Loading and saving a project

In the graphical user interface (GUI), data can be loaded into cApp from binary files in the proprietary cApp-format that stores information from a user-session.

1. Click File in the menu bar, then click Load project.
2. Binary cApp files should, but don't have to carry a '.cpp' extension. This format re-stores all data from a previous user session (i.e. an entire project).
3. To save the current project, use File - Save project.

Add compounds

Compounds can only be added to sets generated by an appraise task. When adding compounds as a new set, the appraise task will be conducted automatically.

Add compounds from external files

Add compounds as a new set
1. Adding compounds as a new set is generally the first step undertaken to begin processing compounds.
2. From the menu bar, select File - Add compounds as new set. In the example here, SDF format has been selected.
3. The file will be loaded and the appraise task will automatically be conducted.
4. The loaded compounds will be added to the project as a new set and displayed as table in a tabbed panel. Sets will be numbered consecutively. The default name displayed is the file name; however, this can be changed using Compound Set - Compound set description from the menu bar.

Add compounds to an existing set
Compounds can also be added to an existing set. This set needs to be selected in the GUI (click on the tab at the top of the panel with the desired set). Then choose File - Add compounds to selected set from the menu bar.

Show meta data

Any calculated property or user annotation of a particular compound constitutes meta data that may accompany the compound in cheminformatics. Among the standard chemical data formats, only the SDF data format allows for encoding of meta data.

When loading compounds into cApp from an SDF file, the meta data in the user-defined properties block are read and stored together with the compound.

When writing an SDF file with cApp, any properties calculated by the program as well as all user-specific data will be added to the user-defined properties block and written out using the key-value syntax in that block (see below).

In the cApp GUI, meta data can be viewed using a feature from the pop-up menu:
1. Select the compound of interest by a left-click in that row.
2. A right-click opens the pop-up menu; select Show meta data.
3. The meta data for the selected compound are displayed in a new window (and can be copied via the clipboard).
4. Optional (this is not cApp-specific): meta data may be edited in the SDF file using an ASCII text editor.
5. Optional (this is not cApp-specific): open the SDF file in a text editor (e.g. textEdit, Notepad etc.) for editing. The key-value syntax for adding properties is as follows:

> <Key>

Query the PubChem database for identical entries

This process queries the PubChem Compound Database with one or multiple compounds from the active dataset for identical entries. If one or more entries are found in PubChem, a URL link is added to the column PubChem CID. If no entry is found, the label 'none' is added instead. Note that each compound query constitutes a separate query process to PubChem database. Therefore, when more than one compound is selected, cApp processes all queries in a queue-like fashion. A wait interval is included between two consecutive queries in order to comply with traffic regulations of the PubChem Power User Gate (PUG).

With cApp, the PubChem Compound Database can also be queried by means of a similarity search. See Examples for a description of this process.

Querying PubChem with all compounds of the active set
1. In order to conduct a search for all compounds of a set, select Tools - Identical entries in PubChem - For active set from the menu bar.

Querying PubChem with individual compounds of the active set
1. Select the query compound by a left-click (not in the structure column, though). Then use a right-click to get the pop-up menu and select Find PubChem entry.
2. In the column PubChem CID, a URL will appear linking to the first found entry in the PubChem Compound Database. The entry can be accessed by a left-click, which will display the content in the user's web browser. If no entry is found, the label 'none' will appear in the PubChem CID column, to indicate that this compound has been processed.

Querying PubChem with multiple selected compounds of the active set
Multiple compounds from the active compound set can be selected by means of table row selections. If this selection is to be subjected to a PubChem query, one should use Tools - Identical entries in PubChem - For selected compounds from the menu bar.

Molecular viewer / 3D structures

cApp uses an embedded version of Jmol as molecular viewer.

Most loaded compounds will be generated as two-dimensional models, because neither SMILES nor InChI strings encode three-dimensional information. Compounds provided as SDF files may or may not be available as 3D models, depending on whether the z-coordinates in the provided SDF file are populated or not (in which case they all read '0.0000').

The generation of 3D molecular models in cApp uses the CDK ModelBuilder3D class which is not a substitute for higher quality QM calculations, but delivers reasonable results for most compounds; there is no guarantee that the stereochemistry is correctly considered.

There is no immediately visible result in cApp upon completion of this process. You will need to open the compound in the molecular viewer to assess the results. Of course, when writing compounds or compound sets to SDF files, the generated three-dimensional conformation is the one written out.

Generation of 3D coordinates

For selected compound Select the compound by a left-click and obtain the pop-up menu by a right-click. Then choose Generate 3D coordinates.
For all compounds in a set From the menu bar, choose Tools - Generate 3D coordinates to generate 3D coordinates for all compounds in the active set. The calculation will be done in the background as indicated by the progress bar. It is possible to abort the calculation by clicking the button Stop 3D coordinates generation above the tabbed panel.

Updating 3D coordinates

For selected compound The three-dimensional coordinates of the selected compound can be updated by loading information from a user-provided SDF file. This feature does not affect any other properties of the compound and just updates the atomic coordinates stored for this compound in the SDF component of the entry. This feature is available from the pop-up menu at Update 3D coordinates from external SDF file. When loading an external SDF file, cApp will perform a check to validate that the imported molecule matches the compound entry. For this check, the unique SMILES codes of compound entry and new molecule are compared.

Molecular viewer

The molecular viewer window is available from the pop-up menu (right-click) for the selected compound. The display of hydorgen atoms in the viewer depends on the settings for the selected compound (available in the feature Image parameters from the pop-up menu).