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2 Operating EROS

2.1 General Information

This graphical user interface was designed to facilitate communication between the user and the EROS7 program for reaction prediction. Instead of repeatedly typing long file names and more or less cryptic command line options or having to develop shell scripts, an intuitive access to EROS7 is provided.

Figure 2-1. The main command center.

In general, all interactions can be performed by clicking buttons with the left mouse button or via keyboard strokes. Pressing the "tab" keys alters the activated widget, which can be set to action by pressing "enter". In the following chapters a description of the capabilities of the graphical user interface will be given.
Guided tour: As you read along, you are invited to perform your first EROS7 run following the instructions given in italics at the end of each chapter. This will allow you to simulate the degradation of s-triazines in soil to illustrate the capabilities of the EROS system and the CACTVS tools.

2.2 Input Specifications

General note:

Figure 2-2. Data input.

2.2.1 Structure Input

The input of the structure of chemical compounds can be made in two ways. If the structures are already available in the CTX file format, you can just click on the tiny folder symbol next to the default file name to open a file browser and select the appropriate file. All sample input files are stored in the directory input relative to the directory you chose to copy the sample files when you started the graphical user interface the first time (usually /home/user/eros7/input).
This file may contain one or more chemical structures serving as starting materials for reaction prediction. The other possibility is to start the CACVTS Editor by clicking the "edit" button to create or edit a structure file. For detailed information on the editor please refer to the CACTVS-Editor manual (see Appendix 7.1 or http://www2.chemie.uni-erlangen.de/software/cactvs/
index.html
). Other structure editors can easily be appended to the EROS system as communication is performed through the CTX ASCII file format and conversion programs to standard structure exchange formats such as MDL SDFile, SMILES strings etc. are available.

Figure 2-3. The CACTVS Editor.

Guided tour: Please select the file named "atrazine.ctx" in your input directory. Alternatively draw the structure of atrazine using the CACTVS Editor.

2.2.2 Selecting a Rule File

The chemical knowledge of EROS7 is stored in rule files in ASCII format. Select an appropriate rule file by clicking the folder symbol next to the default file name. A detailed description of existing reaction rules can be found in the section "Sample EROS Runs". If you are familiar with the scripting language Tcl, you can also edit existing rule files for your needs, which are stored in the directory rules relative to the directory you selected during the first start of the EROS GUI for the samples (usually /home/user/eros7/rules). The "edit" button will start a text editor with the displayed file name. For details about EROS7 reaction rules please refer to the chapter 4 "Writing Your Own Reaction Rules".
Guided tour: Select the rule file named "triazine.tcl" in your "rules" directory. In this file the main degradation pathways of s-triazines in soil, hydrolysis and reductive dealkylation, are coded for the use with EROS7.

2.3 Reaction Generator

Figure 2-4. Setting options for the reaction generator.

In this section all command line options concerning the reaction generators can be set.

Reaction levels:
Increase or decrease the number of desired reaction levels by clicking the up and down arrows next to the number. Alternatively you can click on the number and type in any number higher than zero.

Trace output:
Increase or decrease the amount of trace output written to the logfile. Choose zero for minimum output up to 5 for maximum trace output.

Advanced Options:
By clicking the button "advanced options" a configuration window will appear. Usually, you will not need this options, but in some special cases, e.g., debugging reaction rules, they might be considered as useful.

Figure 2-5. Configuration of advanced options.

Usually, the input of structures will be given as connection tables in the CTX format. Internally, this valence bond representation is converted into a representation that is more related to a MO description (MOSES) so that reaction prediction can deal with the full scope of organic chemistry. For output, the structures are reconverted to a connection table representation in the CTX format. This behavior can be changed by choosing the MOSES format either as input or output format.
The phases in a rule file are numbered from 1 to n. If a reaction rule has 5 phases, all generating reactions, it is possible to stop reaction generation after phase three by checking the box and setting the counter to three.
The next checkbox is used to create and transfer additional variables to the rule file. The variables have to be separated by a comma and follow the syntax: name-separator-value (no blanks at all!). The symbol of the separator also indicates the kind of the variable created: "#" for an integer, ":" for a double and "$" (you have to type \$ for the $ because of the shell wrapper) for const char *, (e.g. pi:3.14,num#7).
The structure file written by EROS7 represents the molecules of that phase that was defined as the "output_phase" in the rule file. With the last checkbox active, it is possible to redirect the molecules of any other phase to the structure file.
Guided tour: For our example please set "reaction levels" to 9 to simulate the degradation all the way to the formation of carbon dioxide, ammonia, and water. Setting trace output or advanced options is not necessary in our example.

