For molecular modelers, efficiently specifying and querying molecular structures is a crucial challenge. SAMSON’s Node Specification Language (NSL) provides a solution by enabling users to target specific molecular features with precision. In this article, we’ll focus on one subset of SAMSON NSL—the bond attribute space—and show how you can use bond attributes to streamline your molecular design and analysis workflows.
What are bond attributes?
In SAMSON NSL, bond attributes allow you to match and filter bond nodes based on various characteristics like bond type, length, order, or custom labels. These attributes are defined in the bond space (short name: b), which ensures queries exclusively target bond nodes within your molecular system.
Examples of bond attributes
Let’s dive into some of the most commonly used bond attributes:
customType (b.ct)
If you’ve assigned custom labels to bonds (e.g., based on experiment or specific use cases), the customType attribute allows you to filter bonds by these integer types. For instance:
b.ct 0: Matches bonds with custom type 0.b.ct >= 0: Matches bonds with custom type values greater than or equal to 0.b.ct 0:2: Matches bonds with custom type values between 0 and 2.
length (b.len)
To analyze structural properties, bond lengths are often essential. With b.len, you can examine specific ranges or compare lengths to thresholds:
b.len >= 1.5A: Matches bonds longer than 1.5 Å.b.len 1.2A:1.4A: Matches bonds with lengths between 1.2 Å and 1.4 Å.b.len 0.15nm:2.1nm: Matches bonds in the range from 0.15 nm to 2.1 nm, combining angstrom and nanometer flexibility.
order (b.o)
Bond order provides insight into the nature of bonds—be it single, double, or otherwise. The b.o attribute helps you select bonds efficiently. For example:
b.o >= 2: Matches bonds with orders greater than or equal to 2.b.o 1.5:3: Targets bonds with orders between 1.5 and 3.
type (b.t)
The bond.type attribute identifies bonds based on pre-defined types such as single, double, triple, or aromatic. Here are a few examples:
b.t s: Matches single bonds.b.t s,d: Matches single and double bonds simultaneously.b.t du,un: Matches dummy and undefined bonds, which might be placeholders in your molecular design.
The bond.type attribute supports a wide variety of predefined bond types, making it easy to focus on specific interactions or structures within complex molecular systems.
Why use bond attributes?
Bond attributes in SAMSON NSL enable molecular modelers to:
- Filter specific bonds in large molecular models quickly.
- Set constraints or analyze data based on bond properties.
- Simplify workflows for exploring and designing molecules with specific bond characteristics.
For example, identifying all bonds of a specific length range or focusing on aromatic bonds within a molecule can be done in seconds using bond attributes. This removes the need for manual inspection and enables efficient data-driven decisions in molecular modeling projects.
Learn more
Interested in exploring all bond attributes in SAMSON NSL? Head over to the detailed documentation page here: https://documentation.samson-connect.net/users/latest/nsl/bond/.
SAMSON and all SAMSON Extensions are free for non-commercial use. Start your molecular modeling journey today by downloading SAMSON from https://www.samson-connect.net.