--- /dev/null 2019-10-21 09:46:46.351315135 +0200 +++ ./Code/PgSQL/rdkit/expected/rdkit-91_1.out 2019-11-02 21:02:13.079044510 +0100 @@ -0,0 +1,878 @@ +-- +-- first, define the datatype. Turn off echoing so that expected file +-- does not depend on contents of rdkit.sql. +-- +SET client_min_messages = warning; +\set ECHO none +RESET client_min_messages; +SELECT is_valid_smiles('c1ccccc1'); + is_valid_smiles +----------------- + t +(1 row) + +SELECT mol_from_smiles('c1ccccc1'); + mol_from_smiles +----------------- + c1ccccc1 +(1 row) + +SELECT is_valid_smiles('c1ccccc'); + is_valid_smiles +----------------- + f +(1 row) + +SELECT mol_from_smiles('c1ccccc'); +WARNING: could not create molecule from SMILES 'c1ccccc' + mol_from_smiles +----------------- + +(1 row) + +SELECT mol_from_smiles('cccccc'); +WARNING: could not create molecule from SMILES 'cccccc' + mol_from_smiles +----------------- + +(1 row) + +SELECT is_valid_smiles('c1cccn1'); + is_valid_smiles +----------------- + f +(1 row) + +SELECT is_valid_smarts('c1ccc[n,c]1'); + is_valid_smarts +----------------- + t +(1 row) + +SELECT mol_from_smarts('c1ccc[n,c]1'); + mol_from_smarts +----------------- + *1cccc1 +(1 row) + +SELECT is_valid_smarts('c1ccc'); + is_valid_smarts +----------------- + f +(1 row) + +SELECT mol_from_smarts('c1ccc'); +WARNING: could not create molecule from SMILES 'c1ccc' + mol_from_smarts +----------------- + +(1 row) + +SELECT mol_to_smiles(mol_from_smiles('c1ccccc1')); + mol_to_smiles +--------------- + c1ccccc1 +(1 row) + +SELECT mol_to_smarts(mol_from_smiles('c1ccccc1')); + mol_to_smarts +---------------------------------- + [#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1 +(1 row) + +SELECT mol_to_smarts('c1cccc[n,c]1'::qmol); + mol_to_smarts +--------------- + c1cccc[n,c]1 +(1 row) + +SELECT mol_to_smiles('c1cccc[n,c]1'::qmol); + mol_to_smiles +--------------- + *1ccccc1 +(1 row) + +SELECT is_valid_smiles(''); + is_valid_smiles +----------------- + t +(1 row) + +SELECT mol_from_smiles(''); + mol_from_smiles +----------------- + +(1 row) + +SELECT mol_to_smiles(mol_from_smiles('')); + mol_to_smiles +--------------- + +(1 row) + +CREATE TABLE pgmol (id int, m mol); +\copy pgmol from 'data/data' +CREATE UNIQUE INDEX mol_ididx ON pgmol (id); +SELECT count(*) FROM pgmol; + count +------- + 1000 +(1 row) + +SELECT count(*) FROM pgmol WHERE m @> 'c1ccccc1'; + count +------- + 901 +(1 row) + +SELECT count(*) FROM pgmol WHERE m @> 'c1cccnc1'; + count +------- + 245 +(1 row) + +SELECT count(*) FROM pgmol WHERE 'c1ccccc1' <@ m; + count +------- + 901 +(1 row) + +SELECT count(*) FROM pgmol WHERE 'c1cccnc1' <@ m; + count +------- + 245 +(1 row) + +SELECT count(*) FROM pgmol WHERE m @> mol_from_smarts('c1ccccc1'); + count +------- + 901 +(1 row) + +SELECT count(*) FROM pgmol WHERE m @> mol_from_smarts('c1cccnc1'); + count +------- + 245 +(1 row) + +SELECT count(*) FROM pgmol WHERE m @> mol_from_smarts('c1ccc[n,c]c1'); + count +------- + 939 +(1 row) + +SELECT count(*) FROM pgmol WHERE mol_from_smarts('c1ccccc1') <@ m; + count +------- + 901 +(1 row) + +SELECT count(*) FROM pgmol WHERE mol_from_smarts('c1ccc[n,c]c1') <@ m; + count +------- + 939 +(1 row) + +SELECT id, rdkit_fp(m) AS f, maccs_fp(m) as maccsf INTO pgbfp FROM pgmol; +CREATE UNIQUE INDEX bfp_ididx ON pgbfp (id); +SELECT id, morgan_fp(m,1) AS f INTO pgsfp FROM pgmol; +CREATE UNIQUE INDEX sfp_ididx ON pgsfp (id); +SELECT id, torsion_fp(m) AS f INTO pgtorsfp FROM pgmol; +SELECT id, atompair_fp(m) AS f INTO pgpairfp FROM pgmol; +set rdkit.tanimoto_threshold=0.5; +set rdkit.dice_threshold=0.5; +SELECT + id, + tanimoto_sml(rdkit_fp('C1C(OC2=CC(=CC(=C2C1=O)O)O)'::mol), f) +FROM + (SELECT * FROM pgbfp ORDER BY id) AS t +WHERE rdkit_fp('C1C(OC2=CC(=CC(=C2C1=O)O)O)'::mol) % f +LIMIT 10; + id | tanimoto_sml +----+-------------- +(0 rows) + +SELECT + id, + dice_sml(rdkit_fp('C1C(OC2=CC(=CC(=C2C1=O)O)O)'::mol), f) +FROM + (SELECT * FROM pgbfp ORDER BY id) AS t +WHERE rdkit_fp('C1C(OC2=CC(=CC(=C2C1=O)O)O)'::mol) % f +LIMIT 10; + id | dice_sml +----+---------- +(0 rows) + +SELECT + id, + tanimoto_sml(rdkit_fp('C1C(OC2=CC(=CC(=C2C1=O)O)O)'::mol), f) +FROM + (SELECT * FROM pgbfp ORDER BY id) AS t +WHERE rdkit_fp('C1C(OC2=CC(=CC(=C2C1=O)O)O)'::mol) # f +LIMIT 10; + id | tanimoto_sml +--------+--------------------- + 66722 | 0.3601036269430052 + 498250 | 0.3682983682983683 + 576770 | 0.35368421052631577 + 644427 | 0.3370165745856354 + 645921 | 0.36594202898550726 + 690546 | 0.402 + 698576 | 0.4226579520697168 + 714484 | 0.3830734966592428 + 771595 | 0.34393638170974156 + 788060 | 0.33386581469648563 +(10 rows) + +SELECT + id, + dice_sml(rdkit_fp('C1C(OC2=CC(=CC(=C2C1=O)O)O)'::mol), f), + size(f) +FROM + (SELECT * FROM pgbfp ORDER BY id) AS t +WHERE rdkit_fp('C1C(OC2=CC(=CC(=C2C1=O)O)O)'::mol) # f +LIMIT 10; + id | dice_sml | size +--------+--------------------+------ + 66722 | 0.5295238095238095 | 1024 + 498250 | 0.5383304940374787 | 1024 + 576770 | 0.5225505443234837 | 1024 + 644427 | 0.5041322314049587 | 1024 + 645921 | 0.5358090185676393 | 1024 + 690546 | 0.5734664764621968 | 1024 + 698576 | 0.5941807044410413 | 1024 + 714484 | 0.5539452495974235 | 1024 + 771595 | 0.5118343195266272 | 1024 + 788060 | 0.5005988023952096 | 1024 +(10 rows) + +set rdkit.tanimoto_threshold=0.4; +SELECT + id, + tanimoto_sml(morgan_fp('C1C(OC2=CC(=CC(=C2C1=O)))'::mol, 1), f) +FROM + (SELECT * FROM pgsfp ORDER BY id) AS t +WHERE morgan_fp('C1C(OC2=CC(=CC(=C2C1=O)))'::mol, 1) % f +LIMIT 10; + id | tanimoto_sml +---------+-------------------- + 3761688 | 0.4418604651162791 +(1 row) + +SELECT + id, + dice_sml(morgan_fp('C1C(OC2=CC(=CC(=C2C1=O)))'::mol, 1), f) +FROM + (SELECT * FROM pgsfp ORDER BY id) AS t +WHERE morgan_fp('C1C(OC2=CC(=CC(=C2C1=O)))'::mol, 1) % f +LIMIT 10; + id | dice_sml +---------+-------------------- + 3761688 | 0.6129032258064516 +(1 row) + +SELECT + id, + tanimoto_sml(morgan_fp('C1C(OC2=CC(=CC(=C2C1=O)O)O)'::mol, 1), f) +FROM + (SELECT * FROM pgsfp ORDER BY id) AS t +WHERE morgan_fp('C1C(OC2=CC(=CC(=C2C1=O)O)O)'::mol, 1) # f +LIMIT 10; + id | tanimoto_sml +----------+--------------------- + 902176 | 0.34782608695652173 + 2952787 | 0.36585365853658536 + 5281628 | 0.34615384615384615 + 10560368 | 0.4358974358974359 + 16196768 | 0.375 +(5 rows) + +SELECT + id, + dice_sml(morgan_fp('C1C(OC2=CC(=CC(=C2C1=O)O)O)'::mol, 1), f) +FROM + (SELECT * FROM pgsfp ORDER BY id) AS t +WHERE morgan_fp('C1C(OC2=CC(=CC(=C2C1=O)O)O)'::mol, 1) # f +LIMIT 10; + id | dice_sml +----------+-------------------- + 902176 | 0.5161290322580645 + 2952787 | 0.5357142857142857 + 5281628 | 0.5142857142857142 + 10560368 | 0.6071428571428571 + 16196768 | 0.5454545454545454 +(5 rows) + +select dice_sml(morgan_fp('C1C(OC2=CC(=CC(=C2C1=O)O)O)'::mol, 1), morgan_fp('C1C(OC2=CC(=CC(=C2C1=O)O)N)'::mol, 1)) sml; + sml +-------------------- + 0.8846153846153846 +(1 row) + +select dice_sml(featmorgan_fp('C1C(OC2=CC(=CC(=C2C1=O)O)O)'::mol, 1), featmorgan_fp('C1C(OC2=CC(=CC(=C2C1=O)O)N)'::mol, 1)) sml; + sml +-------------------- + 0.8846153846153846 +(1 row) + +select dice_sml(morganbv_fp('C1C(OC2=CC(=CC(=C2C1=O)O)O)'::mol, 1), morganbv_fp('C1C(OC2=CC(=CC(=C2C1=O)O)N)'::mol, 1)) sml; + sml +-------------------- + 0.8888888888888888 +(1 row) + +select dice_sml(featmorganbv_fp('C1C(OC2=CC(=CC(=C2C1=O)O)O)'::mol, 1), featmorganbv_fp('C1C(OC2=CC(=CC(=C2C1=O)O)N)'::mol, 1)) sml; + sml +-------------------- + 0.9032258064516129 +(1 row) + +select 'Cc1ccccc1'::mol@='c1ccccc1C'::mol; + ?column? +---------- + t +(1 row) + +select 'Cc1ccccc1'::mol@='c1ccccc1CC'::mol; + ?column? +---------- + f +(1 row) + +select 'Cc1ccccc1'::mol@='c1cccnc1C'::mol; + ?column? +---------- + f +(1 row) + +select subtract(torsion_fp('CCC1CCNCC1'),torsion_fp('OCC1CCNCC1'))=subtract(torsion_fp('CCC1CCOCC1'),torsion_fp('OCC1CCOCC1')); + ?column? +---------- + t +(1 row) + +select subtract(torsion_fp('CCC1CCNCC1'),torsion_fp('OCC1CCNCC1'))=subtract(torsion_fp('CCC1CCOCC1'),torsion_fp('NCC1CCOCC1')); + ?column? +---------- + f +(1 row) + +select add(torsion_fp('CCC1CCNCC1'),torsion_fp('OCC1CCNCC1'))=add(torsion_fp('CCC1CCOCC1'),torsion_fp('OCC1CCOCC1')); + ?column? +---------- + f +(1 row) + +select add(torsion_fp('CCC1CCNCC1'),torsion_fp('OCC1CCNCC1'))=add(torsion_fp('CCC1CCOCC1'),torsion_fp('NCC1CCOCC1')); + ?column? +---------- + f +(1 row) + +select add(torsion_fp('CCC1CCNCC1'),torsion_fp('OCC1CCNCC1'))=subtract(torsion_fp('CCC1CCNCC1'),torsion_fp('OCC1CCNCC1')); + ?column? +---------- + f +(1 row) + +select add(torsion_fp('CCC1CCNCC1'),torsion_fp('OCC1CCNCC1'))=subtract(torsion_fp('CCC1CCOCC1'),torsion_fp('OCC1CCOCC1')); + ?column? +---------- + f +(1 row) + +select is_valid_ctab('chiral1.mol + ChemDraw04200416412D + + 5 4 0 0 0 0 0 0 0 0999 V2000 + -0.0141 0.0553 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.8109 0.0553 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0 + -0.4266 0.7697 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0 0 + -0.0141 -0.7697 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0 + -0.8109 -0.1583 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 1 0 + 1 3 1 0 + 1 4 1 1 + 1 5 1 0 +M END'); + is_valid_ctab +--------------- + t +(1 row) + +select is_valid_ctab('invalid'); + is_valid_ctab +--------------- + f +(1 row) + +select mol_from_ctab('chiral1.mol + ChemDraw04200416412D + + 5 4 0 0 0 0 0 0 0 0999 V2000 + -0.0141 0.0553 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.8109 0.0553 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0 + -0.4266 0.7697 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0 0 + -0.0141 -0.7697 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0 + -0.8109 -0.1583 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 1 0 + 1 3 1 0 + 1 4 1 1 + 1 5 1 0 +M END'); + mol_from_ctab +---------------- + C[C@](F)(Cl)Br +(1 row) + +-- mol_to_ctab() - suppress auto-generation of depiction. +select mol_to_ctab(mol('CCC'), false); + mol_to_ctab +----------------------------------------------------------------------- + + + RDKit 2D + + + + 3 2 0 0 0 0 0 0 0 0999 V2000 + + 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0+ + 1.2990 0.7500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0+ + 2.5981 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0+ + 1 2 1 0 + + 2 3 1 0 + + M END + + +(1 row) + +-- mol_to_ctab() - with auto-generated depiction. +select mol_to_ctab(mol('CCC')); + mol_to_ctab +----------------------------------------------------------------------- + + + RDKit 2D + + + + 3 2 0 0 0 0 0 0 0 0999 V2000 + + 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0+ + 1.2990 0.7500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0+ + 2.5981 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0+ + 1 2 1 0 + + 2 3 1 0 + + M END + + +(1 row) + +-- mol_to_ctab() - should preserve existing/input depiction. Note the +-- extra 'true' parameter to 'mol_from_ctab()' that forces the cartridge +-- to preserve the input conformer. Otherwise the conformer will be lost. +select mol_to_ctab(mol_from_ctab('chiral1.mol + ChemDraw04200416412D + + 5 4 0 0 0 0 0 0 0 0999 V2000 + -0.0141 0.0553 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.8109 0.0553 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0 + -0.4266 0.7697 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0 0 + -0.0141 -0.7697 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0 + -0.8109 -0.1583 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 1 0 + 1 3 1 0 + 1 4 1 1 + 1 5 1 0 +M END', true)); + mol_to_ctab +----------------------------------------------------------------------- + + + RDKit 2D + + + + 5 4 0 0 0 0 0 0 0 0999 V2000 + + -0.0141 0.0553 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0+ + 0.8109 0.0553 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0+ + -0.4266 0.7697 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0 0+ + -0.0141 -0.7697 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0+ + -0.8109 -0.1583 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0+ + 1 2 1 0 + + 1 3 1 0 + + 1 4 1 0 + + 1 5 1 6 + + M END + + +(1 row) + +select all_values_lt(torsion_fp('c1ccccc1C'::mol),2); + all_values_lt +--------------- + f +(1 row) + +select all_values_lt(torsion_fp('c1ccccc1C'::mol),3); + all_values_lt +--------------- + t +(1 row) + +select all_values_gt(torsion_fp('c1ccccc1C'::mol),1); + all_values_gt +--------------- + t +(1 row) + +select all_values_gt(torsion_fp('c1ccccc1C'::mol),2); + all_values_gt +--------------- + f +(1 row) + +select is_valid_mol_pkl('foo'::bytea); + is_valid_mol_pkl +------------------ + f +(1 row) + +select is_valid_mol_pkl(mol_to_pkl('c1ccccc1'::mol)); + is_valid_mol_pkl +------------------ + t +(1 row) + +select mol_from_pkl(mol_to_pkl('c1ccccc1'::mol)); + mol_from_pkl +-------------- + c1ccccc1 +(1 row) + +select tanimoto_sml(morganbv_fp('c1ccccn1'::mol),morganbv_fp('c1ccccc1'::mol)); + tanimoto_sml +-------------------- + 0.3333333333333333 +(1 row) + +select tanimoto_sml(bfp_from_binary_text(bfp_to_binary_text(morganbv_fp('c1ccccn1'::mol))), + bfp_from_binary_text(bfp_to_binary_text(morganbv_fp('c1ccccc1'::mol)))); + tanimoto_sml +-------------------- + 0.3333333333333333 +(1 row) + +-- GitHub issue 9 +select 'C1CC2CC3C45C2C2C6C7C8C9C%10C(C1)C1C%11%10C%109C98C87C76C42C24C65C3C3C56C64C4%12C72C28C79C8%10C9%11C1C1C%109C98C87C42C24C7%12C%116C65C3C3C56C6%11C%117C74C4%12C82C29C8%10C1C1C98C42C24C89C1C1C98C84C4%10C%122C27C7%11C%116C65C3C3C56C6%11C%117C42C24C7%11C%116C65C3C3C56C6%11C%117C74C4%12C%102C28C89C1C1C98C42C24C89C1C1C98C84C4%10C%122C27C7%11C%116C65C3C3C56C6%11C%117C42C24C7%11C%116C65C3C3C56C6%11C%117C74C4%12C%102C28C89C1C1C98C42C24C89C1CC8C4C1C%122C27C4%11C76C65C3CC6C7C4C12'::mol; + mol +---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- + C1CC2CC3C4C5C6C7C8C9C%10C%11C%12C%13C%14C%15C%16CC%17C%18C%19C%20C%21C%22C%23CC%24C%25C%26C%27C%28C%29C%30C%31C%32C%33C%34C%35C%36C%37C(C1)C1C%38C%39C%40C%41C%42C2C32C%423C%41%42C%40%41C%39%40C%38%39C1%37C%361C%35%36C%34%35C%33%34C%32%33C%31%32C%30%31C%29%30C%28%29C%27%28C%26%27C%25%26C%23%24C%22%23C%21%22C%20%21C%19%20C%18%19C%17%16C%15%16C%14%15C%13%14C%12%13C%11%12C%10%11C9%10C89C78C67C56C42C32C%423C%414C%405C%391C%361C%35%17C%34%18C%33%24C%32%25C%31%32C%30%31C%29%30C%28%29C%27%28C%23%26C%22%23C%21%22C%20%21C%19%16C%15%16C%14%15C%13%14C%12%13C%11%12C%10%11C9%10C89C78C62C32C43C51C%171C%184C%245C%256C%327C%31%17C%30%18C%29%19C%23%28C%22%20C%21%16C%15%16C%14%15C%13%14C%12%13C%11%12C%10%11C9%10C82C31C%104C%115C%126C%137C%14%17C%15%18C%20%16%19 +(1 row) + +-- chiral matching +select 'C[C@H](F)Cl'::mol@>'CC(F)Cl'::mol as match; + match +------- + t +(1 row) + +select 'C[C@H](F)Cl'::mol@>'C[C@H](F)Cl'::mol as match; + match +------- + t +(1 row) + +select 'C[C@H](F)Cl'::mol@>'C[C@@H](F)Cl'::mol as match; + match +------- + t +(1 row) + +set rdkit.do_chiral_sss=true; +select 'C[C@H](F)Cl'::mol@>'CC(F)Cl'::mol as match; + match +------- + t +(1 row) + +select 'C[C@H](F)Cl'::mol@>'C[C@H](F)Cl'::mol as match; + match +------- + t +(1 row) + +select 'C[C@H](F)Cl'::mol@>'C[C@@H](F)Cl'::mol as match; + match +------- + f +(1 row) + +set rdkit.do_chiral_sss=false; +-- substructure counts +select substruct_count('c1ccncc1'::mol,'c1ccncc1'::mol); + substruct_count +----------------- + 1 +(1 row) + +select substruct_count('c1ccncc1'::mol,'c1ccncc1'::mol,false); + substruct_count +----------------- + 2 +(1 row) + +-- special queries +select 'c1ccc[nH]1'::mol@>mol_from_smiles('c1cccn1[H]') as match; + match +------- + t +(1 row) + +select 'c1cccn1C'::mol@>mol_from_smiles('c1cccn1[H]') as match; + match +------- + t +(1 row) + +select 'c1ccc[nH]1'::mol@>qmol_from_smiles('c1cccn1[H]') as match; + match +------- + t +(1 row) + +select 'c1cccn1C'::mol@>qmol_from_smiles('c1cccn1[H]') as match; + match +------- + f +(1 row) + +select 'c1ccc[nH]1'::mol@>mol_from_ctab('query + Mrv0541 04021509592D + + 6 6 0 0 0 0 999 V2000 + -0.2652 0.7248 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + -0.9796 1.1373 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -0.9796 1.9623 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.4493 1.9623 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.4493 1.1373 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -0.2652 -0.1002 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 1 0 0 0 0 + 2 3 2 0 0 0 0 + 4 5 2 0 0 0 0 + 1 5 1 0 0 0 0 + 3 4 1 0 0 0 0 + 1 6 1 0 0 0 0 +M END') as match; + match +------- + t +(1 row) + +select 'c1cccn1C'::mol@>mol_from_ctab('query + Mrv0541 04021509592D + + 6 6 0 0 0 0 999 V2000 + -0.2652 0.7248 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + -0.9796 1.1373 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -0.9796 1.9623 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.4493 1.9623 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.4493 1.1373 