from optparse import OptionParser import IMP.em import IMP.multifit import IMP.helper def main(): IMP.set_log_level(IMP.SILENT) usage = "usage: %prog [options] \n Description: The script gets as input a PDB file of a complex and calculates an anchor graph,\n such that nodes corresponds to the centroids of its chains and \n edges are between chains that are close in space." parser = OptionParser(usage) (options, args) = parser.parse_args() if len(args) != 2: parser.error("incorrect number of arguments") pdb_fn=args[0] cmm_fn=args[1] #read the protein mdl=IMP.Model() mh=IMP.atom.read_pdb(pdb_fn,mdl,IMP.atom.CAlphaPDBSelector()) IMP.atom.add_radii(mh) #find the centers of the individual chains chains=IMP.atom.get_by_type(mh,IMP.atom.CHAIN_TYPE) centers=[] rbs=[] for chain in chains: ps=IMP.core.XYZsTemp(IMP.core.get_leaves(chain)) centers.append(IMP.core.get_centroid(ps)) IMP.atom.setup_as_rigid_body(chain) #fast calculations of which chains are close links=[] sdps= IMP.core.SphereDistancePairScore(IMP.core.Linear(0,1)) rdps= IMP.core.RigidBodyDistancePairScore(sdps, IMP.core.LeavesRefiner(IMP.atom.Hierarchy.get_traits())) for id1,chain1 in enumerate(chains): for id2,chain2 in enumerate(chains[id1+1:]): #check if the bounding boxes are intersecting if rdps.evaluate(IMP.ParticlePair(chain1.get_particle(), chain2), None)<0.5: links.append([id1,id1+id2+1]) #write the cmm file output=open(cmm_fn,"w") output.write('\n') for id,c in enumerate(centers): output.write('') for id1,id2 in links: output.write('\n') output.write('\n') if __name__ == "__main__": main()