If you turn off the sanitization the splitting should be super fast too. If that is the only thing you would like to do.
pon., 7 paź 2019, 10:31 użytkownik Téletchéa Stéphane < stephane.teletc...@univ-nantes.fr> napisał: > Le 05/10/2019 à 12:46, Chris Swain via Rdkit-discuss a écrit : > > Hi, > > > > I have a number of PDB files (foo.pdb.gz) and I want to separate each > chain in each file out into a separate file. So if a file contains 4 chains > it will generate 4 separate files. > > > > Can I do this using RDKit, if so how? > > > > Cheers > > > > Chris > > Dear Chris, > > Even this could be performed in rdkit, I would recommend doing it using > an external tool, for instance using Biopython and the Bio.PDB module > (https://biopython.org/wiki/The_Biopython_Structural_Bioinformatics_FAQ), > or even ProDy (http://prody.csb.pitt.edu/). > > Rdkit needs to wrap a lot of atom definitions to load the pdb file > properly, and it takes time (minutes on my machine, which is a decent > workstation :-). > It will be lightning fast using Bio.PDB or prody, compared to rdkit. > > If you still want to use rdkit only, and need to reuse rdkit > representation of the PDB file, then (c)pickle it (python2): > > import cPickle > from rdkit import Chem > > def processReceptor(r): > try: > h=open('receptor.pkl','r') > receptor=cPickle.load(h) > h.close() > except Exception as e: > receptor = Chem.MolFromPDBFile(r) > f=open('receptor.pkl','w') > cPickle.dump(receptor,f) > f.close() > > return receptor > > HTH, > > Stéphane > > -- > Assistant Professor in BioInformatics, UFIP, UMR 6286 CNRS, Team Protein > Design In Silico > UFR Sciences et Techniques, 2, rue de la Houssinière, Bât. 25, 44322 > Nantes cedex 03, France > Tél : +33 251 125 636 / Fax : +33 251 125 632 > http://www.ufip.univ-nantes.fr/ - http://www.steletch.org > > > _______________________________________________ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >
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