Conversion Commands

Conversion Commands
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The conversion module provides functions for converting chemical data. Open Babel supports over 80 chemical file formats. To avoid having to many functions, this module defines a set of two functions for each format: FORMAT_TO_MOLECULE and MOLECULE_TO_FORMAT. However, new functions, like CML_TO_SMILES, can be requested on the feature tracker.

Note

If a function of the conversion module fails, it returns an empty string.

MOLECULE_TO_SERIALIZEDOBMOL(molecule)
MOLECULE_TO_SERIALIZEDOBMOL() converts a molecule in DEFAULT_TYPE format to a serialized OBMol object. The SQL type of a serialized object is a binary string.
```
mysql> SELECT MOLECULE_TO_SERIALIZEDOBMOL(molecule_col)
    -> FROM tbl_name WHERE name='glycine';
        -> binary string
        
```

CML_TO_MOLECULE(molecule)

CML_TO_MOLECULE() converts a molecule in CML format to a molecule in DEFAULT_TYPE format.

mysql> SELECT CML_TO_MOLECULE(cml_col) FROM tbl_name
    -> WHERE name='glycine';
        -> glycine
 OpenBabel11190809032D

  5  4  0  0  0  0  0  0  0  0999 V2000
  206.0000  126.0000    0.0000 C   0  0  0  0  0
  227.0075  113.8713    0.0000 C   0  0  0  0  0
  227.0075   89.6139    0.0000 O   0  0  0  0  0
  248.0151  126.0000    0.0000 O   0  0  0  0  0
  184.9925  113.8713    0.0000 N   0  0  0  0  0
  1  2  1  0  0  0
  1  5  1  0  0  0
  2  3  2  0  0  0
  2  4  1  0  0  0
M  END

MOLECULE_TO_CML(molecule)

MOLECULE_TO_CML() converts a molecule in DEFAULT_TYPE format to a molecule in CML format.

mysql> SELECT MOLECULE_TO_CML(molecule_col) FROM tbl_name
    -> WHERE name='glycine';
        -> <molecule id="glycine">
 <atomArray>
  <atom id="a1" elementType="C" x2="206.000000" y2="126.000000"/>
  <atom id="a2" elementType="C" x2="227.007500" y2="113.871300"/>
  <atom id="a3" elementType="O" x2="227.007500" y2="89.613900"/>
  <atom id="a4" elementType="O" x2="248.015100" y2="126.000000"/>
  <atom id="a5" elementType="N" x2="184.992500" y2="113.871300"/>
 </atomArray>
 <bondArray>
  <bond atomRefs2="a2 a3" order="2"/>
  <bond atomRefs2="a2 a4" order="1"/>
  <bond atomRefs2="a1 a2" order="1"/>
  <bond atomRefs2="a1 a5" order="1"/>
 </bondArray>
</molecule>

FINGERPRINT(molecule,type)
FINGERPRINT() converts a molecule in DEFAULT_TYPE format to a fingerprint. The fingerprint type is specified by the second argument (FP2, FP3 or FP4). The SQL type of the converted molecule is a binary string for all kinds of fingerprint.
```
mysql> SELECT FINGERPRINT(molecule_col,"FP2") FROM tbl_name
    -> WHERE name='glycine';
        -> binary fingerprint (type FP2)
        
```
Note
Tanimoto scoring can be improved by using a concatenation of different fingerprint types. The concatenation of fingerprints can be performed with the following query:
```
mysql> SELECT CONCAT(FINGERPRINT(molecule_col,"FP2"),
    -> FINGERPRINT(molecule_col,"FP3")) FROM tbl_name
    -> WHERE id=9;
        -> binary fingerprint (type FP2 + type FP3)
	  
```

FINGERPRINT2(molecule)

FINGERPRINT2() converts a molecule in DEFAULT_TYPE format to a FP2 fingerprint. The SQL type of FP2 fingerprints is a binary string.

mysql> SELECT FINGERPRINT2(molecule_col) FROM tbl_name
    -> WHERE name='glycine';
        -> binary fingerprint (type FP2)

FINGERPRINT3(molecule)

FINGERPRINT3() converts a molecule in DEFAULT_TYPE format to a FP3 fingerprint. The SQL type of FP3 fingerprints is a binary string.

