Dragon main features
Input files. To run Dragon the user needs molecular structure files previously obtained by other specific molecular modelling software. The most common molecular file formats are accepted.
1. Sybyl © Molfiles (.sm2) as provided by ChemOffice, CambridgeSoft Corp.
2. Sybyl © multiple Molfiles (.mol, .ml2) by Tripos, Inc.
3. Molfiles (.mol) by Molecular Design Ltd. (MDL)
4. Multiple SD files (.sdf) by Molecular Design Ltd. (MDL)
5. HyperChem © files (.hin) by Hypercube, Inc.
6. SMILES notations (.smi)
7. MacroModel © files (.dat, .out) by Schrodinger (*)
To make full use of Dragon calculations, 3D optimised structures with hydrogens should be used. However, Dragon can also deal with H-depleted molecules and 2D-structures; in this case, it's apparent that some restrictions to descriptor calculation are applied. At the moment, Dragon cannot process molecules containing atoms for which some physicochemical properties are undefined, disconnected structures such as salts, and molecules with radicals.
Loading of user-defined variables. Dragon allows the user to import some variables and string fields that can be added to the calculated molecular descriptors such as experimental properties and information on the processed molecules (e.g., CAS number, product code). The variables can be loaded by Dragon and are available, together with calculated molecular descriptors, for a preliminary correlation analysis and saving of the final output file until new variables are loaded by the user.
Principal components of descriptor blocks. Principal components of the descriptor blocks can be selected, along with the descriptors of interest, in order to be available for graphical analysis of molecule distribution and correlation analysis with some user-defined variables before saving of the output file.
Output file. The standard Dragon output file is a text file. It has been organised so that first there are two fixed columns, one containing the sequential number of molecules (No.) and the other the molecule identifier (MolID) chosen by the user. Then, the string variables, eventually loaded by the user, follow. Finally, the selected molecular descriptors, their PCs (if checked) and numerical user-defined variables (if loaded and selected) follow. The possibility of adding string variables in the output file is very important if additional information on molecules e.g., CAS number, product codes or specific names, needs to be stored.
Descriptor saving. It is possible to choose the descriptors to be saved, a title for the output file, the code for missing values, and the format of the output file. Moreover, the user can choose to exclude from the output file the least informative variables and whether to save all of the calculated descriptors in the same file or in different files, one for each descriptor block.
Graphics and statistics. Interactive graph menus are available in Dragon for a preliminary descriptor analysis. Histogram graphs, Pareto plots and univariate statistics are available in the menu devoted to the analysis of each single descriptor. Line plots, 2D and 3D scatter plots are available; these graphs allow a preliminary analysis of molecule distribution in the descriptor or principal component space, as well as a preliminary correlation analysis when user-defined responses have already been loaded.
Dragon is not for... Dragon was not designed as QSAR software, it provides only molecular descriptors and does not perform QSAR analysis. However, DRAGON allows the merging of calculated molecular descriptors and user-defined properties for a set of molecules, providing a complete output file which is easily loaded by any correlation analysis application.
Note that Dragon does not perform geometry optimization, nor transform topological structures into the corresponding 3D geometrical structures. For SMILES notations, connectivities for hydrogens are added, but these calculations are restricted to 0D, 1D and 2D descriptors.
Input files. To run Dragon the user needs molecular structure files previously obtained by other specific molecular modelling software. The most common molecular file formats are accepted.1. Sybyl © Molfiles (.sm2) as provided by ChemOffice, CambridgeSoft Corp.
2. Sybyl © multiple Molfiles (.mol, .ml2) by Tripos, Inc.
3. Molfiles (.mol) by Molecular Design Ltd. (MDL)
4. Multiple SD files (.sdf) by Molecular Design Ltd. (MDL)
5. HyperChem © files (.hin) by Hypercube, Inc.
6. SMILES notations (.smi)
7. MacroModel © files (.dat, .out) by Schrodinger (*)
To make full use of Dragon calculations, 3D optimised structures with hydrogens should be used. However, Dragon can also deal with H-depleted molecules and 2D-structures; in this case, it's apparent that some restrictions to descriptor calculation are applied. At the moment, Dragon cannot process molecules containing atoms for which some physicochemical properties are undefined, disconnected structures such as salts, and molecules with radicals.
Loading of user-defined variables. Dragon allows the user to import some variables and string fields that can be added to the calculated molecular descriptors such as experimental properties and information on the processed molecules (e.g., CAS number, product code). The variables can be loaded by Dragon and are available, together with calculated molecular descriptors, for a preliminary correlation analysis and saving of the final output file until new variables are loaded by the user. Principal components of descriptor blocks. Principal components of the descriptor blocks can be selected, along with the descriptors of interest, in order to be available for graphical analysis of molecule distribution and correlation analysis with some user-defined variables before saving of the output file. Output file. The standard Dragon output file is a text file. It has been organised so that first there are two fixed columns, one containing the sequential number of molecules (No.) and the other the molecule identifier (MolID) chosen by the user. Then, the string variables, eventually loaded by the user, follow. Finally, the selected molecular descriptors, their PCs (if checked) and numerical user-defined variables (if loaded and selected) follow. The possibility of adding string variables in the output file is very important if additional information on molecules e.g., CAS number, product codes or specific names, needs to be stored. Descriptor saving. It is possible to choose the descriptors to be saved, a title for the output file, the code for missing values, and the format of the output file. Moreover, the user can choose to exclude from the output file the least informative variables and whether to save all of the calculated descriptors in the same file or in different files, one for each descriptor block. Graphics and statistics. Interactive graph menus are available in Dragon for a preliminary descriptor analysis. Histogram graphs, Pareto plots and univariate statistics are available in the menu devoted to the analysis of each single descriptor. Line plots, 2D and 3D scatter plots are available; these graphs allow a preliminary analysis of molecule distribution in the descriptor or principal component space, as well as a preliminary correlation analysis when user-defined responses have already been loaded. Dragon is not for... Dragon was not designed as QSAR software, it provides only molecular descriptors and does not perform QSAR analysis. However, DRAGON allows the merging of calculated molecular descriptors and user-defined properties for a set of molecules, providing a complete output file which is easily loaded by any correlation analysis application. Note that Dragon does not perform geometry optimization, nor transform topological structures into the corresponding 3D geometrical structures. For SMILES notations, connectivities for hydrogens are added, but these calculations are restricted to 0D, 1D and 2D descriptors.