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -0.2652 -0.1002 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 1 0 0 0 0 + 2 3 2 0 0 0 0 + 4 5 2 0 0 0 0 + 1 5 1 0 0 0 0 + 3 4 1 0 0 0 0 + 1 6 1 0 0 0 0 +M END') as match; + match +------- + t +(1 row) + +select 'c1ccc[nH]1'::mol@>qmol_from_ctab('query + Mrv0541 04021509592D + + 6 6 0 0 0 0 999 V2000 + -0.2652 0.7248 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + -0.9796 1.1373 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -0.9796 1.9623 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.4493 1.9623 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.4493 1.1373 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -0.2652 -0.1002 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 1 0 0 0 0 + 2 3 2 0 0 0 0 + 4 5 2 0 0 0 0 + 1 5 1 0 0 0 0 + 3 4 1 0 0 0 0 + 1 6 1 0 0 0 0 +M END') as match; + match +------- + t +(1 row) + +select 'c1cccn1C'::mol@>qmol_from_ctab('query + Mrv0541 04021509592D + + 6 6 0 0 0 0 999 V2000 + -0.2652 0.7248 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + -0.9796 1.1373 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -0.9796 1.9623 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.4493 1.9623 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.4493 1.1373 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -0.2652 -0.1002 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 1 0 0 0 0 + 2 3 2 0 0 0 0 + 4 5 2 0 0 0 0 + 1 5 1 0 0 0 0 + 3 4 1 0 0 0 0 + 1 6 1 0 0 0 0 +M END') as match; + match +------- + f +(1 row) + +-- mol_adjust_query_properties +select 'C1CC1OC'::mol @> 'C1CC1O*'::mol; + ?column? +---------- + f +(1 row) + +select 'C1CC1OC'::mol @> mol_adjust_query_properties('C1CC1O*'::mol); + ?column? +---------- + t +(1 row) + +select 'C1CC1OC'::mol @> mol_adjust_query_properties('C1CC1O*'::mol,'{"makeDummiesQueries":false}'); + ?column? +---------- + f +(1 row) + +select 'CC1CC1OC'::mol @> 'C1CC1O*'::mol; + ?column? +---------- + f +(1 row) + +select 'CC1CC1OC'::mol @> mol_adjust_query_properties('C1CC1O*'::mol); + ?column? +---------- + f +(1 row) + +select 'CC1CC1OC'::mol @> mol_adjust_query_properties('C1CC1O*'::mol,'{"adjustDegree":false}'); + ?column? +---------- + t +(1 row) + +select 'C1CC1C(C)OC'::mol @> mol_adjust_query_properties('C1CC1CO*'::mol); + ?column? +---------- + t +(1 row) + +select 'C1CC1C(C)OC'::mol @> mol_adjust_query_properties('C1CC1CO*'::mol,'{"adjustDegreeFlags":"IGNOREDUMMIES"}'); + ?column? +---------- + f +(1 row) + +select 'C1CC1CCCC'::mol @> mol_adjust_query_properties('C1CC1CC'::mol); + ?column? +---------- + t +(1 row) + +select 'C1CC1CCCC'::mol @> mol_adjust_query_properties('C1CC1CC'::mol,'{"adjustDegreeFlags":"IGNORENONE"}'); + ?column? +---------- + f +(1 row) + +select 'C1CC1CCCC'::mol @> mol_adjust_query_properties('C1CC1CC'::mol,'{"adjustDegreeFlags":"IGNOREALL"}'); + ?column? +---------- + t +(1 row) + +select 'C1CC1CCCC'::mol @> mol_adjust_query_properties('C1CC1CC'::mol,'{"adjustDegreeFlags":"IGNORECHAINS"}'); + ?column? +---------- + t +(1 row) + +select 'C1CC1CCCC'::mol @> mol_adjust_query_properties('C1CC1CC'::mol,'{"adjustDegreeFlags":"IGNORERINGS"}'); + ?column? +---------- + f +(1 row) + +select 'C1CC1CCCC'::mol @> mol_adjust_query_properties('C1CC1CC'::mol,'{"adjustDegreeFlags":"IGNORERINGS|IGNORECHAINS"}'); + ?column? +---------- + t +(1 row) + +select 'C1C(C)C1CCCC'::mol @> mol_adjust_query_properties('C1CC1CC'::mol); + ?column? +---------- + f +(1 row) + +select 'C1C(C)C1CCCC'::mol @> mol_adjust_query_properties('C1CC1CC'::mol,'{"adjustDegreeFlags":"IGNORENONE"}'); + ?column? +---------- + f +(1 row) + +select 'C1C(C)C1CCCC'::mol @> mol_adjust_query_properties('C1CC1CC'::mol,'{"adjustDegreeFlags":"IGNOREALL"}'); + ?column? +---------- + t +(1 row) + +select 'C1C(C)C1CCCC'::mol @> mol_adjust_query_properties('C1CC1CC'::mol,'{"adjustDegreeFlags":"IGNORECHAINS"}'); + ?column? +---------- + f +(1 row) + +select 'C1C(C)C1CCCC'::mol @> mol_adjust_query_properties('C1CC1CC'::mol,'{"adjustDegreeFlags":"IGNORERINGS"}'); + ?column? +---------- + f +(1 row) + +select 'C1C(C)C1CCCC'::mol @> mol_adjust_query_properties('C1CC1CC'::mol,'{"adjustDegreeFlags":"IGNORERINGS|IGNORECHAINS"}'); + ?column? +---------- + t +(1 row) + +select 'C1C(C)C1CCCC'::mol @> mol_adjust_query_properties('C1CC1CC'::mol,'{"adjustDegreeFlags":"bogus"}'); +ERROR: bad which string provided 'BOGUS' +select 'C1C([2H])C1CCCC'::mol @> mol_adjust_query_properties('C1CC1CC'::mol); + ?column? +---------- + f +(1 row) + +select 'C1C([2H])C1CCCC'::mol @> mol_adjust_query_properties('C1CC1CC'::mol,'{"adjustDegree":false}'); + ?column? +---------- + t +(1 row) + +select 'C1C([2H])C1CCCC'::mol @> mol_adjust_query_properties('C1CC1CC'::mol,'{"adjustDegree":false,"adjustHeavyDegree":true}'); + ?column? +---------- + t +(1 row) + +-- CXSmiles +SELECT mol_to_smiles(mol_from_smiles('C[C@H](F)[C@H](C)[C@@H](C)Br |a:1,o1:4,5|')); + mol_to_smiles +------------------------------ + C[C@H](F)[C@H](C)[C@@H](C)Br +(1 row) + +SELECT mol_to_cxsmiles(mol_from_smiles('C[C@H](F)[C@H](C)[C@@H](C)Br |a:1,o1:4,5|')); + mol_to_cxsmiles +------------------------------------------- + C[C@H](F)[C@H](C)[C@@H](C)Br |a:1,o1:4,5| +(1 row) + --- /dev/null 2019-10-21 09:46:46.351315135 +0200 +++ ./Code/PgSQL/rdkit/expected/props_1.out 2019-11-02 21:02:17.287019119 +0100 @@ -0,0 +1,479 @@ +SELECT mol_amw('c1ccccc1'::mol) mol_amw; + mol_amw +--------- + 78.114 +(1 row) + +SELECT mol_logp('c1ccccc1'::mol) mol_logp; + mol_logp +---------- + 1.6866 +(1 row) + +SELECT mol_hba('c1ccccc1'::mol) mol_hba; + mol_hba +--------- + 0 +(1 row) + +SELECT mol_hbd('c1ccccc1'::mol) mol_hbd; + mol_hbd +--------- + 0 +(1 row) + +SELECT mol_hba('c1ccncc1'::mol) mol_hba; + mol_hba +--------- + 1 +(1 row) + +SELECT mol_hbd('c1ccncc1'::mol) mol_hbd; + mol_hbd +--------- + 0 +(1 row) + +SELECT mol_hbd('c1ccncc1O'::mol) mol_hbd; + mol_hbd +--------- + 1 +(1 row) + +SELECT mol_hba('c1ccncc1O'::mol) mol_hba; + mol_hba +--------- + 2 +(1 row) + +SELECT mol_logp('c1ccncc1O'::mol) mol_logp; + mol_logp +---------- + 0.7872 +(1 row) + +SELECT mol_chi0n('c1ccccc1O'::mol) v; + v +----------- + 3.8339648 +(1 row) + +SELECT mol_chi1n('c1ccccc1O'::mol) v; + v +----------- + 2.1342905 +(1 row) + +SELECT mol_chi2n('c1ccccc1O'::mol) v; + v +----------- + 1.3355491 +(1 row) + +SELECT mol_chi3n('c1ccccc1O'::mol) v; + v +----------- + 0.7561936 +(1 row) + +SELECT mol_chi4n('c1ccccc1O'::mol) v; + v +----------- + 0.4279941 +(1 row) + +SELECT mol_chi0v('c1ccccc1O'::mol) v; + v +----------- + 3.8339648 +(1 row) + +SELECT mol_chi1v('c1ccccc1O'::mol) v; + v +----------- + 2.1342905 +(1 row) + +SELECT mol_chi2v('c1ccccc1O'::mol) v; + v +----------- + 1.3355491 +(1 row) + +SELECT mol_chi3v('c1ccccc1O'::mol) v; + v +----------- + 0.7561936 +(1 row) + +SELECT mol_chi4v('c1ccccc1O'::mol) v; + v +----------- + 0.4279941 +(1 row) + +SELECT mol_kappa1('C12CC2C3CC13'::mol) v; + v +--------- + 2.34375 +(1 row) + +SELECT mol_kappa2('CC(C)C1CCC(C)CCC1'::mol) v; + v +---------- + 4.132653 +(1 row) + +SELECT mol_kappa3('CC(C)C1CCC(C)CCC1'::mol) v; + v +----------- + 2.8444445 +(1 row) + +SELECT mol_numspiroatoms('C1CCC2(C1)CC1CCC2CC1'::mol) v; + v +--- + 1 +(1 row) + +SELECT mol_numbridgeheadatoms('C1CCC2(C1)CC1CCC2CC1'::mol) v; + v +--- + 2 +(1 row) + +SELECT mol_numspiroatoms('CC1(C)CC2(C)CCC1(C)CC2'::mol) v; + v +--- + 0 +(1 row) + +SELECT mol_numbridgeheadatoms('CC1(C)CC2(C)CCC1(C)CC2'::mol) v; + v +--- + 2 +(1 row) + +-- Mol formula tests - SQL equivalents of tests in testMolDescriptors.py. +select mol_formula('[2H]C([3H])O'::mol); + mol_formula +------------- + CH4O +(1 row) + + -- separateIsotopes = true +select mol_formula('[2H]C([3H])O'::mol, true); + mol_formula +------------- + CH2DTO +(1 row) + + -- abbreviateHIsotopes = false +select mol_formula('[2H]C([3H])O'::mol, true, false); + mol_formula +-------------- + CH2[2H][3H]O +(1 row) + + -- +select mol_formula('[2H][13CH2]CO'::mol); + mol_formula +------------- + C2H6O +(1 row) + +select mol_formula('[2H][13CH2]CO'::mol, true); + mol_formula +------------- + C[13C]H5DO +(1 row) + +select mol_formula('[2H][13CH2]CO'::mol, true, false); + mol_formula +--------------- + C[13C]H5[2H]O +(1 row) + +-- +SELECT mol_numrotatablebonds('CCC'::mol) mol_numrotatablebonds; + mol_numrotatablebonds +----------------------- + 0 +(1 row) + +SELECT