Molecular modelers often face challenges when narrowing down molecular conformations for analysis or simulation. The Node Specification Language (NSL) in SAMSON provides a powerful way to address such challenges by enabling you to query and manipulate specific molecular conformations. This blog post introduces the conformation attributes in NSL, explains their key properties, and demonstrates how to use them for practical purposes.
What are Conformation Attributes?
The conformation attribute space (short name: co) is a predefined set of attributes within NSL designed specifically for managing molecular conformations. With these attributes, you can target and refine your selection of conformation nodes, whether you’re filtering by individual names, number of atoms, or selection criteria.
Inherited vs. Specific Conformation Attributes
The conformation attribute space includes two types of attributes:
- Inherited attributes: Shared with the general
nodeattribute space, such asnameandselectionFlag. - Specific attributes: Unique to the conformation space, such as
numberOfAtoms.
Inherited Attributes
- name: Targets conformations based on their names. You can use quotes to specify exact names or partial matches. For example:
co.n "A"matches a conformation named “A”.co.n "L*"matches any conformation name starting with “L”.
- selectionFlag (
sf): Indicates whether a conformation node is part of the current selection. Examples include:co.sf: Matches conformations where the selection flag istrue.co.sf false: Matches conformations where the selection flag isfalse.
Specific Attributes
One notable specificity in the conformation space is the numberOfAtoms (nat) attribute, which matches conformations based on their number of atoms. This attribute is particularly useful when dealing with large datasets or focusing on specific molecular characteristics.
Examples for numberOfAtoms include:
co.nat > 100: Matches conformations with more than 100 atoms.co.nat 100:200: Matches conformations with 100 to 200 atoms.
These simple yet powerful filters can save you hours of manual refinement when analyzing large molecules.
Streamlining Your Workflow
By combining these attributes, you can create succinct and powerful queries tailored to your specific needs. For example:
co.n "L*" and co.nat > 50: Matches conformations whose name starts with “L” and have more than 50 atoms.
Using such commands, you can customize your modeling process and focus on the exact subset of conformations required for your research.
Where to Learn More
The documentation page provides detailed explanations and additional examples of conformation attributes. It’s highly recommended for molecular modelers looking to refine their skills in SAMSON’s Node Specification Language.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON today from SAMSON Connect.