pdb2sql
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DeepRank
Fast and versatile biomolecular structure PDB file parser using SQL queries
Sometimes we need to set rotation center that is other than the geometric center of the whole protein. This could be fixed by changing this line of pdb2sql.transform.rot_mat(): `xyz =...
Better _pdb2sql_ has an option to select one alternative location for atoms of a residue **Description of problem** While checking the similarity of two PDBs (decoy & ref) when there...
**Describe the bug** If a backbone atom is missing in the Ligand part of one of the two PDBs, _compute_lrmsd_pdb2sql_ does not report it and leads to an error **Environment:**...
StructureSimilarity is a bit of a mess now. We have different ways of computing the metrics and they don't all have the same features and internal checks : - Some...
pdb matching is a very useful step for pdb analysis. It would be nice if we could add this to pdb2sql. Expected performance: INPUT: - a reference pdb file with...
``` >>> ref = "ref.pdb" >>> model = "model.pdb" >>> sim = StructureSimilarity(model,ref) >>> irmsd_fast = sim.compute_irmsd_fast() Traceback (most recent call last): File "", line 1, in File "/home/lixue/tools/anaconda3/lib/python3.7/site-packages/pdb2sql/StructureSimilarity.py", line...