Mercurial > repos > chemteam > biopdb_align_and_rmsd
comparison BioPDB_align_and_rmsd.py @ 1:a40867ca69fe draft default tip
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit e9345f76e3f953eea14bad2287cbc5a9c1ff882e
| author | chemteam |
|---|---|
| date | Tue, 25 Mar 2025 07:25:58 +0000 |
| parents | 6352d6dd74e2 |
| children |
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| 0:6352d6dd74e2 | 1:a40867ca69fe |
|---|---|
| 93 super_imposer.set_atoms(ref_atoms, sample_atoms) | 93 super_imposer.set_atoms(ref_atoms, sample_atoms) |
| 94 super_imposer.apply(sample_model.get_atoms()) | 94 super_imposer.apply(sample_model.get_atoms()) |
| 95 | 95 |
| 96 # Save RMSD into an output file: | 96 # Save RMSD into an output file: |
| 97 with open(args.rmsd, 'w') as rmsd_out: | 97 with open(args.rmsd, 'w') as rmsd_out: |
| 98 rmsd_out.write(str(super_imposer.rms)) | 98 rmsd_out.write("{}\n".format(super_imposer.rms)) |
| 99 | 99 |
| 100 # Save aligned coordinates of the model: | 100 # Save aligned coordinates of the model: |
| 101 io = Bio.PDB.PDBIO() | 101 io = Bio.PDB.PDBIO() |
| 102 io.set_structure(sample_structure) | 102 io.set_structure(sample_structure) |
| 103 io.save(args.aligned_structure) | 103 io.save(args.aligned_structure) |