When analyzing complex molecular systems, identifying bonds of specific lengths can be vital. Whether you’re refining a molecular structure, studying strain in a bond, or just verifying model integrity, being able to query and filter bonds by length saves time and effort.
In SAMSON, the Node Specification Language (NSL) offers users a flexible way to filter molecular elements such as atoms, bonds, and entire molecular groups. This post focuses on querying bonds by length using NSL so that you can isolate and study just the bonds that matter most in your current task.
Why Work with Bond Lengths?
Mismatches in bond lengths can indicate issues in molecular models — such as incorrect geometry, force field misapplications, or artifacts introduced during file import/conversion. Sometimes, science requires focusing only on unusually short or long bonds, for example, in transition states or intermolecular contacts.
How Bond Length Queries Work in NSL
NSL lets you write structured queries to match specific molecular features. For bonds, you use the bond.length attribute, with the short name b.len, to specify conditions based on bond length. SAMSON supports typical query symbols like >, >=, <, <=, and range specifications using :.
Examples of Syntax
b.len >= 1.5A– matches bonds with length greater than or equal to 1.5 angstromsb.len 1.2A:1.4A– matches bonds with length between 1.2A and 1.4Ab.len 0.15nm:2.1nm– matches bonds between 0.15 and 2.1 nanometers
Notice that you can express lengths in units like angstroms (A) or nanometers (nm). This is useful when you’re transitioning between different scales, such as quantum chemistry models and coarse-grained systems.
Tips for Effective Use
- Always specify units when using floating point values in bond length queries. Default units may vary depending on the system configuration, and ambiguity can create mismatches.
- Watch out for default bond types: If you suspect your bond types aren’t defined, remember that bond type filters might not return results.
- Use ranges for flexibility: Instead of picking a single bond length, use a range to include slightly varying geometries (e.g.,
b.len 1.48A:1.52A).
This kind of filtering is especially useful when scripting workflows, analyzing molecular dynamics results, or preparing data for visualization. Combined with other filters (like bond type or order), bond length filtering provides a high level of control over what you see and analyze in SAMSON.
To learn more about bond attributes in NSL, including length, type, customType, and order, visit the official documentation: https://documentation.samson-connect.net/users/latest/nsl/bond/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.