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rdkit/Code/PgSQL/rdkit/sql/rdkit-91.sql
paconius 9d0f15172f Make Cartridge @= operator coordinate agnostic (#8488) 
* Modified CXSmiles comparison to ignore coords

* Added @= tests for coordinate change in mol

* Added test output for Issue #8465
2025-05-01 05:21:08 +02:00

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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;
SET extra_float_digits=0;
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 qmol_from_smarts('c1ccc[n,c]1');
SELECT is_valid_smarts('c1ccc');
SELECT qmol_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(''));
SELECT mol_to_smiles(mol_from_smiles('C[C@H](F)[C@H](C)[C@@H](C)Br'));
SELECT mol_to_smiles(mol_from_smiles('C[C@H](F)[C@H](C)[C@@H](C)Br'), false);
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 @> qmol_from_smarts('c1ccccc1');
SELECT count(*) FROM pgmol WHERE m @> qmol_from_smarts('c1cccnc1');
SELECT count(*) FROM pgmol WHERE m @> qmol_from_smarts('c1ccc[n,c]c1');
SELECT count(*) FROM pgmol WHERE qmol_from_smarts('c1ccccc1') <@ m;
SELECT count(*) FROM pgmol WHERE qmol_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));
-- mol_to_ctab() - force v3000.
select mol_to_ctab(mol('CCC'), false, true);
select mol_to_v3kctab(mol('CCC'), false);
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
set rdkit.do_chiral_sss=false;
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;
-- github #2790
set rdkit.do_chiral_sss=false;
select 'C[C@H](F)Cl'::mol@='C[C@H](F)Cl'::mol;
select 'C[C@H](F)Cl'::mol@='C[C@@H](F)Cl'::mol;
select 'C[C@H](F)Cl'::mol@='CC(F)Cl'::mol;
select 'CC(F)Cl'::mol@='C[C@@H](F)Cl'::mol;
select 'CC(F)Cl'::mol@='C[C@H](F)Cl'::mol;
select 'CC(F)Cl'::mol@='CC(F)Cl'::mol;
set rdkit.do_chiral_sss=true;
select 'C[C@H](F)Cl'::mol@='C[C@H](F)Cl'::mol;
select 'C[C@H](F)Cl'::mol@='C[C@@H](F)Cl'::mol;
select 'C[C@H](F)Cl'::mol@='CC(F)Cl'::mol;
select 'CC(F)Cl'::mol@='C[C@@H](F)Cl'::mol;
select 'CC(F)Cl'::mol@='C[C@H](F)Cl'::mol;
select 'CC(F)Cl'::mol@='CC(F)Cl'::mol;
set rdkit.do_chiral_sss=false;
-- Enhanced stereo
-- Includes Issue# 8465: Demonstrate that modification of molecule coords does not impact identity
set rdkit.do_chiral_sss=false;
set rdkit.do_enhanced_stereo_sss=false; /* has no effect when do_chiral_sss is false */
select 'C[C@@H](O)[C@@H](C)F |&1:1,3,r|'::mol@>'C[C@@H](O)[C@@H](C)F |o1:1,3,r|'::mol;
select 'C[C@@H](O)[C@@H](C)F |o1:1,3,r|'::mol@>'C[C@@H](O)[C@@H](C)F |&1:1,3,r|'::mol;
select 'C[C@H](O)[C@H](C)F |&1:1,3,r|'::mol@>'C[C@@H](O)[C@@H](C)F |o1:1,3,r|'::mol;
select 'C[C@H](O)[C@H](C)F |o1:1,3,r|'::mol@>'C[C@@H](O)[C@@H](C)F |&1:1,3,r|'::mol;
select 'C[C@@H](O)[C@@H](C)F |o1:1,3,r|'::mol@>'C[C@@H](O)[C@@H](C)F'::mol;
