Beispiel #1
0
def get_em2d_restraint(assembly,
                       images_selection_file,
                       restraint_params,
                       mode="fast",
                       n_optimized=1):
    """ Sets a restraint for comparing the model to a set of EM images
    """
    model = assembly.get_model()
    # Setup the restraint
    sc = em2d.EM2DScore()
    r = em2d.Em2DRestraint(model)
    r.setup(sc, restraint_params)
    names = em2d.read_selection_file(images_selection_file)
    names = [base.get_relative_path(images_selection_file, x) for x in names]
    log.debug("names of the images %s", names)
    srw = em2d.SpiderImageReaderWriter()
    imgs = em2d.read_images(names, srw)
    r.set_images(imgs)

    ps = atom.get_leaves(assembly)
    lsc = container.ListSingletonContainer(ps)
    r.set_particles(lsc)

    if (mode == "coarse"):
        r.set_coarse_registration_mode(True)
    elif (mode == "fast"):
        r.set_fast_mode(n_optimized)
    elif (mode == "complete"):
        pass
    else:
        raise ValueError("Em2DRestraint mode not recognized")
    return r
Beispiel #2
0
def get_em2d_restraint( assembly,
                        images_selection_file,
                        restraint_params,
                        mode="fast",
                        n_optimized=1):
    """ Sets a restraint for comparing the model to a set of EM images
    """
    model = assembly.get_model()
    # Setup the restraint
    sc = em2d.EM2DScore()
    r = em2d.Em2DRestraint()
    r.setup(sc, restraint_params)
    names = em2d.read_selection_file(images_selection_file)
    names = [base.get_relative_path(images_selection_file, x) for x in names]
    log.debug("names of the images %s", names)
    srw = em2d.SpiderImageReaderWriter()
    imgs = em2d.read_images(names, srw)
    r.set_images(imgs)

    ps = atom.get_leaves(assembly)
    lsc = container.ListSingletonContainer(ps)
    r.set_particles(lsc)

    if (mode == "coarse"):
        r.set_coarse_registration_mode(True)
    elif (mode == "fast"):
        r.set_fast_mode(n_optimized)
    elif(mode == "complete"):
        pass
    else:
        raise ValueError("Em2DRestraint mode not recognized")
    return r
Beispiel #3
0
def get_experiment_params(fn_params):
    """
        Imports the configuration file
        @param fn_params configuration file
        @return Experiment Class with all the infomation from the config file
    """

    name, ext = os.path.splitext(fn_params)
    import imp
    foo = imp.load_source(name, fn_params)
    exp = foo.Experiment()
    # convert to absolute paths
    exp.fn_pdbs = [base.get_relative_path(fn_params, fn) for fn in exp.fn_pdbs]
    if hasattr(exp, "sampling_positions"):
        exp.sampling_positions.read = base.get_relative_path(fn_params, exp.sampling_positions.read)
    if hasattr(exp, "benchmark"):
        if hasattr(exp.benchmark, "fn_pdb_native"):
            exp.benchmark.fn_pdb_native = base.get_relative_path(
                                    fn_params, exp.benchmark.fn_pdb_native)
        if hasattr(exp.benchmark, "fn_pdbs_native"):
            fns = []
            for fn in exp.benchmark.fn_pdbs_native:
                fns.append( base.get_relative_path(fn_params, fn) )
            exp.benchmark.fn_pdbs_native = fns

    if hasattr(exp, "dock_transforms"):
        for i in range(len(exp.dock_transforms)):
            exp.dock_transforms[i][2] = base.get_relative_path(fn_params, exp.dock_transforms[i][2])
    if hasattr(exp, "em2d_restraints"):
        for i in range(len(exp.em2d_restraints)):
            exp.em2d_restraints[i][1] = base.get_relative_path(fn_params, exp.em2d_restraints[i][1])
    return exp
Beispiel #4
0
def get_experiment_params(fn_params):
    """
        Imports the configuration file
        @param fn_params configuration file
        @return Experiment Class with all the infomation from the config file
    """

    name, ext = os.path.splitext(fn_params)
    import imp
    foo = imp.load_source(name, fn_params)
    exp = foo.Experiment()
    # convert to absolute paths
    exp.fn_pdbs = [base.get_relative_path(fn_params, fn) for fn in exp.fn_pdbs]
    if hasattr(exp, "sampling_positions"):
        exp.sampling_positions.read = base.get_relative_path(
            fn_params, exp.sampling_positions.read)
    if hasattr(exp, "benchmark"):
        if hasattr(exp.benchmark, "fn_pdb_native"):
            exp.benchmark.fn_pdb_native = base.get_relative_path(
                fn_params, exp.benchmark.fn_pdb_native)
        if hasattr(exp.benchmark, "fn_pdbs_native"):
            fns = []
            for fn in exp.benchmark.fn_pdbs_native:
                fns.append(base.get_relative_path(fn_params, fn))
            exp.benchmark.fn_pdbs_native = fns

    if hasattr(exp, "dock_transforms"):
        for i in range(len(exp.dock_transforms)):
            exp.dock_transforms[i][2] = base.get_relative_path(
                fn_params, exp.dock_transforms[i][2])
    if hasattr(exp, "em2d_restraints"):
        for i in range(len(exp.em2d_restraints)):
            exp.em2d_restraints[i][1] = base.get_relative_path(
                fn_params, exp.em2d_restraints[i][1])
    return exp