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FW: Mychem SQL query for Tanimoto function

Martin Morissette
Hi, I would need some help to create a SQL query that returns hits ordered on the tanimoto coefficient of the queried smiles and the fingerprints stored in the database. So far, I was able to set the sql variable as follow :
SET @fp = (SELECT FINGERPRINT2(SMILES_TO_MOLECULE(‘smiles')));
Where the smiles is inserted with php from a JSME input
Then I want to modify the current substructure search query :
$query = "SELECT compounds.name AS No, pdt.fullname as Name FROM pdt,compounds,bin_structures WHERE pdt.name=compounds.name AND compounds.id=bin_structures.compound_id AND MATCH_SUBSTRUCT('".$_POST['smiles']."',obserialized)";
to compute the tanimoto of @fp and bin_structures.fp2
Whenever I try to compute TANIMOTO(@fp, fp2) from bin_structures I get a NULL value.
I tried the TANIMOTO function examples from the documentation but I always get NULL values.
If I use two variables @fp1 and @fp2 and set these values with 2 different smiles fingerprints, I can compute the TANIMOTO(@fp1, @fp2).
I use a LAMP stack on Ubuntu 14.04 64 bits.
Any help is welcome
Thank you
Martin
 
 

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Re: FW: Mychem SQL query for Tanimoto function

Fredrik Wallner
Hi,

What versions of OpenBabel and Mychem do you use?

I also think that this question is best answered in the Mychem list so I forwarded it there. 

Kind regards,
Fredrik 

Skickat från min iPhone

20 okt. 2016 kl. 18:44 skrev Martin Morissette <[hidden email]>:

Hi, I would need some help to create a SQL query that returns hits ordered on the tanimoto coefficient of the queried smiles and the fingerprints stored in the database. So far, I was able to set the sql variable as follow :
SET @fp = (SELECT FINGERPRINT2(SMILES_TO_MOLECULE(‘smiles')));
Where the smiles is inserted with php from a JSME input
Then I want to modify the current substructure search query :
$query = "SELECT compounds.name AS No, pdt.fullname as Name FROM pdt,compounds,bin_structures WHERE pdt.name=compounds.name AND compounds.id=bin_structures.compound_id AND MATCH_SUBSTRUCT('".$_POST['smiles']."',obserialized)";
to compute the tanimoto of @fp and bin_structures.fp2
Whenever I try to compute TANIMOTO(@fp, fp2) from bin_structures I get a NULL value.
I tried the TANIMOTO function examples from the documentation but I always get NULL values.
If I use two variables @fp1 and @fp2 and set these values with 2 different smiles fingerprints, I can compute the TANIMOTO(@fp1, @fp2).
I use a LAMP stack on Ubuntu 14.04 64 bits.
Any help is welcome
Thank you
Martin
 
 
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Re: FW: Mychem SQL query for Tanimoto function

Martin Morissette

Hi Fredrik,

 

I use OpenBabel 2.3.2 and MyChem 0.9.3

 

I use :

PHP 5.5.9-1ubuntu4.17

Server version: 5.6.30-0ubuntu0.14.04.1

 

On a Digital Ocean Ubuntu 14.04 64bits droplet.

 

I installed openbabel with the following command:

sudo apt-get install openbabel

 

I can supply my whole installation procedure if you want. I ran the test module also and 2 conversion failed :

 

Running tests...

Test project /home/studur/mychem-code-0.9.3/build

    Start 1: ConversionTest

1/5 Test #1: ConversionTest ...................***Failed    0.18 sec

    Start 2: HelperTest

2/5 Test #2: HelperTest .......................   Passed    0.01 sec

    Start 3: ModificationTest

3/5 Test #3: ModificationTest .................   Passed    0.02 sec

    Start 4: MolmatchTest

4/5 Test #4: MolmatchTest .....................   Passed    0.06 sec

    Start 5: PropertyTest

5/5 Test #5: PropertyTest .....................***Failed    0.05 sec

 

60% tests passed, 2 tests failed out of 5

 

Total Test time (real) =   0.32 sec

 

The following tests FAILED:

          1 - ConversionTest (Failed)

          5 - PropertyTest (Failed)

Errors while running CTest

make: *** [test] Error 8

 

Here is the log:

 

Start testing: Oct 20 14:27 EDT

----------------------------------------------------------

1/5 Testing: ConversionTest

1/5 Test: ConversionTest

Command: "/home/studur/mychem-code-0.9.3/build/tests/conversion_test" "-h" "localhost" "-u" "studur" "-p" "********" "-b" "mysql" "-d" "/home/studur/mychem-code-0.9.3/tests/data/"

Directory: /home/studur/mychem-code-0.9.3/build/tests

"ConversionTest" start time: Oct 20 14:27 EDT

Output:

----------------------------------------------------------

Testing molfile_to_molecule ...                             [OK]

Testing molecule_to_molfile ...                             [OK]

Testing V3000_to_molecule ...                               [OK]

Testing molecule_to_V3000 ...                               [OK]

Testing smiles_to_molecule ...                              [OK]

Testing molecule_to_smiles ...                              [OK]

Testing molecule_to_molecule ...                            [OK]

Testing cml_to_molecule ...                                 [OK]

Testing molecule_to_cml ...                                 [OK]

Testing fingerprint ...                                     [OK]

Testing molecule_to_canonical_smiles ...                    [OK]

Testing inchi_to_molecule ...                               [OK]

Testing molecule_to_inchi ...                               [OK]

Testing molecule_to_serializedOBMol ...                     [OK]

Testing pdb_to_molecule ...                                 [OK]

Testing mol2_to_molecule ...                              [FAILED]

Testing molecule_to_mol2 ...                              [FAILED]

<end of output>

Test time =   0.18 sec

----------------------------------------------------------

Test Failed.