select 'C[C@@H](O)[C@@H](C)F |&1:1,3,r|'::mol@>'C[C@@H](O)[C@@H](C)F'::mol;
select 'C[C@@H](O)[C@@H](C)F |o1:1,3,r|'::mol@>'C[C@H](O)[C@H](C)F'::mol;
select 'C[C@@H](O)[C@@H](C)F |&1:1,3,r|'::mol@>'C[C@H](O)[C@H](C)F'::mol;
select 'c1ccccc1 |(7.8993,-8.9847,;8.6138,-8.5722,;8.6138,-7.7472,;7.8993,-7.3347,;7.1848,-7.7472,;7.1848,-8.5722,)|'::mol@='c1ccccc1 |(10.3733,-8.9847,;11.0877,-8.5722,;11.0877,-7.7472,;10.3733,-7.3347,;9.6588,-7.7472,;9.6588,-8.5722,)|'::mol;
set rdkit.do_enhanced_stereo_sss=true; /* has no effect when do_chiral_sss is false */
select 'C[C@@H](O)[C@@H](C)F |&1:1,3,r|'::mol@>'C[C@@H](O)[C@@H](C)F |o1:1,3,r|'::mol;
select 'C[C@@H](O)[C@@H](C)F |o1:1,3,r|'::mol@>'C[C@@H](O)[C@@H](C)F |&1:1,3,r|'::mol;
select 'C[C@H](O)[C@H](C)F |&1:1,3,r|'::mol@>'C[C@@H](O)[C@@H](C)F |o1:1,3,r|'::mol;
select 'C[C@H](O)[C@H](C)F |o1:1,3,r|'::mol@>'C[C@@H](O)[C@@H](C)F |&1:1,3,r|'::mol;
select 'C[C@@H](O)[C@@H](C)F |o1:1,3,r|'::mol@>'C[C@@H](O)[C@@H](C)F'::mol;
select 'C[C@@H](O)[C@@H](C)F |&1:1,3,r|'::mol@>'C[C@@H](O)[C@@H](C)F'::mol;
select 'C[C@@H](O)[C@@H](C)F |o1:1,3,r|'::mol@>'C[C@H](O)[C@H](C)F'::mol;
select 'C[C@@H](O)[C@@H](C)F |&1:1,3,r|'::mol@>'C[C@H](O)[C@H](C)F'::mol;
select 'c1ccccc1 |(7.8993,-8.9847,;8.6138,-8.5722,;8.6138,-7.7472,;7.8993,-7.3347,;7.1848,-7.7472,;7.1848,-8.5722,)|'::mol@='c1ccccc1 |(10.3733,-8.9847,;11.0877,-8.5722,;11.0877,-7.7472,;10.3733,-7.3347,;9.6588,-7.7472,;9.6588,-8.5722,)|'::mol;
set rdkit.do_chiral_sss=true;
set rdkit.do_enhanced_stereo_sss=false;
select 'C[C@@H](O)[C@@H](C)F |&1:1,3,r|'::mol@>'C[C@@H](O)[C@@H](C)F |o1:1,3,r|'::mol;
select 'C[C@@H](O)[C@@H](C)F |o1:1,3,r|'::mol@>'C[C@@H](O)[C@@H](C)F |&1:1,3,r|'::mol;
select 'C[C@H](O)[C@H](C)F |&1:1,3,r|'::mol@>'C[C@@H](O)[C@@H](C)F |o1:1,3,r|'::mol;
select 'C[C@H](O)[C@H](C)F |o1:1,3,r|'::mol@>'C[C@@H](O)[C@@H](C)F |&1:1,3,r|'::mol;
select 'C[C@@H](O)[C@@H](C)F |o1:1,3,r|'::mol@>'C[C@@H](O)[C@@H](C)F'::mol;
select 'C[C@@H](O)[C@@H](C)F |&1:1,3,r|'::mol@>'C[C@@H](O)[C@@H](C)F'::mol;
select 'C[C@@H](O)[C@@H](C)F |o1:1,3,r|'::mol@>'C[C@H](O)[C@H](C)F'::mol;
select 'C[C@@H](O)[C@@H](C)F |&1:1,3,r|'::mol@>'C[C@H](O)[C@H](C)F'::mol;
select 'c1ccccc1 |(7.8993,-8.9847,;8.6138,-8.5722,;8.6138,-7.7472,;7.8993,-7.3347,;7.1848,-7.7472,;7.1848,-8.5722,)|'::mol@='c1ccccc1 |(10.3733,-8.9847,;11.0877,-8.5722,;11.0877,-7.7472,;10.3733,-7.3347,;9.6588,-7.7472,;9.6588,-8.5722,)|'::mol;
set rdkit.do_enhanced_stereo_sss=true; /* now we expect to see an effect */
select 'C[C@@H](O)[C@@H](C)F |&1:1,3,r|'::mol@>'C[C@@H](O)[C@@H](C)F |o1:1,3,r|'::mol;
select 'C[C@@H](O)[C@@H](C)F |o1:1,3,r|'::mol@>'C[C@@H](O)[C@@H](C)F |&1:1,3,r|'::mol;
