* I meant

h = IMP.atom.Hierarchy(p) c = p.get_children(h)

this assumes that particle p was already decorated as Hierarchy (let me know if you are not familiar with decorators, Hierarchy, or Particle).

On Wed, Jul 2, 2014 at 3:02 PM, Barak Raveh barak.raveh@gmail.com wrote:

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