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Today's Topics:
 Â1. Re: Sampling and writing to pym/rmf (Barak Raveh) (Josh Bullock)
----------------------------------------------------------------------
Message: 1
Date: Thu, 3 Jul 2014 16:25:53 +0100
From: Josh Bullock <">>
To: ">
Subject: Re: [IMP-users] Sampling and writing to pym/rmf (Barak Raveh)
Message-ID:
    <">>
Content-Type: text/plain; charset="utf-8"
so this is what is looks like with rmf_show:
https://gist.github.com/mysticvision/271d973806603967fd31
i'll email you the rmf now.
thanks !
On 3 July 2014 14:28, <">> wrote:
> Send IMP-users mailing list submissions to
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>
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> or, via email, send a message with subject or body 'help' to
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>
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>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of IMP-users digest..."
>
>
> Today's Topics:
>
> Â Â1. Re: Sampling and writing to pym/rmf (Josh Bullock) (Barak Raveh)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 3 Jul 2014 06:27:55 -0700
> From: Barak Raveh <">>
> To: Help and discussion for users of IMP <">>
> Subject: Re: [IMP-users] Sampling and writing to pym/rmf (Josh
> Â Â Â Â Bullock)
> Message-ID:
> Â Â Â Â <
> ">CAHp+>
> Content-Type: text/plain; charset="utf-8"
>
> You can use rmf_show and rmf_show -v to view your file in human readable
> format
> http://integrativemodeling.org/rmf/nightly/doc/executables.html
>
> About chimera, are you using a latest nightly build? You can send me the
> RMF file and I'll give a look to see if it depends on the chimera version.
>
> Barak
>
>
> On Thu, Jul 3, 2014 at 5:55 AM, Josh Bullock <">>
> wrote:
>
> > oh so there is something in the .rmf file, looks a bit garbled though ...
> > is this normal ?
> >
> > https://gist.github.com/mysticvision/271d973806603967fd31
> >
> >
> > On 3 July 2014 13:44, <">> wrote:
> >
> >> Send IMP-users mailing list submissions to
> >> Â Â Â Â ">
> >>
> >> To subscribe or unsubscribe via the World Wide Web, visit
> >> Â Â Â Â https://salilab.org/mailman/listinfo/imp-users
> >> or, via email, send a message with subject or body 'help' to
> >> Â Â Â Â ">
> >>
> >> You can reach the person managing the list at
> >> Â Â Â Â ">
> >>
> >> When replying, please edit your Subject line so it is more specific
> >> than "Re: Contents of IMP-users digest..."
> >>
> >>
> >> Today's Topics:
> >>
> >> Â Â1. Re: Sampling and writing to pym/rmf (Barak Raveh) (Josh Bullock)
> >>
> >>
> >> ----------------------------------------------------------------------
> >>
> >> Message: 1
> >> Date: Thu, 3 Jul 2014 13:44:22 +0100
> >> From: Josh Bullock <">>
> >> To: ">
> >> Subject: Re: [IMP-users] Sampling and writing to pym/rmf (Barak Raveh)
> >> Message-ID:
> >> Â Â Â Â <CAHh_40_zsUCt4=
> >> ">nZbvDRd0owHzz_v_DHEiB-R+>
> >> Content-Type: text/plain; charset="utf-8"
> >>
> >> 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()):
> >> Â Â cs.load_configuration(i)
> >> Â Â h = IMP.atom.Hierarchy.get_children(all)
> >> Â Â tfn = IMP.create_temporary_file_name("josh%d"%i, ".rmf")
> >> Â Â print "file is", tfn
> >> Â Â rh = RMF.create_rmf_file(tfn)
> >>
> >> Â Â # add the hierarchy to the file
> >> Â Â IMP.rmf.add_hierarchies(rh, h)
> >>
> >> Â Â # add the current configuration to the file as frame 0
> >> Â Â IMP.rmf.save_frame(rh)
> >>
> >>
> >> On 3 July 2014 00:20, <">> wrote:
> >>
> >> > Send IMP-users mailing list submissions to
> >> > Â Â Â Â ">
> >> >
> >> > To subscribe or unsubscribe via the World Wide Web, visit
> >> > Â Â Â Â https://salilab.org/mailman/listinfo/imp-users
> >> > or, via email, send a message with subject or body 'help' to
> >> > Â Â Â Â ">
> >> >
> >> > You can reach the person managing the list at
> >> > Â Â Â Â ">
> >> >
> >> > When replying, please edit your Subject line so it is more specific
> >> > than "Re: Contents of IMP-users digest..."
