コード例 #1
0
 def eval_color(v):
     try:
         if not v:
             v=eval(cmd.get('bg_rgb'))
             v=list(map(sum, list(zip(v,[-1,-1,-1]))))
             v=list(map(abs, v))
             if v[0]==v[1]==v[2]==0.5: # grey
                 v=[0,0,0]
             return v
         if isinstance(v, list):
             return v[0:3]
         if not isinstance(v, str):
             return v[0:3]
         if v.startswith('['):
             return cmd.safe_list_eval(v)[0:3]
         return list(cmd.get_color_tuple(v))
     except:
         return [random.random(),random.random(),random.random()]
コード例 #2
0
ファイル: creating.py プロジェクト: Rasinj/pymol-psico
def ramp_levels(name, levels, quiet=1):
    '''
DESCRIPTION

    Changes the slot levels of a ramp.

SEE ALSO

    ramp_new, isolevel
    '''
    quiet = int(quiet)
    if cmd.is_string(levels):
        levels = cmd.safe_list_eval(levels)

    try:
        position = cmd.get_names('all').index(name)

        odata = cmd.get_session(name, 1, 1, 0, 0)['names'][0]
        if odata[4] != 8:
            raise TypeError('not a ramp')
        data = odata[5]
    except:
        print(' Error: Get session data for ramp "%s" failed' % (name))
        raise CmdException

    if len(levels) != len(data[3]):
        print(' Error: number of levels must agree with existing object')
        raise CmdException

    map_name = data[6]
    colors = [data[4][i:i+3] for i in range(0, len(data[4]), 3)]
    cmd.ramp_new(name, map_name, levels, colors, quiet=quiet)

    # restore original position
    if position == 0:
        cmd.order(name, location='top')
    else:
        cmd.order(cmd.get_names('all')[position-1] + ' ' + name)
コード例 #3
0
def get_coord(v):
    if not isinstance(v, str):
        try:
            return v[:3]
        except:
            return False
    if v.startswith('['):
        return cmd.safe_list_eval(v)[:3]
    try:
        if cmd.count_atoms(v)==1:
            # atom coordinates
            return cmd.get_atom_coords(v)
        else:
            # more than one atom --> use "center"
            # alt check!
            if cmd.count_atoms('(alt *) and not (alt "")')!=0:
                print "distancetoatom: warning! alternative coordinates found for origin, using center!"
            view_temp=cmd.get_view()
            cmd.zoom(v)
            v=cmd.get_position()
            cmd.set_view(view_temp)
            return v
    except:
        return False
コード例 #4
0
ファイル: cgo_arrow.py プロジェクト: FoosN/script4Pymol
 def get_coord(v):
     if not isinstance(v, str):
         return v
     if v.startswith('['):
         return cmd.safe_list_eval(v)
     return cmd.get_atom_coords(v)
コード例 #5
0
ファイル: electrostatics.py プロジェクト: speleo3/pymol-psico
def volume_esp(name, map, stops=[0.1, 1.0], neg='red', pos='blue',
        opacity=0.2, quiet=1):
    '''
DESCRIPTION

    Create a volume object from a map object with default coloring
    for electrostatic potential (similar to positive and negative
    isosurface).

ARGUMENTS

    name = string: name for the new volume object

    map = string: name of the map object to use

    stops = list of floats: 2 or 3 values in standard deviations for creating
    the volume ramp {default: [0.1, 1.0]}

    neg = string: color for negative volume {default: red}

    pos = string: color for positive volume {default: blue}

    opacity = float: maximum opacity in volume ramp {default: 0.2}

SEE ALSO

    volume
    '''
    from .setting import set_temporary

    opacity, quiet = float(opacity), int(quiet)

    if isinstance(stops, str):
        stops = cmd.safe_list_eval(stops)

    try:
        from pymol.colorramping import ColorRamp
    except ImportError:
        print(' Warning: volume_esp is deprecated')
        stdevD = cmd.get_volume_histogram(map, 0)[3]
        stops = [s * stdevD for s in stops]
        ramp = [
            -stops[1], neg, opacity,
            -stops[0], neg, 0.0,
            stops[0], pos, 0.0,
            stops[1], pos, opacity,
        ]
        if len(stops) == 3:
            ramp = [-stops[2], neg, opacity] + ramp + [stops[2], pos, opacity]
        cmd.volume(name, map, ramp, quiet=quiet)
        return

    c_neg = cmd.get_color_tuple(neg)
    c_pos = cmd.get_color_tuple(pos)

    c_pos_0 = c_pos + (0.0,)
    c_pos_1 = c_pos + (opacity,)
    c_neg_0 = c_neg + (0.0,)
    c_neg_1 = c_neg + (opacity,)

    if len(stops) == 2:
        cstops = [(c_neg_1, -999), (c_neg_1, -stops[1]), (c_neg_0, -stops[0]),
                (c_pos_0, stops[0]), (c_pos_1, stops[1]), (c_pos_1, 999)]
    elif len(stops) == 3:
        cstops = [(c_neg_0, -999), (c_neg_0, -stops[2]), (c_neg_1, -stops[1]),
                (c_neg_0, -stops[0]), (c_pos_0, stops[0]), (c_pos_1, stops[1]),
                (c_pos_0, stops[2]), (c_pos_0, 999)]
    else:
        print(' Error: need 2 or 3 stops')
        raise CmdException

    cmd.volume(name, map, quiet=quiet)

