# Consero: assembling 3D fragments of regular polymers Consero assembles 3D fragments (coordinates in PDB format) of polymers made of 2 alternated subunits ( sequence ababa... ). It has been primarily developed to assemble fragments of glycosaminoglycanes docked on a protein with the AutoDock3 software, but can in principle be used in the general case stated above. ################################# # requirements ################################# python2 and numpy python3 and numpy ################################# # Example of usage ################################# ____________________________________________________________ convert data from AutoDock3 !!! you might need to change which frag indices are dp3 or dp3a !!! ./prep-data.sh ____________________________________________________________ assemble fragments args: [first frag index] [last frag index] [Nb_of_chains] [min_overlap rmsd] [max_overlap rmsd] ./assemble.sh 2 4 10000 1.2 3.5 ____________________________________________________________ create library of monomer conformations args: [list of pdbfiles to extract monomers from] [clustering cutoff] ./build-library.sh 0.5 ____________________________________________________________ convert chains of fragments into full all-atom models args: [chains] [first frag index] [last frag index] ./create_chains.sh f2-4_1.5A_1000poses_1000meanrk.chains 2 4 ################################# # Statitics ################################# The fragment library is converted into a flat table for quick search. Queries on the fragment library use 3 dictionaries: _ the data dictionnary, provided by structures.json (written when creating the database, at step 1) _ the chainschema (see make_chainschena.py) that describes the format of the data and how it can be queried _ the query "variables" dictionnary (see query.py), that contains description of the subdata we are interested in For details on the data formats, see make_chainschema.py For an example of query, see the jupyter-notebook exemple_stats.ipynb