Are you working on designing or analyzing molecular systems and looking for ways to filter specific bonds based on their attributes? Understanding and effectively using bond attributes in the Node Specification Language (NSL) of the SAMSON Molecular Design Platform can make this task much easier.
Bond attributes are a powerful way to match specific bond nodes in your molecular models. Whether you’re filtering by bond type, order, length, or custom types, NSL allows you to precisely define the criteria you need. Below, we’ll briefly examine four key bond attributes available in NSL: customType, length, order, and type.
customType Attribute
The bond.customType attribute, which can be shortened to b.ct, allows you to match bonds with specific custom classifications. These classifications are defined using integers.
Example expressions:
bond.customType 0(orb.ct 0) matches bonds of custom type 0.bond.customType >= 0(orb.ct >= 0) matches bonds with custom types greater than or equal to 0.bond.customType 0:2(orb.ct 0:2) matches bonds with custom types ranging from 0 to 2.
length Attribute
The bond.length attribute (short name: b.len) is used to match bonds based on their lengths. This attribute is particularly useful when designing structures that rely on specific bond distances.
Possible values include floating-point numbers, which can also be defined with units like angstroms (A) or nanometers (nm).
Example expressions:
bond.length >= 1.5A(orb.len >= 1.5A): matches bonds longer than 1.5 angstroms.bond.length 1.2A:1.4A(orb.len 1.2A:1.4A): matches bonds with lengths between 1.2 and 1.4 angstroms.
order Attribute
The bond.order attribute (short name: b.o) filters bonds based on their chemical bond order, such as single, double, or higher orders. This attribute accepts floating-point values, making it flexible for precise criteria.
Example expressions:
bond.order >= 2(orb.o >= 2): matches bonds at least double in order.bond.order 1.5:3(orb.o 1.5:3): matches bonds with orders between 1.5 and 3, inclusive.
type Attribute
The bond.type attribute (short name: b.t) lets you match bonds of a specific chemical type. Examples include single, double, triple, aromatic, and dummy bonds. Each has specific shorthand values for convenience.
The table below summarizes the possible bond types and their corresponding shorthand:
| Bond Type | Shorthand |
|---|---|
| single | s, 1 |
| double | d, 2 |
| amide | am |
| aromatic | ar |
Example expressions:
bond.type single(orb.t s): matches single bonds.bond.type single, double(orb.t s,d): matches single and double bonds.
By combining these attributes, you can efficiently search, filter, and interrogate bond-specific data across large molecular models. For more information on bond attributes and NSL syntax, visit the detailed documentation page.
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