def drawIsoSurface(values3d, resolution=1., plot_center=None, viewer=None):
from htmd.vmdviewer import getCurrentViewer
from htmd.molecule.util import writeVoxels
# plot_center should be - molecule.get_center() + 12
if len(values3d.shape) != 3:
raise ValueError("Your provided a box of {} dimensions."
"\nThis only works with dimension of 3".format(len(values3d.shape)))
from htmd.util import tempname
if viewer is None:
viewer = getCurrentViewer()
mincoor = np.zeros(3, dtype=np.float64)
maxcoor = np.array(values3d.shape, dtype=np.float64)
rescoor = np.array([resolution] * 3)
# Adjust the plotting center
if plot_center is None:
plot_center = maxcoor / 2.
else:
plot_center = np.array(plot_center)
mincoor -= (plot_center + 0.5) # TODO: Fix so it will work in case resolution != 1.
maxcoor -= (plot_center + 0.5)
outf = tempname(suffix='.cube')
writeVoxels(values3d, outf, mincoor, maxcoor, rescoor)
viewer.send('mol new {} type cube first 0 last -1 step 1 waitfor 1 volsets {{0 }}'.format(outf))
viewer.send('mol modstyle 0 top Isosurface 0.75 0 2 0 1 1')
def __init__(self, xyz, color='red', radius=1):
""" Displays a sphere in VMD.
The function returns an instance of VMDGraphicsObject. To delete it, use the delete() method.
Parameters
----------
xyz : list
The center of the sphere
color : str
Color of the sphere
radius : float
The radius of the sphere
"""
super().__init__(xyz)
#self._remember('draw materials off')
self._remember('draw color {}'.format(color))
self._remember('draw sphere "{} {} {}" radius {}\n'.format(
xyz[0], xyz[1], xyz[2], radius))
self.script.write("\n")
self.script.write("set htmd_graphics_mol({:d}) [molinfo top]".format(
self.n))
cmd = self.script.getvalue()
vmd = getCurrentViewer()
vmd.send(cmd)
def viewStates(self,
states=None,
statetype='macro',
protein=None,
ligand=None,
viewer=None,
mols=None,
numsamples=50):
""" Visualize macro/micro/cluster states in VMD
Parameters
----------
states : ndarray, optional
A list of states to visualize
statetype : ['macro','micro','cluster'], optional
The type of state to visualize
protein : bool, optional
Set to True to enable pure protein system visualization
ligand : str, optional
Atomselection string for the ligand
viewer : :class:`VMD <htmd.vmdviewer.VMD>` object, optional
A viewer in which to visualize the states
mols : ndarray, optional
An array of :class:`Molecule <htmd.molecule.molecule.Molecule>` objects to visualize
numsamples : int
Number of samples (conformations) for each state.
Examples
--------
>>> model = Model(data)
>>> model.markovModel(100, 5)
>>> model.viewStates(protein=True)
>>> model.viewStates(ligand='resname MOL')
"""
from htmd.config import _config
self._integrityCheck(postmsm=(statetype != 'cluster'))
if _config['viewer'].lower() == 'ngl':
return self._viewStatesNGL(states, statetype, protein, ligand,
mols, numsamples)
if viewer is None:
viewer = getCurrentViewer()
if states is None:
states = range(self.macronum)
if isinstance(states, int):
states = [states]
if mols is None:
mols = self.getStates(states, statetype, numsamples=numsamples)
colors = [0, 1, 3, 4, 5, 6, 7, 9]
for i, s in enumerate(states):
viewer.loadMol(mols[i], name=statetype + ' ' + str(states[i]))
if ligand is not None:
viewer.rep('ligand',
sel=ligand,
color=colors[np.mod(i, len(colors))])
if protein is not None:
viewer.rep('protein')
viewer.send('start_sscache')
def __init__(self, arr, vecMin, vecRes, color=8, isovalue=0.5):
""" Displays an isosurface in VMD
The function returns an instance of VMDGraphicsObject. To delete it, use the delete() method.
