REACT Molecular Database
This menu allows the input of the molecular data into the REACT database (this is what is used primarily by
mechanism generation). There are four tabs:
- Structure To read in individual molecular structural data in SDF format
- Names To read in the correspondence between the full long (IUPAC) name and the short name used in combustion calculations
- Thermo To read in thermodynamic in NASA polynomial form
- Reset To reset the entire database of molecular information
The molecular data, particularly for the standard database, is found in the 'mol/molsdf' directory
of the client (local) directory system. When adding to the database, the files are transfered to the
corresponding directory of the server (for the particular user) and read in. The complete set of
molecular information consists of the following files:
- root.sdfThis is the two dimensional graphical description of the molecule along with its proper
name (by convention, it should be the IUPAC name). This is the minimum information needed for a molecule.
All other associated information is referenced to the name.
- root-names.lst This has the Short and CHEMKIN names for each molecule.
- root.thm This has the thermodynamic information in NASA polynomial format. The name
of the molecule in this form is the CHEMKIN name.
- root.mol This is the corresponding list of full names, one per line, for each of the
molecules in the thermodynamic file.
Input of Structure
This is the minimal required information about a species, the 2D graphical structure (atoms and
how they are bonded) and the name (preferably IUPAC). In the 'Structure' tab is the menu for testing and
inputting a structure from a file:
- SDF File By pressing 'SDF File' a list of files starting in the 'mol' directory of the
client files is shown. The desired file must be in this subdirectory. If the file is to be put in the
database, the file must be in the mol/molsdf subdirectory.
- Root Name This extracts the given root name from the selected file (this root name will be
used in the further menus involving molecular information.
- Test It is very important to test the structure file before trying to put it in the database.
Since information for the database (including the index) is derived from the structure, a wrong structure
could corrupt the molecule database. The output of the molecule with some calculated quantites (including
semi-empirical quantities such as partial charge, electronegativity, etc.) is given in the text field. Upone
pressing 'Test SDF File', the file is transfered to the server and the file read into the REACT database.
- Database Once the file has been tested and verified, it can be read into the database. The
'Read to Database' key is only turned on after the test has been made.
Names
With this menu, the alternative names are read into the database. The name is referenced to the
name given by the structure data. The format of the files is the 'Property' format. The procedure is as follows:
- Setup Using the 'Setup Table from File' button, a menu for reading in the alternative names
in molecule property format is read in. The convention is to use the rootname with the
'-name.lst' extension and the file should be in the mol/molsdf directory. The table of names is displayed.
- Table Changes The alternative names of the table can be changed.
- Database When the table is ready, pressing the 'Read to Database' button will write the table
information to a file (using the root name of the 'Structures' tab, the alternative name
file is setup with a '-names.lst' extension), transfer it to the server and read the
information into the REACT database.
Thermo
The thermodynamic information is read in using NASA polynomial format:
- Setup Pressing the 'Setup Thermo information from file' button, a file list (starting in the
mol directory) appears. The expected extension is 'thm'. Upon selection, a table appears with the
full name, CHEMKIN name and formula of each of the read in polynomials.
- ChangesIf a row is selected, and the 'Modify Selected' button is pressed, a window pops up
with the polynomial information displayed. Any field can be changed. In addition, if a new NASA polynomial
is put into the text field (in the proper format), then this information can be transfered to the table.
After the changes, pressing 'Transfer Thermo Data' transfer the new information to the original table.
- Database By pressing 'Read Thermodynamics to Database', the information is written to a file
(in the mol/sdf directory), transfered to the server and read into the database.
Reset
It is recommened that when a molecule set has been debugged and added to the REACT database,
that the entire database be reinitialized. The main reason for this is that the indexing depends on
the molecular structure and, this, in turn, makes the index dependent on the order in which the molecule
was added to the database.
To reset the database, the following steps are taken:
- Clear By pressing the 'Clear Molecule Database' button, all the molecule information is erased
from the REACT database
- Table of files The set of files for the molecule information are to be found in the mol/molsdf
directory. When the 'Read Full File Set' is pressed, those molecular sets which have all the molecule information
defined (structure, names and thermo), are listed in the table with just the root name. File sets can be deleted
with the 'Delete Selected' button. The whole table can be cleared with the 'Clear Table' button.
- Read Pressing the 'Read in Molecule Database' button systematically reads in all the
file sets. The lamp turns to green if the read is successful.
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