mol_numrotatablebonds('CCCC'::mol) mol_numrotatablebonds; + mol_numrotatablebonds +----------------------- + 1 +(1 row) + +SELECT mol_numrotatablebonds('c1ccccc1c1ccc(CCC)cc1'::mol) mol_numrotatablebonds; + mol_numrotatablebonds +----------------------- + 3 +(1 row) + +SELECT mol_numheavyatoms('CCC'::mol) val; + val +----- + 3 +(1 row) + +SELECT mol_numatoms('CCC'::mol) val; + val +----- + 11 +(1 row) + +SELECT mol_numheteroatoms('CCC'::mol) val; + val +----- + 0 +(1 row) + +SELECT mol_numheteroatoms('CCO'::mol) val; + val +----- + 1 +(1 row) + +SELECT mol_tpsa('CCC'::mol) val; + val +----- + 0 +(1 row) + +SELECT mol_tpsa('CCO'::mol) val; + val +------- + 20.23 +(1 row) + +SELECT mol_numrings('CCC'::mol) val; + val +----- + 0 +(1 row) + +SELECT mol_numrings('C1CC1'::mol) val; + val +----- + 1 +(1 row) + +SELECT mol_murckoscaffold('c1ccccc1CCC'::mol) val; + val +---------- + c1ccccc1 +(1 row) + +SELECT mol_murckoscaffold('CSC(C)=O'::mol) is NULL; + ?column? +---------- + t +(1 row) + +SELECT mol_to_svg('CCO'::mol) svg; + svg +----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- + + + + + + + + + + + + + + + OH+ + + + +(1 row) + +SELECT mol_to_svg('CCO'::mol,'legend') svg; + svg +------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ + + + + + + + + + + + + + + + OH + + legend+ + + + +(1 row) + +SELECT mol_to_svg('CCO'::mol,'legend',250,200, + '{"atomLabels":{"1":"foo"},"legendColour":[0.5,0.5,0.5]}') svg; + svg +------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- + + + + + + + + + + + + + + + foo+ + OH + + legend + + + + +(1 row) + +-- GitHub Issue 2174 - mol_to_svg() should not change input mol. +/** + Check that mol_to_svg() does not change the_mol. + In previous versions, the atom+bond count would + change from '10 11' in "before_mol" to '11 12' + in "after_mol", due to mol_to_svg()'s call to + MolDraw2DUtils::prepareMolForDrawing(). +**/ +with t as ( + select 'C[C@H]1CC[C@H]2CCCCC12'::mol as the_mol +) +select + substring(mol_to_ctab(the_mol)::text, 1, 65) as before_mol + , substring(mol_to_svg(the_mol)::text, 1, 20) as the_svg + , substring(mol_to_ctab(the_mol)::text, 1, 65) as after_mol + from t; + before_mol | the_svg | after_mol +-----------------------------------------+----------------------+----------------------------------------- + +| f,id limit 10; + id | sml +----+----- +(0 rows) + +SELECT + id, tanimoto_sml(maccs_fp('O=C1CC(OC2=CC=CC=C12)C1=CC=CC=C1'::mol), maccsf) AS sml +FROM + pgbfp +WHERE maccs_fp('O=C1CC(OC2=CC=CC=C12)C1=CC=CC=C1'::mol) % maccsf +ORDER BY sml DESC, id limit 10; + id | sml +----------+-------------------- + 2055076 | 0.7407407407407407 + 5281628 | 0.65625 + 10560368 | 0.5714285714285714 + 755497 | 0.5277777777777778 + 718644 | 0.5263157894736842 + 902176 | 0.5161290322580645 + 687554 | 0.5 + 1380883 | 0.5 +(8 rows) + +DROP INDEX fpidx; +DROP INDEX maccsfpidx; --- /dev/null 2019-10-21 09:46:46.351315135 +0200 +++ ./Code/PgSQL/rdkit/expected/bfpgin_1.out 2019-11-02 21:02:25.106971846 +0100 @@ -0,0 +1,111 @@ +CREATE INDEX fpidx ON pgbfp USING gin (f); +CREATE INDEX maccsfpidx ON pgbfp USING gin (maccsf); +SET rdkit.tanimoto_threshold = 0.5; +SET rdkit.dice_threshold = 0.6; +SET enable_indexscan=off; +SET enable_bitmapscan=off; +SET enable_seqscan=on; +SELECT + id, tanimoto_sml(rdkit_fp('O=C1CC(OC2=CC=CC=C12)C1=CC=CC=C1'::mol), f) AS sml +FROM + pgbfp +WHERE rdkit_fp('O=C1CC(OC2=CC=CC=C12)C1=CC=CC=C1'::mol) % f +ORDER BY sml DESC, id limit 10; + id | sml +----+----- +(0 rows) + +SELECT + id, dice_sml(rdkit_fp('O=C1CC(OC2=CC=CC=C12)C1=CC=CC=C1'::mol), f) AS sml +FROM + pgbfp +WHERE rdkit_fp('O=C1CC(OC2=CC=CC=C12)C1=CC=CC=C1'::mol) # f +ORDER BY sml DESC, id limit 10; + id | sml +--------+-------------------- + 698576 | 0.6049723756906077 +(1 row) + +SELECT + id, tanimoto_sml(maccs_fp('O=C1CC(OC2=CC=CC=C12)C1=CC=CC=C1'::mol), maccsf) AS sml +FROM + pgbfp +WHERE maccs_fp('O=C1CC(OC2=CC=CC=C12)C1=CC=CC=C1'::mol) % maccsf +ORDER BY sml DESC, id limit 10; + id | sml +----------+-------------------- + 2055076 | 0.7407407407407407 + 5281628 | 0.65625 + 10560368 | 0.5714285714285714 + 755497 | 0.5277777777777778 + 718644 | 0.5263157894736842 + 902176 | 0.5161290322580645 + 687554 | 0.5 + 1380883 | 0.5 +(8 rows) + +SET enable_indexscan=on; +SET enable_bitmapscan=on; +SET enable_seqscan=off; +SELECT + id, tanimoto_sml(rdkit_fp('O=C1CC(OC2=CC=CC=C12)C1=CC=CC=C1'::mol), f) AS sml +FROM + pgbfp +WHERE rdkit_fp('O=C1CC(OC2=CC=CC=C12)C1=CC=CC=C1'::mol) % f +ORDER BY sml DESC, id limit 10; + id | sml +----+----- +(0 rows) + +SELECT + id, dice_sml(rdkit_fp('O=C1CC(OC2=CC=CC=C12)C1=CC=CC=C1'::mol), f) AS sml +FROM + pgbfp +WHERE rdkit_fp('O=C1CC(OC2=CC=CC=C12)C1=CC=CC=C1'::mol) # f +ORDER BY sml DESC, id limit 10; + id | sml +--------+-------------------- + 698576 | 0.6049723756906077 +(1 row) + +SELECT + id, tanimoto_sml(maccs_fp('O=C1CC(OC2=CC=CC=C12)C1=CC=CC=C1'::mol), maccsf) AS sml +FROM + pgbfp +WHERE maccs_fp('O=C1CC(OC2=CC=CC=C12)C1=CC=CC=C1'::mol) % maccsf +ORDER BY sml DESC, id limit 10; + id | sml +----------+-------------------- + 2055076 | 0.7407407407407407 + 5281628 | 0.65625 + 10560368 | 0.5714285714285714 + 755497 | 0.5277777777777778 + 718644 | 0.5263157894736842 + 902176 | 0.5161290322580645 + 687554 | 0.5 + 1380883 | 0.5 +(8 rows) + +SET enable_indexscan=on; +SET enable_bitmapscan=on; +SET enable_seqscan=on; +SELECT + id, tanimoto_sml(maccs_fp('O=C1CC(OC2=CC=CC=C12)C1=CC=CC=C1'::mol), maccsf) AS sml +FROM + pgbfp +WHERE maccs_fp('O=C1CC(OC2=CC=CC=C12)C1=CC=CC=C1'::mol) % maccsf +ORDER BY sml DESC, id limit 10; + id | sml +----------+-------------------- + 2055076 | 0.7407407407407407 + 5281628 | 0.65625 + 10560368 | 0.5714285714285714 + 755497 | 0.5277777777777778 + 718644 | 0.5263157894736842 + 902176 | 0.5161290322580645 + 687554 | 0.5 + 1380883 | 0.5 +(8 rows) + +DROP INDEX fpidx; +DROP INDEX maccsfpidx; --- /dev/null 2019-10-21 09:46:46.351315135 +0200 +++ ./Code/PgSQL/rdkit/expected/sfpgist_1.out 2019-11-02 21:02:29.498945246 +0100 @@ -0,0 +1,89 @@ +CREATE INDEX fpidx ON pgsfp USING gist (f); +SET rdkit.tanimoto_threshold = 0.6; +SET rdkit.dice_threshold = 0.6; +SET enable_indexscan=off; +SET enable_bitmapscan=off; +SET enable_seqscan=on; +SELECT + id, tanimoto_sml(morgan_fp('O=C1CC(OC2=CC=CC=C12)C1=CC=CC=C1'::mol, 1), f) AS sml +FROM + pgsfp +WHERE morgan_fp('O=C1CC(OC2=CC=CC=C12)C1=CC=CC=C1'::mol, 1) % f +ORDER BY sml DESC, id; + id | sml +----+----- +(0 rows) + +SELECT + id, dice_sml(morgan_fp('O=C1CC(OC2=CC=CC=C12)C1=CC=CC=C1'::mol, 1), f) AS sml +FROM + pgsfp +WHERE morgan_fp('O=C1CC(OC2=CC=CC=C12)C1=CC=CC=C1'::mol, 1) # f +ORDER BY sml DESC, id; + id | sml +---------+-------------------- + 659725 | 0.6857142857142857 + 63248 | 0.6486486486486487 + 6266272 | 0.6410256410256411 + 5359275 | 0.6388888888888888 + 5718138 | 0.6388888888888888 + 917183 | 0.6285714285714286 + 161167 | 0.6216216216216216 + 230488 | 0.6216216216216216 + 328013 | 0.6216216216216216 + 564008 | 0.6190476190476191 + 2910597 | 0.6153846153846154 + 3963948 | 0.6153846153846154 + 5407397 | 0.6153846153846154 + 3784792 | 0.6136363636363636 + 3096571 | 0.6097560975609756 + 801655 | 0.6052631578947368 + 3157044 | 0.6052631578947368 + 807628 | 0.6 +(18 rows) + +SET enable_indexscan=on; +SET enable_bitmapscan=on; +SET enable_seqscan=off; +SELECT + id, tanimoto_sml(morgan_fp('O=C1CC(OC2=CC=CC=C12)C1=CC=CC=C1'::mol, 1), f) AS sml +FROM + pgsfp +WHERE morgan_fp('O=C1CC(OC2=CC=CC=C12)C1=CC=CC=C1'::mol, 1) % f +ORDER BY sml DESC, id; + id | sml +----+----- +(0 rows) + +SELECT + id, dice_sml(morgan_fp('O=C1CC(OC2=CC=CC=C12)C1=CC=CC=C1'::mol, 1), f) AS sml +FROM + pgsfp +WHERE morgan_fp('O=C1CC(OC2=CC=CC=C12)C1=CC=CC=C1'::mol, 1) # f +ORDER BY sml DESC, id; + id | sml +---------+-------------------- + 659725 | 0.6857142857142857 + 63248 | 0.6486486486486487 + 6266272 | 0.6410256410256411 + 5359275 | 0.6388888888888888 + 5718138 | 0.6388888888888888 + 917183 | 0.6285714285714286 + 161167 | 0.6216216216216216 + 230488 | 0.6216216216216216 + 328013 | 0.6216216216216216 + 564008 | 0.6190476190476191 + 2910597 | 0.6153846153846154 + 3963948 | 0.6153846153846154 + 5407397 | 0.6153846153846154 + 3784792 | 0.6136363636363636 + 3096571 | 0.6097560975609756 + 801655 | 0.6052631578947368 + 3157044 | 0.6052631578947368 + 807628 | 0.6 +(18 rows) + +SET enable_indexscan=on; +SET enable_bitmapscan=on; +SET enable_seqscan=on; +DROP INDEX fpidx; --- /dev/null 2019-10-21 09:46:46.351315135 +0200 +++ ./Code/PgSQL/rdkit/expected/fps_1.out 2019-11-02 21:02:37.786894956 +0100 @@ -0,0 +1,270 @@ +SELECT dice_sml(rdkit_fp('c1ccccc1'::mol),rdkit_fp('c1ccncc1'::mol)); + dice_sml +--------------------- + 0.37209302325581395 +(1 row) + +SELECT tversky_sml(rdkit_fp('c1ccccc1'::mol),rdkit_fp('c1ccncc1'::mol),0.5,0.5); + tversky_sml +--------------------- + 0.37209302325581395 +(1 row) + +SELECT tanimoto_sml(rdkit_fp('c1ccccc1'::mol),rdkit_fp('c1ccncc1'::mol)); + tanimoto_sml +--------------------- + 0.22857142857142856 +(1 row) + +SELECT tversky_sml(rdkit_fp('c1ccccc1'::mol),rdkit_fp('c1ccncc1'::mol),1.0,1.0); + tversky_sml +--------------------- + 0.22857142857142856 +(1 row) + +SELECT dice_sml(atompair_fp('c1ccccc1'::mol),atompair_fp('c1ccncc1'::mol)); + dice_sml +-------------------- + 0.6666666666666666 +(1 row) + +SELECT dice_sml(torsion_fp('c1ccccc1'::mol),torsion_fp('c1ccncc1'::mol)); + dice_sml +-------------------- + 0.3333333333333333 +(1 row) + +SELECT dice_sml(morgan_fp('c1ccccc1'::mol,2),morgan_fp('c1ccncc1'::mol,2)); + dice_sml +---------- + 0.5 +(1 row) + +SELECT dice_sml(morgan_fp('c1ccccc1'::mol),morgan_fp('c1ccncc1'::mol)); + dice_sml +---------- + 0.5 +(1 row) + +SELECT dice_sml(morganbv_fp('c1ccccc1'::mol,2),morganbv_fp('c1ccncc1'::mol,2)); + dice_sml +---------- + 0.5 +(1 row) + +SELECT dice_sml(morganbv_fp('c1ccccc1'::mol),morganbv_fp('c1ccncc1'::mol)); + dice_sml +---------- + 0.5 +(1 row) + +SELECT dice_sml(featmorgan_fp('c1ccccc1'::mol,2),featmorgan_fp('c1ccncc1'::mol,2)); + dice_sml +---------- + 0.5 +(1 row) + +SELECT dice_sml(featmorgan_fp('c1ccccc1'::mol),featmorgan_fp('c1ccncc1'::mol)); + dice_sml +---------- + 0.5 +(1 row) + +SELECT dice_sml(featmorganbv_fp('c1ccccc1'::mol,2),featmorganbv_fp('c1ccncc1'::mol,2)); + dice_sml +---------- + 0.5 +(1 row) + +SELECT dice_sml(featmorganbv_fp('c1ccccc1'::mol),featmorganbv_fp('c1ccncc1'::mol)); + dice_sml +---------- + 0.5 +(1 row) + +SELECT tanimoto_sml(maccs_fp('c1ccccc1'::mol),maccs_fp('c1ccncc1'::mol)); + tanimoto_sml +-------------- + 0.375 +(1 row) + +SELECT dice_sml(maccs_fp('c1ccccc1'::mol),maccs_fp('c1ccncc1'::mol)); + dice_sml +-------------------- + 0.5454545454545454 +(1 row) + +SET rdkit.tanimoto_threshold = 0.4; +SELECT + id, tanimoto_sml(rdkit_fp('O=C1CC(OC2=CC=CC=C12)C1=CC=CC=C1'::mol), f) AS sml +FROM +pgbfp +WHERE rdkit_fp('O=C1CC(OC2=CC=CC=C12)C1=CC=CC=C1'::mol) % f +ORDER BY sml DESC, id LIMIT 10; + id | sml +----------+--------------------- + 698576 | 0.43366336633663366 + 16000816 | 0.4232902033271719 + 1959267 | 0.4227504244482173 + 576770 | 0.42231075697211157 + 16746067 | 0.4204398447606727 + 5770965 | 0.4124783362218371 + 24747640 | 0.41237113402061853 + 15945163 | 0.4092465753424658 + 5770966 | 0.4088397790055249 + 690546 | 0.40875912408759124 +(10 rows) + +SET rdkit.tanimoto_threshold = 0.5; +SET rdkit.dice_threshold = 0.5; +SELECT + id, dice_sml(torsion_fp('O=C1CC(OC2=CC=CC=C12)C1=CC=CC=C1'::mol), f) AS sml +FROM +pgtorsfp +WHERE torsion_fp('O=C1CC(OC2=CC=CC=C12)C1=CC=CC=C1'::mol) # f +ORDER BY sml DESC, id; + id | sml +---------+----- + 3790017 | 0.5 +(1 row) + +SELECT + id, dice_sml(atompair_fp('O=C1CC(OC2=CC=CC=C12)C1=CC=CC=C1'::mol), f) AS sml +FROM +pgpairfp +WHERE atompair_fp('O=C1CC(OC2=CC=CC=C12)C1=CC=CC=C1'::mol) # f +ORDER BY sml DESC, id LIMIT 10; + id | sml +----------+-------------------- + 659725 | 0.6366782006920415 + 917183 | 0.5951557093425606 + 10713707 | 0.5950920245398773 + 3790017 | 0.5885558583106267 + 230488 | 0.5766871165644172 + 16193886 | 0.5501285347043702 + 3236648 | 0.5390625 + 5359275 | 0.5342019543973942 + 6213987 | 0.532871972318339 + 161167 | 0.5276073619631901 +(10 rows) + +select tanimoto_sml(rdkit_fp('O=C1CC(OC2=CC=CC=C12)C1=CC=CC=C1'::mol), rdkit_fp('N=C1CC(NC2=CC=CC=C12)C1=CC=CC=C1'::mol)) AS sml; + sml +--------------------- + 0.31539888682745826 +(1 row) + +set rdkit.rdkit_fp_size = 512; +select tanimoto_sml(rdkit_fp('O=C1CC(OC2=CC=CC=C12)C1=CC=CC=C1'::mol), rdkit_fp('N=C1CC(NC2=CC=CC=C12)C1=CC=CC=C1'::mol)) AS sml; + sml +--------------------- + 0.47103274559193953 +(1 row) + +set rdkit.rdkit_fp_size = 1024; +select tanimoto_sml(rdkit_fp('O=C1CC(OC2=CC=CC=C12)C1=CC=CC=C1'::mol), rdkit_fp('N=C1CC(NC2=CC=CC=C12)C1=CC=CC=C1'::mol)) AS sml; + sml +--------------------- + 0.31539888682745826 +(1 row) + +select tanimoto_sml(layered_fp('O=C1CC(OC2=CC=CC=C12)C1=CC=CC=C1'::mol), layered_fp('N=C1CC(NC2=CC=CC=C12)C1=CC=CC=C1'::mol)) AS sml; + sml +-------------------- + 0.7249417249417249 +(1 row) + +set rdkit.layered_fp_size = 512; +select tanimoto_sml(layered_fp('O=C1CC(OC2=CC=CC=C12)C1=CC=CC=C1'::mol), layered_fp('N=C1CC(NC2=CC=CC=C12)C1=CC=CC=C1'::mol)) AS sml; + sml +------------------- + 0.788235294117647 +(1 row) + +set rdkit.layered_fp_size = 1024; +select tanimoto_sml(layered_fp('O=C1CC(OC2=CC=CC=C12)C1=CC=CC=C1'::mol), layered_fp('N=C1CC(NC2=CC=CC=C12)C1=CC=CC=C1'::mol)) AS sml; + sml +-------------------- + 0.7249417249417249 +(1 row) + +select tanimoto_sml(morganbv_fp('O=C1CC(OC2=CC=CC=C12)C1=CC=CC=C1'::mol), morganbv_fp('N=C1CC(NC2=CC=CC=C12)C1=CC=CC=C1'::mol)) AS sml; + sml +------- + 0.325 +(1 row) + +set rdkit.morgan_fp_size = 512; +select tanimoto_sml(morganbv_fp('O=C1CC(OC2=CC=CC=C12)C1=CC=CC=C1'::mol), morganbv_fp('N=C1CC(NC2=CC=CC=C12)C1=CC=CC=C1'::mol)) AS sml; + sml +------- + 0.325 +(1 row) + +set rdkit.morgan_fp_size = 1024; +select tanimoto_sml(morganbv_fp('O=C1CC(OC2=CC=CC=C12)C1=CC=CC=C1'::mol), morganbv_fp('N=C1CC(NC2=CC=CC=C12)C1=CC=CC=C1'::mol)) AS sml; + sml +-------------------- + 0.3170731707317073 +(1 row) + +select tanimoto_sml(featmorganbv_fp('O=C1CC(OC2=CC=CC=C12)C1=CC=CC=C1'::mol), featmorganbv_fp('N=C1CC(NC2=CC=CC=C12)C1=CC=CC=C1'::mol)) AS sml; + sml +--------------------- + 0.20588235294117646 +(1 row) + +set rdkit.featmorgan_fp_size = 512; +select tanimoto_sml(featmorganbv_fp('O=C1CC(OC2=CC=CC=C12)C1=CC=CC=C1'::mol), featmorganbv_fp('N=C1CC(NC2=CC=CC=C12)C1=CC=CC=C1'::mol)) AS sml; + sml +--------------------- + 0.20588235294117646 +(1 row) + +set rdkit.featmorgan_fp_size = 1024; +select tanimoto_sml(featmorganbv_fp('O=C1CC(OC2=CC=CC=C12)C1=CC=CC=C1'::mol), featmorganbv_fp('N=C1CC(NC2=CC=CC=C12)C1=CC=CC=C1'::mol)) AS sml; + sml +--------------------- + 0.20588235294117646 +(1 row) + +select tanimoto_sml(torsionbv_fp('O=C1CC(OC2=CC=CC=C12)C1=CC=CC=C1'::mol), torsionbv_fp('N=C1CC(NC2=CC=CC=C12)C1=CC=CC=C1'::mol)) AS sml; + sml +--------------------- + 0.45454545454545453 +(1 row) + +set rdkit.hashed_torsion_fp_size = 512; +select tanimoto_sml(torsionbv_fp('O=C1CC(OC2=CC=CC=C12)C1=CC=CC=C1'::mol), torsionbv_fp('N=C1CC(NC2=CC=CC=C12)C1=CC=CC=C1'::mol)) AS sml; + sml +--------------------- + 0.47619047619047616 +(1 row) + +set rdkit.hashed_torsion_fp_size = 1024; +select tanimoto_sml(torsionbv_fp('O=C1CC(OC2=CC=CC=C12)C1=CC=CC=C1'::mol), torsionbv_fp('N=C1CC(NC2=CC=CC=C12)C1=CC=CC=C1'::mol)) AS sml; + sml +--------------------- + 0.45454545454545453 +(1 row) + +select tanimoto_sml(atompairbv_fp('O=C1CC(OC2=CC=CC=C12)C1=CC=CC=C1'::mol), atompairbv_fp('N=C1CC(NC2=CC=CC=C12)C1=CC=CC=C1'::mol)) AS sml; + sml +-------------------- + 0.5619834710743802 +(1 row) + +set rdkit.hashed_atompair_fp_size = 512; +select tanimoto_sml(atompairbv_fp('O=C1CC(OC2=CC=CC=C12)C1=CC=CC=C1'::mol), atompairbv_fp('N=C1CC(NC2=CC=CC=C12)C1=CC=CC=C1'::mol)) AS sml; + sml +-------------------- + 0.5826086956521739 +(1 row) + +set rdkit.hashed_atompair_fp_size = 1024; +select tanimoto_sml(atompairbv_fp('O=C1CC(OC2=CC=CC=C12)C1=CC=CC=C1'::mol), atompairbv_fp('N=C1CC(NC2=CC=CC=C12)C1=CC=CC=C1'::mol)) AS sml; + sml +-------------------- + 0.5714285714285714 +(1 row) + --- /dev/null 2019-10-21 09:46:46.351315135 +0200 +++ ./Code/PgSQL/rdkit/expected/reaction_1.out 2019-11-02 21:02:41.322873463 +0100 @@ -0,0 +1,963 @@ +PREPARE dummy AS SELECT rdkit_version(); +SET rdkit.ignore_reaction_agents=false; +SET rdkit.agent_FP_bit_ratio=0.2; +SET rdkit.difference_FP_weight_agents=1; +SET rdkit.difference_FP_weight_nonagents=10; +SET rdkit.move_unmmapped_reactants_to_agents=true; +SET rdkit.threshold_unmapped_reactant_atoms=0.2; +SET rdkit.init_reaction=true; +SELECT reaction_from_smiles('c1ccccc1>>c1cccnc1'); + reaction_from_smiles +---------------------- + c1ccccc1>>c1ccncc1 +(1 row) + +SELECT reaction_from_smiles('c1ccccc1>CC(=O)O>c1cccnc1'); + reaction_from_smiles +--------------------------- + c1ccccc1>CC(=O)O>c1ccncc1 +(1 row) + +SELECT reaction_from_smarts('[c1:1][c:2][c:3][c:4]c[c1:5]>CC(=O)O>[c1:1][c:2][c:3][c:4]n[c1:5]'); + reaction_from_smarts +--------------------------------------------------------------------------------- + c([cH:4][cH:3][cH:2][cH2:1])[cH2:5]>CC(=O)O>n([cH:4][cH:3][cH:2][cH2:1])[cH2:5] +(1 row) + +SELECT reaction_from_smarts('C(F)(F)F.