When working with molecular models, filtering and querying based on electrostatic properties can be essential for selecting molecules of interest, especially in tasks like charge optimization, molecular docking, or interaction prediction. One commonly used property for this is the partial charge.
In SAMSON, the integrative platform for molecular design, the Node Specification Language (NSL) allows for precise selection of structural models based on their partial charges. This short guide introduces how to leverage the partialCharge attribute in NSL to make your search and workflow more efficient.
Why Partial Charge Matters
Partial charges are key to understanding and modeling electrostatic interactions in molecular systems. These charges influence how molecules interact with each other, bind to surfaces, or participate in chemical reactions.
Finding molecular models with unusually high or low partial charges, or within specific numeric ranges, helps researchers study trends or identify candidates for further investigation. Manually tagging and sorting molecules by charge in large datasets can be tedious—so NSL’s search language becomes a helpful tool to automate and refine this process.
The Attribute You Need: partialCharge
In the NSL, the total partial charge of a structural model is accessed via:
sm.pc
This shorthand stands for structuralModel.partialCharge.
How to Query
Use sm.pc followed by the value or range you’re interested in. Here are some examples:
sm.pc 1→ Matches structural models with a total partial charge of exactly 1.sm.pc 1.5:2.0→ Selects all models with total partial charge between 1.5 and 2.0.sm.pc > 2.5→ Filters models with total partial charge greater than 2.5.not sm.pc→ (if implemented contextually) Might be used to exclude models where this attribute isn’t defined.
This kind of selection helps narrow down a dataset to candidates with electrochemical properties you’re targeting in your analysis or design workflow.
Practical Example
Imagine you’re working on a dataset of drug-like molecules, and you’re interested in evaluating candidates with partial charges close to neutrality, say between -0.5 and +0.5. A simple NSL query would be:
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sm.pc -0.5:0.5 |
This will instantly filter out charged species, letting you focus on neutral or minimally charged compounds—useful especially when looking to reduce off-target electrostatic interactions in biological environments.
Combining Queries
NSL supports logical constructs, so you can combine partial charge filters with other criteria. For example, to find non-hidden models with a partial charge above 1.5, use:
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sm.pc > 1.5 and not sm.h |
Such combinations are powerful in curating datasets before simulations or when exporting structures.
Final Thoughts
Being able to filter by partial charge enhances the value of your modeling sessions considerably. It helps reduce clutter, focus your dataset, and conduct meaningful analysis faster than by scanning manually. If you’ve never used sm.pc before, try it now to see how it streamlines your workflow.
To learn more about structural model attributes in NSL, visit the original documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.