When working on molecular modeling, one common challenge is effectively analyzing and managing molecular conformations to extract useful insights. SAMSON, with its powerful integrative molecular design platform, offers tools to address this challenge efficiently. One particularly useful system within SAMSON is the Node Specification Language (NSL), which includes conformation attributes for managing and specifying conformation nodes in your models. If you’re working on molecular conformations, understanding how to use these attributes can simplify your workflows and improve precision.
What Are Conformation Attributes?
Conformation attributes are part of the conformation attribute space (identified by the short name co). This system is specifically designed to match conformation nodes in a molecular model. With powerful filtering options, this feature allows molecular modelers to isolate, analyze, and manipulate specific conformations easily.
These attributes belong to two categories:
- Inherited attributes: Attributes that are shared with the broader node attribute space.
- Specific attributes: Attributes that are unique to the
conformationspace.
Key Attributes Inherited from Node
The following inherited attributes often come in handy:
| Attribute name | Short name | Possible values | Examples |
|---|---|---|---|
| name | n |
Strings in quotes | co.n "A", co.n "L*" |
| selected | true, false |
co.selected, not co.selected |
|
| selectionFlag | sf |
true, false |
co.sf false, co.sf |
For example, the co.n "A" expression can be used to match conformations with a specific name.
Attributes Specific to the Conformation Space
Among the attributes unique to the conformation space, one of the most impactful is numberOfAtoms (short name: nat). This attribute helps when filtering conformations based on the number of atoms they contain.
Possible values: Integers (e.g., the number of atoms).
Here are some example expressions for using numberOfAtoms:
conformation.nat > 100(short version:co.nat > 100): Matches conformations with more than 100 atoms.conformation.nat 100:200(short version:co.nat 100:200): Matches conformations with the number of atoms between 100 and 200.
These expressions enable you to isolate conformations based on size, which is crucial when focusing on specific molecular scales or filtering irrelevant conformations from large datasets.
How to Get Started
Using conformation attributes in SAMSON offers flexibility and precision for molecular modelers. Combined with the ability to chain commands and apply filtering logic, these tools can dramatically improve your efficiency.
To explore these attributes in more detail, visit the official documentation. Start experimenting with the examples provided, and see how easily you can analyze and filter conformations in your models!
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON for free at samson-connect.net.