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name: selections-topology description: "Use and debug MDAnalysis atom selections, topology attributes, groups, fragments, topology guessing, and selection exporters." disable-model-invocation: true metadata: disco-role: operating license: NOASSERTION

MDAnalysis Selections and Topology

Use this sub-skill when a task involves select_atoms(), AtomGroup/ResidueGroup/SegmentGroup, topology attributes, group or updating selections, bonds/fragments, topology guessing, or exporting selections for another molecular tool.

Read First

• Start with Selection Language for selection grammar, keyword behavior, sorting, dynamic selections, selection groups, geometry, SMARTS, and exporters.
• Use Topology and Groups for group operations, topology attribute access, custom attributes, fragments/bonds, and topology guessing.
• Use Troubleshooting when selections are empty, reordered, slow, dependency-sensitive, or raise SelectionError, NoDataError, ValueError, or optional RDKit-related errors.
• Run python scripts/selection_probe.py from this sub-skill directory to confirm the installed MDAnalysis selection/topology basics with only synthetic data.

Common Task Routes

• Selection text: Prefer u.select_atoms("...") or ag.select_atoms("..."); remember keywords and string values are case-sensitive and selections are unique/sorted by topology index unless sorted=False is passed.
• Preserve order: For manually ordered groups such as ag[[5, 1, 0]], pass sorted=False to select_atoms() or use group concatenation/slicing when duplicates must be preserved.
• Dynamic selections: Pass updating=True for an UpdatingAtomGroup that lazily re-evaluates after trajectory frame changes; avoid it for static topology-only selections in tight loops.
• Topology attributes: Add built-in attributes with u.add_TopologyAttr("masses", values) or custom TopologyAttr subclasses; selectable custom attributes need supported dtype values (bool, integer, float, string/object).
• Cross-skill routing: Send file loading/writing format decisions to ../universe-io/SKILL.md, converter interoperability to ../formats-converters/SKILL.md, and numerical distance/analysis algorithms to ../analysis-workflows/SKILL.md.