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()]
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)
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
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)
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)
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)
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)
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)