> >> >
> >> >
> >> > Today's Topics:
> >> >
> >> > Â Â1. Re: Sampling and writing to pym/rmf (Barak Raveh)
> >> >
> >> >
> >> > ----------------------------------------------------------------------
> >> >
> >> > Message: 1
> >> > Date: Wed, 2 Jul 2014 16:20:19 -0700
> >> > From: Barak Raveh <">>
> >> > To: Help and discussion for users of IMP <">>
> >> > Subject: Re: [IMP-users] Sampling and writing to pym/rmf
> >> > Message-ID:
> >> > Â Â Â Â <
> >> > ">CAHp+_Uoq-HAyca9AX_pFcEje32ke3J3KuKZWYfuj+>
> >> > 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 <">>
> >> > 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()):
> >> > > Â Â cs.load_configuration(i)
> >> > > Â Â h = IMP.atom.Hierarchy(m) Â Â# <------- how do i call the
> >> hierarchy
> >> > of
> >> > > the current loaded configuration ?
> >> > > Â Â c = p.get_children(h)
> >> > > Â Â Âtfn = IMP.create_temporary_file_name("josh%d"%i, ".rmf")
> >> > > Â Â rh = RMF.create_rmf_file(tfn)
> >> > >
> >> > > Â Â # add the hierarchy to the file
> >> > > Â Â IMP.rmf.add_hierarchies(rh, h)
> >> > >
> >> > > Â Â # add the current configuration to the file as frame 0
> >> > > Â Â IMP.rmf.save_frame(rh)
> >> > >
> >> > > On 2 July 2014 23:03, <">> wrote:
> >> > >
> >> > >> Send IMP-users mailing list submissions to
> >> > >> Â Â Â Â ">
> >> > >>
> >> > >> To subscribe or unsubscribe via the World Wide Web, visit
> >> > >> Â Â Â Â https://salilab.org/mailman/listinfo/imp-users
> >> > >> or, via email, send a message with subject or body 'help' to
> >> > >> Â Â Â Â ">
> >> > >>
> >> > >> You can reach the person managing the list at
> >> > >> Â Â Â Â ">
> >> > >>
> >> > >> When replying, please edit your Subject line so it is more specific
> >> > >> than "Re: Contents of IMP-users digest..."
> >> > >>
> >> > >>
> >> > >> Today's Topics:
> >> > >>
> >> > >> Â Â1. Re: Sampling and writing to pym/rmf (Barak Raveh)
> >> > >>
> >> > >>
> >> > >>
> >> ----------------------------------------------------------------------
> >> > >>
> >> > >> Message: 1
> >> > >> Date: Wed, 2 Jul 2014 15:03:19 -0700
> >> > >>
> >> > >> From: Barak Raveh <">>
> >> > >> To: Help and discussion for users of IMP <">>
> >> > >> Subject: Re: [IMP-users] Sampling and writing to pym/rmf
> >> > >> Message-ID:
> >> > >> Â Â Â Â <CAHp+_UqO8rXRMsUSndbg-c0jyDxnswDe9aFKvW889gGMU=
> >> > >> ">>
> >> > >> 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 <">
> >
> >> > >> 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 <
> >> ">>
> >> > >> > wrote:
> >> > >> >
> >> > >> >> ah sorry ! this line gives me the error
> >> > >> >>
> >> > >> >> h= IMP.atom.Hierarchy.get_children(cs)
> >> > >> >>
> >> > >> >> thanks
> >> > >> >>
> >> > >> >> josh
> >> > >> >>
> >> > >> >> On 2 July 2014 17:45, <">> wrote:
> >> > >> >>
> >> > >> >>> Send IMP-users mailing list submissions to
> >> > >> >>> Â Â Â Â ">
> >> > >> >>>
> >> > >> >>> To subscribe or unsubscribe via the World Wide Web, visit
> >> > >> >>> Â Â Â Â https://salilab.org/mailman/listinfo/imp-users
> >> > >> >>> or, via email, send a message with subject or body 'help' to
> >> > >> >>> Â Â Â Â ">
> >> > >> >>>
> >> > >> >>> You can reach the person managing the list at
> >> > >> >>> Â Â Â Â ">
> >> > >> >>>
> >> > >> >>> When replying, please edit your Subject line so it is more
> >> specific
> >> > >> >>> than "Re: Contents of IMP-users digest..."
