Understanding Conformation Attributes in SAMSON’s Node Specification Language

Molecular modelers often need tools to organize and analyze complex molecular data efficiently. One such pain point arises when handling specific properties of molecular conformations. SAMSON, an integrative molecular design platform, offers a solution with its Node Specification Language (NSL). In this article, we will explore a key aspect of NSL for molecular modeling: conformation attributes.

What Are Conformation Attributes?

The conformation attributes are a subset of attributes in SAMSON’s Node Specification Language (NSL) that help you interact with conformation nodes specifically. This allows you to filter, query, and manipulate molecular data according to properties unique to molecular conformations.

Inherited and Specific Attributes

Conformation attributes are divided into two categories: inherited attributes from the more general “node” attribute space, and attributes specific to conformations.

Inherited Attributes

• name (n): Enables you to filter conformation nodes by name, using strings in quotes. For example:
  
  co.n "A"

  1

  co.n "A"

  matches conformations named “A” or
  
  co.n "L*"

  1

  co.n "L*"

  matches all conformations whose names start with “L”.
• selected: Allows you to target only selected conformations using true or false values. For example:
  
  co.selected

  1	co.selected

  matches selected conformations, while
  
  not co.selected

  1	not co.selected

  matches unselected ones.
• selectionFlag (sf): Similar to “selected” but with the added short name “sf” for convenience. Example usage includes:
  
  co.sf false

  1	co.sf false

  to find conformations without this flag, or
  
  co.sf

  1

  co.sf

  to check directly for flagged conformations.

Specific Conformation Attributes

Unique to the conformation attribute space, the key attribute numberOfAtoms (nat) empowers you to filter by the number of atoms in conformations:

• To find conformations with more than 100 atoms:
  
  co.nat > 100

  1	co.nat > 100

• To target those with atom counts between 100 and 200:
  
  co.nat 100:200

  1	co.nat 100:200

Practical Example

Imagine you are working with a protein structure and want to identify all conformations with names beginning with “L,” that are not selected, and have between 150 and 300 atoms. Using NSL, you can craft a single query that achieves this efficiently:

This flexibility eliminates the need for manual filtering and speeds up your workflows significantly.

Why Learn About NSL Conformation Attributes?

Understanding NSL’s conformation attributes gives you the power to streamline your molecular modeling tasks in SAMSON. These attributes provide precision in targeting specific nodes, saving you time and effort in your research or design projects.

For a comprehensive list of all conformation attributes and their usage, visit the official documentation page: https://documentation.samson-connect.net/users/latest/nsl/conformation/.

SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON at www.samson-connect.net.