def __setstate__(self, state):
name, files, types, reps = state
self.id = molecule.new(name, 0)
for file, type in zip(files, types):
self.load(file, type)
self.clearReps()
for rep in reps:
self.addRep(rep)
def __setstate__(self, state):
name, files, types, reps = state
self.id = molecule.new(name, 0)
for file, type in zip(files, types):
self.load(file, type)
self.clearReps()
for rep in reps:
self.addRep(rep)
def __init__(self, name=None, id=None, atoms=0):
"""
Creating a new Molecule instance with no arguments will create a new
empty molecule in VMD. Passing a valid molecule id will make the
Molecule instance mirror the state of the corresponding molecule in VMD.
If id is None, and a name is given, the new molecule will have that name.
"""
if id is None:
if name is None:
name = "molecule"
self.id = molecule.new(name, atoms)
else:
self.id = id
self.atoms = molecule.numatoms(self.id)
if not molecule.exists(self.id):
raise ValueError, "Molecule with id %d does not exist." % self.id
def __init__(self, name=None, id=None, atoms=0):
"""
Creating a new Molecule instance with no arguments will create a new
empty molecule in VMD. Passing a valid molecule id will make the
Molecule instance mirror the state of the corresponding molecule in VMD.
If id is None, and a name is given, the new molecule will have that name.
"""
if id is None:
if name is None:
name = "molecule"
self.id = molecule.new(name, atoms)
else:
self.id = id
self.atoms = molecule.numatoms(self.id)
if not molecule.exists(self.id):
raise ValueError, "Molecule with id %d does not exist." % self.id
def vmd_draw_angle(molid,
frame,
atomids=None,
atm_coords=None,
canvas=False,
resolution=200,
radius=0.5,
drawcolor="blue",
cylinder_radius=0.01):
"""
Draws part of a circle to visualize the measured angle.
Input:
> moldid int; index of molecule to draw the angle for
> frame int; frame number to draw the angle for
> atomids tuple; all three atom ids with second one as angular
point
> canvas boolean; draw a canvas between bow and angle axis
> resolution int; number of cylinders and spheres that form the angle
"""
if atomids is not None:
id1, id2, id3 = atomids
# select all atoms
sel = atomsel.atomsel("all", molid, frame)
# get coordinates
x = sel.get("x")
y = sel.get("y")
z = sel.get("z")
# get rotational axis
atm1Crds = np.array([x[id1], y[id1], z[id1]])
atm2Crds = np.array([x[id2], y[id2], z[id2]])
atm3Crds = np.array([x[id3], y[id3], z[id3]])
elif atm_coords is not None:
atm1Crds, atm2Crds, atm3Crds = atm_coords
else:
raise Warning(
"At least atomic coordinates or atom ids have to be provided!")
# draw bows in the current molecule, transparent canvas in a new molecule
if canvas is True:
molecule.new("angle canvas")
graphics_id = molecule.num() - 1 # ids start with 0
else:
graphics_id = molid
graphics.color(graphics_id, drawcolor)
#pdb.set_trace()
# define angle and rotational axis
vt1 = atm1Crds - atm2Crds
vt2 = atm3Crds - atm2Crds
vtRot = np.cross(vt1, vt2)
# unit vectors for quaternions
vt1 /= np.linalg.norm(vt1)
vt2 /= np.linalg.norm(vt2)
vtRot /= np.linalg.norm(vtRot)
# define angle offset
max_angle = np.arccos(np.dot(
vt1, vt2)) # denominator is 1 since vectors are normed
print("Measured angles: {}".format(np.degrees(max_angle)))
angle_offset = np.pi / resolution
vt1 *= radius
vt2 *= radius
for cntr, theta in enumerate(np.arange(0, max_angle, angle_offset)):
# previous vector
if cntr == 0:
vt_pre = vt1 + atm2Crds
# define quaternion
q = Quaternion(axis=vtRot, angle=theta)
#print(q)
# rotate vector
vt_cur = q.rotate(vt1)
vt_cur += atm2Crds
if canvas is True and cntr != 0:
graphics.triangle(graphics_id, tuple(vt_pre), tuple(atm2Crds),
tuple(vt_cur))
else:
graphics.cylinder(graphics_id,
tuple(vt_pre),
tuple(vt_cur),
radius=cylinder_radius,
resolution=20,
filled=1)
vt_pre = vt_cur
if canvas is True:
graphics.triangle(graphics_id, tuple(vt_pre), tuple(atm2Crds),
tuple(vt2 + atm2Crds))
graphics.material(graphics_id, "Transparent")
else:
graphics.cylinder(graphics_id,
tuple(vt_pre),
tuple(vt2 + atm2Crds),
radius=cylinder_radius,
resolution=20,
filled=1)
def draw_torsion(molid,
frame,
atomids,
canvas=False,
resolution=50,
radius=0.5,
drawcolor="blue"):
"""
"""
id1, id2, id3, id4 = atomids
# draw bows in the current molecule, transparent canvas in a new molecule
if canvas is True:
molecule.new("angle canvas")
graphics_id = molecule.num() - 1 # ids start with 0
else:
graphics_id = molid
graphics.color(graphics_id, drawcolor)
# select all atoms
sel = atomsel.atomsel("all", molid, frame)
# get coordinates
x = sel.get("x")
y = sel.get("y")
z = sel.get("z")
# get rotational axis
atm1Crds = np.array([x[id1], y[id1], z[id1]])
atm2Crds = np.array([x[id2], y[id2], z[id2]])
atm3Crds = np.array([x[id3], y[id3], z[id3]])
atm4Crds = np.array([x[id4], y[id4], z[id4]])
# define angle and rotational axis
#vt1 = atm1Crds - atm2Crds
#vt2 = atm3Crds - atm2Crds
#vtRot = np.cross(vt1, vt2)
# unit vectors for quaternions
#vt1 /= np.linalg.norm(vt1)
#vt2 /= np.linalg.norm(vt2)
#vtRot /= np.linalg.norm(vtRot)
#print(atm1Crds)
_, cp1, cp2 = ag_geometry.get_dihedral(atm1Crds,
atm2Crds,
atm3Crds,
atm4Crds,
return_cross=True)
# draw vectors between id2 and id3, therefor get the relevant vector
center_pt = atm2Crds + (atm3Crds - atm2Crds) * 0.5
cp1 += center_pt
cp2 += center_pt
vmd_draw_angle(molid,
frame,
atm_coords=[cp1, center_pt, cp2],
canvas=False,
resolution=resolution,
radius=radius,
drawcolor="blue")