> >> > >> >>>
> >> > >> >>>
> >> > >> >>> Today's Topics:
> >> > >> >>>
> >> > >> >>> Â Â1. 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 <">>
> >> > >> >>> To: Help and discussion for users of IMP <
> ">>
> >> > >> >>> Subject: Re: [IMP-users] Sampling and writing to pym/rmf (Barak
> >> > Raveh)
> >> > >> >>> Message-ID:
> >> > >> >>> Â Â Â Â <CAHp+_Uo19VasJDJYi+2CoUUu=
> >> > >> >>> ">u_6duKCraVetU4dW45+>
> >> > >> >>> Content-Type: text/plain; charset="utf-8"
> >> > >> >>>
> >> > >> >>> Which lines throws the error?
> >> > >> >>>
> >> > >> >>>
> >> > >> >>> On Wed, Jul 2, 2014 at 4:56 AM, Josh Bullock <
> >> ">
> >> > >
> >> > >> >>> 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()):
> >> > >> >>> > Â Â JOSH = cs.load_configuration(i)
> >> > >> >>> > Â Â S= IMP.atom.Selection
> >> > >> >>> > Â Â h= IMP.atom.Hierarchy.get_children(cs)
> >> > >> >>> > Â Â tfn = IMP.create_temporary_file_name("josh%d"%i, ".rmf")
> >> > >> >>> > Â Â rh = RMF.create_rmf_file(tfn)
> >> > >> >>> >
> >> > >> >>> > On 1 July 2014 17:31, <">> wrote:
> >> > >> >>> >
> >> > >> >>> >> Send IMP-users mailing list submissions to
> >> > >> >>> >> Â Â Â Â ">
> >> > >> >>> >>
> >> > >> >>> >> To subscribe or unsubscribe via the World Wide Web, visit
> >> > >> >>> >> Â Â Â Â https://salilab.org/mailman/listinfo/imp-users
> >> > >> >>> >> or, via email, send a message with subject or body 'help' to
> >> > >> >>> >> Â Â Â Â ">
> >> > >> >>> >>
> >> > >> >>> >> You can reach the person managing the list at
> >> > >> >>> >> Â Â Â Â ">
> >> > >> >>> >>
> >> > >> >>> >> When replying, please edit your Subject line so it is more
> >> > specific
> >> > >> >>> >> than "Re: Contents of IMP-users digest..."
> >> > >> >>> >>
> >> > >> >>> >>
> >> > >> >>> >> Today's Topics:
> >> > >> >>> >>
> >> > >> >>> >> Â Â1. Re: Sampling and writing to pym/rmf (Barak Raveh)
> >> > >> >>> >>
> >> > >> >>> >>
> >> > >> >>> >>
> >> > >>
> >> ----------------------------------------------------------------------
> >> > >> >>> >>
> >> > >> >>> >> Message: 1
> >> > >> >>> >> Date: Tue, 1 Jul 2014 09:31:33 -0700
> >> > >> >>> >> From: Barak Raveh <">>
> >> > >> >>> >> To: Help and discussion for users of IMP <
> >> ">>
> >> > >> >>> >> Subject: Re: [IMP-users] Sampling and writing to pym/rmf
> >> > >> >>> >> Message-ID:
> >> > >> >>> >> Â Â Â Â <CAHp+_UowiBwJozbwOfi8yFEVt7Z8o2tEZ=
> >> > >> >>> >> ">>
> >> > >> >>> >> 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 <
> >> > >> ">>
> >> > >> >>> >> 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),
> >> > >> >>> >> > Â Â Â Â Â Â Â Â Â Â Â Â Â Â ÂIMP.algebra.Vector3D(300,
> 300,
> >> > 300))
> >> > >> >>> >> >
> >> > >> >>> >> >
> >> > >> >>> >> > # this function creates the molecular hierarchies for the
> >> > various
> >> > >> >>> >> involved
> >> > >> >>> >> > proteins
> >> > >> >>> >> > def create_representation():
> >> > >> >>> >> > Â Â m= IMP.Model()
> >> > >> >>> >> > Â Â all=IMP.atom.Hierarchy.setup_particle(IMP.Particle(m))
> >> > >> >>> >> > Â Â all.set_name("the universe")
> >> > >> >>> >> > Â Â # create a protein, represented as a set of connected
> >> balls
> >> > >> of
> >> > >> >>> >> > appropriate
> >> > >> >>> >> > Â Â # radii and number, chose by the resolution parameter
> >> and
> >> > the
> >> > >> >>> >> number of
> >> > >> >>> >> > Â Â # amino acids.