    # get_volume_histogram returns zeros without refresh
    with set_temporary(suspend_updates='off'):
        cmd.refresh()

    minD, maxD, meanD, stdevD = cmd.get_volume_histogram(name)[:4]

    v_ramp = []
    c_ramp = ColorRamp(360)
    for c, s in cstops:
        i = int(360 * ((s * stdevD) - minD) / (maxD - minD))
        i = min(max(i, 0), 359)
        v_ramp.append(i)
        v_ramp.extend(c)
        c_ramp.addColor(i, c)

    cmd.set_volume_ramp(name, v_ramp)
    cmd.volume_color(name, c_ramp.getRamp())
    cmd.recolor(name)
コード例 #6
0
ファイル: plotting.py プロジェクト: Rasinj/pymol-psico
def pca_plot(
    aln_object,
    ref="all",
    state=0,
    maxlabels=20,
    size=20,
    invert="",
    which=(0, 1),
    alpha=0.75,
    filename=None,
    quiet=1,
    load_b=0,
):
    """
DESCRIPTION

    Principal Component Analysis on a set of superposed conformations, given
    by an alignment object. By default all states in all objects are
    considered. Generates a 2d-plot of the first two principal components.

USAGE

    pca_plot aln_object [, ref [, state [, maxlabels ]]]

ARGUMENTS

    aln_object = string: name of alignment object, defines the selection
    and the atom mapping between objects

    ref = string: object names for which to calculate PCA for {default: all}

    state = integer: if state=0 use all states {default: 0}

    maxlabels = integer: label dots in plot if maxlabels<0 or number of models
    not more than maxlabels {default: 20}

    size = float: size of plot points in px^2 {default: 20}

    invert = string: invert plotting axes x, y or xy {default: ''}

    which = (int,int): indices of principal components to plot {default: (0,1)}

    alpha = float: opacity of plotting points

    filename = string: if given, plot to file {default: None}

EXAMPLE

    fetch 1ake 4ake 1dvr 1ak2, async=0
    split_chains
    extra_fit (*_*) and name CA, reference=1ake_A, cycles=0, object=aln
    pca_plot aln, 1ake_* 4ake_*

    fetch 1ubq 2k39, async=0
    align 2k39, 1ubq and guide, cycles=0, object=aln2
    color blue, 1ubq
    color orange, 2k39
    pca_plot aln2, filename=pca-ubq.pdf
    """
    from numpy import array, dot
    from numpy.linalg import svd, LinAlgError
    from . import matplotlib_fix
    from matplotlib.pyplot import figure

    state, quiet = int(state), int(quiet)
    maxlabels = int(maxlabels)
    if cmd.is_string(which):
        which = cmd.safe_list_eval(which)

    if aln_object not in cmd.get_names_of_type("object:"):
        print(" Warning: first argument should be an alignment object")

        from .fitting import extra_fit

        selection = aln_object
        aln_object = cmd.get_unused_name("aln")
        extra_fit(selection, cycles=0, transform=0, object=aln_object)

    if state == 0:
        states = list(range(1, cmd.count_states() + 1))
    elif state < 0:
        states = [cmd.get_state()]
    else:
        states = [state]

    models = cmd.get_object_list(aln_object)
    references = set(cmd.get_object_list("(" + ref + ")")).intersection(models)
    others = set(models).difference(references)
    aln = cmd.get_raw_alignment(aln_object)

    if not quiet:
        print(" PCA References:", ", ".join(references))
        print(" PCA Others:", ", ".join(others))

    if len(references) == 0:
        print(" PCA Error: No reference objects")
        raise CmdException

    model_count = len(models)
    coords = dict((model, []) for model in models)
    aln = [pos for pos in aln if len(pos) == model_count]

    for state in states:
        idx2xyz = dict()
        cmd.iterate_state(state, aln_object, "idx2xyz[model,index] = (x,y,z)", space={"idx2xyz": idx2xyz})

        for pos in aln:
            for idx in pos:
                if idx not in idx2xyz:
                    continue

                c = coords[idx[0]]
                if len(c) < state:
                    c.append([])
                c[-1].extend(idx2xyz[idx])

    c_iter = lambda models: ((c, model, i + 1) for model in models for (i, c) in enumerate(coords[model]))
    X = array([i[0] for i in c_iter(references)])
    Y = array([i[0] for i in c_iter(others)])
    center = X.mean(0)
    X = X - center

    try:
        U, L, V = svd(X)
    except LinAlgError as e:
        print(" PCA Error: ", e)
        raise CmdException

    if int(load_b):
        cmd.alter("byobj " + aln_object, "b=-0.01")
        b_dict = {}
        i = which[0]
        b_array = (V[i].reshape((-1, 3)) ** 2).sum(1) ** 0.5
        for pos, b in zip(aln, b_array):
            for idx in pos:
                b_dict[idx] = b
        cmd.alter(aln_object, "b=b_dict.get((model,index), -0.01)", space=locals())
        cmd.color("yellow", "byobj " + aln_object)
        cmd.spectrum("b", "blue_red", aln_object + " and b > -0.01")

