def extend(model, nodes, atoms):
"""Returns mapping indices and an :class:`.AtomMap`."""
try:
n_atoms = model.numAtoms()
is3d = model.is3d()
except AttributeError:
raise ValueError('model must be an NMA instance')
try:
n_nodes = nodes.numAtoms()
i_nodes = nodes.iterAtoms()
except AttributeError:
raise ValueError('nodes must be an Atomic instance')
if n_atoms != n_nodes:
raise ValueError('atom numbers must be the same')
if not nodes in atoms:
raise ValueError('nodes must be a subset of atoms')
atom_indices = []
indices = []
get = HierView(atoms).getResidue
for i, node in enumerate(i_nodes):
res = get(node.getChid() or None, node.getResnum(),
node.getIcode() or None,
node.getSegname() or None)
if res is None:
raise ValueError('atoms must contain a residue for all atoms')
atom_indices.append(res._getIndices())
if is3d:
indices.append(list(range(i * 3, (i + 1) * 3)) * len(res))
else:
indices.append([i] * len(res))
atom_indices = np.concatenate(atom_indices)
indices = np.concatenate(indices)
try:
ag = atoms.getAtomGroup()
except AttributeError:
ag = atoms
atommap = AtomMap(ag,
atom_indices,
atoms.getACSIndex(),
title=str(atoms),
intarrays=True)
return indices, atommap
def showProtein(*atoms, **kwargs):
"""Show protein representation using :meth:`~mpl_toolkits.mplot3d.Axes3D`.
This function is designed for generating a quick view of the contents of a
:class:`~.AtomGroup` or :class:`~.Selection`.
Protein atoms matching ``"calpha"`` selection are displayed using solid
lines by picking a random and unique color per chain. Line with can
be adjusted using *lw* argument, e.g. ``lw=12``. Default width is 4.
Chain colors can be overwritten using chain identifier as in ``A='green'``.
Water molecule oxygen atoms are represented by red colored circles. Color
can be changed using *water* keyword argument, e.g. ``water='aqua'``.
Water marker and size can be changed using *wmarker* and *wsize* keywords,
defaults values are ``wmarker='.', wsize=6``.
Hetero atoms matching ``"hetero and noh"`` selection are represented by
circles and unique colors are picked at random on a per residue basis.
Colors can be customized using residue name as in ``NAH='purple'``. Note
that this will color all distinct residues with the same name in the same
color. Hetero atom marker and size can be changed using *hmarker* and
*hsize* keywords, default values are ``hmarker='o', hsize=6``.
ProDy will set the size of axis so the representation is not distorted when
the shape of figure window is close to a square. Colors are picked at
random, except for water oxygens which will always be colored red."""
alist = atoms
for atoms in alist:
if not isinstance(atoms, Atomic):
raise TypeError('atoms must be an Atomic instance')
import matplotlib.pyplot as plt
from mpl_toolkits.mplot3d import Axes3D
cf = plt.gcf()
show = None
for child in cf.get_children():
if isinstance(child, Axes3D):
show = child
break
if show is None:
show = Axes3D(cf)
from matplotlib import colors
cnames = dict(colors.cnames)
wcolor = kwargs.get('water', 'red').lower()
avoid = np.array(colors.hex2color(cnames.pop(wcolor, cnames.pop('red'))))
for cn, val in cnames.items(): # PY3K: OK
clr = np.array(colors.hex2color(val))
if clr.sum() > 2.4:
cnames.pop(cn)
elif np.abs(avoid - clr).sum() <= 0.6:
cnames.pop(cn)
cnames = list(cnames)
import random
random.shuffle(cnames)
min_ = list()
max_ = list()
for atoms in alist:
if isinstance(atoms, AtomGroup):
title = atoms.getTitle()
else:
title = atoms.getAtomGroup().getTitle()
calpha = atoms.select('calpha')
if calpha:
for ch in HierView(calpha, chain=True):
xyz = ch._getCoords()
