Start the program without a dataset and show the GUI.

java -jar capp_v.1.5.1_java1.7.jar or
java -jar capp_v.1.5.1_java1.7.jar -gui


Run an appraise task on the collection of SMILES codes in the file 'test.smi', and show results in the GUI.

java -jar capp_v.1.5.1_java1.7.jar -i test.smi -smi -gui


Run an appraise task on the collection of SMILES codes in the file 'test.smi', and produce an HTML report (to be found in the folder 'capp_results_html') of the results (do not show GUI).

java -jar capp_v.1.5.1_java1.7.jar -i test.smi -smi -html


Run an appraise task on the collection of SMILES codes in the file 'test.smi', and produce an HTML report (to be found in the folder 'capp_results_html') of the results and also show the GUI.

java -jar capp_v.1.5.1_java1.7.jar -i test.smi -smi -gui -html


Run an appraise task on a compound library (SDF format) which has not been curated for single molecule entries. In such cases, individual entries in the SDF file may contain more than one molecule. The autoselect feature will select the largest entity for each entry. While this yields the desired molecule in most cases, the largest molecule may not be the desired one in every case.

java -jar capp_v.1.5.1_java1.7.jar -i library.sdf -sdf -autoselect -gui

Start the program with the GUI

java -jar capp_v1.5.1_java1.7.jar -gui

and establish a new compound set (e.g. test.smi) by using File - Add compounds as new set - SMILES. A new tab is added and labelled 'Set 1: test.smi'.

Select a compound by a left-click on any cell in the row of the desired compound. Then right-click to obtain the pop-up menu. Select Similarity search and provide a compound set to be searched as library in SDF format (e.g. test.sdf).

The similarity search will start and a new tab will be added containing the compound set of the library. The table in the new set will be updated continuously until the search is done. In the above example, the compound selected as query molecule will be found with a Tanimoto similarity of 1.0.

Please note: For similarity searches, cApp processes the target library one entry at a time. However, if you choose to run the similarity search with the GUI, this may result in exhaustion of computer resources, since a set with many compounds will need to be rendered on the screen. For similarity searches of large libraries we therefore recommend to use the non-interactive mode (see below), whereby a summary file with the results will be generated.

In order to conduct a similarity search using a single compound as query and a user-provided library as target from the terminal, the query molecule needs to be defined in a single file (e.g. aspirin.smi), and the library needs to be available in SDF format (e.g. test.sdf). A similarity search with results output as PDF can be conducted from the terminal with

java -jar capp_v1.5.1_java1.7.jar -i aspirin.smi -smi -smsd test.sdf -pdf

The output file ('smsd_aspirin_test_sdf.pdf') can be found in the folder capp_results_pdf.

In order to conduct subsequent similarity searches using a a set of compounds as query molecules and a user-provided library as target, the same procedure as in the previous section can be followed. Instead of using 'aspirin.smi' which has just one compound, a compound set such as test.smi can be used to search a library in SDF format (e.g. test.sdf). The command to use is:

java -jar capp_v1.2_java1.7.jar -i test.smi -smi -smsd test.sdf -pdf

At present, this procedure can only be conducted from the terminal.

Compounds can be read into cApp from either SMILES, InChI or SDF information. When running the software with the GUI, compound sets can be conveniently exported as any of those formats using the File - Write features.

In terminal mode (without the GUI), compound sets are easily converted into all chemical data formats at once when running an appraise task with HTML output. For example, to convert a set of compounds provided as SMILES codes, the command

java -jar {capp_jar_file} -i test.smi -html

will appraise the compound set contained in the file 'test.smi' and write SMILES, InChI, InChI Key and SDF files for all individual compounds as well as multi-compound files with those formats to the directory capp_results_html/files_1.