select 'C[C@H](O)[C@H](C)F |&1:1,3,r|'::mol@>'C[C@@H](O)[C@@H](C)F |o1:1,3,r|'::mol;
select 'C[C@H](O)[C@H](C)F |o1:1,3,r|'::mol@>'C[C@@H](O)[C@@H](C)F |&1:1,3,r|'::mol;
select 'C[C@@H](O)[C@@H](C)F |o1:1,3,r|'::mol@>'C[C@@H](O)[C@@H](C)F'::mol;
select 'C[C@@H](O)[C@@H](C)F |&1:1,3,r|'::mol@>'C[C@@H](O)[C@@H](C)F'::mol;
select 'C[C@@H](O)[C@@H](C)F |o1:1,3,r|'::mol@>'C[C@H](O)[C@H](C)F'::mol;
select 'C[C@@H](O)[C@@H](C)F |&1:1,3,r|'::mol@>'C[C@H](O)[C@H](C)F'::mol;
select 'c1ccccc1 |(7.8993,-8.9847,;8.6138,-8.5722,;8.6138,-7.7472,;7.8993,-7.3347,;7.1848,-7.7472,;7.1848,-8.5722,)|'::mol@='c1ccccc1 |(10.3733,-8.9847,;11.0877,-8.5722,;11.0877,-7.7472,;10.3733,-7.3347,;9.6588,-7.7472,;9.6588,-8.5722,)|'::mol;
set rdkit.do_chiral_sss=false;
set rdkit.do_enhanced_stereo_sss=false;
-- forcing chiral queries
select substruct_chiral('C[C@@H](O)[C@@H](C)F |&1:1,3,r|'::mol,'C[C@@H](O)[C@@H](C)F |o1:1,3,r|'::mol);
select substruct_chiral('C[C@@H](O)[C@@H](C)F |o1:1,3,r|'::mol,'C[C@@H](O)[C@@H](C)F |&1:1,3,r|'::mol);
select rsubstruct_chiral('C[C@@H](O)[C@@H](C)F |&1:1,3,r|'::mol,'C[C@@H](O)[C@@H](C)F |o1:1,3,r|'::mol);
select rsubstruct_chiral('C[C@@H](O)[C@@H](C)F |o1:1,3,r|'::mol,'C[C@@H](O)[C@@H](C)F |&1:1,3,r|'::mol);
-- substructure counts
select substruct_count('c1ccncc1'::mol,'c1ccncc1'::mol);
select substruct_count('c1ccncc1'::mol,'c1ccncc1'::mol,false);
select substruct_count('c1ccccc1C[C@@H](O)[C@@H](C)F |&1:7,9,r|'::mol,'c1ccccc1C[C@@H](O)[C@@H](C)F |o1:7,9,r|'::mol);
select substruct_count('c1ccccc1C[C@@H](O)[C@@H](C)F |o1:7,9,r|'::mol,'c1ccccc1C[C@@H](O)[C@@H](C)F |&1:7,9,r|'::mol);
select substruct_count_chiral('c1ccccc1C[C@@H](O)[C@@H](C)F |&1:7,9,r|'::mol,'c1ccccc1C[C@@H](O)[C@@H](C)F |o1:7,9,r|'::mol);
select substruct_count_chiral('c1ccccc1C[C@@H](O)[C@@H](C)F |o1:7,9,r|'::mol,'c1ccccc1C[C@@H](O)[C@@H](C)F |&1:7,9,r|'::mol);
select substruct_count_chiral('c1ccccc1C[C@@H](O)[C@@H](C)F |&1:7,9,r|'::mol,'c1ccccc1C[C@@H](O)[C@@H](C)F |o1:7,9,r|'::mol,false);
select substruct_count_chiral('c1ccccc1C[C@@H](O)[C@@H](C)F |o1:7,9,r|'::mol,'c1ccccc1C[C@@H](O)[C@@H](C)F |&1:7,9,r|'::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;
-- github #4787:
select mol_to_smarts(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'));
select mol_to_smarts(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 4 0 0 0 0
2 3 4 0 0 0 0
4 5 4 0 0 0 0
1 5 4 0 0 0 0
3 4 4 0 0 0 0
1 6 1 0 0 0 0
M END'));
select mol_to_smarts(qmol_from_ctab('Boronate acid/ester(aryl)
SciTegic12012112112D
5 4 0 0 0 0 999 V2000
1.7243 -2.7324 0.0000 A 0 0
2.7559 -2.1456 0.0000 C 0 0
3.7808 -2.7324 0.0000 B 0 0
4.8057 -2.1456 0.0000 O 0 0
3.7808 -3.9190 0.0000 O 0 0
1 2 4 0 0 1 0
2 3 1 0
3 4 1 0
3 5 1 0
M END'));