[c1:1][c:2][c:3][c:4]c[c1:5]>CC(=O)O>[c1:1][c:2][c:3][c:4]n[c1:5]'); + reaction_from_smarts +---------------------------------------------------------------------------------------- + c([cH:4][cH:3][cH:2][cH2:1])[cH2:5]>CC(=O)O.FC(F)F>n([cH:4][cH:3][cH:2][cH2:1])[cH2:5] +(1 row) + +SELECT reaction_from_smarts('c1ccc[n,c]c1>>c1nccnc1'); + reaction_from_smarts +---------------------- + *1ccccc1>>c1cnccn1 +(1 row) + +SELECT reaction_to_smiles(reaction_from_smiles('c1ccccc1>>c1cccnc1')); + reaction_to_smiles +-------------------- + c1ccccc1>>c1ccncc1 +(1 row) + +SELECT reaction_to_smiles(reaction_from_smarts('c1ccc[n,c]c1>>c1nccnc1')); + reaction_to_smiles +-------------------- + *1ccccc1>>c1cnccn1 +(1 row) + +SELECT reaction_to_smarts(reaction_from_smarts('c1ccc[n,c]c1>>c1nccnc1')); + reaction_to_smarts +------------------------ + c1ccc[n,c]c1>>c1nccnc1 +(1 row) + +SELECT reaction_to_smarts('c1cccnc1>>c1nccnc1'::reaction); + reaction_to_smarts +-------------------------------------------------------------------- + [#6]1:[#6]:[#6]:[#6]:[#7]:[#6]:1>>[#6]1:[#7]:[#6]:[#6]:[#7]:[#6]:1 +(1 row) + +SELECT reaction_to_ctab(reaction_from_smiles('c1ccccc1>>c1cccnc1')); + reaction_to_ctab +----------------------------------------------------------------------- + $RXN + + + + RDKit + + + + 1 1 + + $MOL + + + + RDKit 2D + + + + 6 6 0 0 0 0 0 0 0 0999 V2000 + + 1.5000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0+ + 0.7500 -1.2990 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0+ + -0.7500 -1.2990 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0+ + -1.5000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0+ + -0.7500 1.2990 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0+ + 0.7500 1.2990 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0+ + 1 2 4 0 + + 2 3 4 0 + + 3 4 4 0 + + 4 5 4 0 + + 5 6 4 0 + + 6 1 4 0 + + M END + + $MOL + + + + RDKit 2D + + + + 6 6 0 0 0 0 0 0 0 0999 V2000 + + 1.5000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0+ + 0.7500 -1.2990 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0+ + -0.7500 -1.2990 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0+ + -1.5000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0+ + -0.7500 1.2990 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0+ + 0.7500 1.2990 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0+ + 1 2 4 0 + + 2 3 4 0 + + 3 4 4 0 + + 4 5 4 0 + + 5 6 4 0 + + 6 1 4 0 + + M END + + +(1 row) + +SELECT reaction_numreactants(reaction_from_smiles('[Cl].c1ccccc1>>c1cccnc1.[OH2]')); + reaction_numreactants +----------------------- + 2 +(1 row) + +SELECT reaction_numproducts(reaction_from_smiles('[Cl].c1ccccc1>>c1cccnc1.[OH2]')); + reaction_numproducts +---------------------- + 2 +(1 row) + +SELECT reaction_numagents(reaction_from_smiles('[Cl].c1ccccc1>CC(=O)O.[Na+]>c1cccnc1.[OH2]')); + reaction_numagents +-------------------- + 2 +(1 row) + +SELECT reaction_numagents(reaction_from_smarts('C(F)(F)F.[c1:1][c:2][c:3][c:4]c[c1:5]>CC(=O)O>[c1:1][c:2][c:3][c:4]n[c1:5]')); + reaction_numagents +-------------------- + 2 +(1 row) + +SET rdkit.move_unmmapped_reactants_to_agents=false; +SELECT reaction_numagents(reaction_from_smarts('C(F)(F)F.[c1:1][c:2][c:3][c:4]c[c1:5]>CC(=O)O>[c1:1][c:2][c:3][c:4]n[c1:5]')); + reaction_numagents +-------------------- + 1 +(1 row) + +SET rdkit.move_unmmapped_reactants_to_agents=true; +SET rdkit.threshold_unmapped_reactant_atoms=0.9; +SELECT reaction_numagents(reaction_from_smarts('C(F)(F)F.[c1:1][c:2][c:3][c:4]c[c1:5]>CC(=O)O>[c1:1][c:2][c:3][c:4]n[c1:5]')); + reaction_numagents +-------------------- + 3 +(1 row) + +SET rdkit.threshold_unmapped_reactant_atoms=0.2; +SELECT 'c1ccccc1>>c1cccnc1'::reaction @= 'c1ccccc1>>c1cccnc1'::reaction; + ?column? +---------- + t +(1 row) + +SELECT 'c1ccccc1>>c1cccnc1'::reaction @= 'c1ccccc1>>c1cncnc1'::reaction; + ?column? +---------- + f +(1 row) + +SELECT reaction_from_ctab('$RXN + + RDKit + + 1 1 +$MOL + + RDKit + + 6 6 0 0 0 0 0 0 0 0999 V2000 + 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 4 0 + 2 3 4 0 + 3 4 4 0 + 4 5 4 0 + 5 6 4 0 + 6 1 4 0 +M END +$MOL + + RDKit + + 6 6 0 0 0 0 0 0 0 0999 V2000 + 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.0000 0.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 4 0 + 2 3 4 0 + 3 4 4 0 + 4 5 4 0 + 5 6 4 0 + 6 1 4 0 +M END'); + reaction_from_ctab +-------------------- + c1ccccc1>>c1ccncc1 +(1 row) + +CREATE TABLE tmp (id integer, tmprxn text); +\copy tmp from 'data/reaction_test_data.out.rsmi'; +select * into pgreactions from (select id,reaction_from_smiles(tmprxn::cstring) rxn from tmp) as r where r is not null; +SET rdkit.move_unmmapped_reactants_to_agents=false; +select * into pgreactions_unchanged from (select id,reaction_from_smiles(tmprxn::cstring) rxn from tmp) as r where r is not null; +DROP table tmp; +SET rdkit.move_unmmapped_reactants_to_agents=true; +SELECT count(*) FROM pgreactions; + count +------- + 1000 +(1 row) + +SELECT count(*) FROM pgreactions_unchanged; + count +------- + 1000 +(1 row) + +SELECT SUM(reaction_numreactants(rxn)) FROM pgreactions; + sum +------ + 1898 +(1 row) + +SELECT SUM(reaction_numreactants(rxn)) FROM pgreactions_unchanged; + sum +------ + 3517 +(1 row) + +SELECT SUM(reaction_numproducts(rxn)) FROM pgreactions; + sum +------ + 1157 +(1 row) + +SELECT SUM(reaction_numproducts(rxn)) FROM pgreactions_unchanged; + sum +------ + 1157 +(1 row) + +SELECT SUM(reaction_numagents(rxn)) FROM pgreactions; + sum +------ + 2528 +(1 row) + +SELECT SUM(reaction_numagents(rxn)) FROM pgreactions_unchanged; + sum +----- + 909 +(1 row) + +CREATE INDEX rxnidx ON pgreactions USING gist(rxn); +SET enable_indexscan=off; +SET enable_bitmapscan=off; +SET enable_seqscan=on; +SELECT count(*) FROM pgreactions WHERE rxn@>'c1ccccc1>>c1ccncc1'; + count +------- + 47 +(1 row) + +SELECT count(*) FROM pgreactions WHERE rxn@>'c1cnccc1>>c1ccccc1'; + count +------- + 50 +(1 row) + +SELECT count(*) FROM pgreactions WHERE 'c1ccccc1>>c1ccncc1'<@rxn; + count +------- + 47 +(1 row) + +SELECT count(*) FROM pgreactions WHERE 'c1cnccc1>>c1ccccc1'<@rxn; + count +------- + 50 +(1 row) + +SELECT count(*) FROM pgreactions WHERE rxn@>'c1ccccc1>>'; + count +------- + 667 +(1 row) + +SELECT count(*) FROM pgreactions WHERE rxn@>'c1cnccc1>>'; + count +------- + 83 +(1 row) + +SELECT count(*) FROM pgreactions WHERE 'c1ccccc1>>'<@rxn; + count +------- + 667 +(1 row) + +SELECT count(*) FROM pgreactions WHERE 'c1cnccc1>>'<@rxn; + count +------- + 83 +(1 row) + +SELECT count(*) FROM pgreactions WHERE rxn@>'>>c1ccncc1'; + count +------- + 79 +(1 row) + +SELECT count(*) FROM pgreactions WHERE rxn@>'>>c1ccccc1'; + count +------- + 650 +(1 row) + +SELECT count(*) FROM pgreactions WHERE '>>c1ccncc1'<@rxn; + count +------- + 79 +(1 row) + +SELECT count(*) FROM pgreactions WHERE '>>c1ccccc1'<@rxn; + count +------- + 650 +(1 row) + +SET enable_indexscan=on; +SET enable_bitmapscan=on; +SET enable_seqscan=off; +SELECT count(*) FROM pgreactions WHERE rxn@>'c1ccccc1>>c1ccncc1'; + count +------- + 47 +(1 row) + +SELECT count(*) FROM pgreactions WHERE rxn@>'c1cnccc1>>c1ccccc1'; + count +------- + 50 +(1 row) + +SELECT count(*) FROM pgreactions WHERE 'c1ccccc1>>c1ccncc1'<@rxn; + count +------- + 47 +(1 row) + +SELECT count(*) FROM pgreactions WHERE 'c1cnccc1>>c1ccccc1'<@rxn; + count +------- + 50 +(1 row) + +SELECT count(*) FROM pgreactions WHERE rxn@>'c1ccccc1>>'; + count +------- + 667 +(1 row) + +SELECT count(*) FROM pgreactions WHERE rxn@>'c1cnccc1>>'; + count +------- + 83 +(1 row) + +SELECT count(*) FROM pgreactions WHERE 'c1ccccc1>>'<@rxn; + count +------- + 667 +(1 row) + +SELECT count(*) FROM pgreactions WHERE 'c1cnccc1>>'<@rxn; + count +------- + 83 +(1 row) + +SELECT count(*) FROM pgreactions WHERE rxn@>'>>c1ccncc1'; + count +------- + 79 +(1 row) + +SELECT count(*) FROM pgreactions WHERE rxn@>'>>c1ccccc1'; + count +------- + 650 +(1 row) + +SELECT count(*) FROM pgreactions WHERE '>>c1ccncc1'<@rxn; + count +------- + 79 +(1 row) + +SELECT count(*) FROM pgreactions WHERE '>>c1ccccc1'<@rxn; + count +------- + 650 +(1 row) + +SELECT count(*) FROM pgreactions WHERE rxn?