When working with complex molecular systems, identifying specific structural groups based on electrostatic properties can be essential. Whether you’re screening ligands, analyzing biomolecular systems, or designing new compounds, partial charges help determine how molecules interact. Yet, combing through thousands of structural groups to find those with distinct charge values can be tedious — especially without an efficient filtering mechanism.
This is exactly where the partialCharge attribute in SAMSON’s Node Specification Language (NSL) becomes useful. It allows molecular modelers to isolate structural groups with specific electrostatic features in seconds.
Why Filter by Partial Charge?
Partial charges indicate the distribution of electrons across atoms in a structure and are critical for:
- Predicting intermolecular interactions
- Identifying polar regions in molecules
- Optimizing docking calculations
- Grouping structural motifs across a database based on charge state
But unless you can rapidly filter and visualize these groups by partial charge, you can’t fully leverage this information.
Meet sg.pc: A Targeted Attribute
In the structuralGroup attribute space within SAMSON’s NSL, the partialCharge attribute is accessible via the short name sg.pc. This lets you create expressive filters to work directly on structural group nodes with:
- Exact charge match:
sg.pc 1 - Range filter:
sg.pc 1.5:2.0— selects any group with a partial charge between 1.5 and 2.0 - Inequalities:
sg.pc > 1.5— selects groups where the partial charge exceeds 1.5
Example Use Case: Ligand Screening
Imagine you’re analyzing a biomolecular structure and want to filter structural groups that are likely to participate in hydrogen bonding due to their polarity. Setting sg.pc > 1.5 in the query tool instantly isolates candidate regions of interest. From there, you can prioritize those structures for further simulation or binding affinity checks.
Combining with Other Filters
What makes this even more powerful is you can combine the sg.pc filter with other attributes such as number of atoms (sg.nat) or type of group, narrowing down matches efficiently. A few examples:
sg.pc > 1.5 and sg.nat < 100— small charged groupssg.pc 0.5:1.0 and not sg.h— visible, moderately charged groups
This targeted querying removes manual guesswork, giving you more time to analyze, simulate, or iterate.
Where to Use It
You can use this attribute directly in SAMSON’s advanced selection tools, filtering scripts, or any NSL-compatible extensions. It helps make navigation through large molecular models significantly more manageable.
For more examples and technical details, visit the official documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.