select mol_to_smarts(qmol_from_smiles('c:c'));
select mol_to_smarts(qmol_from_smiles('C1=CC=CC=C1'));
-- 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}');
select mol_to_smarts(mol_adjust_query_properties('*c1ncc(*)cc1'::mol));
select mol_to_smarts(mol_adjust_query_properties('*c1ncc(*)cc1'::qmol));
-- CXSmiles
SELECT mol_to_smiles(mol_from_smiles('C[C@H](F)[C@H](C)[C@@H](C)Br |a:1,o1:3,5|'));
SELECT mol_to_cxsmiles(mol_from_smiles('C[C@H](F)[C@H](C)[C@@H](C)Br |a:1,o1:3,5|'));
SELECT mol_to_cxsmiles(mol_from_smiles('C[C@H](F)[C@H](C)[C@@H](C)Br |a:1,o1:3,5|'), false);
SELECT mol_to_cxsmarts(mol_from_smiles('C[C@H](F)[C@H](C)[C@@H](C)Br |a:1,o1:3,5|'));
SELECT mol_to_cxsmarts(qmol_from_smarts('C[C@H]([F,Cl,Br])[C@H](C)[C@@H](C)Br |a:1,o1:3,5|'));
-- CXSmiles from mol_out
SELECT mol_out(mol_from_smiles('C[C@H](F)[C@H](C)[C@@H](C)Br |a:1,o1:3,5|'));
-- github #3688: bad input to qmol_from_ctab() crashes db
select qmol_from_ctab('a'::cstring,false);
-- github #3689: bad input to qmol_from_smiles() crashes db
select qmol_from_smiles('a'::cstring);
select qmol_from_smiles('C1C'::cstring);
-- casting from mol to qmol
select mol_from_smiles('C=C')::qmol;
-- github #5095: cannot restore molecule
select mol_in('c1cccc'::cstring);
select mol_in('c1cccc1'::cstring);
select mol_in('c1co(C)cc1'::cstring);
select mol_in('c1cccc'::cstring);
select mol_in('CN(=O)=O'::cstring);
select 'CN(=O)=O'::mol;
select 'c1cccc1'::mol;
select 'c1co(C)cc1'::mol;
select mol_in('c1cccc1'::cstring) @> '[r5]'::qmol;
select 'c1cccc1'::mol @> '[r5]'::qmol;
select mol_in('Cc1ccc2c(c1)-n1-c(=O)c=cc(=O)-n-2-c2cc(C)ccc2-1');
select 'c1cccc1'::text::mol;
select 'c1cccc1'::varchar::mol;
select mol_from_smiles('CCN(=O)=O') @> 'CN(=O)=O';
-- github #6002: molcmp failure
select mol_cmp(mol_from_ctab('
Mrv2211 02092314292D
5 4 0 0 0 0 999 V2000
0.0000 3.6020 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
0.7145 4.0145 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0
1.4290 4.4270 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
1.1270 3.3001 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
0.3020 4.7291 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
1 2 6 0 0 0 0
2 3 2 0 0 0 0
2 4 2 0 0 0 0
2 5 6 0 0 0 0
M END'),mol_from_ctab('
Mrv2211 02092314292D
5 4 0 0 0 0 999 V2000
0.0000 3.6020 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
0.7145 4.0145 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0
1.4290 4.4270 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
1.1270 3.3001 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
0.3020 4.7291 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
1 2 6 0 0 0 0
2 3 2 0 0 0 0
2 4 2 0 0 0 0
2 5 6 0 0 0 0
M END'));
