Streamline Molecular Modeling with Path-Specific Attributes in SAMSON

For molecular modelers, efficiently navigating and analyzing molecular conformations is key to unlocking insights. SAMSON’s Node Specification Language (NSL) provides advanced tools to address this challenge, particularly through the use of path attribute space. This attribute space, with the short name p, is designed to match and manipulate conformation nodes effectively. Below, we’ll explore how leveraging path-specific attributes can make your workflow more precise and productive.

What are Path Attributes?

Path attributes in NSL allow users to identify and filter molecular paths based on defined criteria. These attributes, categorized under the path attribute space, can integrate inherited node attributes while offering functionality specific to paths. This combination provides exceptional flexibility and power for selecting and processing molecular data.

Key Attributes and Their Uses

1. Inherited Attributes

The path attribute space makes use of several inherited attributes from the node attribute space:

  • name (n): Helps identify paths based on string names (supports wildcards). Example:
    p.n "L*" finds all paths starting with ‘L’.
  • selected: Boolean value (true or false) indicating whether a path is currently selected.
    Example: p.selected filters selected paths, while not p.selected captures unselected ones.
  • selectionFlag (sf): Another boolean attribute often used to refine selection queries.
    Example: p.sf false excludes paths flagged for selection.

2. Path-Specific Attributes

These attributes provide unique capabilities specific to path analysis:

  • numberOfAtoms (nat): Matches paths based on the number of atoms present.
    – To find paths containing over 100 atoms: p.nat > 100.
    – To target a range of atom numbers: p.nat 100:200 for paths with between 100 and 200 atoms.

By combining these attributes, you can create powerful queries for specific cases, such as identifying long polymer chains or excluding smaller conformational fragments.

Practical Benefits

For molecular design tasks involving complex systems, path attributes significantly enhance your ability to focus on relevant data. For example, by using p.n "A", you can isolate all paths associated with a specific molecular component labeled “A”. Additionally, combining p.nat > 500 and p.selected enables you to find large, selected conformations with minimal effort. This precision can save time when conducting simulations or evaluating structural properties.

Learn More

SAMSON’s Path Attributes are a robust tool for molecular modelers seeking precision and efficiency in conformation filtering and manipulation. To dive further into the details and examples, visit the original documentation page here.

SAMSON and all SAMSON Extensions are free for non-commercial use. Explore SAMSON and simplify your molecular modeling tasks by downloading it today: Get SAMSON.

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