Similarity based Molecular Generation - ZnDraw

 Integration Tutorial

In this tutorial you'll learn how...

... to generate linkers

... to generate on a canvas

... to use advanced SiMGen featues

Linker generation

Genarate linkers in three steps:

1. Select two (or more) atoms
2. Click

Use Shift+Click to select atoms!

Linker generation

Genarate linkers in three steps:

1. Select two (or more) atoms
2. Click

3. Click

Tip: You can click midpoints of all segments to create new points. Clicking on a point allows you to move it and create curved linkers!

Linker generation

Genarate linkers in three steps:

1. Select two (or more) atoms

2. Click

3. Click

That's it! SiMGen will generate, hydrogenate and relax the full structure all in one click!

Generate a molecule

Genarating on a canvas is also simple:

1. Click on                                

Generate a molecule

Genarating on a canvas is also simple:

1. Click on

2. Place guiding points by clicking on the canvas.
   
   Once you're done click anywhere outside the canvas.

Tip: Red colour indicates you're outside the canvas

Generate a molecule

Genarating on a canvas is also simple:

1. Click on

2. Place guiding points by clicking on the canvas.
   
   Once you're done click anywhere outside the canvas.

3. Click

Generate a molecule

Genarating on a canvas is also simple:

1. Click on

2. Place guiding points by clicking on the canvas.
   
   Once you're done click anywhere outside the canvas.

3. Click

Tip: Click this button to remove the canvas and all placed points

You're done!

Advanced controls

You now know enough to play around with the generation tool.

We encourage you to first try out the two generation modes already explained before returning here.

Enter Draw mode by clicking the Draw button (or X on your keyboard).

Advanced Drawing

Place guiding points by clicking on atoms.

click!

Advanced Drawing

click!

click!

Move guiding points by clicking and then using on-screen controls.

Click Esc to deselect points.

click+drag

Advanced Drawing

Delete a selected point by clicking Backspace on your keyboard.

Advanced Drawing

Open the Interaction menu and select SiMGen

Generation controls

This opens the generation controls.

Note, you'll find two modifiers corresponding to SiMGen:

SiMGen and SiMGenDemo

The latter offers limited controls as it carries out all generation stages as a single action.

The former offers more control and lets you run the generation stages individually.

SiMGen

Generation controls

Change the run type using a drop-down menu.

Usual workflow is:
Generate → Hydrogenate → Relax

SiMGen

Generation controls

Tip: SiMGenDemo does all of these as a single modification

Num Steps controls the number of steps for each run type.

Default values should work for most use cases.

SiMGen

Generation controls

Specify the number of atoms to generate via:

• FixedNumber

• PerAngstrom which uses the length of the guiding curve

SiMGen

Generation controls

If generated structures are fragmented, increase the guiding force multiplier.

We recommend changing in multiples of 2.

SiMGen

Generation controls

Click Run Modifier to launch the generation!

Each step creates a clickable bookmark, allowing to easily jump back to the starting point.

The console contains useful information!

Generation controls

Open the Geometry menu by clicking the map icon on the sidebar

Generation in free 3D space

In the Geometry menu, select the type of canvas to add.

Click Add to add the selected canvas to the scene.

Generation in free 3D space

Guiding points can be attached to the canvas.

Click me in Draw mode!

Generation in free 3D space

Click Remove once you're done with the canvas.

Generation in free 3D space