> >> > >> >>> >> >
> >> > >> >>> >> > Â Â def create_protein_from_pdbs(name, files):
> >> > >> >>> >> >
> >> > >> >>> >> > Â Â Â Â def create_from_pdb(file):
> >> > >> >>> >> > Â Â Â Â Â Â sls=IMP.SetLogState(IMP.NONE)
> >> > >> >>> >> > Â Â Â Â Â Â datadir = os.getcwd()
> >> > >> >>> >> > Â Â Â Â Â Â print datadir
> >> > >> >>> >> > Â Â t=IMP.atom.read_pdb( datadir+'/' + file, m,
> >> > >> >>> >> >
> ÂIMP.atom.ATOMPDBSelector())
> >> > >> >>> >> > Â Â Â Â Â Â del sls
> >> > >> >>> >> > Â Â Â Â Â Â #IMP.atom.show_molecular_hierarchy(t)
> >> > >> >>> >> > Â Â Â Â Â Â c=IMP.atom.Chain(IMP.atom.get_by_type(t,
> >> > >> >>> >> > IMP.atom.CHAIN_TYPE)[0])
> >> > >> >>> >> > Â Â Â Â Â Â if c.get_number_of_children()==0:
> >> > >> >>> >> > Â Â Â Â Â Â Â Â IMP.atom.show_molecular_hierarchy(t)
> >> > >> >>> >> > Â Â Â Â Â Â # there is no reason to use all atoms, just
> >> > >> approximate
> >> > >> >>> the
> >> > >> >>> >> > pdb shape instead
> >> > >> >>> >> > Â Â Â Â Â Â s=IMP.atom.create_simplified_along_backbone(c,
> >> > >> >>> >> >
> >> > >> >>> >> resolution/300.0)
> >> > >> >>> >> > Â Â Â Â Â Â IMP.atom.destroy(t)
> >> > >> >>> >> > Â Â Â Â Â Â # make the simplified structure rigid
> >> > >> >>> >> > Â Â Â Â Â Â rb=IMP.atom.create_rigid_body(s)
> >> > >> >>> >> > # Â Â Â Â Â Ârb=IMP.atom.create_rigid_body(c)
> >> > >> >>> >> > Â Â Â Â Â Â rb.set_coordinates_are_optimized(True)
> >> > >> >>> >> > Â Â Â Â Â Â return s
> >> > >> >>> >> > # Â Â Â Â Â Âreturn c
> >> > >> >>> >> >
> >> > >> >>> >> > Â Â Â Â h= create_from_pdb(files[0])
> >> > >> >>> >> > Â Â Â Â h.set_name(name)
> >> > >> >>> >> > Â Â Â Â all.add_child(h)
> >> > >> >>> >> >
> >> > >> >>> >> > Â Â create_protein_from_pdbs("A", [Firstpdb])
> >> > >> >>> >> > Â Â create_protein_from_pdbs("B", [Secondpdb])
> >> > >> >>> >> > Â Â create_protein_from_pdbs("C", [Thirdpdb])
> >> > >> >>> >> > Â Â create_protein_from_pdbs("D", [Fourthpdb])
> >> > >> >>> >> > Â Â #create_protein_from_pdbs("C", ["rpt3_imp.pdb"])
> >> > >> >>> >> > Â Â return (m, all)
> >> > >> >>> >> >
> >> > >> >>> >> > # create the needed restraints and add them to the model
> >> > >> >>> >> >
> >> > >> >>> >> > def create_restraints(m, all):
> >> > >> >>> >> > Â Â def add_connectivity_restraint(s):
> >> > >> >>> >> >
> >> > >> >>> >> > Â Â Â Â tr= IMP.core.TableRefiner()
> >> > >> >>> >> > Â Â Â Â rps=[]
> >> > >> >>> >> > Â Â Â Â for sc in s:
> >> > >> >>> >> > Â Â Â Â Â Â ps= sc.get_selected_particles()
> >> > >> >>> >> > Â Â Â Â Â Â rps.append(ps[0])
> >> > >> >>> >> > Â Â Â Â Â Â tr.add_particle(ps[0], ps)
> >> > >> >>> >> >
> >> > >> >>> >> > Â Â Â Â # duplicate the
> >> IMP.atom.create_connectivity_restraint
> >> > >> >>> >> > functionality
> >> > >> >>> >> >
> >> > >> >>> >> > Â Â Â Â score=
> >> > >> >>> >> >
> >> > >> >>> >>
> >> > >> >>>
> >> > >>
> >> >
> >>
> IMP.core.KClosePairsPairScore(IMP.core.HarmonicSphereDistancePairScore(0,1),tr)
> >> > >> >>> >> >
> >> > >> >>> >> > Â Â Â Â r= IMP.core.MSConnectivityRestraint(m,score)
