<div dir="ltr">* I meantÂ <div><br></div><div><div style="font-family:arial,sans-serif;font-size:13px">h = IMP.atom.Hierarchy(p)</div><div style="font-family:arial,sans-serif;font-size:13px">c = p.get_children(h)</div></div> <div style="font-family:arial,sans-serif;font-size:13px"><br></div><div style="font-family:arial,sans-serif;font-size:13px">this assumes that particle p was already decorated as Hierarchy (let me know if you are not familiar with decorators, Hierarchy, or Particle).</div> <div style="font-family:arial,sans-serif;font-size:13px"><br></div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Wed, Jul 2, 2014 at 3:02 PM, Barak Raveh <span dir="ltr"><<a href="mailto:barak.raveh@gmail.com" target="_blank">barak.raveh@gmail.com</a>></span> wrote:<br> <blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Hi Josh,Â <div><br><div>I think get_children() is only a member function of Hierarchy, so you should do something like</div> <div><br></div><div>IMP.atom.Hierarchy(p)</div><div>c = p.get_children()<br><div><div class="gmail_extra"> <br></div><div class="gmail_extra">'cs' seems to be a ConfigurationSet object - are you sure that you expect it to have children?</div><div class="gmail_extra"><br></div><div class="gmail_extra">What do you want to do?</div> <div class="gmail_extra"><br></div><div class="gmail_extra">Cheers,</div><div class="gmail_extra">Barak</div><div><div class="h5"><div class="gmail_extra"><br><div class="gmail_quote">On Wed, Jul 2, 2014 at 1:42 PM, Josh Bullock <span dir="ltr"><<a href="mailto:jma.bullock@gmail.com" target="_blank">jma.bullock@gmail.com</a>></span> wrote:<br> <blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">ah sorry ! this line gives me the error<div class="gmail_extra"><br></div><div class="gmail_extra"><span style="font-family:arial,sans-serif;font-size:13px">h= IMP.atom.Hierarchy.get_</span><span style="font-family:arial,sans-serif;font-size:13px">children(cs)</span></div> <div class="gmail_extra"><font face="arial, sans-serif"><br></font></div><div class="gmail_extra"><font face="arial, sans-serif">thanks</font></div><div class="gmail_extra"><font face="arial, sans-serif"><br></font></div> <div class="gmail_extra"><font face="arial, sans-serif">josh<br></font><br><div class="gmail_quote">On 2 July 2014 17:45, <span dir="ltr"><<a href="mailto:imp-users-request@salilab.org" target="_blank">imp-users-request@salilab.org</a>></span> wrote:<br> <blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">Send IMP-users mailing list submissions to<br> Â Â Â Â <a href="mailto:imp-users@salilab.org" target="_blank">imp-users@salilab.org</a><br> <br> To subscribe or unsubscribe via the World Wide Web, visit<br> Â Â Â Â <a href="https://salilab.org/mailman/listinfo/imp-users" target="_blank">https://salilab.org/mailman/listinfo/imp-users</a><br> or, via email, send a message with subject or body 'help' to<br> Â Â Â Â <a href="mailto:imp-users-request@salilab.org" target="_blank">imp-users-request@salilab.org</a><br> <br> You can reach the person managing the list at<br> Â Â Â Â <a href="mailto:imp-users-owner@salilab.org" target="_blank">imp-users-owner@salilab.org</a><br> <br> When replying, please edit your Subject line so it is more specific<br> than "Re: Contents of IMP-users digest..."