For molecular modelers working in complex environments, efficiently finding and managing conformation nodes can be a challenge. SAMSON’s conformation attribute space provides a targeted and systematic way to handle this, allowing you to focus on the specific molecular attributes that are most relevant to your work.
The conformation attribute space (short name: co) is designed specifically for conformation nodes and offers both inherited attributes from the more general node attribute space and a set of attributes unique to conformations. This blog post will guide you through how to use these attributes effectively, providing practical examples to help streamline your molecular design process.
Inherited Attributes
Some attributes in the conformation attribute space are inherited from the general node attribute space, ensuring consistency and interoperability across your projects. These include:
- Name (
n): A string identifier for conformations. For instance,co.n "A"matches conformations named “A”, whileco.n "L*"matches conformations whose names start with “L”. - Selected: A Boolean attribute that matches selected nodes. Example:
co.selectedmatches selected conformations, andnot co.selectedexcludes them. - SelectionFlag (
sf): Similar toSelected, this Boolean attribute can be used to find specific flagged conformations. Example:co.sf falsematches unflagged conformations.
Specific to Conformations: numberOfAtoms
Among the conformation-specific attributes, numberOfAtoms (short name: nat) is especially useful for modelers handling complex molecular systems. This attribute allows you to query conformations by the number of atoms, making it easier to focus on molecular structures of interest.
Some ways to use co.nat include:
co.nat > 100: Matches conformations with more than 100 atoms.co.nat 100:200: Matches conformations containing between 100 and 200 atoms.
This feature can save significant time when working with large datasets, helping you quickly identify conformations that meet specific criteria.
Why Use Conformation Attributes?
The conformation attribute space offers a structured way to make precise selections and filter data, reducing the manual effort required in molecular modeling. By combining inherited attributes like name or selected with conformation-specific attributes like numberOfAtoms, you can construct highly targeted queries tailored to your project’s needs.
For instance, if you are trying to isolate conformations within a specific range of atom counts and that are also selected, you could combine attributes like so: co.nat 50:150 and co.selected.
Start Exploring
The examples shared in this article are just a starting point. By familiarizing yourself with the full set of available attributes and experimenting with queries, you’ll be able to unlock a more streamlined and efficient workflow in SAMSON. To explore more advanced examples and understand all possible use cases, see the full documentation at Conformation Attributes Documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. Download SAMSON now from www.samson-connect.net.