def draw(self, rbcoords, index, shift_com=True): # pragma: no cover
from pele.systems._opengl_tools import draw_atoms, draw_cylinder
from matplotlib.colors import cnames, hex2color
coords = self.aasystem.to_atomistic(rbcoords).copy()
coords = coords.reshape([-1,3])
if shift_com:
com=np.mean(coords, axis=0)
coords -= com[np.newaxis, :]
else:
com = np.zeros(3)
radius = 0.42
red = hex2color(cnames["red"])
c2 = hex2color(cnames["grey"])
draw_atoms(coords, self.harmonic_atoms, c2, radius=radius)
draw_atoms(coords, self.lj_atoms, red, radius=radius)
draw_atoms(coords, self.extra_atoms, c2, radius=radius)
for i1, i2 in self.draw_bonds:
draw_cylinder(coords[i1,:], coords[i2,:], color=c2)
def draw(self, rbcoords, index, shift_com=True): # pragma: no cover
from pele.systems._opengl_tools import draw_atoms, draw_cylinder
from matplotlib.colors import cnames, hex2color
coords = self.aasystem.to_atomistic(rbcoords).copy()
coords = coords.reshape([-1,3])
if shift_com:
com=np.mean(coords, axis=0)
coords -= com[np.newaxis, :]
else:
com = np.zeros(3)
radius = 0.42
red = hex2color(cnames["red"])
c2 = hex2color(cnames["grey"])
draw_atoms(coords, self.harmonic_atoms, c2, radius=radius)
draw_atoms(coords, self.lj_atoms, red, radius=radius)
draw_atoms(coords, self.extra_atoms, c2, radius=radius)
for i1, i2 in self.draw_bonds:
draw_cylinder(coords[i1,:], coords[i2,:], color=c2)
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)
def draw(self, rbcoords, index, shift_com=True): # pragma: no cover
from OpenGL import GL, GLUT
coords = self.aasystem.to_atomistic(rbcoords)
if shift_com:
com = np.mean(coords, axis=0)
else:
com = np.zeros(3)
i = 0
for atom_type, xx in zip(self.atom_types, coords):
color = [1.0, 0.0, 0.0]
radius = 0.3
if elements.has_key(atom_type):
color = elements[atom_type]["color"]
radius = elements[atom_type]["radius"] * self.render_scale
if index == 2:
color = [0.5, 1.0, .5]
i += 1
GL.glMaterialfv(GL.GL_FRONT_AND_BACK, GL.GL_DIFFUSE, color)
x = xx - com
GL.glPushMatrix()
GL.glTranslate(x[0], x[1], x[2])
GLUT.glutSolidSphere(radius, 10, 10)
GL.glPopMatrix()
color = [1.0, 1.0, 1.0]
if index == 2:
color = [0.5, 1.0, .5]
GL.glMaterialfv(GL.GL_FRONT_AND_BACK, GL.GL_DIFFUSE, color)
if hasattr(self, "draw_bonds"):
from pele.systems._opengl_tools import draw_cylinder
for i1, i2 in self.draw_bonds:
draw_cylinder(coords[i1] - com, coords[i2] - com)
def draw(self, rbcoords, index, shift_com=True): # pragma: no cover
from OpenGL import GL, GLUT
coords = self.aasystem.to_atomistic(rbcoords)
if shift_com:
com=np.mean(coords, axis=0)
else:
com = np.zeros(3)
i=0
for atom_type, xx in zip(self.atom_types, coords):
color = [1.0, 0.0, 0.0]
radius = 0.3
if elements.has_key(atom_type):
color = elements[atom_type]["color"]
radius = elements[atom_type]["radius"]*self.render_scale
if index == 2:
color = [0.5, 1.0, .5]
i+=1
GL.glMaterialfv(GL.GL_FRONT_AND_BACK, GL.GL_DIFFUSE, color)
x=xx-com
GL.glPushMatrix()
GL.glTranslate(x[0],x[1],x[2])
GLUT.glutSolidSphere(radius,10,10)
GL.glPopMatrix()
color = [1.0, 1.0, 1.0]
if index == 2:
color = [0.5, 1.0, .5]
GL.glMaterialfv(GL.GL_FRONT_AND_BACK, GL.GL_DIFFUSE, color)
if hasattr(self, "draw_bonds"):
from pele.systems._opengl_tools import draw_cylinder
for i1, i2 in self.draw_bonds:
draw_cylinder(coords[i1]-com, coords[i2]-com)