Parameters
----------
arr: np.ndarray
3D array with volumetric data.
vecMin: np.ndarray
3D vector denoting the minimal corner of the grid
vecRes: np.ndarray
3D vector denoting the resolution of the grid in each dimension
color: str
The color to be used for the isosurface
"""
super().__init__(arr)
from htmd.util import tempname
import numpy as np
import os
filename = tempname(suffix='.cube')
outFile = open(filename, 'w')
# conversion to gaussian units
L = 1 / 0.52917725
gauss_bin = vecRes * L
# minCorner = 0.5*L*(vecMin - vecMax + vecRes)
minCorner = L * (vecMin + 0.5 * vecRes)
ngrid = arr.shape
# write header
outFile.write("CUBE FILE\n")
outFile.write("OUTER LOOP: X, MIDDLE LOOP: Y, INNER LOOP: Z\n")
outFile.write("%5d %12.6f %12.6f %12.6f\n" % (1, minCorner[0], minCorner[1], minCorner[2]))
outFile.write("%5d %12.6f %12.6f %12.6f\n" % (ngrid[0], gauss_bin[0], 0, 0))
outFile.write("%5d %12.6f %12.6f %12.6f\n" % (ngrid[1], 0, gauss_bin[1], 0))
outFile.write("%5d %12.6f %12.6f %12.6f\n" % (ngrid[2], 0, 0, gauss_bin[2]))
outFile.write("%5d %12.6f %12.6f %12.6f %12.6f\n" % (1, 0, minCorner[0], minCorner[1], minCorner[2]))
# main loop
cont = 0
for i in range(ngrid[0]):
for j in range(ngrid[1]):
for k in range(ngrid[2]):
outFile.write("%13.5g" % arr[i][j][k])
if np.mod(cont, 6) == 5:
outFile.write("\n")
cont += 1
outFile.close()
vmd = getCurrentViewer()
vmd.send('mol new {} type cube first 0 last -1 step 1 waitfor 1 volsets {{0 }}'.format(filename))
vmd.send('mol modstyle top top Isosurface {} 0 2 0 2 1'.format(isovalue))
vmd.send('mol modcolor top top ColorID {}'.format(color))
vmd.send('set htmd_graphics_mol({:d}) [molinfo top]'.format(self.n))
os.unlink(filename)
def __init__(self, text, xyz, color='red'):
""" Displays a text in VMD.
The function returns an instance of VMDGraphicsObject. To delete it, use the delete() method.
Parameters
----------
text : str
The text
xyz : list
The position of the text
color : str
Color of the text
"""
super().__init__(xyz)
self._remember('draw materials off')
self._remember('draw color {}'.format(color))
self._remember('draw text "{} {} {}" "{}"\n'.format(
xyz[0], xyz[1], xyz[2], text))
self.script.write("\n")
self.script.write("set htmd_graphics_mol({:d}) [molinfo top]".format(
self.n))
cmd = self.script.getvalue()
vmd = getCurrentViewer()
vmd.send(cmd)
def drawCube(mi, ma, viewer=None):
from htmd.vmdviewer import getCurrentViewer
if viewer is None:
viewer = getCurrentViewer()
viewer.send('draw materials off')
viewer.send('draw color red')
c = ''
c += 'draw line "{} {} {}" "{} {} {}"\n'.format(mi[0], mi[1], mi[2], ma[0], mi[1], mi[2])
c += 'draw line "{} {} {}" "{} {} {}"\n'.format(mi[0], mi[1], mi[2], mi[0], ma[1], mi[2])
c += 'draw line "{} {} {}" "{} {} {}"\n'.format(mi[0], mi[1], mi[2], mi[0], mi[1], ma[2])
c += 'draw line "{} {} {}" "{} {} {}"\n'.format(ma[0], mi[1], mi[2], ma[0], ma[1], mi[2])
c += 'draw line "{} {} {}" "{} {} {}"\n'.format(ma[0], mi[1], mi[2], ma[0], mi[1], ma[2])
c += 'draw line "{} {} {}" "{} {} {}"\n'.format(mi[0], ma[1], mi[2], ma[0], ma[1], mi[2])