mysql> SELECT FINGERPRINT3(molecule_col) FROM tbl_name
    -> WHERE name='glycine';
        -> binary fingerprint (type FP3)

FINGERPRINT4(molecule)

FINGERPRINT4() converts a molecule in DEFAULT_TYPE format to a FP4 fingerprint. The SQL type of FP4 fingerprints is a binary string.

mysql> SELECT FINGERPRINT4(molecule_col) FROM tbl_name
    -> WHERE name='glycine';
        -> binary fingerprint (type FP4)

INCHI_TO_MOLECULE(molecule)

INCHI_TO_MOLECULE() converts a molecule in InChI format to a molecule in DEFAULT_TYPE format.

mysql> SELECT INCHI_TO_MOLECULE(inchi_col) FROM tbl_name
    -> WHERE name='glycine';
        -> 
 OpenBabel11190809142D

  5  4  0  0  0  0  0  0  0  0999 V2000
    0.0000    0.0000    0.0000 C   0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0
    0.0000    0.0000    0.0000 O   0  0  0  0  0
    0.0000    0.0000    0.0000 O   0  0  0  0  0
    0.0000    0.0000    0.0000 N   0  0  0  0  0
  1  2  1  0  0  0
  1  5  1  0  0  0
  2  3  2  0  0  0
  2  4  1  0  0  0
M  END

MOLECULE_TO_INCHI(molecule)
MOLECULE_TO_INCHI converts a molecule in DEFAULT_TYPE format to a molecule in InChI format.
```
mysql> SELECT MOLECULE_TO_INCHI(molecule_col) FROM tbl_name
    -> WHERE name='glycine';
        -> InChI=1/C2H5NO2/c3-1-2(4)5/h1,3H2,(H,4,5)/f/h4H
        
```
Note
The INCHI_VERSION() function permit to know which version of the InChI library is used.

MOL2_TO_MOLECULE(molecule)

MOL2_TO_MOLECULE() converts a molecule in Sybyl Mol2 format to a molecule in DEFAULT_TYPE format.

mysql> SELECT MOL2_TO_MOLECULE(mol2_col) FROM tbl_name
    -> WHERE name='glycine';
        -> glycine
 OpenBabel11190809032D

  5  4  0  0  0  0  0  0  0  0999 V2000
  206.0000  126.0000    0.0000 C   0  0  0  0  0
  227.0075  113.8713    0.0000 C   0  0  0  0  0
  227.0075   89.6139    0.0000 O   0  0  0  0  0
  248.0151  126.0000    0.0000 O   0  0  0  0  0
  184.9925  113.8713    0.0000 N   0  0  0  0  0
  1  2  1  0  0  0
  1  5  1  0  0  0
  2  3  2  0  0  0
  2  4  1  0  0  0
M  END

MOLECULE_TO_MOL2(molecule)

MOLECULE_TO_MOL2() converts a molecule in DEFAULT_TYPE format to a molecule in Sybyl Mol2 format.

mysql> SELECT MOLECULE_TO_MOL2(molecule_col) FROM tbl_name
    -> WHERE name='glycine';
        ->@<TRIPOS>MOLECULE
glycine
 5 4 0 0 0
SMALL
GASTEIGER
Energy = 0

@<TRIPOS>ATOM
   1 CA      206.0000  126.0000  0.0000 C.3   1  GLY1    0.2227
   2 C       227.0075  113.8713  0.0000 C.2   1  GLY1    0.3839
   3 O       227.0075   89.6139  0.0000 O.co2 1  GLY1   -0.2440
   4 OXT     248.0151  126.0000  0.0000 O.co2 1  GLY1   -0.2440
   5 N       184.9925  113.8713  0.0000 N.3   1  GLY1   -0.1186
@<TRIPOS>BOND
   1   1   2  1
   2   1   5  1
   3   2   3 ar
   4   2   4 ar

MOLECULE_TO_MOLECULE(molecule)

MOLECULE_TO_MOLECULE() converts a molecule in the old DEFAULT_TYPE format (InChI) to a molecule in the current DEFAULT_TYPE format (MDL Molfile). This function is useful when updating a database with a new version of Mychem.

mysql> SELECT MOLECULE_TO_MOLECULE(molecule_col) FROM tbl_name
    -> WHERE name='glycine';
        -> 
 OpenBabel11190809092D

