Re: [IMP-users] Sampling and writing to pym/rmf (Barak Raveh) - IMP-users

3 Jul 2014


      aha okay, so now i'm generating .rmf files however when trying to open them
in chimera I get the following error:
"Invalid handle returned from H5Fopen(name.c_str(), H5F_ACC_RDONLY, plist)"
in file "
I'm not sure whether this is because I've created empty .rmf files or
something else is wrong ...
the code for making the rmf files:
for i in range(0, cs.get_number_of_configurations()):
    cs.load_configuration(i)
    h = IMP.atom.Hierarchy.get_children(all)
    tfn = IMP.create_temporary_file_name("josh%d"%i, ".rmf")
    print "file is", tfn
    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)
On 3 July 2014 00:20, imp-users-request@salilab.org wrote:
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> Today's Topics:
>
>    1. Re: Sampling and writing to pym/rmf (Barak Raveh)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 2 Jul 2014 16:20:19 -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+_Uoq-HAyca9AX_pFcEje32ke3J3KuKZWYfuj+M8SZWUkCw@mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hi Josh,
>
> An IMP model contains a list of particles that are tightly associated with
> it (a particle does not exist outside the context of a model). Given the
> disclaimer that I have never used ConfigurationSet, my understanding from
> its documentation is that when you load a configuration, the values of the
> particles within the model are updated accordingly. If I understand your
> code correctly, 'all' is the root of the hierarchy in your model, so it is
> 'all' that you should add to the rmf. The values of 'all' and all of its
> children are supposed to update when you load a configuration,
> automatically.
>
> All that being said said - use this advice at own risk, perhaps someone
> could advise you better. Let me know if you have more questions.
>
> Barak
>
>
> On Wed, Jul 2, 2014 at 3:42 PM, Josh Bullock jma.bullock@gmail.com
> wrote:
>
> >
> >
> > Conceptually I do ( i think ... ) but not practically. I'm hoping to view
> > each of the models i created - with MSrestraints - separately as an .rmf
> in
> > chimera, just so i can see what i'm making !
> >
> > so i have created my models using:
> >
> > cs= get_conformations(m)
> >
> > do i have to assign each model to a particle before i can write it to an
> > .rmf ? Or is each model already a particle with hierarchy ?
> >
> > -------------------------------------------
> >
> > for i in range(0, cs.get_number_of_configurations()):
> >     cs.load_configuration(i)
> >     h = IMP.atom.Hierarchy(m)    # <------- how do i call the hierarchy
> of
> > the current loaded configuration ?
> >     c = p.get_children(h)
> >      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)
> >
> > On 2 July 2014 23:03, imp-users-request@salilab.org wrote:
> >
> >> Send IMP-users mailing list submissions to
> >>         imp-users@salilab.org
> >>
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> >>         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: Wed, 2 Jul 2014 15:03:19 -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+_UqO8rXRMsUSndbg-c0jyDxnswDe9aFKvW889gGMU=
> >> 4MMQ@mail.gmail.com>
> >> Content-Type: text/plain; charset="utf-8"
> >>
> >>
> >> * 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
> >> >>> >>