For molecular modelers, the ability to efficiently explore backbone attributes in complex molecular models can significantly enhance design workflows. If you’re using the SAMSON Molecular Design Platform, you might find the Backbone Node Specification Language (NSL) attributes to be a powerful way to gain precise control over your modeling process. This comprehensive guide introduces you to the backbone attribute space and highlights how to benefit from it.
Understanding Backbone Attribute Spaces
In SAMSON, backbone attributes are defined in the backbone attribute space (short name: s), meaning they specifically correspond to the backbone nodes in your molecular model. These attributes include names, possible values, and examples for defining queries or filtering structures. Leveraging this system allows you to organize, analyze, and modify your molecules with greater simplicity.
Key Attributes You Must Know
The table below highlights some backbone attributes, their corresponding short names, possible values, and examples. This quick reference can make your modeling tasks much easier:
| Attribute name | Short name | Possible values | Usage examples |
|---|---|---|---|
| hasMaterial | hm |
true, false |
bb.hm, not bb.hm |
| name | n |
Strings in quotes | bb.n "A", bb.n "L*" |
| numberOfAtoms | nat |
Integers | bb.nat < 1000, bb.nat 100:200 |
| numberOfCarbons | nC |
Integers | bb.nC < 10, bb.nC 10:20 |
These attributes allow you to specify certain conditions and extract only the details you care most about. For instance, the bb.n "L*" query filters backbone nodes with names starting with “L”.
Practical Use Cases
- Selecting Nodes with Specific Materials: Use
bb.hmfor molecule backbones that have material ornot bb.hmfor those without material. - Counting Carbon Atoms: To examine models based on the number of carbon atoms, query with
bb.nC 10:20to include backbones with 10 to 20 carbons. - Probing Partial Charges: Use attributes like
partialCharge(bb.pc > 1.5) to isolate nodes based on charge values efficiently.
Going Beyond: Why It Matters
Molecular research often requires granular data exploration at different structural levels. By mastering backbone attributes in NSL, the precision modeling of molecules becomes intuitive. Whether you’re identifying reactive groups, analyzing structures, or simulating functionalities, attributes such as selected, hidden, and visibilityFlag provide a path to quickly focus on the most relevant nodes.
To dive deeper into the full set of backbone attributes and their creative applications, visit the official SAMSON documentation page here: https://documentation.samson-connect.net/users/latest/nsl/backbone/.
SAMSON and all SAMSON Extensions are free for non-commercial use. To get your copy, visit https://www.samson-connect.net.