Molecular modeling often requires precise targeting of specific molecular bonds to modify, analyze, or categorize them based on their physical or chemical properties. If you’ve ever wrestled with finding specific bonds in complex structures, the NSL in SAMSON offers a flexible and efficient solution. Today, let’s dive into SAMSON’s ‘bond’ attribute space and explore how to target bonds with unparalleled precision using the provided bond attributes.
What are Bond Attributes?
Bond attributes are part of the bond attribute space in NSL, commonly abbreviated as b. These attributes simplify the selection or filtering of bond nodes in molecular models, based on properties like bond type, length, order, or custom definitions.
Here’s a breakdown of the main bond attributes and how they work:
1. b.ct: Custom Bond Types
The bond.customType (b.ct) attribute helps you locate bonds with any custom-defined type. For example:
b.ct 0: Matches bonds with a custom type of 0.b.ct >= 0: Matches bonds with custom types larger than or equal to 0.b.ct 0:2: Matches bonds with custom types between 0 and 2.
Custom bond types allow you to categorize bonds based on criteria unique to your modeling projects.
2. b.len: Bond Length
bond.length (b.len) enables filtering based on precise bond lengths. Whether you’re working in angstroms (A) or nanometers (nm), this attribute provides flexibility:
b.len >= 1.5A: Matches bonds greater 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 from 0.15 to 2.1 nanometers.
Being able to specify ranges or thresholds makes it easy to find bonds that meet exact structural criteria.
3. b.o: Bond Order
With the bond.order (b.o) attribute, you can identify bonds based on their bond orders. For example:
b.o >= 2: Matches bonds with orders greater than or equal to 2.b.o 1.5:3: Matches bonds with orders between 1.5 and 3.
This is especially useful for filtering common bond types like single, double, or triple bonds—or for combinations of partial bonding in intermediates.
4. b.t: Bond Type
The bond.type (b.t) attribute provides a concise way to locate bonds based on predefined types such as single, double, or aromatic bonds. Supported types include:
| Attribute Name | Short Name | Meaning |
|---|---|---|
single |
s, 1 |
Single bond |
double |
d, 2 |
Double bond |
amide |
am |
Amide bond |
aromatic |
ar |
Aromatic bond |
Examples include:
b.t s: Matches single bonds.b.t s,d: Matches single and double bonds.b.t du,un: Matches dummy and undefined bonds.
Conclusion
Whether you’re targeting bonds by their custom type, length, order, or classification, NSL’s bond attributes offer unparalleled flexibility for molecular modelers. Apply these tools to isolate and analyze exact bond types in your simulations.
For more detailed information, visit the official documentation page here: https://documentation.samson-connect.net/users/latest/nsl/bond/.
SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON at https://www.samson-connect.net.