c += 'draw line "{} {} {}" "{} {} {}"\n'.format(mi[0], ma[1], mi[2], mi[0], ma[1], ma[2])
c += 'draw line "{} {} {}" "{} {} {}"\n'.format(mi[0], mi[1], ma[2], ma[0], mi[1], ma[2])
c += 'draw line "{} {} {}" "{} {} {}"\n'.format(mi[0], mi[1], ma[2], mi[0], ma[1], ma[2])
c += 'draw line "{} {} {}" "{} {} {}"\n'.format(ma[0], ma[1], ma[2], ma[0], ma[1], mi[2])
c += 'draw line "{} {} {}" "{} {} {}"\n'.format(ma[0], ma[1], ma[2], mi[0], ma[1], ma[2])
c += 'draw line "{} {} {}" "{} {} {}"\n'.format(ma[0], ma[1], ma[2], ma[0], mi[1], ma[2])
viewer.send(c)
"""
def viewStates(self, states=None, statetype='macro', protein=None, ligand=None, viewer=None, mols=None,
numsamples=50, wrapsel='protein', alignsel='name CA', gui=False, simlist=None):
""" Visualize macro/micro/cluster states in VMD
Parameters
----------
states : ndarray, optional
A list of states to visualize
statetype : ['macro','micro','cluster'], optional
The type of state to visualize
protein : bool, optional
Set to True to enable pure protein system visualization
ligand : str, optional
Atom selection string for the ligand.
See more `here <http://www.ks.uiuc.edu/Research/vmd/vmd-1.9.2/ug/node89.html>`__
viewer : :class:`VMD <htmd.vmdviewer.VMD>` object, optional
A viewer in which to visualize the states
mols : ndarray, optional
An array of :class:`Molecule <htmd.molecule.molecule.Molecule>` objects to visualize
numsamples : int
Number of samples (conformations) for each state.
wrapsel : str, optional, default='protein'
Atom selection string to use for wrapping.
See more `here <http://www.ks.uiuc.edu/Research/vmd/vmd-1.9.2/ug/node89.html>`__
alignsel : str, optional, default='name CA'
Atom selection string used for aligning all frames. See to None to disable aligning.
See more `here <http://www.ks.uiuc.edu/Research/vmd/vmd-1.9.2/ug/node89.html>`__
simlist : numpy.ndarray of :class:`Sim <htmd.simlist.Sim>` objects
Optionally pass a different (but matching, i.e. filtered) simlist for visualizing the states.
Examples
--------
>>> model = Model(data)
>>> model.markovModel(100, 5)
>>> model.viewStates(protein=True)
>>> model.viewStates(ligand='resname MOL')
"""
from htmd.config import _config
self._integrityCheck(postmsm=(statetype != 'cluster'))
if _config['viewer'].lower() == 'ngl' or _config['viewer'].lower() == 'webgl':
return self._viewStatesNGL(states, statetype, protein, ligand, mols, numsamples, gui=gui)
if viewer is None:
viewer = getCurrentViewer()
if states is None:
states = range(self.macronum)
if isinstance(states, int):
states = [states]
if mols is None:
mols = self.getStates(states, statetype, numsamples=numsamples, wrapsel=wrapsel, alignsel=alignsel, simlist=simlist)
colors = [0, 1, 3, 4, 5, 6, 7, 9]
for i, s in enumerate(states):
viewer.loadMol(mols[i], name=statetype+' '+str(states[i]))
if ligand is not None:
viewer.rep('ligand', sel=ligand, color=colors[np.mod(i, len(colors))])
if protein is not None:
viewer.rep('protein')
viewer.send('start_sscache')
def __init__(self, m, style="", preamble="", solid=False):
"""Display the convex hull of the given molecule.