> >> > >> >>> >> >
> >> > >> >>> >> > Â Â Â Â iA = r.add_type([rps[0]])
> >> > >> >>> >> > Â Â Â Â iB = r.add_type([rps[1]])
> >> > >> >>> >> > Â Â Â Â iC = r.add_type([rps[2]])
> >> > >> >>> >> > Â Â Â Â iD = r.add_type([rps[3]])
> >> > >> >>> >> > Â Â Â Â n1 = r.add_composite([iA, iB, iC, iD])
> >> > >> >>> >> > Â Â Â Â n2 = r.add_composite([iA, iB], n1)
> >> > >> >>> >> > Â Â Â Â n3 = r.add_composite([iC, iD], n1)
> >> > >> >>> >> > Â Â Â Â n4 = r.add_composite([iB, iC, iD], n1)
> >> > >> >>> >> >
> >> > >> >>> >> > Â Â Â Â m.add_restraint(r)
> >> > >> >>> >> >
> >> > >> >>> >> > Â Â evr=IMP.atom.create_excluded_volume_restraint([all])
> >> > >> >>> >> > Â Â m.add_restraint(evr)
> >> > >> >>> >> > Â Â # a Selection allows for natural specification of what
> >> the
> >> > >> >>> >> restraints
> >> > >> >>> >> > act on
> >> > >> >>> >> > Â Â S= IMP.atom.Selection
> >> > >> >>> >> > Â Â sA=S(hierarchy=all, molecule="A")
> >> > >> >>> >> > Â Â sB=S(hierarchy=all, molecule="B")
> >> > >> >>> >> > Â Â sC=S(hierarchy=all, molecule="C")
> >> > >> >>> >> > Â Â sD=S(hierarchy=all, molecule="D")
> >> > >> >>> >> > Â Â add_connectivity_restraint([sA, sB, sC, sD])
> >> > >> >>> >> >
> >> > >> >>> >> >
> >> > >> >>> >> > # find acceptable conformations of the model
> >> > >> >>> >> > def get_conformations(m):
> >> > >> >>> >> > Â Â sampler= IMP.core.MCCGSampler(m)
> >> > >> >>> >> > Â Â sampler.set_bounding_box(bb)
> >> > >> >>> >> > Â Â # magic numbers, experiment with them and make them
> >> large
> >> > >> >>> enough for
> >> > >> >>> >> > things to work
> >> > >> >>> >> > Â Â sampler.set_number_of_conjugate_gradient_steps(100)
> >> > >> >>> >> > Â Â sampler.set_number_of_monte_carlo_steps(20)
> >> > >> >>> >> > Â Â sampler.set_number_of_attempts(models)
> >> > >> >>> >> > Â Â # We don't care to see the output from the sampler
> >> > >> >>> >> > Â Â sampler.set_log_level(IMP.SILENT)
> >> > >> >>> >> > Â Â # return the IMP.ConfigurationSet storing all the
> found
> >> > >> >>> >> configurations
> >> > >> >>> >> > that
> >> > >> >>> >> > Â Â # meet the various restraint maximum scores.
> >> > >> >>> >> > Â Â cs= sampler.create_sample()
> >> > >> >>> >> > Â Â return cs
> >> > >> >>> >> >
> >> > >> >>> >> >
> >> > >> >>> >> > # cluster the conformations and write them to a file
> >> > >> >>> >> > def analyze_conformations(cs, all, gs):
> >> > >> >>> >> > Â Â # we want to cluster the configurations to make them
> >> easier
> >> > >> to
> >> > >> >>> >> > understand
> >> > >> >>> >> > Â Â # in the case, the clustering is pretty meaningless
> >> > >> >>> >> > Â Â embed= IMP.statistics.ConfigurationSetXYZEmbedding(cs,
> >> > >> >>> >> >
> >> > >> >>> >> >
> >> > ÂIMP.container.ListSingletonContainer(IMP.atom.get_leaves(all)),
> >> > >> >>> True)
> >> > >> >>> >> > Â Â cluster= IMP.statistics.create_lloyds_kmeans(embed,
> 10,
> >> > >> 10000)
> >> > >> >>> >> > Â Â # dump each cluster center to a file so it can be
> >> viewed.