<br> <br> <br> Today's Topics:<br> <br> Â Â 1. Re: Sampling and writing to pym/rmf (Barak Raveh) (Barak Raveh)<br> <br> <br> ----------------------------------------------------------------------<br> <br> Message: 1<br> Date: Wed, 2 Jul 2014 09:45:30 -0700<br> From: Barak Raveh <<a href="mailto:barak.raveh@gmail.com" target="_blank">barak.raveh@gmail.com</a>><br> To: Help and discussion for users of IMP <<a href="mailto:imp-users@salilab.org" target="_blank">imp-users@salilab.org</a>><br> Subject: Re: [IMP-users] Sampling and writing to pym/rmf (Barak Raveh)<br> Message-ID:<br> Â Â Â Â <CAHp+_Uo19VasJDJYi+2CoUUu=<a href="mailto:u_6duKCraVetU4dW45%2BoDhTAw@mail.gmail.com" target="_blank">u_6duKCraVetU4dW45+oDhTAw@mail.gmail.com</a>><br> Content-Type: text/plain; charset="utf-8"<br> <br> Which lines throws the error?<br> <br> <br> On Wed, Jul 2, 2014 at 4:56 AM, Josh Bullock <<a href="mailto:jma.bullock@gmail.com" target="_blank">jma.bullock@gmail.com</a>> wrote:<br> <br> > Hi Barek,<br> ><br> > So I'm not giving hierarchy.get_children the correct input:<br> ><br> > TypeError: unbound method get_children() must be called with Hierarchy<br> > instance as first argument (got ConfigurationSet instance instead)<br> ><br> > I'm not sure which argument is the hierarchy instance.<br> ><br> > Thanks,<br> ><br> > Josh<br> ><br> > -------------------------------------------------<br> ><br> > cs= get_conformations(m)<div><br> ><br> > for i in range(0, cs.get_number_of_configurations()):<br> > Â Â JOSH = cs.load_configuration(i)<br> > Â Â S= IMP.atom.Selection<br> > Â Â h= IMP.atom.Hierarchy.get_children(cs)<br> > Â Â tfn = IMP.create_temporary_file_name("josh%d"%i, ".rmf")<br> > Â Â rh = RMF.create_rmf_file(tfn)<br> ><br></div> > On 1 July 2014 17:31, <<a href="mailto:imp-users-request@salilab.org" target="_blank">imp-users-request@salilab.org</a>> wrote:<br> ><br> >> Send IMP-users mailing list submissions to<br> >> Â Â Â Â <a href="mailto:imp-users@salilab.org" target="_blank">imp-users@salilab.org</a><br> >><br> >> To subscribe or unsubscribe via the World Wide Web, visit<br> >> Â Â Â Â <a href="https://salilab.org/mailman/listinfo/imp-users" target="_blank">https://salilab.org/mailman/listinfo/imp-users</a><br> >> or, via email, send a message with subject or body 'help' to<br> >> Â Â Â Â <a href="mailto:imp-users-request@salilab.org" target="_blank">imp-users-request@salilab.org</a><br> >><br> >> You can reach the person managing the list at<br> >> Â Â Â Â <a href="mailto:imp-users-owner@salilab.org" target="_blank">imp-users-owner@salilab.org</a><br> >><br> >> When replying, please edit your Subject line so it is more specific<br> >> than "Re: Contents of IMP-users digest..."<br> >><br> >><br> >> Today's Topics:<br> >><br> >> Â Â 1. Re: Sampling and writing to pym/rmf (Barak Raveh)<br> >><br> >><br> >> ----------------------------------------------------------------------<br> >><br> >> Message: 1<br> >> Date: Tue, 1 Jul 2014 09:31:33 -0700<br> >> From: Barak Raveh <<a href="mailto:barak.raveh@gmail.com" target="_blank">barak.raveh@gmail.com</a>><br> >> To: Help and discussion for users of IMP <<a href="mailto:imp-users@salilab.org" target="_blank">imp-users@salilab.org</a>><br> >> Subject: Re: [IMP-users] Sampling and writing to pym/rmf<br> >> Message-ID:<br> >> Â Â Â Â <CAHp+_UowiBwJozbwOfi8yFEVt7Z8o2tEZ=<br> >> <a href="mailto:LvYPnJh-LjpC2cSA@mail.gmail.com" target="_blank">LvYPnJh-LjpC2cSA@mail.gmail.com</a>><br> >> Content-Type: text/plain; charset="utf-8"<div><br> >><br> >> Hi Josh, from a very superficial look, your code to write the RMF files<br> >> seems fine - do you get an output RMF file? Could you load it in Chimera?