For preamble and color, see http://www.ks.uiuc.edu/Research/vmd/vmd-1.9.2/ug/node129.html
The function returns an instance of VMDGraphicsObject. To delete it, use the delete() method.
Parameters
----------
m: Molecule
The object of which to show the hull (only 1 frame)
style: str
Style for wireframe lines
preamble: str
Commands (material, color) to be prefixed to the output.
E.g.: "draw color red; graphics top materials on; graphics top material Transparent".
Note that this affects later preamble-less commands.
solid: bool
Solid or wireframe
Examples
--------
>>> m=Molecule("3PTB")
>>> m.view()
>>> mf=m.copy()
>>> mf.filter("protein ")
>>> gh=htmd.vmdgraphics.VMDConvexHull(mf) # doctest: +ELLIPSIS
>>> gh.delete()
"""
from scipy.spatial import ConvexHull
if m.coords.shape[2] != 1:
raise Exception("Only one frame is supported")
cc = m.coords[:, :, 0]
hull = ConvexHull(cc)
super().__init__(hull)
self.script.write(preamble + "\n")
for i in range(hull.nsimplex):
v1, v2, v3 = hull.simplices[i, :]
c1s = VMDGraphicObject.tq(cc[v1, :])
c2s = VMDGraphicObject.tq(cc[v2, :])
c3s = VMDGraphicObject.tq(cc[v3, :])
if solid:
self._remember("draw triangle {:s} {:s} {:s}".format(c1s, c2s, c3s))
else:
self._remember("draw line {:s} {:s} {:s}".format(c1s, c2s, style))
self._remember("draw line {:s} {:s} {:s}".format(c1s, c3s, style))
self._remember("draw line {:s} {:s} {:s}".format(c2s, c3s, style))
self.script.write("\n")
self.script.write("set htmd_graphics_mol({:d}) [molinfo top]".format(self.n))
cmd = self.script.getvalue()
vmd = getCurrentViewer()
vmd.send(cmd)
def viewStates(self, states=None, statetype='macro', protein=None, ligand=None, viewer=None, mols=None,
numsamples=50, wrapsel='protein', alignsel='name CA', gui=False, simlist=None):
""" Visualize macro/micro/cluster states in VMD
Parameters
----------
states : ndarray, optional
A list of states to visualize
statetype : ['macro','micro','cluster'], optional
The type of state to visualize
protein : bool, optional
Set to True to enable pure protein system visualization
ligand : str, optional
Atomselection string for the ligand
viewer : :class:`VMD <htmd.vmdviewer.VMD>` object, optional
A viewer in which to visualize the states
mols : ndarray, optional
An array of :class:`Molecule <htmd.molecule.molecule.Molecule>` objects to visualize
numsamples : int
Number of samples (conformations) for each state.
wrapsel : str, optional, default='protein'
A selection to use for wrapping
alignsel : str, optional, default='name CA'
A selection used for aligning all frames
simlist : simlist
Optionally pass a different (but matching, i.e. filtered) simlist for visualizing the states.