  5  4  0  0  0  0  0  0  0  0999 V2000
    0.0000    0.0000    0.0000 C   0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0
    0.0000    0.0000    0.0000 N   0  0  0  0  0
    0.0000    0.0000    0.0000 O   0  0  0  0  0
    0.0000    0.0000    0.0000 O   0  0  0  0  0
  1  2  1  0  0  0
  1  3  1  0  0  0
  2  4  2  0  0  0
  2  5  1  0  0  0
M  END

MOLFILE_TO_MOLECULE(molecule)

MOLFILE_TO_MOLECULE() converts a molecule in MDL Molfile (V2000) format to a molecule in DEFAULT_TYPE format.

mysql> SELECT MOLFILE_TO_MOLECULE(molfile_col) FROM tbl_name
    -> WHERE name='glycine';
        -> glycine
 OpenBabel11190809052D

  5  4  0  0  0  0  0  0  0  0999 V2000
  206.0000  126.0000    0.0000 C   0  0  0  0  0
  227.0075  113.8713    0.0000 C   0  0  0  0  0
  227.0075   89.6139    0.0000 O   0  0  0  0  0
  248.0151  126.0000    0.0000 O   0  0  0  0  0
  184.9925  113.8713    0.0000 N   0  0  0  0  0
  1  2  1  0  0  0
  1  5  1  0  0  0
  2  3  2  0  0  0
  2  4  1  0  0  0
M  END

MOLECULE_TO_MOLFILE(molecule)

MOLECULE_TO_MOLFILE() converts a molecule in DEFAULT_TYPE format to a molecule in MDL Molfile (V2000) format.

mysql> SELECT MOLECULE_TO_MOLFILE(molecule_col) FROM tbl_name
    -> WHERE name='glycine';
        -> glycine
 OpenBabel11190809062D

  5  4  0  0  0  0  0  0  0  0999 V2000
  206.0000  126.0000    0.0000 C   0  0  0  0  0
  227.0075  113.8713    0.0000 C   0  0  0  0  0
  227.0075   89.6139    0.0000 O   0  0  0  0  0
  248.0151  126.0000    0.0000 O   0  0  0  0  0
  184.9925  113.8713    0.0000 N   0  0  0  0  0
  1  2  1  0  0  0
  1  5  1  0  0  0
  2  3  2  0  0  0
  2  4  1  0  0  0
M  END

PDB_TO_MOLECULE(molecule)

PDB_TO_MOLECULE() converts a molecule in PDB format to a molecule in DEFAULT_TYPE format.

mysql> SELECT PDB_TO_MOLECULE(pdb_col) FROM tbl_name
    -> WHERE name='1CRN';
        ->
 OpenBabel08210907243D

327337  0  0  0  0  0  0  0  0999 V2000
   17.0470   14.0990    3.6250 N   0  0  0  0  0
   16.9670   12.7840    4.3380 C   0  0  0  0  0
   15.6850   12.7550    5.1330 C   0  0  0  0  0
   15.2680   13.8250    5.5940 O   0  0  0  0  0
   18.1700   12.7030    5.3370 C   0  0  0  0  0
   19.3340   12.8290    4.4630 O   0  0  0  0  0
   18.1500   11.5460    6.3040 C   0  0  0  0  0
   15.1150   11.5550    5.2650 N   0  0  0  0  0
   13.8560   11.4690    6.0660 C   0  0  0  0  0
   14.1640   10.7850    7.3790 C   0  0  0  0  0
   14.9930    9.8620    7.4430 O   0  0  0  0  0
   12.7320   10.7110    5.2610 C   0  0  0  0  0
   13.3080    9.4390    4.9260 O   0  0  0  0  0
   12.4840   11.4420    3.8950 C   0  0  0  0  0
   13.4880   11.2410    8.4170 N   0  0  0  0  0
   13.6600   10.7070    9.7870 C   0  0  0  0  0
   12.2690   10.4310   10.3230 C   0  0  0  0  0
   11.3930   11.3080   10.1850 O   0  0  0  0  0
   14.3680   11.7480   10.6910 C   0  0  0  0  0
   15.8850   12.4260   10.0160 S   0  0  0  0  0
   12.0190    9.2720   10.9280 N   0  0  0  0  0
   10.6460    8.9910   11.4080 C   0  0  0  0  0
   10.6540    8.7930   12.9190 C   0  0  0  0  0
   11.6590    8.2960   13.4910 O   0  0  0  0  0
   10.0570    7.7520   10.6820 C   0  0  0  0  0
    9.8370    8.0180    8.9040 S   0  0  0  0  0
    9.5610    9.1080   13.5630 N   0  0  0  0  0
    9.4480    9.0340   15.0120 C   0  0  0  0  0
    9.2880    7.6700   15.6060 C   0  0  0  0  0
...

