Designing custom polymers often requires handling complex monomer sequences—whether you’re modeling repetitive structures, testing new arrangements, or building realistic polymers for simulations. One time-consuming step many molecular designers face is the repetitive reconstruction of commonly used monomer sequences.
With SAMSON’s Polymer Builder Extension, you can now save valuable time by easily registering and reusing monomer sequences—just like templates—for your polymers. This blog post walks you through how to make the most of this feature to streamline your polymer design workflows.
Why save monomer sequences?
When building polymers, especially synthetic ones or copolymers, researchers often reuse the same arrangements repeatedly. Rather than typing them again or risking mistakes, you can:
- Store sequence patterns with clear IDs like
S1,S2, etc. - Easily reuse and combine them in more elaborate polymers.
- Quickly visualize connected fragments via built-in highlighting tools.
- Specify precise bonding (single, double, triple) between monomers.
How to register sequences from monomers
After creating and registering your monomers:
- Click Add new sequence in the Polymer Builder.
- Use monomer IDs (like
A,B) to define a pattern, e.g.,ABBA. - Need a double or triple bond? Use
=or#symbols:A=B,A#B. - If the sequence is valid, it’s added to the table and instantly ready for use.
- Give it a name to group the result into a defined structural group, helpful for later export or simulation.
Convenience when building larger polymers
Once multiple sequences are defined, they can be easily referenced in compound expressions during the polymer generation step. For instance:
|
1 |
S1 + 2*S2 + AB=BA |
This expression will use sequence S1, then two repeats of sequence S2, then the sequence AB connected with a double bond to BA. SAMSON automatically shows the predicted length and molecular weight of the resulting polymer.
If there’s a mistake in your syntax, you’ll get a clear error label in the Status column to identify and fix it quickly.
Flexible editing and deletion
You can adjust your sequences and their names right from the table. To delete one, just right-click on it and select Delete sequence. Or click Clear all to remove the full list and start fresh.
With organized sequence management, polymer design becomes modular and efficient—particularly useful for repeat testing, simulations, and versioning experiments.
To learn more about how to build, modify, and generate entire molecular structures using the Polymer Builder, visit the full documentation here: https://documentation.samson-connect.net/tutorials/polymer-builder/polymer-builder/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.