Examples
--------
>>> model = Model(data)
>>> model.markovModel(100, 5)
>>> model.viewStates(protein=True)
>>> model.viewStates(ligand='resname MOL')
"""
from htmd.config import _config
self._integrityCheck(postmsm=(statetype != 'cluster'))
if _config['viewer'].lower() == 'ngl':
return self._viewStatesNGL(states, statetype, protein, ligand, mols, numsamples, gui=gui)
if viewer is None:
viewer = getCurrentViewer()
if states is None:
states = range(self.macronum)
if isinstance(states, int):
states = [states]
if mols is None:
mols = self.getStates(states, statetype, numsamples=numsamples, wrapsel=wrapsel, alignsel=alignsel, simlist=simlist)
colors = [0, 1, 3, 4, 5, 6, 7, 9]
for i, s in enumerate(states):
viewer.loadMol(mols[i], name=statetype+' '+str(states[i]))
if ligand is not None:
viewer.rep('ligand', sel=ligand, color=colors[np.mod(i, len(colors))])
if protein is not None:
viewer.rep('protein')
viewer.send('start_sscache')
def _prepareViewer(mol, ligandsel):
mol.view(sel='protein', style='lines', hold=True)
mol.view(sel=ligandsel, style='licorice', hold=True)
mol.view()
viewer = getCurrentViewer()
viewer.send('draw color red')
viewer.send('color Display Background black')
viewer.send('draw materials off')
return viewer
def __init__(self, box, color='red'):
""" Displays a box in VMD as lines of its edges.
The function returns an instance of VMDGraphicsObject. To delete it, use the delete() method.
Parameters
----------
box : list
The min and max positions of the edges. Given as [xmin, xmax, ymin, ymax, zmin, zmax]
color : str
Color of the lines
"""
super().__init__(box)
xmin, xmax, ymin, ymax, zmin, zmax = box
mi = [xmin, ymin, zmin]
ma = [xmax, ymax, zmax]
self._remember('draw materials off')
self._remember('draw color {}'.format(color))
self._remember('draw line "{} {} {}" "{} {} {}"\n'.format(
mi[0], mi[1], mi[2], ma[0], mi[1], mi[2]))
self._remember('draw line "{} {} {}" "{} {} {}"\n'.format(
mi[0], mi[1], mi[2], mi[0], ma[1], mi[2]))
self._remember('draw line "{} {} {}" "{} {} {}"\n'.format(
mi[0], mi[1], mi[2], mi[0], mi[1], ma[2]))
self._remember('draw line "{} {} {}" "{} {} {}"\n'.format(
ma[0], mi[1], mi[2], ma[0], ma[1], mi[2]))
self._remember('draw line "{} {} {}" "{} {} {}"\n'.format(
ma[0], mi[1], mi[2], ma[0], mi[1], ma[2]))
self._remember('draw line "{} {} {}" "{} {} {}"\n'.format(
mi[0], ma[1], mi[2], ma[0], ma[1], mi[2]))
self._remember('draw line "{} {} {}" "{} {} {}"\n'.format(
mi[0], ma[1], mi[2], mi[0], ma[1], ma[2]))
self._remember('draw line "{} {} {}" "{} {} {}"\n'.format(
mi[0], mi[1], ma[2], ma[0], mi[1], ma[2]))
self._remember('draw line "{} {} {}" "{} {} {}"\n'.format(
mi[0], mi[1], ma[2], mi[0], ma[1], ma[2]))
self._remember('draw line "{} {} {}" "{} {} {}"\n'.format(
ma[0], ma[1], ma[2], ma[0], ma[1], mi[2]))
self._remember('draw line "{} {} {}" "{} {} {}"\n'.format(
ma[0], ma[1], ma[2], mi[0], ma[1], ma[2]))
self._remember('draw line "{} {} {}" "{} {} {}"\n'.format(
ma[0], ma[1], ma[2], ma[0], mi[1], ma[2]))
self.script.write("\n")
self.script.write("set htmd_graphics_mol({:d}) [molinfo top]".format(
self.n))
cmd = self.script.getvalue()
vmd = getCurrentViewer()
vmd.send(cmd)
def _drawForce(start, vec):
assert start.ndim == 1 and vec.ndim == 1
from htmd.vmdviewer import getCurrentViewer
vmd = getCurrentViewer()
vmd.send("""
proc vmd_draw_arrow {start end} {
# an arrow is made of a cylinder and a cone
draw color green
set middle [vecadd $start [vecscale 0.9 [vecsub $end $start]]]
graphics top cylinder $start $middle radius 0.15
graphics top cone $middle $end radius 0.25
}
""")
vmd.send('vmd_draw_arrow {{ {} }} {{ {} }}'.format(' '.join(map(str, start)), ' '.join(map(str, start + vec))))
def _drawForce(start, vec):
assert start.ndim == 1 and vec.ndim == 1
from htmd.vmdviewer import getCurrentViewer
vmd = getCurrentViewer()
vmd.send("""
proc vmd_draw_arrow {start end} {
# an arrow is made of a cylinder and a cone
draw color green
set middle [vecadd $start [vecscale 0.9 [vecsub $end $start]]]
graphics top cylinder $start $middle radius 0.15
graphics top cone $middle $end radius 0.25
}
""")
vmd.send('vmd_draw_arrow {{ {} }} {{ {} }}'.format(' '.join(map(str, start)), ' '.join(map(str, start + vec))))
def __init__(self,
mol,
selection,
molid='top',
textsize=0.5,
textcolor='green'):
""" Displays labels on atoms in VMD.
