0.692308
      
0.96
    
    

      
MSWZFWKMSRAUBD-TVIMKVIFSA-N
      
C6H13NO5
      
25
      
25
      
0.777778
      
0.96
    
    

      
WCWOEQFAYSXBRK-BYIBVSMXSA-N
      
C6H13NO5
      
25
      
25
      
0.692308
      
0.96
    
    

      
MSWZFWKMSRAUBD-HGVZOGFYSA-N
      
C6H13NO5
      
25
      
25
      
0.777778
      
0.96
    
    

      
WCWOEQFAYSXBRK-RWOPYEJCSA-N
      
C6H13NO5
      
25
      
25
      
0.692308
      
0.96
    
    

      
MSWZFWKMSRAUBD-PHYPRBDBSA-N
      
C6H13NO5
      
25
      
25
      
0.777778
      
0.96
    
    

      
MSWZFWKMSRAUBD-FPRJBGLDSA-N
      
C6H13NO5
      
25
      
25
      
0.777778
      
0.96
    
  

In [10]:

    

from marsi.io.db import Metabolite


    

In [11]:

    

Metabolite.get('WCWOEQFAYSXBRK-FPRJBGLDSA-N')


    

    
Out[11]:






    

        
Formula
C6H13NO5
        
InChi
InChI=1S/C6H13NO5/c7-6-5(11)4(10)3(9)2(1-8)12-6/h2-6,8-11H,1,7H2/t2-,3+,4+,5-,6-/m1/s1
        
InChi Key
WCWOEQFAYSXBRK-FPRJBGLDSA-N
        
Structure


        
DBs
zinc: ZINC13544123
        
Synonyms

    

In [12]:

    

Metabolite.get('WCWOEQFAYSXBRK-QBFJYBIGSA-N')


    

    
Out[12]:






    

        
Formula
C6H13NO5
        
InChi
InChI=1S/C6H13NO5/c7-6-5(11)4(10)3(9)2(1-8)12-6/h2-6,8-11H,1,7H2/t2-,3+,4+,5+,6-/m1/s1
        
InChi Key
WCWOEQFAYSXBRK-QBFJYBIGSA-N
        
Structure


        
DBs
zinc: ZINC22059796
        
Synonyms

    

In [13]:

    

Metabolite.get('BQCCAEOLPYCBAE-UKFBFLRUSA-N')


    

    
Out[13]:






    

        
Formula
C6H13NO5
        
InChi
InChI=1S/C6H13NO5/c7-3-4(9)2(1-8)12-6(11)5(3)10/h2-6,8-11H,1,7H2/t2-,3-,4-,5-,6+/m1/s1
        
InChi Key
BQCCAEOLPYCBAE-UKFBFLRUSA-N
        
Structure


        
DBs
zinc: ZINC83295854
        
Synonyms

    

In [ ]: