2.2 Find analogs for target

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.

from marsi.chemistry.common import dynamic_fingerprint_cut

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"

from marsi.chemistry.molecule import Molecule

glucose_molecule = Molecule.from_inchi(glucose_inchi)

glucose_molecule

cutoff = dynamic_fingerprint_cut(glucose_molecule.num_atoms); cutoff

0.439615

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.

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

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

	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

from marsi.io.db import Metabolite

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

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

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

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

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

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