Molecule identifier

In each stage of Dragon, molecules are identified by

▪an integer number (ID), corresponding to the rank in the import list. The molecule identifier (ID) depends on the order of loading.
▪the molecule name stored into a specific field of the structure file. When loading a multiple structure file and the chemical names are not specified in it, then the filename with a sequential integer attached at the end will be used as the molecule name.

 

If the user needs to load specific text labels for molecule identification, this can be done by adding external variables to the calculated molecular descriptors.

 

Example of MDL structure file (*.sdf) where the chemical name field is highlighted in boldface. The text DRG1 2-methylbenzo-1,4-quinone will be used by Dragon as the molecule name:

DRG1 2-methylbenzo-1,4-quinone

xxxxx 0   0.00000     xxxxx xxxxx

 

15 15  0  0  0  0  0  0  0  0999 V2000

   1.8890    1.7851   -0.0009 C   0  0  0  0  0  0  0  0  0  0  0  0

   0.7730    0.7724   -0.0022 C   0  0  0  0  0  0  0  0  0  0  0  0

   1.0858   -0.6712    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0

  -0.5031    1.1816    0.0003 C   0  0  0  0  0  0  0  0  0  0  0  0

   2.2422   -1.0420    0.0024 O   0  0  0  0  0  0  0  0  0  0  0  0

  -0.0081   -1.6639   -0.0002 C   0  0  0  0  0  0  0  0  0  0  0  0

  -1.5969    0.1889   -0.0004 C   0  0  0  0  0  0  0  0  0  0  0  0

  -1.2842   -1.2547   -0.0029 C   0  0  0  0  0  0  0  0  0  0  0  0

  -2.7534    0.5597    0.0023 O   0  0  0  0  0  0  0  0  0  0  0  0

   1.4675    2.7903   -0.0028 H   0  0  0  0  0  0  0  0  0  0  0  0

   2.5015    1.6497    0.8905 H   0  0  0  0  0  0  0  0  0  0  0  0

   2.5052    1.6479   -0.8894 H   0  0  0  0  0  0  0  0  0  0  0  0

  -0.7317    2.2371    0.0033 H   0  0  0  0  0  0  0  0  0  0  0  0

   0.2206   -2.7194    0.0013 H   0  0  0  0  0  0  0  0  0  0  0  0

  -2.0840   -1.9805   -0.0034 H   0  0  0  0  0  0  0  0  0  0  0  0

 1  2  1  0  0  0  0

 2  3  1  0  0  0  0

 2  4  2  0  0  0  0

 3  5  2  0  0  0  0

 3  6  1  0  0  0  0

 4  7  1  0  0  0  0

 6  8  2  0  0  0  0

 7  9  2  0  0  0  0

 7  8  1  0  0  0  0

 1 10  1  0  0  0  0

 1 11  1  0  0  0  0

 1 12  1  0  0  0  0

 4 13  1  0  0  0  0

 6 14  1  0  0  0  0

 8 15  1  0  0  0  0

M  END

> <E_NSC>

1

 

> <E_CAS>

553-97-9

 

> <E_SMILES>

CC1=CC(=O)C=CC1=O

 

$$$$

 

Example of SMILES structure file (*.smi) where the chemical name field is on the rigth. For instance, the text Methane will be used by Dragon as the molecule name for the first molecule:

C                Methane

CC                Ethane

CCC                Propane

CCCC                n-Butane

CCCCC                n-Pentane

CCCCCC        n-Hexane

C(C)(C)C        isobutane

C(C)(C)(C)C        neopentane

CC(C)CCC        2-Methylpentane

CC=CC                cis-2-Butene

CC=CC                trans-2-Butene

CC#CC                2-Butyne

C1CC1                Cyclopropane

C1CCC1        Cyclobutane

C1CCCC1        Cyclopentane

 

Example of Sybyl structure file (*.mol2) where the chemical name field is highlighted in boldface. It will be used by Dragon as the molecule name:

@<TRIPOS>MOLECULE

Methane

5 4 0 0 0

SMALL

GASTEIGER

Energy = 0

 

@<TRIPOS>ATOM

     1 C           0.2863   -0.1795    0.1402 C.3     1  LIG1       -0.0776

     2 H           0.4043   -0.5980   -0.8593 H       1  LIG1        0.0194

     3 H          -0.7741   -0.1128    0.3833 H       1  LIG1        0.0194

     4 H           0.7296    0.8158    0.1721 H       1  LIG1        0.0194

     5 H           0.7854   -0.8229    0.8648 H       1  LIG1        0.0194

@<TRIPOS>BOND

    1     1     2    1

    2     1     3    1

    3     1     4    1

    4     1     5    1