<br> >><br> >><br> >> On Tue, Jul 1, 2014 at 2:40 AM, Josh Bullock <<a href="mailto:jma.bullock@gmail.com" target="_blank">jma.bullock@gmail.com</a>><br> >> wrote:<br> >><br> >> > Hello,<br> >> ><br> >> > I'm relatively new to all this so please let me know if i'm making any<br> >> > obvious errors ...<br> >> ><br></div><div> >> > Essentially all i'm trying to do is generate an ensemble of models made<br> >> > from four subunits - constrained by MS connectivity restraints. The<br> >> models<br> >> > get scored but nothing seems to write to the pymol file. Ideally i'd<br> >> like<br> >> > to write to an .rmf but i haven't worked that one out either ...<br> >> ><br></div><div><div> >> > Is this a reasonable way to go about my problem ?<br> >> ><br> >> > Many thanks,<br> >> ><br> >> > Josh<br> >> ><br> >> > -------------------------------------------<br> >> ><br> >> > import IMP<br> >> > import IMP.atom<br> >> > import IMP.rmf<br> >> > import inspect<br> >> > import IMP.container<br> >> > import IMP.display<br> >> > import IMP.statistics<br> >> > #import IMP.example<br> >> > import sys, math, os, optparse<br> >> > import RMF<br> >> ><br> >> > from optparse import OptionParser<br> >> ><br> >> ><br> >> > # Convert the arguments into strings and number<br> >> > Firstpdb = str(sys.argv[1])<br> >> > Secondpdb = str(sys.argv[2])<br> >> > Thirdpdb = str(sys.argv[3])<br> >> > Fourthpdb = str(sys.argv[4])<br> >> > models = float(sys.argv[5])<br> >> ><br> >> > #*****************************************<br> >> ><br> >> > # the spring constant to use, it doesnt really matter<br> >> > k=100<br> >> > # the target resolution for the representation, this is used to specify<br> >> > how detailed<br> >> > # the representation used should be<br> >> > resolution=300<br> >> > # the box to perform everything<br> >> > bb=IMP.algebra.BoundingBox3D(IMP.algebra.Vector3D(0,0,0),<br> >> > Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â IMP.algebra.Vector3D(300, 300, 300))<br> >> ><br> >> ><br> >> > # this function creates the molecular hierarchies for the various<br> >> involved<br> >> > proteins<br> >> > def create_representation():<br> >> > Â Â m= IMP.Model()<br> >> > Â Â all=IMP.atom.Hierarchy.setup_particle(IMP.Particle(m))<br> >> > Â Â all.set_name("the universe")<br> >> > Â Â # create a protein, represented as a set of connected balls of<br> >> > appropriate<br> >> > Â Â # radii and number, chose by the resolution parameter and the<br> >> number of<br> >> > Â Â # amino acids.