User Guide

EasyHybrid is a “graphical environment for pDynamo3” designed to be easy to visualize, edit, inspect e simulate molecular systems and view. It runs on Windows and Linux.This user guide was made on a Mint Linux, but the interface should be very similar on any computer. If your EasyHybrid is properly installed, you can initialize running the following command at the EasyHybrid main folder.

~/something/EasyHybrid3$ python3 EasyHybrid.py 

EasyHybrid's main window can be divided into 5 parts as shown in Figure 1. Later we will discuss in more detail how each tool works and what it is capable of.

A brief description for the parts mentioned in Figure 1: 

1 - main menu: Contain all the functions available in EasyHybrid. 

2 - main toolbar: Contains the main features of EasyHybrid and can be divided into file tools, selection toolbar, pDynamo toolbar and selection type box (Figure 2). 

3 - GL area: is the interactive space for visualization of three-dimensional objects, here all active objects are displayed. The basic commands associated with the mouse (Figure 3) and keyboard for interacting with 3D models are as follows:

Button 1: Selects objects in the GL area (applicable to both view and edit mode).

Button 2: Invokes the GL area menus.

Button 3: Centers the viewable object on the selected atom.

Button 1 + Mouse Movement: Rotates the 3D models.

Button 2 + Mouse Movement: Zooms in or out of the field of view.

Button 1 + Mouse Movement + Shift: Enables area selection when the 'viewing' option of the selection box is active.

Button 1 + Mouse Movement + Ctrl: Rotates the camera on the Z axis (depth).

4 - System Treeview: The system treeview  (Figure 4) displays all the systems currently loaded in memory and their respective viewable objects. Since it is possible to work with multiple systems simultaneously, the active system, which undergoes simulation routines, is indicated by a radiobutton in the first column of the treeview. Each loaded system has a collapsible header (treeview item) for easy navigation. The interface utilizes reference colors for each system, and by default, new viewable objects assign the system's reference color to the carbon atoms. You have the option to customize the color on your preferences. Additionally, the treeview presents two columns, labeled "V" and "F," for viewable objects. The "V" column indicates active viewable objects that can be observed in the GL area, while the "F" column shows the number of frames for each object. 

A double click with Button 1 on an object in the treeview updates the minimum/maximum limits on the trajectory player scroll bar. Button 3 opens the treeview menu, providing options to change system settings and other functionalities.

5 - Status bar: The properties of the active system in memory (identified by the selected radiobutton in the first column of the system treeview) are displayed in the status bar. When the selected system is changed, the content of the status bar updates accordingly. The properties shown include the total number of atoms, frozen (fixed) atoms, atoms in the QC region, force field, QC method, non-bonded model, and more.

6 -status notebook: It shows the history of the main routines executed within the interface. The colors are used to associate the record with the receptive systems (color of references).