> >> > >> >>> >> > Â Â for i in range(cluster.get_number_of_clusters()):
> >> > >> >>> >> > Â Â Â Â center= cluster.get_cluster_center(i)
> >> > >> >>> >> > Â Â Â Â cs.load_configuration(i)
> >> > >> >>> >> > Â Â Â Â w= IMP.display.PymolWriter("cluster.%d.pym"%i)
> >> > >> >>> >> > Â Â Â Â for g in gs:
> >> > >> >>> >> > Â Â Â Â Â Â 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()):
> >> > >> >>> >> > Â Â color= IMP.display.get_display_color(i)
> >> > >> >>> >> > Â Â n= all.get_child(i)
> >> > >> >>> >> > Â Â name= n.get_name()
> >> > >> >>> >> > Â Â g= IMP.atom.HierarchyGeometry(n)
> >> > >> >>> >> > Â Â g.set_color(color)
> >> > >> >>> >> > Â Â 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()):
> >> > >> >>> >> > Â Â Â Â cs.load_configuration(i)
> >> > >> >>> >> > Â Â Â Â # print the configuration
> >> > >> >>> >> > Â Â Â Â print "solution number: ",i,"scored :",
> >> > m.evaluate(False)
> >> > >> >>> >> > Â Â Â Â 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()):
> >> > >> >>> >> > Â Â JOSH = cs.load_configuration(i)
> >> > >> >>> >> > Â Â S= IMP.atom.Selection
> >> > >> >>> >> > Â Â h= IMP.atom.Hierarchy.get_children(cs)
> >> > >> >>> >> > Â Â tfn = IMP.create_temporary_file_name("josh%d"%i,
> ".rmf")
> >> > >> >>> >> > Â Â rh = RMF.create_rmf_file(tfn)
> >> > >> >>> >> >
> >> > >> >>> >> > Â Â # add the hierarchy to the file
> >> > >> >>> >> > Â Â IMP.rmf.add_hierarchies(rh, h)
> >> > >> >>> >> >
> >> > >> >>> >> > Â Â # add the current configuration to the file as frame 0
> >> > >> >>> >> > Â Â IMP.rmf.save_frame(rh)
> >> > >> >>> >> >
> >> > >> >>> >> > Â Â for g in gs:
> >> > >> >>> >> > Â Â Â Â w.add_geometry(g)
> >> > >> >>> >> >
> >> > >> >>> >> > analyze_conformations(cs, all, gs)
> >> > >> >>> >> >
> >> > >> >>> >> >
> >> > >> >>> >> > _______________________________________________
> >> > >> >>> >> > IMP-users mailing list
> >> > >> >>> >> > ">
> >> > >> >>> >> > https://salilab.org/mailman/listinfo/imp-users
> >> > >> >>> >> >
> >> > >> >>> >> >
> >> > >> >>> >>
> >> > >> >>> >>
> >> > >> >>> >> --
> >> > >> >>> >> Barak
> >> > >> >>> >> -------------- next part --------------
> >> > >> >>> >> An HTML attachment was scrubbed...
> >> > >> >>> >> URL: <
> >> > >> >>> >>
> >> > >> >>>
> >> > >>
> >> >
> >>
> http://salilab.org/archives/imp-users/attachments/20140701/7b0e5f9f/attachment.html
> >> > >> >>> >> >
> >> > >> >>> >>
> >> > >> >>> >> ------------------------------
> >> > >> >>>
> >> > >> >>> >>
> >> > >> >>> >> _______________________________________________
> >> > >> >>> >> IMP-users mailing list
> >> > >> >>> >> ">
> >> > >> >>> >> https://salilab.org/mailman/listinfo/imp-users
> >> > >> >>> >>
> >> > >> >>> >>
> >> > >> >>> >> End of IMP-users Digest, Vol 38, Issue 2
> >> > >> >>> >> ****************************************
> >> > >> >>>
> >> > >> >>> >>
> >> > >> >>> >
> >> > >> >>> >
> >> > >> >>> > _______________________________________________
> >> > >> >>> > IMP-users mailing list
> >> > >> >>> > ">
> >> > >> >>> > https://salilab.org/mailman/listinfo/imp-users
> >> > >> >>> >
> >> > >> >>> >
> >> > >> >>>
> >> > >> >>>
> >> > >> >>> --
> >> > >> >>> Barak
> >> > >> >>> -------------- next part --------------
> >> > >> >>> An HTML attachment was scrubbed...