SMILES_TO_MOLECULE(molecule)

SMILES_TO_MOLECULE() converts a molecule in SMILES format to a molecule in DEFAULT_TYPE format.

mysql> SELECT SMILES_TO_MOLECULE(smiles_col) FROM tbl_name
    -> WHERE name='glycine';
        -> 
 OpenBabel11190809142D

  5  4  0  0  0  0  0  0  0  0999 V2000
    0.0000    0.0000    0.0000 C   0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0
    0.0000    0.0000    0.0000 O   0  0  0  0  0
    0.0000    0.0000    0.0000 O   0  0  0  0  0
    0.0000    0.0000    0.0000 N   0  0  0  0  0
  1  2  1  0  0  0
  1  5  1  0  0  0
  2  3  2  0  0  0
  2  4  1  0  0  0
M  END

MOLECULE_TO_SMILES(molecule)
MOLECULE_TO_SMILES converts a molecule in DEFAULT_TYPE format to molecule in SMILES format.
```
mysql> SELECT MOLECULE_TO_SMILES(molecule_col) FROM tbl_name
    -> WHERE name='glycine';
        -> C(C(=O)O)N
        
```
Note
If you need a single canonical form for any particular molecule, regardless of atom order, the use of the MOLECULE_TO_CANONICAL_SMILES() function should be preferred.

MOLECULE_TO_CANONICAL_SMILES(molecule)

MOLECULE_TO_CANONICAL_SMILES converts a molecule in DEFAULT_TYPE format to a molecule in Canonical SMILES format.

mysql> SELECT MOLECULE_TO_CANONICAL_SMILES(molecule_col)
    -> FROM tbl_name WHERE name='glycine';
        -> NCC(=O)O

V3000_TO_MOLECULE(molecule)

V3000_TO_MOLECULE() converts a molecule in MDL Molfile (V3000) format to a molecule in DEFAULT_TYPE format.

mysql> SELECT V3000_TO_MOLECULE(V3000_col) FROM tbl_name
    -> WHERE name='glycine';
        -> glycine
 OpenBabel11190809082D

  5  4  0  0  0  0  0  0  0  0999 V2000
  206.0000  126.0000    0.0000 C   0  0  0  0  0
  227.0075  113.8713    0.0000 C   0  0  0  0  0
  227.0075   89.6139    0.0000 O   0  0  0  0  0
  248.0151  126.0000    0.0000 O   0  0  0  0  0
  184.9925  113.8713    0.0000 N   0  0  0  0  0
  1  2  1  0  0  0
  1  5  1  0  0  0
  2  3  2  0  0  0
  2  4  1  0  0  0
M  END

MOLECULE_TO_V3000(molecule)

MOLECULE_TO_V3000() converts a molecule in DEFAULT_TYPE format to a molecule in MDL Molfile (V3000) format.

mysql> SELECT MOLECULE_TO_V3000(molecule_col) FROM tbl_name
    -> WHERE name='glycine';
        -> glycine
 OpenBabel11190809132D

  0  0  0     0  0            999 V3000
M  V30 BEGIN CTAB
M  V30 COUNTS 5 4 0 0 0
M  V30 BEGIN ATOM
M  V30 1 C 206 126 0 0
M  V30 2 C 227.007 113.871 0 0
M  V30 3 O 227.007 89.6139 0 0
M  V30 4 O 248.015 126 0 0
M  V30 5 N 184.993 113.871 0 0
M  V30 END ATOM
M  V30 BEGIN BOND
M  V30 1 1 1 2
M  V30 2 1 1 5
M  V30 3 2 2 3
M  V30 4 1 2 4
M  V30 END BOND
M  V30 END CTAB
M  END