Examples
--------
>>> from htmd.ui import *
>>> from htmd.vmdgraphics import *
>>> mol = Molecule('3ptb')
>>> mol.view()
>>> x = VMDLabels(mol, 'resid 40')
>>> y = VMDLabels(mol, 'resid 50')
>>> y.delete()
>>> x.delete()
"""
# TODO: After deleting labels it breaks. Better don't delete or fix the code
super().__init__(None)
print(VMDLabels.count)
idx = mol.atomselect(selection, indexes=True)
cmd = '''label textsize {s}
color Labels Atoms {c}
set molnum [molinfo {molid}]
set i {start}
foreach n [list {idx}] {{
label add Atoms $molnum/$n
label textformat Atoms $i {{%a}}
incr i
}}'''.format(s=textsize,
c=textcolor,
sel=selection,
molid=molid,
idx=' '.join(map(str, idx)),
start=VMDLabels.count)
self.labelidx = list(range(VMDLabels.count,
VMDLabels.count + len(idx)))
VMDLabels.count += len(idx)
vmd = getCurrentViewer()
vmd.send(cmd)
def viewStates(self, protein=None, ligand=None, nsamples=20):
from htmd.projections.metric import _singleMolfile
from htmd.molecule.molecule import Molecule
from htmd.vmdviewer import getCurrentViewer
(single, molfile) = _singleMolfile(self.data.simlist)
if not single:
raise RuntimeError('Can'
't visualize states without unique molfile')
viewer = getCurrentViewer()
colors = [0, 1, 3, 4, 5, 6, 7, 9]
print('Active set includes macrostates: {}'.format(
self.hmm.active_set))
# dtraj = np.vstack(self.hmm.discrete_trajectories_full)
res = self.hmm.sample_by_observation_probabilities(nsamples)
refmol = Molecule(molfile)
for i, s in enumerate(self.hmm.active_set):
mol = Molecule(molfile)
mol.coords = []
mol.box = []
# idx = np.where(dtraj == i)[0]
# samples = np.random.choice(idx, 20)
# frames = self.data.abs2sim(samples)
frames = self.data.rel2sim(res[i])
for f in frames:
mol._readTraj(f.sim.trajectory[f.piece],
frames=[f.frame],
append=True)
mol.wrap('protein')
mol.align('protein', refmol=refmol)
viewer.loadMol(mol, name='hmm macro ' + str(s))
if ligand is not None:
viewer.rep('ligand',
sel=ligand,
color=colors[np.mod(i, len(colors))])
if protein is not None:
viewer.rep('protein')
viewer.send('start_sscache')
def __init__(self, box, color='red'):
""" Displays a box in VMD as lines of its edges.
The function returns an instance of VMDGraphicsObject. To delete it, use the delete() method.
