Understanding Folder Attributes for Molecular Modeling in SAMSON

In molecular design and modeling, efficiently organizing and filtering structural data is critical for productivity. The Node Specification Language (NSL) in SAMSON offers powerful tools to help you work with nodes and their attributes, and specifically, folder attributes that greatly simplify managing complex molecular structures. This blog post delves into folder attributes and examples of how to utilize them effectively.

Why Folder Attributes Matter

As a molecular modeler, you are likely managing extensive amounts of data, often involving multiple chains, atoms, molecules, and other structural elements. Folder attributes allow you to filter and analyze your models without manually sifting through each component, directly targeting the information you need, saving you valuable time.

Attributes Inherited from Nodes

Folders in SAMSON inherit several attributes from nodes that let you query common properties, for instance:

  • hasMaterial (f.hm): Does the folder have material? Possible values: true or false.
  • hidden (f.h): Is the folder hidden? Possible values: true or false.
  • name (f.n): The folder’s name, allowing string matching, such as prefixes or patterns.
  • visible (f.v): Is the folder visible? Possible values: true or false.

For instance, you can use the following expressions to match folders:

  • f.v: Matches visible folders.
  • not f.h: Matches folders that are not hidden.
  • f.n "Protein_A*": Matches folders with names starting with “Protein_A”.

Folder-Specific Attributes

Beyond inherited attributes, folders have unique features that let you explore specific molecular details, such as:

  • formalCharge (f.fc): Filters based on the folder’s total formal charge. Example: f.fc 6:8 matches charges between 6 and 8.
  • numberOfAtoms (f.nat): Matches folders containing models with a specific number of atoms. Example: f.nat > 1000 finds folders with more than 1,000 atoms.
  • numberOfChains (f.nc): Filters by model chains. Example: f.nc 2:4 matches folders containing between 2 and 4 chains.
  • numberOfHydrogens (f.nH): Targets folders with a specific number of hydrogen atoms, using expressions like f.nH 10:20.

With these attributes, you can directly query structural features across your datasets with valuable precision.

Examples of Practical Use

Let’s say you’re working with a dataset of molecular structures and want to focus on folders meeting specific criteria:

  • Analyze models that include more than 2 structural chains: f.nc > 2.
  • Identify folders with partial charges between 1.5 and 2.0: f.pc 1.5:2.0.
  • Find models with fewer than 10 sulfur atoms: f.nS < 10.

By combining these attributes with logical operators like and, or, and not, you can further customize your queries. For example, f.hm and not f.h selects folders with material that are not hidden.

Learning More

The full range of folder attributes and their corresponding short names enable a level of flexibility and precision that will significantly enhance your molecular modeling workflows. You can explore more about these capabilities in the official documentation.

SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON here.

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