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26f1f4cf01fe992f5f7c1056d5ab8df72daa3f36
rdkit/Code/PgSQL/rdkit/sql/rdkit-91.sql
Greg Landrum db89172bf8 handle the heavy-atom degree queries differently (#1560) 
* handle the heavy-atom degree queries differently

* Fixes #1563

* add a test for the heavy atom degree option

* Support (and test) adjustHeavyDegree in the cartridge too.

* test results
2017-09-12 16:10:15 -04:00

328 lines
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--
-- 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
CREATE EXTENSION rdkit;
\set ECHO all
RESET client_min_messages;
SELECT is_valid_smiles('c1ccccc1');
SELECT mol_from_smiles('c1ccccc1');
SELECT is_valid_smiles('c1ccccc');
SELECT mol_from_smiles('c1ccccc');
SELECT mol_from_smiles('cccccc');
SELECT is_valid_smiles('c1cccn1');
SELECT is_valid_smarts('c1ccc[n,c]1');
SELECT mol_from_smarts('c1ccc[n,c]1');
SELECT is_valid_smarts('c1ccc');
SELECT mol_from_smarts('c1ccc');
SELECT mol_to_smiles(mol_from_smiles('c1ccccc1'));
SELECT mol_to_smarts(mol_from_smiles('c1ccccc1'));
SELECT mol_to_smarts('c1cccc[n,c]1'::qmol);
SELECT mol_to_smiles('c1cccc[n,c]1'::qmol);
SELECT is_valid_smiles('');
SELECT mol_from_smiles('');
SELECT mol_to_smiles(mol_from_smiles(''));
CREATE TABLE pgmol (id int, m mol);
\copy pgmol from 'data/data'
CREATE UNIQUE INDEX mol_ididx ON pgmol (id);
SELECT count(*) FROM pgmol;
SELECT count(*) FROM pgmol WHERE m @> 'c1ccccc1';
SELECT count(*) FROM pgmol WHERE m @> 'c1cccnc1';
SELECT count(*) FROM pgmol WHERE 'c1ccccc1' <@ m;
SELECT count(*) FROM pgmol WHERE 'c1cccnc1' <@ m;
SELECT count(*) FROM pgmol WHERE m @> mol_from_smarts('c1ccccc1');
SELECT count(*) FROM pgmol WHERE m @> mol_from_smarts('c1cccnc1');
SELECT count(*) FROM pgmol WHERE m @> mol_from_smarts('c1ccc[n,c]c1');
SELECT count(*) FROM pgmol WHERE mol_from_smarts('c1ccccc1') <@ m;
SELECT count(*) FROM pgmol WHERE mol_from_smarts('c1ccc[n,c]c1') <@ m;
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;
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;
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;
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;
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;
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;
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;
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;
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;
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;
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;
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;
select 'Cc1ccccc1'::mol@='c1ccccc1C'::mol;
select 'Cc1ccccc1'::mol@='c1ccccc1CC'::mol;
select 'Cc1ccccc1'::mol@='c1cccnc1C'::mol;
select subtract(torsion_fp('CCC1CCNCC1'),torsion_fp('OCC1CCNCC1'))=subtract(torsion_fp('CCC1CCOCC1'),torsion_fp('OCC1CCOCC1'));
select subtract(torsion_fp('CCC1CCNCC1'),torsion_fp('OCC1CCNCC1'))=subtract(torsion_fp('CCC1CCOCC1'),torsion_fp('NCC1CCOCC1'));
select add(torsion_fp('CCC1CCNCC1'),torsion_fp('OCC1CCNCC1'))=add(torsion_fp('CCC1CCOCC1'),torsion_fp('OCC1CCOCC1'));
select add(torsion_fp('CCC1CCNCC1'),torsion_fp('OCC1CCNCC1'))=add(torsion_fp('CCC1CCOCC1'),torsion_fp('NCC1CCOCC1'));
select add(torsion_fp('CCC1CCNCC1'),torsion_fp('OCC1CCNCC1'))=subtract(torsion_fp('CCC1CCNCC1'),torsion_fp('OCC1CCNCC1'));
select add(torsion_fp('CCC1CCNCC1'),torsion_fp('OCC1CCNCC1'))=subtract(torsion_fp('CCC1CCOCC1'),torsion_fp('OCC1CCOCC1'));
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');
select is_valid_ctab('invalid');
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_to_ctab() - suppress auto-generation of depiction.
select mol_to_ctab(mol('CCC'), false);
-- mol_to_ctab() - with auto-generated depiction.
select mol_to_ctab(mol('CCC'));
-- 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));
select all_values_lt(torsion_fp('c1ccccc1C'::mol),2);