<br> >> ><br> >> > Â Â def create_protein_from_pdbs(name, files):<br> >> ><br> >> > Â Â Â Â def create_from_pdb(file):<br> >> > Â Â Â Â Â Â sls=IMP.SetLogState(IMP.NONE)<br> >> > Â Â Â Â Â Â datadir = os.getcwd()<br> >> > Â Â Â Â Â Â print datadir<br> >> > Â Â t=IMP.atom.read_pdb( datadir+'/' + file, m,<br> >> > Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â IMP.atom.ATOMPDBSelector())<br> >> > Â Â Â Â Â Â del sls<br> >> > Â Â Â Â Â Â #IMP.atom.show_molecular_hierarchy(t)<br> >> > Â Â Â Â Â Â c=IMP.atom.Chain(IMP.atom.get_by_type(t,<br> >> > IMP.atom.CHAIN_TYPE)[0])<br> >> > Â Â Â Â Â Â if c.get_number_of_children()==0:<br> >> > Â Â Â Â Â Â Â Â IMP.atom.show_molecular_hierarchy(t)<br> >> > Â Â Â Â Â Â # there is no reason to use all atoms, just approximate the<br> >> > pdb shape instead<br> >> > Â Â Â Â Â Â s=IMP.atom.create_simplified_along_backbone(c,<br> >> ><br> >> resolution/300.0)<br> >> > Â Â Â Â Â Â IMP.atom.destroy(t)<br> >> > Â Â Â Â Â Â # make the simplified structure rigid<br> >> > Â Â Â Â Â Â rb=IMP.atom.create_rigid_body(s)<br> >> > # Â Â Â Â Â Â rb=IMP.atom.create_rigid_body(c)<br> >> > Â Â Â Â Â Â rb.set_coordinates_are_optimized(True)<br> >> > Â Â Â Â Â Â return s<br> >> > # Â Â Â Â Â Â return c<br> >> ><br> >> > Â Â Â Â h= create_from_pdb(files[0])<br> >> > Â Â Â Â h.set_name(name)<br> >> > Â Â Â Â all.add_child(h)<br> >> ><br> >> > Â Â create_protein_from_pdbs("A", [Firstpdb])<br> >> > Â Â create_protein_from_pdbs("B", [Secondpdb])<br> >> > Â Â create_protein_from_pdbs("C", [Thirdpdb])<br> >> > Â Â create_protein_from_pdbs("D", [Fourthpdb])<br> >> > Â Â #create_protein_from_pdbs("C", ["rpt3_imp.pdb"])<br> >> > Â Â return (m, all)<br> >> ><br> >> > # create the needed restraints and add them to the model<br> >> ><br> >> > def create_restraints(m, all):<br> >> > Â Â def add_connectivity_restraint(s):<br> >> ><br> >> > Â Â Â Â tr= IMP.core.TableRefiner()<br> >> > Â Â Â Â rps=[]<br> >> > Â Â Â Â for sc in s:<br> >> > Â Â Â Â Â Â ps= sc.get_selected_particles()<br> >> > Â Â Â Â Â Â rps.append(ps[0])<br> >> > Â Â Â Â Â Â tr.add_particle(ps[0], ps)<br> >> ><br> >> > Â Â Â Â # duplicate the IMP.atom.create_connectivity_restraint<br> >> > functionality<br> >> ><br> >> > Â Â Â Â score=<br> >> ><br> >> IMP.core.KClosePairsPairScore(IMP.core.HarmonicSphereDistancePairScore(0,1),tr)<br> >> ><br> >> > Â Â Â Â r= IMP.core.MSConnectivityRestraint(m,score)<br> >> ><br> >> > Â Â Â Â iA = r.add_type([rps[0]])<br> >> > Â Â Â Â iB = r.add_type([rps[1]])<br> >> > Â Â Â Â iC = r.add_type([rps[2]])<br> >> > Â Â Â Â iD = r.add_type([rps[3]])<br> >> > Â Â Â Â n1 = r.add_composite([iA, iB, iC, iD])<br> >> > Â Â Â Â n2 = r.add_composite([iA, iB], n1)<br> >> > Â Â Â Â n3 = r.add_composite([iC, iD], n1)<br> >> > Â Â Â Â n4 = r.add_composite([iB, iC, iD], n1)<br> >> ><br> >> > Â Â Â Â m.add_restraint(r)<br> >> ><br> >> > Â Â evr=IMP.atom.create_excluded_volume_restraint([all])<br> >> > Â Â m.add_restraint(evr)<br> >> > Â Â # a Selection allows for natural specification of what the<br> >> restraints<br> >> > act on<br> >> > Â Â S= IMP.atom.Selection<br> >> > Â Â sA=S(hierarchy=all, molecule="A")<br> >> > Â Â sB=S(hierarchy=all, molecule="B")<br> >> > Â Â sC=S(hierarchy=all, molecule="C")<br> >> > Â Â sD=S(hierarchy=all, molecule="D")<br> >> > Â Â add_connectivity_restraint([sA, sB, sC, sD])<br> >> ><br> >> ><br> >> > # find acceptable conformations of the model<br> >> > def get_conformations(m):<br> >> > Â Â sampler= IMP.core.MCCGSampler(m)<br> >> > Â Â