"ConversionTest" end time: Oct 20 14:27 EDT

"ConversionTest" time elapsed: 00:00:00

----------------------------------------------------------

 

2/5 Testing: HelperTest

2/5 Test: HelperTest

Command: "/home/studur/mychem-code-0.9.3/build/tests/helper_test" "-h" "localhost" "-u" "studur" "-p" "********" "-b" "mysql" "-d" "/home/studur/mychem-code-0.9.3/tests/data/"

Directory: /home/studur/mychem-code-0.9.3/build/tests

"HelperTest" start time: Oct 20 14:27 EDT

Output:

----------------------------------------------------------

Testing mychem_version ...                                  [OK]

Testing openbabel_version ...                               [OK]

<end of output>

Test time =   0.01 sec

----------------------------------------------------------

Test Passed.

"HelperTest" end time: Oct 20 14:27 EDT

"HelperTest" time elapsed: 00:00:00

----------------------------------------------------------

 

3/5 Testing: ModificationTest

3/5 Test: ModificationTest

Command: "/home/studur/mychem-code-0.9.3/build/tests/modification_test" "-h" "localhost" "-u" " studur " "-p" "********" "-b" "mysql" "-d" "/home/studur/mychem-code-0.9.3/tests/data/"

Directory: /home/studur/mychem-code-0.9.3/build/tests

"ModificationTest" start time: Oct 20 14:27 EDT

Output:

----------------------------------------------------------

Testing add_hydrogens ...                                   [OK]

Testing remove_hydrogens ...                                [OK]

Testing strip_salts ...                                     [OK]

<end of output>

Test time =   0.02 sec

----------------------------------------------------------

Test Passed.

"ModificationTest" end time: Oct 20 14:27 EDT

"ModificationTest" time elapsed: 00:00:00

----------------------------------------------------------

 

4/5 Testing: MolmatchTest

4/5 Test: MolmatchTest

Command: "/home/studur/mychem-code-0.9.3/build/tests/molmatch_test" "-h" "localhost" "-u" " studur " "-p" "********" "-b" "mysql" "-d" "/home/studur/mychem-code-0.9.3/tests/data/"

Directory: /home/studur/mychem-code-0.9.3/build/tests

"MolmatchTest" start time: Oct 20 14:27 EDT

Output:

----------------------------------------------------------

Testing match_substruct ...                                 [OK]

Testing substruct_atom_ids ...                              [OK]

Testing substruct_count ...                                 [OK]

Testing tanimoto ...                                        [OK]

Testing bit_fp_and ...                                      [OK]

Testing bit_fp_or ...                                       [OK]

Testing bit_fp_count ...                                    [OK]

<end of output>

Test time =   0.06 sec

----------------------------------------------------------

Test Passed.

"MolmatchTest" end time: Oct 20 14:27 EDT

"MolmatchTest" time elapsed: 00:00:00

----------------------------------------------------------

 

5/5 Testing: PropertyTest

5/5 Test: PropertyTest

Command: "/home/studur/mychem-code-0.9.3/build/tests/property_test" "-h" "localhost" "-u" " studur " "-p" "********" "-b" "mysql" "-d" "/home/studur/mychem-code-0.9.3/tests/data/"

Directory: /home/studur/mychem-code-0.9.3/build/tests

"PropertyTest" start time: Oct 20 14:27 EDT

Output:

----------------------------------------------------------

Testing molweight ...                                       [OK]

Testing exactmass ...                                       [OK]

Testing number_of_atoms ...                                 [OK]

Testing number_of_heavy_atoms ...                           [OK]

Testing number_of_bonds ...                                 [OK]

Testing number_of_rotable_bonds ...                         [OK]

Testing total_charge ...                                    [OK]

Testing molformula ...                                      [OK]

Testing number_of_acceptors ...                             [OK]

Testing number_of_donors ...                                [OK]

Testing molpsa ...                                        [FAILED]

Testing molmr ...                                         [FAILED]

Testing mollogp ...                                       [FAILED]

Testing is_2D ...                                           [OK]

Testing is_3D ...                                           [OK]

Testing is_chiral ...                                       [OK]

Testing number_of_rings ...                                 [OK]

<end of output>

Test time =   0.05 sec

----------------------------------------------------------

Test Failed.

"PropertyTest" end time: Oct 20 14:27 EDT

"PropertyTest" time elapsed: 00:00:00

----------------------------------------------------------

 

 


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