To open an SDF file either launch the application and use the open dialog to select the molecule file or drag and drop your file on the application icon.
Multiple SDF files can be opened at the same time.
A dialog requests you to choose the property to use to cluster (grouping) the molecules into groups:
The mouse wheel zoom/unzoom the view
Instead of using the toolbar buttons you can:
To perform a substructure search do as follows:
To perform a clustering based on structural similarity do as follows:
To perform a structural similarity clustering on the molecules of a single group do as follows:
To display the molecule properties contained in the SDF file do as follows:
To display one of the molecule properties inside its frame, select the property in the “Display” dropdown menu:
To perform a text search in the whole dataset:
To select the result of the query check the “Select” checkbox before performing the search.
To add the current selection to the following search result use the “Select” and the “Append” checkboxes.
Complex text searches can be performed using regular expressions. To do so check the “RegEx” checkbox.
To cluster the molecules by a property, select the property of your choice in the “Organize by:” dropdown menu. The molecules change group but keep the color of their original group, the one selected in the open file dialog box (see 1. Open a Molecule file.)
If the clustering property is numerical (like molecular weight), every group will likely contain only a single molecule. To merge a range of numerical values inside a single group enter a binning value in the “Bins:” input field and press enter.
Enter 0 as a binning value in the “Bins:” input field and press enter to revert to a numerical clustering based on unique property values.
To go back to the initial clustering property press the home button .
To create a new group:
The new group is placed at the mouse cursor position if you use the keyboard shortcut. Otherwise it is placed at one of the edges of the working area.
To create a super-group, a group containing other groups:
To move a group into a supergroup:
To visually compact all the super-groups use the menu “Groups -> compact group“.
To visually compact a single super-group, press the shortcut key ‘C‘ while the cursor is on the super-group.
The “Tree view” button opens a hierarchical display of the groups. Double on any group name to center the view on it.
Molecules can be sorted by property inside the groups. To sort Molecules:
Press the “reorganize groups” button or press ‘v‘ to tidy up the screen and the position of the groups. The reorganization is purely visual to minimize the space occupied by the groups on the screen.
Alternatively, groups can also be sorted by various properties using the “Groups” menu:
To quickly navigate from molecule to molecule within a group do as follows:
To quickly navigate from group to group do as follows:
The Molecule cell background can be colored simultaneously by four different properties:
The colored property can also be displayed as 3D bars with the molecules on the top:
Note that for very large datasets, the 3D Property Bar view may significantly decrease the performance of the display.
Press the “Disable filters” to temporarily show all molecules.
Clusters can be placed on a 2D plot with X and Y axis defined as molecule properties:
To attach a graph to each cluster:
To activate the dataset spreadsheet:
Use the “formula” button to create new properties from existing ones:
Some tips and shortcuts to accelerate the navigation on a dataset:
To prevent some groups from moving when the view is reorganized :
Alternative to the context menu:
Note: The frozen groups will still apparently move on the screen when is pressed (or ‘v‘) but their position relative to each other will stay the same.
Cluster can be hidden when there are too many groups to work easily and some of them are not of immediate interest:
To show all hidden groups at once use the menu “Groups->Show all“.
To delete a molecule:
Press + ‘Z‘ to undo the delete molecule (or use the menu “Edit->Undo“).
If a selection is active and you delete one of the selected molecules, all the selected molecules are deleted.
To delete a group (and all its content):
To delete a supergroup (but not its content):
Subgrouping consists of assigning the molecules of each group to new groups based on selected property. Theses new groups are added to the original group which becomes a supergroup.
To perform a subgrouping:
To perform a subgrouping on a single group:
Note: This operation cannot be undone at the moment (v1.00).
The property selector is used to select which properties loaded from the SDF file are to be displayed/hidden.
To make a selection of displayed properties:
Important note: properties that have been hidden are not saved when using “File->Save“, “File->Save as” or “File->Save Selected“.
Each molecule of the dataset has an internal clock measuring the viewing time i.e. the time it has been displayed at a high zoom level. When this viewing time is displayed, it is possible to easily spot the zones of the dataset that have been overlooked.
To display the viewing time:
The circle is hidden at high zoom level to avoid overlapping with the molecule.
The molecules can be displayed in 3 different ways: wire, sticks and spheres. These 3 modes are accessible from the “Molecules” menu.