def draw(self, coordsl, index):
from pele.systems._opengl_tools import draw_sphere
coords = coordsl.reshape([-1, 3])
com = np.mean(coords, axis=0)
# draw atoms as spheres
for i, name in enumerate(self.atom_names): # in self.potential.prmtop.topology.atoms():
x = coords[i, :] - com
col = elements[name]['color']
if index == 2:
col = [0.5, 1.0, .5]
rad = elements[name]['radius'] / 5
draw_sphere(x, radius=rad, color=col)
# draw bonds
for atomPairs in self.bonds: # self.potential.prmtop.topology.bonds():
# note that atom numbers in topology start at 0
xyz1 = coords[atomPairs[0]] - com
xyz2 = coords[atomPairs[1]] - com
self.drawCylinder(xyz1, xyz2)
def draw(self, coordsl, index):
from pele.systems._opengl_tools import draw_sphere
coords = coordsl.reshape([-1, 3])
com = np.mean(coords, axis=0)
# draw atoms as spheres
for i, name in enumerate(
self.atom_names): # in self.potential.prmtop.topology.atoms():
x = coords[i, :] - com
col = elements[name]['color']
if index == 2:
col = [0.5, 1.0, .5]
rad = elements[name]['radius'] / 5
draw_sphere(x, radius=rad, color=col)
# draw bonds
for atomPairs in self.bonds: # self.potential.prmtop.topology.bonds():
# note that atom numbers in topology start at 0
xyz1 = coords[atomPairs[0]] - com
xyz2 = coords[atomPairs[1]] - com
self.drawCylinder(xyz1, xyz2)
def draw(self, rbcoords, index, shift_com=True): # pragma: no cover
from pele.systems._opengl_tools import draw_sphere, draw_cylinder
coords = self.aasystem.to_atomistic(rbcoords).reshape(-1, 3)
if shift_com:
com = np.mean(coords, axis=0)
coords = coords - com[np.newaxis, :]
for atom_type, xx in zip(self.atom_types, coords):
color = [1.0, 0.0, 0.0]
radius = 0.3
if atom_type in elements:
color = elements[atom_type]["color"]
radius = elements[atom_type]["radius"] * self.render_scale
if index == 2:
color = [0.5, 1.0, .5]
draw_sphere(xx, radius, color)
if hasattr(self, "draw_bonds"):
color = [1.0, 1.0, 1.0]
if index == 2:
color = [0.5, 1.0, .5]
for i1, i2 in self.draw_bonds:
draw_cylinder(coords[i1], coords[i2], color=color)
def draw(self, rbcoords, index, shift_com=True): # pragma: no cover
from pele.systems._opengl_tools import draw_sphere, draw_cylinder
coords = self.aasystem.to_atomistic(rbcoords).reshape(-1, 3)
if shift_com:
com = np.mean(coords, axis=0)
coords = coords - com[np.newaxis, :]
for atom_type, xx in zip(self.atom_types, coords):
color = [1.0, 0.0, 0.0]
radius = 0.3
if atom_type in elements:
color = elements[atom_type]["color"]
radius = elements[atom_type]["radius"] * self.render_scale
if index == 2:
color = [0.5, 1.0, .5]
draw_sphere(xx, radius, color)
if hasattr(self, "draw_bonds"):
color = [1.0, 1.0, 1.0]
if index == 2:
color = [0.5, 1.0, .5]
for i1, i2 in self.draw_bonds:
draw_cylinder(coords[i1], coords[i2], color=color)