Structure files

A structure is intended as a representation of an individual chemical compound. The minimum information for a structure must include the types of atoms and their connectivity. Note that only connected structures can be dealt by dProperties.

The structure files, which are the input files for dProperties calculation, cannot be generated in dProperties. They can be obtained by specific chemical drawing applications or, in the case of SMILES notations, by a simple text editor.


Sometimes molecule files may be not correctly read if created by old software version or modified in some way by the user. Therefore, the molecule file formats supported by dProperties are reported in the following with information on the software which produces them.


1. Sybyl © molecule files (.ml2, .mol, sm2, mol2) by Tripos, Inc.

2. MDL files (.mol, .mdl, .sdf) by Symyx Solutions, Inc.

3. HyperChem © files (.hin) by Hypercube, Inc.

4. SMILES notations (.smi) by Daylight Chemical Information Systems, Inc.

5. CML files (.cml)

6. MacroModel © files (.mmd, .mmod, .out, .dat) by Schrodinger, LLC


To calculate all the molecular properties, hydrogen-filled molecular structures are suggested. If hydrogens are missing, dProperties attaches hydrogens to atoms in order to complete the rest of their usual valence consistent with explicit bond specification. See details here.


If molecules are entered by SMILES notations, hydrogen atoms are automatically added to the molecule structure.


The SMILES conventions adopted in dProperties are those proposed by Weininger (Weininger D., J.Chem.Inf.Comput.Sci. 1988, 28, 31-36). The SMILES molecule file must be a tabbed text file with any extension. It can include one or more molecular structure. The SMILES file must only include the list of molecules, without any heading. The molecule name is optional and, if present, is separated from the molecule line notation by TAB or SPACE.