> >> > >> >>> URL: <
> >> > >> >>>
> >> > >>
> >> >
> >>
> http://salilab.org/archives/imp-users/attachments/20140702/081e70ca/attachment.html
> >> > >> >>> >
> >> > >> >>>
> >> > >> >>> ------------------------------
> >> > >> >>>
> >> > >> >>>
> >> > >> >>> _______________________________________________
> >> > >> >>> IMP-users mailing list
> >> > >> >>> ">
> >> > >> >>> https://salilab.org/mailman/listinfo/imp-users
> >> > >> >>>
> >> > >> >>>
> >> > >> >>> End of IMP-users Digest, Vol 38, Issue 4
> >> > >> >>> ****************************************
> >> > >> >>>
> >> > >> >>
> >> > >> >>
> >> > >> >> _______________________________________________
> >> > >> >> IMP-users mailing list
> >> > >> >> ">
> >> > >> >> https://salilab.org/mailman/listinfo/imp-users
> >> > >> >>
> >> > >> >>
> >> > >> >
> >> > >> >
> >> > >> > --
> >> > >> > Barak
> >> > >> >
> >> > >>
> >> > >>
> >> > >>
> >> > >> --
> >> > >> Barak
> >> > >> -------------- next part --------------
> >> > >> An HTML attachment was scrubbed...
> >> > >> URL: <
> >> > >>
> >> >
> >>
> http://salilab.org/archives/imp-users/attachments/20140702/74f552a1/attachment.html
> >> > >> >
> >> > >>
> >> > >>
> >> > >> ------------------------------
> >> > >>
> >> > >> _______________________________________________
> >> > >> IMP-users mailing list
> >> > >> ">
> >> > >> https://salilab.org/mailman/listinfo/imp-users
> >> > >>
> >> > >>
> >> > >> End of IMP-users Digest, Vol 38, Issue 7
> >> > >> ****************************************
> >> > >>
> >> > >
> >> > >
> >> > > _______________________________________________
> >> > > IMP-users mailing list
> >> > > ">
> >> > > https://salilab.org/mailman/listinfo/imp-users
> >> > >
> >> > >
> >> >
> >> >
> >> > --
> >> > Barak
> >> > -------------- next part --------------
> >> > An HTML attachment was scrubbed...
> >> > URL: <
> >> >
> >>
> http://salilab.org/archives/imp-users/attachments/20140702/2f1fb30c/attachment.html
> >> > >
> >> >
> >> > ------------------------------
> >> >
> >> > _______________________________________________
> >> > IMP-users mailing list
> >> > ">
> >> > https://salilab.org/mailman/listinfo/imp-users
> >> >
> >> >
> >> > End of IMP-users Digest, Vol 38, Issue 9
> >> > ****************************************
> >> >
> >> -------------- next part --------------
> >> An HTML attachment was scrubbed...
> >> URL: <
> >>
> http://salilab.org/archives/imp-users/attachments/20140703/fe3a183b/attachment.html
> >> >
> >>
> >> ------------------------------
> >>
> >> _______________________________________________
> >> IMP-users mailing list
> >> ">
> >> https://salilab.org/mailman/listinfo/imp-users
> >>
> >>
> >> End of IMP-users Digest, Vol 38, Issue 10
> >> *****************************************
> >>
> >
> >
> > _______________________________________________
> > IMP-users mailing list
> > ">
> > https://salilab.org/mailman/listinfo/imp-users
> >
> >
>
>
> --
> Barak
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL: <
> http://salilab.org/archives/imp-users/attachments/20140703/ebc4da96/attachment.html
> >
>
> ------------------------------
>
> _______________________________________________
> IMP-users mailing list
> ">
> https://salilab.org/mailman/listinfo/imp-users
>
>
> End of IMP-users Digest, Vol 38, Issue 12
> *****************************************
>
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_______________________________________________
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">
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End of IMP-users Digest, Vol 38, Issue 13
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