Parameters
----------
box : list
The min and max positions of the edges. Given as [xmin, xmax, ymin, ymax, zmin, zmax]
color : str
Color of the lines
"""
super().__init__(box)
xmin, xmax, ymin, ymax, zmin, zmax = box
mi = [xmin, ymin, zmin]
ma = [xmax, ymax, zmax]
self._remember('draw materials off')
self._remember('draw color {}'.format(color))
self._remember('draw line "{} {} {}" "{} {} {}"\n'.format(mi[0], mi[1], mi[2], ma[0], mi[1], mi[2]))
self._remember('draw line "{} {} {}" "{} {} {}"\n'.format(mi[0], mi[1], mi[2], mi[0], ma[1], mi[2]))
self._remember('draw line "{} {} {}" "{} {} {}"\n'.format(mi[0], mi[1], mi[2], mi[0], mi[1], ma[2]))
self._remember('draw line "{} {} {}" "{} {} {}"\n'.format(ma[0], mi[1], mi[2], ma[0], ma[1], mi[2]))
self._remember('draw line "{} {} {}" "{} {} {}"\n'.format(ma[0], mi[1], mi[2], ma[0], mi[1], ma[2]))
self._remember('draw line "{} {} {}" "{} {} {}"\n'.format(mi[0], ma[1], mi[2], ma[0], ma[1], mi[2]))
self._remember('draw line "{} {} {}" "{} {} {}"\n'.format(mi[0], ma[1], mi[2], mi[0], ma[1], ma[2]))
self._remember('draw line "{} {} {}" "{} {} {}"\n'.format(mi[0], mi[1], ma[2], ma[0], mi[1], ma[2]))
self._remember('draw line "{} {} {}" "{} {} {}"\n'.format(mi[0], mi[1], ma[2], mi[0], ma[1], ma[2]))
self._remember('draw line "{} {} {}" "{} {} {}"\n'.format(ma[0], ma[1], ma[2], ma[0], ma[1], mi[2]))
self._remember('draw line "{} {} {}" "{} {} {}"\n'.format(ma[0], ma[1], ma[2], mi[0], ma[1], ma[2]))
self._remember('draw line "{} {} {}" "{} {} {}"\n'.format(ma[0], ma[1], ma[2], ma[0], mi[1], ma[2]))
self.script.write("\n")
self.script.write("set htmd_graphics_mol({:d}) [molinfo top]".format(self.n))
cmd = self.script.getvalue()
vmd = getCurrentViewer()
vmd.send(cmd)
def drawCube(mi, ma, viewer=None):
from htmd.vmdviewer import getCurrentViewer
if viewer is None:
viewer = getCurrentViewer()
viewer.send('draw materials off')
viewer.send('draw color red')
c = ''
c += 'draw line "{} {} {}" "{} {} {}"\n'.format(mi[0], mi[1], mi[2], ma[0],
mi[1], mi[2])
c += 'draw line "{} {} {}" "{} {} {}"\n'.format(mi[0], mi[1], mi[2], mi[0],
ma[1], mi[2])
c += 'draw line "{} {} {}" "{} {} {}"\n'.format(mi[0], mi[1], mi[2], mi[0],
mi[1], ma[2])
c += 'draw line "{} {} {}" "{} {} {}"\n'.format(ma[0], mi[1], mi[2], ma[0],
ma[1], mi[2])
c += 'draw line "{} {} {}" "{} {} {}"\n'.format(ma[0], mi[1], mi[2], ma[0],
mi[1], ma[2])
c += 'draw line "{} {} {}" "{} {} {}"\n'.format(mi[0], ma[1], mi[2], ma[0],
ma[1], mi[2])
c += 'draw line "{} {} {}" "{} {} {}"\n'.format(mi[0], ma[1], mi[2], mi[0],
ma[1], ma[2])
c += 'draw line "{} {} {}" "{} {} {}"\n'.format(mi[0], mi[1], ma[2], ma[0],
mi[1], ma[2])
c += 'draw line "{} {} {}" "{} {} {}"\n'.format(mi[0], mi[1], ma[2], mi[0],
ma[1], ma[2])
c += 'draw line "{} {} {}" "{} {} {}"\n'.format(ma[0], ma[1], ma[2], ma[0],
ma[1], mi[2])
c += 'draw line "{} {} {}" "{} {} {}"\n'.format(ma[0], ma[1], ma[2], mi[0],
ma[1], ma[2])
c += 'draw line "{} {} {}" "{} {} {}"\n'.format(ma[0], ma[1], ma[2], ma[0],
mi[1], ma[2])
viewer.send(c)
"""
def __init__(self, text, xyz, color='red'):
""" Displays a text in VMD.
