Understanding Folder Attributes: A Helpful Guide for Molecular Modelers

For molecular modelers, managing and organizing complex molecular designs is a key part of the modeling workflow. The folder attribute space in SAMSON provides powerful options to efficiently organize and query folder nodes based on various properties. This blog post introduces the folder attributes available in SAMSON’s Node Specification Language (NSL), helping you streamline your modeling process and save time.

What Are Folder Attributes?

In SAMSON, folder attributes allow you to work with folder nodes that group different elements in your molecular model. By using the folder attribute space (short name: f), you can query and filter folder nodes based on specific properties. For example, you can select folders containing a defined range of atoms, chains, or structural models, among many other criteria.

Examples of Common Folder Attributes

Here are some folder attributes that can make a real difference in your workflow:

  • Formal Charge (formalCharge): Specify folders with structures having a particular formal charge. For instance, folder.fc 6:8 (short version f.fc 6:8) selects folders with a formal charge between 6 and 8.
  • Number of Atoms (numberOfAtoms): Filter folders based on the number of atoms in their structures using folder.numberOfAtoms or its short name f.nat. For example, f.nat < 1000 selects folders with fewer than 1,000 atoms.
  • Number of Carbon Atoms (numberOfCarbons): Target folders based on the count of carbon atoms with f.nC < 10 or f.nC 10:20.
  • Number of Structural Groups (numberOfStructuralGroups): Use the short name f.nsg to narrow down folders with a specified range of structural groups, such as f.nsg 10:13.

Advanced Use: Combining Folder Attributes

One of the strengths of folder attributes in SAMSON is their versatility. For example, you can combine queries to pinpoint specific folders:

  • f.nat > 200 and f.nC < 10: Finds folders with more than 200 atoms but fewer than 10 carbon atoms.
  • f.nm 3:5 and f.nsg 20: Matches folders containing 3 to 5 molecules and exactly 20 structural groups.

Benefits for Your Workflow

By leveraging folder attributes, you can simplify the organization and modification of molecular designs. Searching for specific structures based on properties like atomic composition, selected molecules, or formal charges no longer needs to be a time-consuming task. Folder attributes allow you to focus on your research rather than managing unwieldy datasets.

Learn More

The documentation offers a detailed breakdown of folder attributes along with examples. For further exploration, visit SAMSON’s official documentation.

SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON at SAMSON Connect.

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