sampler.set_bounding_box(bb)<br> >> > Â Â # magic numbers, experiment with them and make them large enough for<br> >> > things to work<br> >> > Â Â sampler.set_number_of_conjugate_gradient_steps(100)<br> >> > Â Â sampler.set_number_of_monte_carlo_steps(20)<br> >> > Â Â sampler.set_number_of_attempts(models)<br> >> > Â Â # We don't care to see the output from the sampler<br> >> > Â Â sampler.set_log_level(IMP.SILENT)<br> >> > Â Â # return the IMP.ConfigurationSet storing all the found<br> >> configurations<br> >> > that<br> >> > Â Â # meet the various restraint maximum scores.<br> >> > Â Â cs= sampler.create_sample()<br> >> > Â Â return cs<br> >> ><br> >> ><br> >> > # cluster the conformations and write them to a file<br> >> > def analyze_conformations(cs, all, gs):<br> >> > Â Â # we want to cluster the configurations to make them easier to<br> >> > understand<br> >> > Â Â # in the case, the clustering is pretty meaningless<br> >> > Â Â embed= IMP.statistics.ConfigurationSetXYZEmbedding(cs,<br> >> ><br> >> > Â IMP.container.ListSingletonContainer(IMP.atom.get_leaves(all)), True)<br> >> > Â Â cluster= IMP.statistics.create_lloyds_kmeans(embed, 10, 10000)<br> >> > Â Â # dump each cluster center to a file so it can be viewed.<br> >> > Â Â for i in range(cluster.get_number_of_clusters()):<br> >> > Â Â Â Â center= cluster.get_cluster_center(i)<br> >> > Â Â Â Â cs.load_configuration(i)<br> >> > Â Â Â Â w= IMP.display.PymolWriter("cluster.%d.pym"%i)<br> >> > Â Â Â Â for g in gs:<br> >> > Â Â Â Â Â Â w.add_geometry(g)<br> >> ><br> >> ><br> >> ><br> >> ><br> >> #******************************************************************************************<br> >> > # now do the actual work<br> >> ><br> >> > (m,all)= create_representation()<br> >> > IMP.atom.show_molecular_hierarchy(all)<br> >> > create_restraints(m, all)<br> >> ><br> >> > # in order to display the results, we need something that maps the<br> >> > particles onto<br> >> > # geometric objets. The IMP.display.Geometry objects do this mapping.<br> >> > # IMP.display.XYZRGeometry map an IMP.core.XYZR particle onto a sphere<br> >> > gs=[]<br> >> > for i in range(all.get_number_of_children()):<br> >> > Â Â color= IMP.display.get_display_color(i)<br> >> > Â Â n= all.get_child(i)<br> >> > Â Â name= n.get_name()<br> >> > Â Â g= IMP.atom.HierarchyGeometry(n)<br> >> > Â Â g.set_color(color)<br> >> > Â Â gs.append(g)<br> >> ><br> >> > cs= get_conformations(m)<br> >> ><br> >> > print "found", cs.get_number_of_configurations(), "solutions"<br> >> ><br> >> > ListScores = []<br> >> > for i in range(0, cs.get_number_of_configurations()):<br> >> > Â Â Â Â cs.load_configuration(i)<br> >> > Â Â Â Â # print the configuration<br> >> > Â Â Â Â print "solution number: ",i,"scored :", m.evaluate(False)<br> >> > Â Â Â Â ListScores.append(m.evaluate(False))<br> >> ><br> >> > f1 = open("out_scores.csv", "w")<br> >> > f1.write("\n".join(map(lambda x: str(x), ListScores)))<br> >> > f1.close()<br> >> ><br> >> > # for each of the configuration, dump it to a file to view in pymol<br> >> > for i in range(0, cs.get_number_of_configurations()):<br> >> > Â Â JOSH = cs.load_configuration(i)<br> >> > Â Â S= IMP.atom.Selection<br> >> > Â Â h= IMP.atom.Hierarchy.get_children(cs)<br> >> > Â Â tfn = IMP.create_temporary_file_name("josh%d"%i, ".rmf")<br> >> > Â Â rh = RMF.create_rmf_file(tfn)<br> >> ><br> >> > Â Â # add the hierarchy to the file<br> >> > Â Â IMP.rmf.add_hierarchies(rh, h)<br> >> ><br> >> > Â Â # add the current configuration to the file as frame 0<br> >> > Â Â IMP.rmf.save_frame(rh)<br> >> ><br> >> > Â Â for g in gs:<br> >> > Â Â Â Â w.add_geometry(g)<br> >> ><br> >> > analyze_conformations(cs, all, gs)<br> >> ><br> >> ><br></div></div><div> >> > _______________________________________________<br> >> > IMP-users mailing list<br> >> > <a href="mailto:IMP-users@salilab.org" target="_blank">IMP-users@salilab.org</a><br> >> > <a href="https://salilab.org/mailman/listinfo/imp-users" target="_blank">https://salilab.org/mailman/listinfo/imp-users</a><br> >> ><br> >> ><br> >><br> >><br></div> >> --<br> >> Barak<br> >> -------------- next part --------------<br> >> An HTML attachment was scrubbed...<br> >> URL: <<br> >> <a href="http://salilab.org/archives/imp-users/attachments/20140701/7b0e5f9f/attachment.html" target="_blank">http://salilab.org/archives/imp-users/attachments/20140701/7b0e5f9f/attachment.html</a><br> >> ><br> >><br> >> ------------------------------<div><br> >><br> >> _______________________________________________<br> >> IMP-users mailing list<br> >> <a href="mailto:IMP-users@salilab.org" target="_blank">IMP-users@salilab.org</a><br> >> <a href="https://salilab.org/mailman/listinfo/imp-users" target="_blank">https://salilab.org/mailman/listinfo/imp-users</a><br> >><br> >><br></div> >> End of IMP-users Digest, Vol 38, Issue 2<br> >> ****************************************<div><br> >><br> ><br> ><br> > _______________________________________________<br> > IMP-users mailing list<br> > <a href="mailto:IMP-users@salilab.org" target="_blank">IMP-users@salilab.org</a><br> > <a href="https://salilab.org/mailman/listinfo/imp-users" target="_blank">https://salilab.org/mailman/listinfo/imp-users</a><br> ><br> ><br> <br> <br></div> --<br> Barak<br> -------------- next part --------------<br> An HTML attachment was scrubbed...<br> URL: <<a href="http://salilab.org/archives/imp-users/attachments/20140702/081e70ca/attachment.html" target="_blank">http://salilab.org/archives/imp-users/attachments/20140702/081e70ca/attachment.html</a>><br> <br> ------------------------------<div><br> <br> _______________________________________________<br> IMP-users mailing list<br> <a href="mailto:IMP-users@salilab.org" target="_blank">IMP-users@salilab.org</a><br> <a href="https://salilab.org/mailman/listinfo/imp-users" target="_blank">https://salilab.org/mailman/listinfo/imp-users</a><br> <br> <br></div> End of IMP-users Digest, Vol 38, Issue 4<br> ****************************************<br> </blockquote></div><br></div></div> <br>_______________________________________________<br> IMP-users mailing list<br> <a href="mailto:IMP-users@salilab.org" target="_blank">IMP-users@salilab.org</a><br> <a href="https://salilab.org/mailman/listinfo/imp-users" target="_blank">https://salilab.org/mailman/listinfo/imp-users</a><br> <br></blockquote></div><br><br clear="all"><div><br></div>-- <br>Barak </div></div></div></div></div></div></div> </blockquote></div><br><br clear="all"><div><br></div>-- <br>Barak </div>