The function returns an instance of VMDGraphicsObject. To delete it, use the delete() method.
Parameters
----------
text : str
The text
xyz : list
The position of the text
color : str
Color of the text
"""
super().__init__(xyz)
self._remember('draw materials off')
self._remember('draw color {}'.format(color))
self._remember('draw text "{} {} {}" "{}"\n'.format(xyz[0], xyz[1], xyz[2], text))
self.script.write("\n")
self.script.write("set htmd_graphics_mol({:d}) [molinfo top]".format(self.n))
cmd = self.script.getvalue()
vmd = getCurrentViewer()
vmd.send(cmd)
def __init__(self, xyz, color='red', radius=1):
""" Displays a sphere in VMD.
The function returns an instance of VMDGraphicsObject. To delete it, use the delete() method.
Parameters
----------
xyz : list
The center of the sphere
color : str
Color of the sphere
radius : float
The radius of the sphere
"""
super().__init__(xyz)
#self._remember('draw materials off')
self._remember('draw color {}'.format(color))
self._remember('draw sphere "{} {} {}" radius {}\n'.format(xyz[0], xyz[1], xyz[2], radius))
self.script.write("\n")
self.script.write("set htmd_graphics_mol({:d}) [molinfo top]".format(self.n))
cmd = self.script.getvalue()
vmd = getCurrentViewer()
vmd.send(cmd)
def viewStates(self, protein=None, ligand=None, nsamples=20):
from htmd.projections.metric import _singleMolfile
from htmd.molecule.molecule import Molecule
from htmd.vmdviewer import getCurrentViewer
(single, molfile) = _singleMolfile(self.data.simlist)
if not single:
raise RuntimeError('Can''t visualize states without unique molfile')
viewer = getCurrentViewer()
colors = [0, 1, 3, 4, 5, 6, 7, 9]
print('Active set includes macrostates: {}'.format(self.hmm.active_set))
# dtraj = np.vstack(self.hmm.discrete_trajectories_full)
res = self.hmm.sample_by_observation_probabilities(nsamples)
refmol = Molecule(molfile)
for i, s in enumerate(self.hmm.active_set):
mol = Molecule(molfile)
mol.coords = []
mol.box = []
# idx = np.where(dtraj == i)[0]
# samples = np.random.choice(idx, 20)
# frames = self.data.abs2sim(samples)
frames = self.data.rel2sim(res[i])
for f in frames:
mol._readTraj(f.sim.trajectory[f.piece], frames=[f.frame], append=True)
mol.wrap('protein')
mol.align('protein', refmol=refmol)
viewer.loadMol(mol, name='hmm macro ' + str(s))
if ligand is not None:
viewer.rep('ligand', sel=ligand, color=colors[np.mod(i, len(colors))])
if protein is not None:
viewer.rep('protein')
viewer.send('start_sscache')
def delete(self):
vmd = getCurrentViewer()
for i in self.labelidx[::-1]:
vmd.send('label delete Atoms {}'.format(i))
VMDLabels.count -= 1
def delete(self):
vmd = getCurrentViewer()
vmd.send('mol delete htmd_graphics_mol({:d})'.format(self.n))