>'c1ccccc1>>c1ccncc1'; + count +------- + 47 +(1 row) + +SELECT count(*) FROM pgreactions WHERE rxn?>'c1cnccc1>>c1ccccc1'; + count +------- + 50 +(1 row) + +SELECT count(*) FROM pgreactions WHERE 'c1ccccc1>>c1ccncc1'?>c1ccccc1'?'c1ccccc1>>'; + count +------- + 667 +(1 row) + +SELECT count(*) FROM pgreactions WHERE rxn?>'c1cnccc1>>'; + count +------- + 83 +(1 row) + +SELECT count(*) FROM pgreactions WHERE 'c1ccccc1>>'?>'?'>>c1ccncc1'; + count +------- + 79 +(1 row) + +SELECT count(*) FROM pgreactions WHERE rxn?>'>>c1ccccc1'; + count +------- + 650 +(1 row) + +SELECT count(*) FROM pgreactions WHERE '>>c1ccncc1'?>c1ccccc1'?>c1ccncc1',1), reaction_difference_fp('c1ccccc1>>c1ccncc1',1)); + tanimoto_sml +-------------- + 1 +(1 row) + +SELECT tanimoto_sml(reaction_difference_fp('c1ccccc1>>c1ccncc1',1), reaction_difference_fp('c1ncccc1>>c1ncncc1',1)); + tanimoto_sml +-------------------- + 0.6363636363636364 +(1 row) + +SELECT tanimoto_sml(reaction_difference_fp('c1ccccc1>CC(=O)O.[Na+]>c1ccncc1',1), reaction_difference_fp('c1ccccc1>CC(=O)O.[Na+]>c1ccncc1',1)); + tanimoto_sml +-------------- + 1 +(1 row) + +SELECT tanimoto_sml(reaction_difference_fp('c1ccccc1>CC(=O)O.[Na+]>c1ccncc1',1), reaction_difference_fp('c1ncccc1>[Na+]>c1ncncc1',1)); + tanimoto_sml +------------------- + 0.603448275862069 +(1 row) + +SELECT tanimoto_sml(reaction_difference_fp('c1ccccc1>>c1ccncc1',2), reaction_difference_fp('c1ccccc1>>c1ccncc1',2)); + tanimoto_sml +-------------- + 1 +(1 row) + +SELECT tanimoto_sml(reaction_difference_fp('c1ccccc1>>c1ccncc1',2), reaction_difference_fp('c1ncccc1>>c1ncncc1',2)); + tanimoto_sml +-------------- + 0.2 +(1 row) + +SELECT tanimoto_sml(reaction_difference_fp('c1ccccc1>CC(=O)O.[Na+]>c1ccncc1',2), reaction_difference_fp('c1ccccc1>CC(=O)O.[Na+]>c1ccncc1',2)); + tanimoto_sml +-------------- + 1 +(1 row) + +SELECT tanimoto_sml(reaction_difference_fp('c1ccccc1>CC(=O)O.[Na+]>c1ccncc1',2), reaction_difference_fp('c1ncccc1>[Na+]>c1ncncc1',2)); + tanimoto_sml +-------------- + 0.2 +(1 row) + +SELECT tanimoto_sml(reaction_difference_fp('c1ccccc1>>c1ccncc1',3), reaction_difference_fp('c1ccccc1>>c1ccncc1',3)); + tanimoto_sml +-------------- + 1 +(1 row) + +SELECT tanimoto_sml(reaction_difference_fp('c1ccccc1>>c1ccncc1',3), reaction_difference_fp('c1ncccc1>>c1ncncc1',3)); + tanimoto_sml +--------------------- + 0.45454545454545453 +(1 row) + +SELECT tanimoto_sml(reaction_difference_fp('c1ccccc1>CC(=O)O.[Na+]>c1ccncc1',3), reaction_difference_fp('c1ccccc1>CC(=O)O.[Na+]>c1ccncc1',3)); + tanimoto_sml +-------------- + 1 +(1 row) + +SELECT tanimoto_sml(reaction_difference_fp('c1ccccc1>CC(=O)O.[Na+]>c1ccncc1',3), reaction_difference_fp('c1ncccc1>[Na+]>c1ncncc1',3)); + tanimoto_sml +--------------------- + 0.44493392070484583 +(1 row) + +SELECT tanimoto_sml(reaction_structural_bfp('c1ccccc1>>c1ccncc1',1), reaction_structural_bfp('c1ccccc1>>c1ccncc1',1)); + tanimoto_sml +-------------- + 1 +(1 row) + +SELECT tanimoto_sml(reaction_structural_bfp('c1ccccc1>>c1ccncc1',1), reaction_structural_bfp('c1ncccc1>>c1ncncc1',1)); + tanimoto_sml +-------------------- + 0.6206896551724138 +(1 row) + +SELECT tanimoto_sml(reaction_structural_bfp('c1ccccc1>CC(=O)O.[Na+]>c1ccncc1',1), reaction_structural_bfp('c1ccccc1>CC(=O)O.[Na+]>c1ccncc1',1)); + tanimoto_sml +-------------- + 1 +(1 row) + +SELECT tanimoto_sml(reaction_structural_bfp('c1ccccc1>CC(=O)O.[Na+]>c1ccncc1',1), reaction_structural_bfp('c1ncccc1>[Na+]>c1ncncc1',1)); + tanimoto_sml +-------------------- + 0.5142857142857142 +(1 row) + +--SELECT tanimoto_sml(reaction_structural_bfp('c1ccccc1>>c1ccncc1',2), reaction_structural_bfp('c1ccccc1>>c1ccncc1',2)); +--SELECT tanimoto_sml(reaction_structural_bfp('c1ccccc1>>c1ccncc1',2), reaction_structural_bfp('c1ncccc1>>c1ncncc1',2)); +--SELECT tanimoto_sml(reaction_structural_bfp('c1ccccc1>CC(=O)O.[Na+]>c1ccncc1',2), reaction_structural_bfp('c1ccccc1>CC(=O)O.[Na+]>c1ccncc1',2)); +--SELECT tanimoto_sml(reaction_structural_bfp('c1ccccc1>CC(=O)O.[Na+]>c1ccncc1',2), reaction_structural_bfp('c1ncccc1>[Na+]>c1ncncc1',2)); +SELECT tanimoto_sml(reaction_structural_bfp('c1ccccc1>>c1ccncc1',3), reaction_structural_bfp('c1ccccc1>>c1ccncc1',3)); + tanimoto_sml +-------------- + 1 +(1 row) + +SELECT tanimoto_sml(reaction_structural_bfp('c1ccccc1>>c1ccncc1',3), reaction_structural_bfp('c1ncccc1>>c1ncncc1',3)); + tanimoto_sml +-------------------- + 0.4090909090909091 +(1 row) + +SELECT tanimoto_sml(reaction_structural_bfp('c1ccccc1>CC(=O)O.[Na+]>c1ccncc1',3), reaction_structural_bfp('c1ccccc1>CC(=O)O.[Na+]>c1ccncc1',3)); + tanimoto_sml +-------------- + 1 +(1 row) + +SELECT tanimoto_sml(reaction_structural_bfp('c1ccccc1>CC(=O)O.[Na+]>c1ccncc1',3), reaction_structural_bfp('c1ncccc1>[Na+]>c1ncncc1',3)); + tanimoto_sml +-------------------- + 0.3225806451612903 +(1 row) + +SELECT tanimoto_sml(reaction_structural_bfp('c1ccccc1>>c1ccncc1',4), reaction_structural_bfp('c1ccccc1>>c1ccncc1',4)); + tanimoto_sml +-------------- + 1 +(1 row) + +SELECT tanimoto_sml(reaction_structural_bfp('c1ccccc1>>c1ccncc1',4), reaction_structural_bfp('c1ncccc1>>c1ncncc1',4)); + tanimoto_sml +--------------------- + 0.27710843373493976 +(1 row) + +SELECT tanimoto_sml(reaction_structural_bfp('c1ccccc1>CC(=O)O.[Na+]>c1ccncc1',4), reaction_structural_bfp('c1ccccc1>CC(=O)O.[Na+]>c1ccncc1',4)); + tanimoto_sml +-------------- + 1 +(1 row) + +SELECT tanimoto_sml(reaction_structural_bfp('c1ccccc1>CC(=O)O.[Na+]>c1ccncc1',4), reaction_structural_bfp('c1ncccc1>[Na+]>c1ncncc1',4)); + tanimoto_sml +--------------------- + 0.23711340206185566 +(1 row) + +SELECT tanimoto_sml(reaction_structural_bfp('c1ccccc1>>c1ccncc1',5), reaction_structural_bfp('c1ccccc1>>c1ccncc1',5)); + tanimoto_sml +-------------- + 1 +(1 row) + +SELECT tanimoto_sml(reaction_structural_bfp('c1ccccc1>>c1ccncc1',5), reaction_structural_bfp('c1ncccc1>>c1ncncc1',5)); + tanimoto_sml +-------------------- + 0.7933884297520661 +(1 row) + +SELECT tanimoto_sml(reaction_structural_bfp('c1ccccc1>CC(=O)O.[Na+]>c1ccncc1',5), reaction_structural_bfp('c1ccccc1>CC(=O)O.[Na+]>c1ccncc1',5)); + tanimoto_sml +-------------- + 1 +(1 row) + +SELECT tanimoto_sml(reaction_structural_bfp('c1ccccc1>CC(=O)O.[Na+]>c1ccncc1',5), reaction_structural_bfp('c1ncccc1>[Na+]>c1ncncc1',5)); + tanimoto_sml +-------------------- + 0.6049382716049383 +(1 row) + +SET rdkit.agent_FP_bit_ratio=0.5; +SET rdkit.difference_FP_weight_agents=-3; +SET rdkit.difference_FP_weight_nonagents=7; +SELECT tanimoto_sml(reaction_difference_fp('c1ccccc1>>c1ccncc1',1), reaction_difference_fp('c1ccccc1>>c1ccncc1',1)); + tanimoto_sml +-------------- + 1 +(1 row) + +SELECT tanimoto_sml(reaction_difference_fp('c1ccccc1>>c1ccncc1',1), reaction_difference_fp('c1ncccc1>>c1ncncc1',1)); + tanimoto_sml +-------------------- + 0.6363636363636364 +(1 row) + +SELECT tanimoto_sml(reaction_difference_fp('c1ccccc1>CC(=O)O.[Na+]>c1ccncc1',1), reaction_difference_fp('c1ccccc1>CC(=O)O.[Na+]>c1ccncc1',1)); + tanimoto_sml +-------------- + 1 +(1 row) + +SELECT tanimoto_sml(reaction_difference_fp('c1ccccc1>CC(=O)O.[Na+]>c1ccncc1',1), reaction_difference_fp('c1ncccc1>[Na+]>c1ncncc1',1)); + tanimoto_sml +-------------------- + 0.5157894736842106 +(1 row) + +SELECT tanimoto_sml(reaction_difference_fp('c1ccccc1>>c1ccncc1',2), reaction_difference_fp('c1ccccc1>>c1ccncc1',2)); + tanimoto_sml +-------------- + 1 +(1 row) + +SELECT tanimoto_sml(reaction_difference_fp('c1ccccc1>>c1ccncc1',2), reaction_difference_fp('c1ncccc1>>c1ncncc1',2)); + tanimoto_sml +-------------- + 0.2 +(1 row) + +SELECT tanimoto_sml(reaction_difference_fp('c1ccccc1>CC(=O)O.[Na+]>c1ccncc1',2), reaction_difference_fp('c1ccccc1>CC(=O)O.[Na+]>c1ccncc1',2)); + tanimoto_sml +-------------- + 1 +(1 row) + +SELECT tanimoto_sml(reaction_difference_fp('c1ccccc1>CC(=O)O.[Na+]>c1ccncc1',2), reaction_difference_fp('c1ncccc1>[Na+]>c1ncncc1',2)); + tanimoto_sml +-------------- + 0.2 +(1 row) + +SELECT tanimoto_sml(reaction_difference_fp('c1ccccc1>>c1ccncc1',3), reaction_difference_fp('c1ccccc1>>c1ccncc1',3)); + tanimoto_sml +-------------- + 1 +(1 row) + +SELECT tanimoto_sml(reaction_difference_fp('c1ccccc1>>c1ccncc1',3), reaction_difference_fp('c1ncccc1>>c1ncncc1',3)); + tanimoto_sml +--------------------- + 0.45454545454545453 +(1 row) + +SELECT tanimoto_sml(reaction_difference_fp('c1ccccc1>CC(=O)O.[Na+]>c1ccncc1',3), reaction_difference_fp('c1ccccc1>CC(=O)O.