chid = ch.getChid()
show.plot(xyz[:, 0],
xyz[:, 1],
xyz[:, 2],
label=title + '_' + chid,
color=kwargs.get(chid, cnames.pop()).lower(),
lw=kwargs.get('lw', 4))
water = atoms.select('water and noh')
if water:
xyz = atoms.select('water')._getCoords()
show.plot(xyz[:, 0],
xyz[:, 1],
xyz[:, 2],
label=title + '_water',
color=wcolor,
ls='None',
marker=kwargs.get('wmarker', '.'),
ms=kwargs.get('wsize', 6))
hetero = atoms.select('not protein and not nucleic and not water')
if hetero:
for res in HierView(hetero).iterResidues():
xyz = res._getCoords()
resname = res.getResname()
resnum = str(res.getResnum())
chid = res.getChid()
show.plot(xyz[:, 0],
xyz[:, 1],
xyz[:, 2],
ls='None',
color=kwargs.get(resname, cnames.pop()).lower(),
label=title + '_' + chid + '_' + resname + resnum,
marker=kwargs.get('hmarker', 'o'),
ms=kwargs.get('hsize', 6))
xyz = atoms._getCoords()
min_.append(xyz.min(0))
max_.append(xyz.max(0))
show.set_xlabel('x')
show.set_ylabel('y')
show.set_zlabel('z')
min_ = np.array(min_).min(0)
max_ = np.array(max_).max(0)
center = (max_ + min_) / 2
half = (max_ - min_).max() / 2
show.set_xlim3d(center[0] - half, center[0] + half)
show.set_ylim3d(center[1] - half, center[1] + half)
show.set_zlim3d(center[2] - half, center[2] + half)
if kwargs.get('legend', False):
show.legend(prop={'size': 10})
if SETTINGS['auto_show']:
showFigure()
return show
def showProtein(*atoms, **kwargs):
"""Show protein representation using :meth:`~mpl_toolkits.mplot3d.Axes3D`.
This function is designed for generating a quick view of the contents of a
:class:`~.AtomGroup` or :class:`~.Selection`.
Protein atoms matching ``"calpha"`` selection are displayed using solid
lines by picking a random and unique color per chain. Line with can
be adjusted using *lw* argument, e.g. ``lw=12``. Default width is 4.
Chain colors can be overwritten using chain identifier as in ``A='green'``.
Water molecule oxygen atoms are represented by red colored circles. Color
can be changed using *water* keyword argument, e.g. ``water='aqua'``.
Water marker and size can be changed using *wmarker* and *wsize* keywords,
defaults values are ``wmarker='.', wsize=6``.
Hetero atoms matching ``"hetero and noh"`` selection are represented by
circles and unique colors are picked at random on a per residue basis.
Colors can be customized using residue name as in ``NAH='purple'``. Note
that this will color all distinct residues with the same name in the same
color. Hetero atom marker and size can be changed using *hmarker* and
*hsize* keywords, default values are ``hmarker='o', hsize=6``.
ProDy will set the size of axis so the representation is not distorted when
the shape of figure window is close to a square. Colors are picked at
random, except for water oxygens which will always be colored red.
*** Interactive 3D Rendering in Jupyter Notebook ***
If py3Dmol has been imported then it will be used instead to display
an interactive viewer. See :func:`view3D`
"""
from prody.dynamics.mode import Mode
method = kwargs.pop('draw', None)
modes = kwargs.get('mode', None)
scale = kwargs.get('scale', 100)
# modes need to be specifically a list or a tuple (cannot be an array)
if modes is None:
n_modes = 0
else:
modes = wrapModes(modes)
n_modes = len(modes)
if method is None:
import sys
if 'py3Dmol' in sys.modules:
method = 'py3Dmol'
else:
method = 'matplotlib'
method = method.lower()
alist = atoms
for atoms in alist:
if not isinstance(atoms, Atomic):
raise TypeError('atoms must be an Atomic instance')
if n_modes and n_modes != len(alist):
raise RuntimeError(
'the number of proteins ({0}) does not match that of the modes ({1}).'
