The SPECTCOL client tool


Spectcol is a tool dedicated to handling XSAMS formatted data for the purpose of extracting and merging Einstein and rate coefficients from different sources.

Spectcol is an executable software, developed in Java language. The tool is provided with a guide in PDF format. The document gives a help on Spectcol’s functionality and how to use it. Several versions have been developed since the beginning of the project, but the latest version is the “12.07-r1”.

This application has a direct access to data from 4 databases :

Task 1: Discovering database content

When the application launches, the main window appears. For this first task we will use the “Species Search” tab, it is selected by default at startup. It allows the user to display datasets contained in the database.

There are 6 query parameters. The only “exotic” one is the molecular species inchikey. The InChI identifier identifiers describes chemical substances in terms of layers of information — the atoms and their bond connectivity, tautomeric information, isotope information, stereochemistry, and electronic charge information.

It is human readable. The InChIKey is a 25 characters long hash of an InChI identifier and as such is not human readable. It is used in VAMDC species database as an unique identifier for species.

Let’s look for available data related to the CO molecule in the Basecol database. Verify that this database is the only checked one. Then, in the Molecular Stoichiometric Formula field, seize “CO”.

Expected result:

Looking for data with Spectcol

Task 4 : Grouping data

A very convenient features of this application is the possibility to merge data from Basecol and from a transitional database. The software will identify equivalent levels in energy tables according to their quantum numbers. Then it will produce a table containing levels exisiting in both tables, using ernergy values from the transitional database. Finally, it will give rate and Einstein coefficients for the levels available after merging the tables.

The first thing to do is looking for CO data available in transitional databases. We did that in task 2. Secondly, we have to look for CO+H collisions, as we did in task 3.

Expected result :

Merging data from CDMS and Basecol

The “Group by hand” and “Group by species” buttons can be used for merging. The former will let the user choose manually which datasets he wants to merge. The latter will search in the collision datasets the ones whose collider corresponds to the currently selected transitions dataset.

The link between species will be performed thanks to the InChIKey value.

Click on the transitions dataset labelled “29501”, then click on “Group by species”. A window will appear with no corresponding collisional set. Indeed none of them uses the same InChIKey, which means it is a different CO isotope.

Now select the dataset labelled 28503. There are now 3 corresponding datasets.

Expected result :

Grouping datasets by inchikey

You will notice that all the transitional datasets with a similar InChIKey have been selected as well.

Now we can merge data. You have to select one transitional and one collisional dataset and click on “Show selection”. We will use the dataset labelled 28503 in CDMS, with v=0. These rotational data corresponds to those found in the Basecol datasets labelled “Rotational de-excitation of CO by H”. The merging can be made on one among the three Basecol datasets.

A window will ask you if you want to choose the quantum numbers.

choose quantum numbers on which merging will be based

If you choose “Yes”, you will be able to choose manually which quantum numbers will be used to identify similar levels in each table. If you choose “No”, the choice will be made automatically by the software according to the quantum numbers available in both tables.

Let’s choose “Yes”. A new window will show the energy tables. You can click on one or several columns to choose the quantum numbers. Here we will choose the rotational quantum number J.

The result is a new energy table containing levels available in both original tables. All related informations are provided too (Einstein and rate coefficients, sources, partition function values). You have multiple export functionnalities so that you can use those merged data easily.

Expected result :

Merging result in spectcol.