Convert molecular formats and generate 3D coordinates with Open Babel.
npx skills add https://github.com/Hello-QM/catgo-LRG --skill openbabel-hello-qm
Please help me install this Agent Skill. Skill: openbabel Source: https://github.com/Hello-QM/catgo-LRG/tree/main/server/catgo/workflow/skills/data/openbabel Command: npx skills add https://github.com/Hello-QM/catgo-LRG --skill openbabel-hello-qm
Convert molecular formats and generate 3D coordinates for molecular structures, enabling seamless interconversion and structure generation in computational chemistry workflows.
Convert a SMILES string to a 3D geometry using Open Babel.
High-intent search queries and answers about installing and using this skill.
Open Babel generates 3D coordinates from 2D representations like SMILES to create input geometries for docking or quantum chemistry calculations. It handles interconversion between common molecular formats seamlessly.
Open Babel supports interconversion among SMILES, SDF/MOL, PDB, MOL2, XYZ, and CIF formats for cheminformatics workflows. You can convert PDB files to SDF or MOL2 to prepare structures for molecular dynamics.
Open Babel provides hydrogen handling features to add or adjust hydrogens as needed during format conversion. This ensures correct protonation states when preparing molecular structures for downstream analysis.
You must have Open Babel installed via apt or conda to generate 3D coordinates for CIF files. Optional Python bindings are also available if you need to script the coordinate generation process.
Open Babel supports XYZ format conversion for HPC computational workflows. It enables seamless interconversion of XYZ files with other common formats to prepare input geometries for large-scale calculations.
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