-- mol properties being properly serialized
select 'COC1=NNC=C1 |LN:1:1.3|'::mol;
-- bond properties all preserved
select mol_to_v3kctab(mol_from_ctab('
Mrv2211 09062306242D
0 0 0 0 0 999 V3000
M V30 BEGIN CTAB
M V30 COUNTS 5 3 0 0 0
M V30 BEGIN ATOM
M V30 1 C -7.7917 4.0833 0 0
M V30 2 C -6.458 4.8533 0 0
M V30 3 C -5.1243 4.0833 0 0
M V30 4 * -6.458 4.34 0 0
M V30 5 C -5.303 6.3405 0 0
M V30 END ATOM
M V30 BEGIN BOND
M V30 1 1 1 2
M V30 2 2 2 3
M V30 3 1 4 5 ENDPTS=(3 1 2 3) ATTACH=ANY
M V30 END BOND
M V30 END CTAB
M END'));
-- sanitization and Hs: do not sanitize, removing Hs has no effect
select mol_to_smiles(mol_from_ctab('
RDKit 2D
0 0 0 0 0 0 0 0 0 0999 V3000
M V30 BEGIN CTAB
M V30 COUNTS 3 2 0 0 0
M V30 BEGIN ATOM
M V30 1 C 0.000000 0.000000 0.000000 0
M V30 2 F 1.299038 0.750000 0.000000 0
M V30 3 H 2.598076 -0.000000 0.000000 0
M V30 END ATOM
M V30 BEGIN BOND
M V30 1 1 1 2
M V30 2 1 2 3
M V30 END BOND
M V30 END CTAB
M END
',false,false,true));
-- sanitization and Hs: do not sanitize, do not remove Hs
select mol_to_smiles(mol_from_ctab('
RDKit 2D
0 0 0 0 0 0 0 0 0 0999 V3000
M V30 BEGIN CTAB
M V30 COUNTS 3 2 0 0 0
M V30 BEGIN ATOM
M V30 1 C 0.000000 0.000000 0.000000 0
M V30 2 F 1.299038 0.750000 0.000000 0
M V30 3 H 2.598076 -0.000000 0.000000 0
M V30 END ATOM
M V30 BEGIN BOND
M V30 1 1 1 2
M V30 2 1 2 3
M V30 END BOND
M V30 END CTAB
M END
',false,false,false));
-- sanitization and Hs: sanitize, do not remove Hs
select mol_to_smiles(mol_from_ctab('
RDKit 2D
0 0 0 0 0 0 0 0 0 0999 V3000
M V30 BEGIN CTAB
M V30 COUNTS 3 2 0 0 0
M V30 BEGIN ATOM
M V30 1 C 0.000000 0.000000 0.000000 0
M V30 2 O 1.299038 0.750000 0.000000 0
M V30 3 H 2.598076 -0.000000 0.000000 0
M V30 END ATOM
M V30 BEGIN BOND
M V30 1 1 1 2
M V30 2 1 2 3
M V30 END BOND
M V30 END CTAB
M END
',false,true,false));
-- sanitization and Hs: default is to sanitize and remove Hs
select mol_to_smiles(mol_from_ctab('
RDKit 2D
0 0 0 0 0 0 0 0 0 0999 V3000
M V30 BEGIN CTAB
M V30 COUNTS 3 2 0 0 0
M V30 BEGIN ATOM
M V30 1 C 0.000000 0.000000 0.000000 0
M V30 2 O 1.299038 0.750000 0.000000 0
M V30 3 H 2.598076 -0.000000 0.000000 0
M V30 END ATOM
M V30 BEGIN BOND
M V30 1 1 1 2
M V30 2 1 2 3
M V30 END BOND
M V30 END CTAB
M END
',false));
-- sanitization and Hs: sanitize, do not remove Hs, input coords manipulated
select mol_to_v3kctab(mol_from_ctab('
RDKit 2D
0 0 0 0 0 0 0 0 0 0999 V3000
M V30 BEGIN CTAB
M V30 COUNTS 3 2 0 0 0
M V30 BEGIN ATOM
M V30 1 C 0.000000 0.000000 0.000000 0
M V30 2 O 1.000000 0.500000 0.000000 0
M V30 3 H 2.598076 -0.000000 0.000000 0
M V30 END ATOM
M V30 BEGIN BOND
M V30 1 1 1 2
M V30 2 1 2 3
M V30 END BOND
M V30 END CTAB
M END
',false,true,false));
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