Understanding Property Model Attributes in SAMSON’s Node Specification Language

Molecular modelers seeking better control and precision in handling molecular data often face the challenge of managing and querying specific node properties efficiently. SAMSON’s property model attributes offer a structured way to address this issue by enabling the use of the Node Specification Language (NSL) to interact directly with property model nodes. Below, we’ll explore these attributes and their utility in simplifying molecular modeling workflows.

What Are Property Model Attributes?

Property model attributes belong to the propertyModel attribute space, denoted by its short name, pm. These attributes allow users to work specifically with property model nodes in SAMSON, helping to filter, manipulate, or query key properties of molecular data. For example, attributes like hasMaterial, name, and visibilityFlag provide granular control over how nodes are classified and visualized.

Key Attributes and Their Usage

Let’s dive into some of the most relevant property model attributes and how they are used:

  • hasMaterial (hm): Indicates whether a property model node has material. Possible values are true or false. For instance, you can check if a node has material using pm.hm, or exclude such nodes with not pm.hm.
  • hidden (h): Specifies whether a node is hidden. Use pm.h to target hidden nodes or not pm.h for nodes that are visible.
  • name (n): Refers to the name of the node, represented as strings in quotes. For instance, pm.n "A" targets nodes whose name is exactly “A,” while pm.n "L*" targets nodes with names starting with “L.”
  • ownsMaterial (om): Denotes whether the node owns its material. This is a boolean attribute (true or false) accessible via pm.om.
  • visibilityFlag (vf): Determines the visibility flag of the node. For example, you can query nodes with visibility flags set to false using pm.vf false.

Practical Use Cases

One common pain point for molecular modelers is filtering out unnecessary model elements during analysis or visualization. Property model attributes help specify criteria like visibility or material presence to focus solely on the desired components.

For example, to focus on visible and named nodes that own material, you can combine filters as follows:

pm.v and pm.om and pm.n "TargetName"

Such queries are invaluable when handling complex molecular structures where selecting or isolating specific components is critical.

Dive Deeper Into Attribute Details

Each property model attribute ties back to underlying attributes inherited from the node attribute space. This ensures consistency and integration across the platform. For example, propertyModel.hasMaterial is derived from node.hasMaterial, and so on. For modelers familiar with node-level attributes, this inheritance simplifies adopting property model workflows.

Curious to explore more about property model attributes? Head over to the full documentation page on Property Model Attributes in SAMSON.

SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.

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