For molecular modelers, fine control over bond specifications is a critical aspect of modeling and analysis. SAMSON’s Node Specification Language (NSL) offers a dedicated bond attribute space that enables precise targeting and filtering of bond nodes, enhancing model customization. In this blog post, we’ll explore how to leverage bond attributes in SAMSON to achieve better results with minimal effort.
What Are Bond Attributes?
The bond attribute space in NSL is a powerful way to work specifically with bond nodes. It provides users with several predefined attributes, each offering its own filtering capabilities:
- customType: Matches bonds based on custom integer types.
- length: Matches bonds based on bond length values, specified in physical units.
- order: Matches bonds based on chemical bond orders (e.g., single, double, triple).
- type: Matches bonds of specific types like single, double, aromatic, etc.
Let’s dive deeper into these attributes with examples to show how they can simplify your molecular modeling workflow.
customType
Need to filter bonds by custom-defined types or categories? The customType attribute allows you to achieve this with ease. Simply use integers to define and target specific bond types. For example:
b.ct 0: Matches bonds withcustomTypeequal to 0.b.ct >= 1: Matches bonds withcustomTypegreater than or equal to 1.b.ct 1:3: Matches bonds withcustomTypevalues between 1 and 3.
length
When it comes to analyzing bond lengths, precision is key. The length attribute allows for detailed filtering based on bond lengths expressed in units like Angstroms (A) or nanometers (nm). Examples include:
b.len >= 1.5A: Matches bonds longer than or equal to 1.5 Angstroms.b.len 1.2A:1.4A: Matches bonds with lengths between 1.2 and 1.4 Angstroms.b.len 0.15nm:2.1nm: Matches bonds within the length range of 0.15 to 2.1 nanometers.
order
Finding bonds with specific bond orders? The order attribute lets you filter bonds by their chemical bond order with simple syntax:
b.o >= 2: Matches bonds with order greater than or equal to 2.b.o 1.5:3: Matches bonds with bond orders between 1.5 and 3.
type
The type attribute is perfect for selecting bonds of specific types, like single or aromatic. Each type is represented by easily recognizable symbols (or short names):
| Attribute name | Short name | Meaning |
|---|---|---|
single |
s, 1 |
single bond |
double |
d, 2 |
double bond |
triple |
t, 3 |
triple bond |
amide |
am |
amide bond |
aromatic |
ar |
aromatic bond |
dummy |
du |
dummy bond |
undefined |
un |
undefined bonds |
For instance:
b.t s: Matches single bonds.b.t ar: Matches aromatic bonds.b.t du,un: Matches dummy and undefined bonds.
Why Use Bond Attributes?
Bond attributes drastically simplify the way you query bond nodes in your molecular models. Whether you need to analyze specific bond lengths, target chemical orders, or isolate particular types of bonds, NSL’s bond attributes offer the flexibility and precision you need to save time and effort.
To explore the full documentation related to SAMSON’s bond attributes in NSL, visit the official documentation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. Get started by downloading SAMSON at https://www.samson-connect.net.