2.4 Data Output

Figure 2-6. Configuration of data output.

In this section the output of a program run can be configured. In most cases, the structure and reaction file will be sufficient. The structure file lists all different molecules handled in this program run. The molecules can be sorted by molecule numbers (default), by concentration or by their persistence. The reaction file stores the molecules for every generated reaction.
Change the default file names according to your needs simply by editing the file entries or clicking the folder symbols to browse your directories for existing file names. If any of the file checkboxes are unchecked the respective file will not be written (the EROS7 logfile will be written in any case).

If you are using EROS7 reaction rules designed for the simulation of mass spectra, check the "Mass spectra" button to write the generated mass spectra to a file.
Guided tour: Make sure that the buttons "Structure file" and "Reaction file" are checked. Sort the molecules in the structure file by their persistence.

2.5 Visualization of Results

Figure 2-7. Visualize the EROS7 results.

After the first EROS7 program run a "Visualization" frame will appear. These buttons are generated according to the selected "Data Output" options. This means if the buttons for "Structure file" and "Mass spectra" were unchecked, the visualization of the structure file and the mass spectra is not possible.

Molecules:
This button will open the CACTVS Browser csbr to display the molecules of the EROS7 structure file.

Figure 2-8. Visualization of the EROS7 structure file with the CACTVS Browser.

Guided tour: Please click on "Molecules" to visualize the EROS7 structure file. For each molecule, information about the predicted end concentration (c), the overall first order formation and degradation rates (k+, k-) and the persistence of the compound will be displayed. The molecules will be sorted by their persistence (P).

Note: In the case of the appearance of bimolecular reactions and the probability kinetics the values displayed for k+ and k- are not valid.

Reactions:
This will open the CACTVS Browser csbr with the EROS7 reaction file. The starting materials and products for each reaction will be displayed connected by an arrow.

Figure 2-9. Visualization of the EROS7 reaction file with the CACTVS Browser.

Guided tour: Click the "Reactions" button to see starting materials and products for each reaction.

Reaction network:
By clicking this button the EROS7 reaction file will be visualized as a reaction tree by CACTVS Tree cstr. For details about CACTVS Tree please refer to the manual (see Appendix 7.2 or http://www2.chemie.uni-erlangen.de/software/cactvs/cstree/frame.html). CACTVS Tree was designed to display only reactions that were generated by EROS7 with the reaction mode "MONOMOLEC" set in the rule file

Figure 2-10. Visualization of the EROS7 reaction file with CACTVS Tree.

Guided tour: Visualize the reaction tree by clicking "Reaction Network".

Logfile:
Clicking this button will start the default text editor with the EROS7 logfile.
Guided tour: If you like, view the EROS7 logfile by clicking the appropriate button.

Concentration Time Plots
Click this button to see the concentration time plots of all compounds involved in this EROS run. This feature is enabled when kinetic calculations were done with Gear’s algorithm (to be set in the rule file). The plots will be displayed for 120 seconds. Additionally a postscript file of the curves will be written to the output directory. If there is no valid data an empty plot with an error message will appear.

Mass Spectra:
Simulated mass spectra will be displayed with the spectra visualization tool CACTVS IR csir.

Figure 2-11. Visualization of predicted mass spectra with CACTVS IR.

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Prof. Dr. J. Gasteiger
Computer Chemie Centrum, Org. Chem., Uni. Erlangen
Nägelsbachstraße 25
D-91052 Erlangen

Gasteiger@CCC.Chemie.Uni-Erlangen.DE