.format(len(alist), n_modes))
if '3dmol' in method:
mol = view3D(*alist, **kwargs)
return mol
else:
kwargs.pop('mode', None)
kwargs.pop('scale', 100)
import matplotlib.pyplot as plt
from mpl_toolkits.mplot3d import Axes3D
cf = plt.gcf()
show = None
for child in cf.get_children():
if isinstance(child, Axes3D):
show = child
break
if show is None:
show = Axes3D(cf)
from matplotlib import colors
cnames = dict(colors.cnames)
wcolor = kwargs.get('water', 'red').lower()
avoid = np.array(
colors.hex2color(cnames.pop(wcolor, cnames.pop('red'))))
for cn, val in cnames.copy().items(): # PY3K: OK
clr = np.array(colors.hex2color(val))
if clr.sum() > 2.4:
cnames.pop(cn)
elif np.abs(avoid - clr).sum() <= 0.6:
cnames.pop(cn)
cnames = list(cnames)
import random
random.shuffle(cnames)
cnames_copy = list(cnames)
min_ = list()
max_ = list()
for i, atoms in enumerate(alist):
if isinstance(atoms, AtomGroup):
title = atoms.getTitle()
else:
title = atoms.getAtomGroup().getTitle()
calpha = atoms.select('calpha')
if calpha:
partition = False
mode = modes[i] if n_modes else None
if mode is not None:
is3d = False
try:
arr = mode.getArray()
is3d = mode.is3d()
n_nodes = mode.numAtoms()
except AttributeError:
arr = mode
is3d = len(arr) == len(calpha) * 3
n_nodes = len(arr) // 3 if is3d else len(arr)
if n_nodes != len(calpha):
raise RuntimeError(
'size mismatch between the protein ({0} residues) and the mode ({1} nodes).'
.format(len(calpha), n_nodes))
partition = not is3d
if partition:
xyz = calpha._getCoords()
chids = calpha.getChids()
rbody = []
last_sign = np.sign(arr[0])
last_chid = chids[0]
rcolor = ['red', 'red', 'blue']
n = 1
for i, a in enumerate(arr):
s = np.sign(a)
ch = chids[i]
if s == 0: s = last_sign
if last_sign != s or i == len(
arr) - 1 or last_chid != ch:
if last_chid == ch:
rbody.append(i)
show.plot(xyz[rbody, 0],
xyz[rbody, 1],
xyz[rbody, 2],
label=title + '_regid%d' % n,
color=rcolor[int(last_sign + 1)],
lw=kwargs.get('lw', 4))
rbody = []
n += 1
last_sign = s
last_chid = ch
rbody.append(i)
else:
for ch in HierView(calpha, chain=True):
xyz = ch._getCoords()
chid = ch.getChid()
if len(cnames) == 0:
cnames = list(cnames_copy)
show.plot(xyz[:, 0],
xyz[:, 1],
xyz[:, 2],
label=title + '_' + chid,
color=kwargs.get(chid, cnames.pop()).lower(),
lw=kwargs.get('lw', 4))
if mode is not None:
from prody.utilities.drawtools import drawArrow3D
XYZ = calpha._getCoords()
arr = arr.reshape((n_nodes, 3))
XYZ2 = XYZ + arr * scale
for i, xyz in enumerate(XYZ):
xyz2 = XYZ2[i]
mutation_scale = kwargs.pop('mutation_scale', 10)
drawArrow3D(xyz,
xyz2,
mutation_scale=mutation_scale,
**kwargs)
water = atoms.select('water and noh')
if water:
xyz = atoms.select('water')._getCoords()
show.plot(xyz[:, 0],
xyz[:, 1],
xyz[:, 2],
label=title + '_water',
color=wcolor,
ls='None',
marker=kwargs.get('wmarker', '.'),
ms=kwargs.get('wsize', 6))
hetero = atoms.select(
'not protein and not nucleic and not water and not dummy')
if hetero:
for res in HierView(hetero).iterResidues():
xyz = res._getCoords()
resname = res.getResname()
resnum = str(res.getResnum())
chid = res.getChid()
if len(cnames) == 0:
cnames = list(cnames_copy)
show.plot(xyz[:, 0],
xyz[:, 1],
xyz[:, 2],
ls='None',
color=kwargs.get(resname, cnames.pop()).lower(),
label=title + '_' + chid + '_' + resname +
resnum,
marker=kwargs.get('hmarker', 'o'),
ms=kwargs.get('hsize', 6))
xyz = atoms._getCoords()
min_.append(xyz.min(0))
max_.append(xyz.max(0))
show.set_xlabel('x')
show.set_ylabel('y')
show.set_zlabel('z')
min_ = np.array(min_).min(0)
max_ = np.array(max_).max(0)
center = (max_ + min_) / 2
half = (max_ - min_).max() / 2
show.set_xlim3d(center[0] - half, center[0] + half)
show.set_ylim3d(center[1] - half, center[1] + half)
show.set_zlim3d(center[2] - half, center[2] + half)
if kwargs.get('legend', False):
show.legend(prop={'size': 10})
if SETTINGS['auto_show']:
showFigure()
return show