    X_labels = [i[1:3] for i in c_iter(references)]
    Y_labels = [i[1:3] for i in c_iter(others)]

    x_list = []
    y_list = []
    colors = []
    text_list = []

    def plot_pc_2d(X, labels):
        pca_12 = dot(X, V.T)[:, which]
        for (x, y), (model, state) in zip(pca_12, labels):
            x_list.append(x)
            y_list.append(y)
            colors.append(get_model_color(model))
            if maxlabels < 0 or len(pca_12) <= maxlabels:
                text_list.append("%s(%d)" % (model, state))
            else:
                text_list.append(None)

    plot_pc_2d(X, X_labels)
    if len(Y) > 0:
        Y = Y - center
        plot_pc_2d(Y, Y_labels)

    if "x" in invert:
        x_list = [-x for x in x_list]
    if "y" in invert:
        y_list = [-y for y in y_list]

    fig = figure()
    plt = fig.add_subplot(111, xlabel="PC %d" % (which[0] + 1), ylabel="PC %d" % (which[1] + 1))
    plt.scatter(x_list, y_list, float(size), colors, linewidths=0, alpha=float(alpha))

    for (x, y, text) in zip(x_list, y_list, text_list):
        if text is not None:
            plt.text(x, y, text, horizontalalignment="left")

    _showfigure(fig, filename, quiet)
コード例 #7
0
 def get_coord(v):
     if not isinstance(v, str):
         return v
     if v.startswith('['):
         return cmd.safe_list_eval(v)
     return cmd.get_atom_coords(v)
コード例 #8
0
def volume_esp(name,
               map,
               stops=[0.1, 1.0],
               neg='red',
               pos='blue',
               opacity=0.2,
               quiet=1):
    '''
DESCRIPTION

    Create a volume object from a map object with default coloring
    for electrostatic potential (similar to positive and negative
    isosurface).

ARGUMENTS

    name = string: name for the new volume object

    map = string: name of the map object to use

    stops = list of floats: 2 or 3 values in standard deviations for creating
    the volume ramp {default: [0.1, 1.0]}

    neg = string: color for negative volume {default: red}

    pos = string: color for positive volume {default: blue}

    opacity = float: maximum opacity in volume ramp {default: 0.2}

SEE ALSO

    volume
    '''
    from .setting import set_temporary

    opacity, quiet = float(opacity), int(quiet)

    if isinstance(stops, str):
        stops = cmd.safe_list_eval(stops)

    try:
        from pymol.colorramping import ColorRamp
    except ImportError:
        print(' Warning: volume_esp is deprecated')
        stdevD = cmd.get_volume_histogram(map, 0)[3]
        stops = [s * stdevD for s in stops]
        ramp = [
            -stops[1],
            neg,
            opacity,
            -stops[0],
            neg,
            0.0,
            stops[0],
            pos,
            0.0,
            stops[1],
            pos,
            opacity,
        ]
        if len(stops) == 3:
            ramp = [-stops[2], neg, opacity] + ramp + [stops[2], pos, opacity]
        cmd.volume(name, map, ramp, quiet=quiet)
        return

    c_neg = cmd.get_color_tuple(neg)
    c_pos = cmd.get_color_tuple(pos)

    c_pos_0 = c_pos + (0.0, )
    c_pos_1 = c_pos + (opacity, )
    c_neg_0 = c_neg + (0.0, )
    c_neg_1 = c_neg + (opacity, )

    if len(stops) == 2:
        cstops = [(c_neg_1, -999), (c_neg_1, -stops[1]), (c_neg_0, -stops[0]),
                  (c_pos_0, stops[0]), (c_pos_1, stops[1]), (c_pos_1, 999)]
    elif len(stops) == 3:
        cstops = [(c_neg_0, -999), (c_neg_0, -stops[2]), (c_neg_1, -stops[1]),
                  (c_neg_0, -stops[0]), (c_pos_0, stops[0]),
                  (c_pos_1, stops[1]), (c_pos_0, stops[2]), (c_pos_0, 999)]
    else:
        print(' Error: need 2 or 3 stops')
        raise CmdException

    cmd.volume(name, map, quiet=quiet)

    # get_volume_histogram returns zeros without refresh
    with set_temporary(suspend_updates='off'):
        cmd.refresh()

    minD, maxD, meanD, stdevD = cmd.get_volume_histogram(name)[:4]

    v_ramp = []
    c_ramp = ColorRamp(360)
    for c, s in cstops:
        i = int(360 * ((s * stdevD) - minD) / (maxD - minD))
        i = min(max(i, 0), 359)
        v_ramp.append(i)
        v_ramp.extend(c)
        c_ramp.addColor(i, c)

    cmd.set_volume_ramp(name, v_ramp)
    cmd.volume_color(name, c_ramp.getRamp())
    cmd.recolor(name)