[Na+]>c1ccncc1',3)); + tanimoto_sml +-------------- + 1 +(1 row) + +SELECT tanimoto_sml(reaction_difference_fp('c1ccccc1>CC(=O)O.[Na+]>c1ccncc1',3), reaction_difference_fp('c1ncccc1>[Na+]>c1ncncc1',3)); + tanimoto_sml +--------------------- + 0.40331491712707185 +(1 row) + +SELECT tanimoto_sml(reaction_structural_bfp('c1ccccc1>>c1ccncc1',1), reaction_structural_bfp('c1ccccc1>>c1ccncc1',1)); + tanimoto_sml +-------------- + 1 +(1 row) + +SELECT tanimoto_sml(reaction_structural_bfp('c1ccccc1>>c1ccncc1',1), reaction_structural_bfp('c1ncccc1>>c1ncncc1',1)); + tanimoto_sml +-------------------- + 0.6206896551724138 +(1 row) + +SELECT tanimoto_sml(reaction_structural_bfp('c1ccccc1>CC(=O)O.[Na+]>c1ccncc1',1), reaction_structural_bfp('c1ccccc1>CC(=O)O.[Na+]>c1ccncc1',1)); + tanimoto_sml +-------------- + 1 +(1 row) + +SELECT tanimoto_sml(reaction_structural_bfp('c1ccccc1>CC(=O)O.[Na+]>c1ccncc1',1), reaction_structural_bfp('c1ncccc1>[Na+]>c1ncncc1',1)); + tanimoto_sml +-------------------- + 0.5142857142857142 +(1 row) + +--SELECT tanimoto_sml(reaction_structural_bfp('c1ccccc1>>c1ccncc1',2), reaction_structural_bfp('c1ccccc1>>c1ccncc1',2)); +--SELECT tanimoto_sml(reaction_structural_bfp('c1ccccc1>>c1ccncc1',2), reaction_structural_bfp('c1ncccc1>>c1ncncc1',2)); +--SELECT tanimoto_sml(reaction_structural_bfp('c1ccccc1>CC(=O)O.[Na+]>c1ccncc1',2), reaction_structural_bfp('c1ccccc1>CC(=O)O.[Na+]>c1ccncc1',2)); +--SELECT tanimoto_sml(reaction_structural_bfp('c1ccccc1>CC(=O)O.[Na+]>c1ccncc1',2), reaction_structural_bfp('c1ncccc1>[Na+]>c1ncncc1',2)); +SELECT tanimoto_sml(reaction_structural_bfp('c1ccccc1>>c1ccncc1',3), reaction_structural_bfp('c1ccccc1>>c1ccncc1',3)); + tanimoto_sml +-------------- + 1 +(1 row) + +SELECT tanimoto_sml(reaction_structural_bfp('c1ccccc1>>c1ccncc1',3), reaction_structural_bfp('c1ncccc1>>c1ncncc1',3)); + tanimoto_sml +--------------------- + 0.42857142857142855 +(1 row) + +SELECT tanimoto_sml(reaction_structural_bfp('c1ccccc1>CC(=O)O.[Na+]>c1ccncc1',3), reaction_structural_bfp('c1ccccc1>CC(=O)O.[Na+]>c1ccncc1',3)); + tanimoto_sml +-------------- + 1 +(1 row) + +SELECT tanimoto_sml(reaction_structural_bfp('c1ccccc1>CC(=O)O.[Na+]>c1ccncc1',3), reaction_structural_bfp('c1ncccc1>[Na+]>c1ncncc1',3)); + tanimoto_sml +-------------------- + 0.3448275862068966 +(1 row) + +SELECT tanimoto_sml(reaction_structural_bfp('c1ccccc1>>c1ccncc1',4), reaction_structural_bfp('c1ccccc1>>c1ccncc1',4)); + tanimoto_sml +-------------- + 1 +(1 row) + +SELECT tanimoto_sml(reaction_structural_bfp('c1ccccc1>>c1ccncc1',4), reaction_structural_bfp('c1ncccc1>>c1ncncc1',4)); + tanimoto_sml +-------------------- + 0.2857142857142857 +(1 row) + +SELECT tanimoto_sml(reaction_structural_bfp('c1ccccc1>CC(=O)O.[Na+]>c1ccncc1',4), reaction_structural_bfp('c1ccccc1>CC(=O)O.[Na+]>c1ccncc1',4)); + tanimoto_sml +-------------- + 1 +(1 row) + +SELECT tanimoto_sml(reaction_structural_bfp('c1ccccc1>CC(=O)O.[Na+]>c1ccncc1',4), reaction_structural_bfp('c1ncccc1>[Na+]>c1ncncc1',4)); + tanimoto_sml +--------------------- + 0.24489795918367346 +(1 row) + +SELECT tanimoto_sml(reaction_structural_bfp('c1ccccc1>>c1ccncc1',5), reaction_structural_bfp('c1ccccc1>>c1ccncc1',5)); + tanimoto_sml +-------------- + 1 +(1 row) + +SELECT tanimoto_sml(reaction_structural_bfp('c1ccccc1>>c1ccncc1',5), reaction_structural_bfp('c1ncccc1>>c1ncncc1',5)); + tanimoto_sml +-------------- + 0.8 +(1 row) + +SELECT tanimoto_sml(reaction_structural_bfp('c1ccccc1>CC(=O)O.[Na+]>c1ccncc1',5), reaction_structural_bfp('c1ccccc1>CC(=O)O.[Na+]>c1ccncc1',5)); + tanimoto_sml +-------------- + 1 +(1 row) + +SELECT tanimoto_sml(reaction_structural_bfp('c1ccccc1>CC(=O)O.[Na+]>c1ccncc1',5), reaction_structural_bfp('c1ncccc1>[Na+]>c1ncncc1',5)); + tanimoto_sml +-------------------- + 0.6086956521739131 +(1 row) + +SET rdkit.ignore_reaction_agents=true; +SELECT tanimoto_sml(reaction_difference_fp('c1ccccc1>>c1ccncc1',1), reaction_difference_fp('c1ccccc1>>c1ccncc1',1)); + tanimoto_sml +-------------- + 1 +(1 row) + +SELECT tanimoto_sml(reaction_difference_fp('c1ccccc1>>c1ccncc1',1), reaction_difference_fp('c1ncccc1>>c1ncncc1',1)); + tanimoto_sml +-------------------- + 0.6363636363636364 +(1 row) + +SELECT tanimoto_sml(reaction_difference_fp('c1ccccc1>CC(=O)O.[Na+]>c1ccncc1',1), reaction_difference_fp('c1ccccc1>CC(=O)O.[Na+]>c1ccncc1',1)); + tanimoto_sml +-------------- + 1 +(1 row) + +SELECT tanimoto_sml(reaction_difference_fp('c1ccccc1>CC(=O)O.[Na+]>c1ccncc1',1), reaction_difference_fp('c1ncccc1>[Na+]>c1ncncc1',1)); + tanimoto_sml +-------------------- + 0.6363636363636364 +(1 row) + +SELECT tanimoto_sml(reaction_structural_bfp('c1ccccc1>>c1ccncc1',5), reaction_structural_bfp('c1ccccc1>>c1ccncc1',5)); + tanimoto_sml +-------------- + 1 +(1 row) + +SELECT tanimoto_sml(reaction_structural_bfp('c1ccccc1>>c1ccncc1',5), reaction_structural_bfp('c1ncccc1>>c1ncncc1',5)); + tanimoto_sml +-------------- + 0.8 +(1 row) + +SELECT tanimoto_sml(reaction_structural_bfp('c1ccccc1>CC(=O)O.[Na+]>c1ccncc1',5), reaction_structural_bfp('c1ccccc1>CC(=O)O.[Na+]>c1ccncc1',5)); + tanimoto_sml +-------------- + 1 +(1 row) + +SELECT tanimoto_sml(reaction_structural_bfp('c1ccccc1>CC(=O)O.[Na+]>c1ccncc1',5), reaction_structural_bfp('c1ncccc1>[Na+]>c1ncncc1',5)); + tanimoto_sml +-------------- + 0.8 +(1 row) + +SELECT reaction_to_svg('[C:1][O:2].[C:3][C:4]>>[C:1][O:2][C:3][C:4]'::reaction) svg; + svg +------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- + + + + + + + + + + + + + + + + + + + + + + + + + C:1+ + O:2+ + C:3+ + C:4+ + C:1+ + O:2 + + C:3+ + C:4+ + + + + + + + + + + + + +(1 row) + +SELECT reaction_to_svg('[C:1][O:2].[C:3][C:4]>>[C:1][O:2][C:3][C:4]'::reaction, true) svg; + svg +----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + O+ + O+ + + + + + + + + + + + + +(1 row) + +SET enable_indexscan=on; +SET enable_bitmapscan=on; +SET enable_seqscan=on; +DROP INDEX rxnidx; --- /dev/null 2019-10-21 09:46:46.351315135 +0200 +++ ./Code/PgSQL/rdkit/expected/slfpgist_1.out 2019-11-02 21:02:33.390921646 +0100 @@ -0,0 +1,89 @@ +CREATE INDEX fpidx ON pgsfp USING gist (f gist_sfp_low_ops); +SET rdkit.tanimoto_threshold = 0.6; +SET rdkit.dice_threshold = 0.6; +SET enable_indexscan=off; +SET enable_bitmapscan=off; +SET enable_seqscan=on; +SELECT + id, tanimoto_sml(morgan_fp('O=C1CC(OC2=CC=CC=C12)C1=CC=CC=C1'::mol, 1), f) AS sml +FROM + pgsfp +WHERE morgan_fp('O=C1CC(OC2=CC=CC=C12)C1=CC=CC=C1'::mol, 1) % f +ORDER BY sml DESC, id; + id | sml +----+----- +(0 rows) + +SELECT + id, dice_sml(morgan_fp('O=C1CC(OC2=CC=CC=C12)C1=CC=CC=C1'::mol, 1), f) AS sml +FROM + pgsfp +WHERE morgan_fp('O=C1CC(OC2=CC=CC=C12)C1=CC=CC=C1'::mol, 1) # f +ORDER BY sml DESC, id; + id | sml +---------+-------------------- + 659725 | 0.6857142857142857 + 63248 | 0.6486486486486487 + 6266272 | 0.6410256410256411 + 5359275 | 0.6388888888888888 + 5718138 | 0.6388888888888888 + 917183 | 0.6285714285714286 + 161167 | 0.6216216216216216 + 230488 | 0.6216216216216216 + 328013 | 0.6216216216216216 + 564008 | 0.6190476190476191 + 2910597 | 0.6153846153846154 + 3963948 | 0.6153846153846154 + 5407397 | 0.6153846153846154 + 3784792 | 0.6136363636363636 + 3096571 | 0.6097560975609756 + 801655 | 0.6052631578947368 + 3157044 | 0.6052631578947368 + 807628 | 0.6 +(18 rows) + +SET enable_indexscan=on; +SET enable_bitmapscan=on; +SET enable_seqscan=off; +SELECT + id, tanimoto_sml(morgan_fp('O=C1CC(OC2=CC=CC=C12)C1=CC=CC=C1'::mol, 1), f) AS sml +FROM + pgsfp +WHERE morgan_fp('O=C1CC(OC2=CC=CC=C12)C1=CC=CC=C1'::mol, 1) % f +ORDER BY sml DESC, id; + id | sml +----+----- +(0 rows) + +SELECT + id, dice_sml(morgan_fp('O=C1CC(OC2=CC=CC=C12)C1=CC=CC=C1'::mol, 1), f) AS sml +FROM + pgsfp +WHERE morgan_fp('O=C1CC(OC2=CC=CC=C12)C1=CC=CC=C1'::mol, 1) # f +ORDER BY sml DESC, id; + id | sml +---------+-------------------- + 659725 | 0.6857142857142857 + 63248 | 0.6486486486486487 + 6266272 | 0.6410256410256411 + 5359275 | 0.6388888888888888 + 5718138 | 0.6388888888888888 + 917183 | 0.6285714285714286 + 161167 | 0.6216216216216216 + 230488 | 0.6216216216216216 + 328013 | 0.6216216216216216 + 564008 | 0.6190476190476191 + 2910597 | 0.6153846153846154 + 3963948 | 0.6153846153846154 + 5407397 | 0.6153846153846154 + 3784792 | 0.6136363636363636 + 3096571 | 0.6097560975609756 + 801655 | 0.6052631578947368 + 3157044 | 0.6052631578947368 + 807628 | 0.6 +(18 rows) + +SET enable_indexscan=on; +SET enable_bitmapscan=on; +SET enable_seqscan=on; +DROP INDEX fpidx;