select all_values_lt(torsion_fp('c1ccccc1C'::mol),3);
select all_values_gt(torsion_fp('c1ccccc1C'::mol),1);
select all_values_gt(torsion_fp('c1ccccc1C'::mol),2);
select is_valid_mol_pkl('foo'::bytea);
select is_valid_mol_pkl(mol_to_pkl('c1ccccc1'::mol));
select mol_from_pkl(mol_to_pkl('c1ccccc1'::mol));
select tanimoto_sml(morganbv_fp('c1ccccn1'::mol),morganbv_fp('c1ccccc1'::mol));
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))));
-- 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;
-- chiral matching
select 'C[C@H](F)Cl'::mol@>'CC(F)Cl'::mol as match;
select 'C[C@H](F)Cl'::mol@>'C[C@H](F)Cl'::mol as match;
select 'C[C@H](F)Cl'::mol@>'C[C@@H](F)Cl'::mol as match;
set rdkit.do_chiral_sss=true;
select 'C[C@H](F)Cl'::mol@>'CC(F)Cl'::mol as match;
select 'C[C@H](F)Cl'::mol@>'C[C@H](F)Cl'::mol as match;
select 'C[C@H](F)Cl'::mol@>'C[C@@H](F)Cl'::mol as match;
set rdkit.do_chiral_sss=false;
-- substructure counts
select substruct_count('c1ccncc1'::mol,'c1ccncc1'::mol);
select substruct_count('c1ccncc1'::mol,'c1ccncc1'::mol,false);
-- special queries
select 'c1ccc[nH]1'::mol@>mol_from_smiles('c1cccn1[H]') as match;
select 'c1cccn1C'::mol@>mol_from_smiles('c1cccn1[H]') as match;
select 'c1ccc[nH]1'::mol@>qmol_from_smiles('c1cccn1[H]') as match;
select 'c1cccn1C'::mol@>qmol_from_smiles('c1cccn1[H]') as match;
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;
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;
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;
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;
-- mol_adjust_query_properties
select 'C1CC1OC'::mol @> 'C1CC1O*'::mol;
select 'C1CC1OC'::mol @> mol_adjust_query_properties('C1CC1O*'::mol);
select 'C1CC1OC'::mol @> mol_adjust_query_properties('C1CC1O*'::mol,'{"makeDummiesQueries":false}');
select 'CC1CC1OC'::mol @> 'C1CC1O*'::mol;
select 'CC1CC1OC'::mol @> mol_adjust_query_properties('C1CC1O*'::mol);
select 'CC1CC1OC'::mol @> mol_adjust_query_properties('C1CC1O*'::mol,'{"adjustDegree":false}');
select 'C1CC1C(C)OC'::mol @> mol_adjust_query_properties('C1CC1CO*'::mol);
select 'C1CC1C(C)OC'::mol @> mol_adjust_query_properties('C1CC1CO*'::mol,'{"adjustDegreeFlags":"IGNOREDUMMIES"}');
select 'C1CC1CCCC'::mol @> mol_adjust_query_properties('C1CC1CC'::mol);
select 'C1CC1CCCC'::mol @> mol_adjust_query_properties('C1CC1CC'::mol,'{"adjustDegreeFlags":"IGNORENONE"}');
select 'C1CC1CCCC'::mol @> mol_adjust_query_properties('C1CC1CC'::mol,'{"adjustDegreeFlags":"IGNOREALL"}');
select 'C1CC1CCCC'::mol @> mol_adjust_query_properties('C1CC1CC'::mol,'{"adjustDegreeFlags":"IGNORECHAINS"}');
select 'C1CC1CCCC'::mol @> mol_adjust_query_properties('C1CC1CC'::mol,'{"adjustDegreeFlags":"IGNORERINGS"}');
select 'C1CC1CCCC'::mol @> mol_adjust_query_properties('C1CC1CC'::mol,'{"adjustDegreeFlags":"IGNORERINGS|IGNORECHAINS"}');
select 'C1C(C)C1CCCC'::mol @> mol_adjust_query_properties('C1CC1CC'::mol);
select 'C1C(C)C1CCCC'::mol @> mol_adjust_query_properties('C1CC1CC'::mol,'{"adjustDegreeFlags":"IGNORENONE"}');
select 'C1C(C)C1CCCC'::mol @> mol_adjust_query_properties('C1CC1CC'::mol,'{"adjustDegreeFlags":"IGNOREALL"}');
select 'C1C(C)C1CCCC'::mol @> mol_adjust_query_properties('C1CC1CC'::mol,'{"adjustDegreeFlags":"IGNORECHAINS"}');
select 'C1C(C)C1CCCC'::mol @> mol_adjust_query_properties('C1CC1CC'::mol,'{"adjustDegreeFlags":"IGNORERINGS"}');
select 'C1C(C)C1CCCC'::mol @> mol_adjust_query_properties('C1CC1CC'::mol,'{"adjustDegreeFlags":"IGNORERINGS|IGNORECHAINS"}');
select 'C1C(C)C1CCCC'::mol @> mol_adjust_query_properties('C1CC1CC'::mol,'{"adjustDegreeFlags":"bogus"}');
select 'C1C([2H])C1CCCC'::mol @> mol_adjust_query_properties('C1CC1CC'::mol);
select 'C1C([2H])C1CCCC'::mol @> mol_adjust_query_properties('C1CC1CC'::mol,'{"adjustDegree":false}');
select 'C1C([2H])C1CCCC'::mol @> mol_adjust_query_properties('C1CC1CC'::mol,'{"adjustDegree":false,"adjustHeavyDegree":true}');
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