def MOIsub():
v = list()
box = uni.dimensions[:3]
for s, vr in zip(sel, vref):
v0 = vft.pbc_pos(s.positions.T, box)
v1 = vft.principle_axis_MOI(v0)[:, 0]
v.append(v1 * np.sign(np.dot(v1, vr)))
return np.array(v).T
def sub():
vnorm = list()
box = uni.dimensions[:3]
for s in sel:
v0 = vft.pbc_pos(s.positions.T, box)
vnorm.append(vft.principle_axis_MOI(v0)[:, 0])
vnorm = np.array(vnorm)
#Pre-allocate output vector, to point along z
v1 = np.zeros([3, sel1.n_atoms])
v1[2] = 1
v2 = v1.copy()
v0 = vft.pbc_corr((sel1.positions - sel2.positions).T, box)
for k, vn in enumerate(vnorm):
v1[:, k == index] = vft.projXY(v0[:, k == index], vn)
v2[:, k == index] = np.array([vn]).T.repeat((k == index).sum(),
axis=1)
return v1, v2
def MOIz(molecule, sel, resids=None, segids=None, filter_str=None):
"""
Defines a frame for which the moment of inertia of a set of atoms remains
aligned along the z-axis. Note, atomic mass is NOT considered, all atoms
have equal influence.
MOIz(sel,resids,segids,filter_str)
"""
sel = selt.sel_lists(molecule, sel, resids, segids, filter_str)
uni = molecule.mda_object
uni.trajectory[0]
box = uni.dimensions[:3]
for k, s in enumerate(sel):
vr = s.positions
i0 = vft.sort_by_dist(vr)
sel[k] = sel[k][i0]
vref = list()
for s in sel:
v0 = vft.pbc_pos(s.positions.T, box)
vref.append(vft.principle_axis_MOI(v0)[:, 0])
def sub():
v = list()
box = uni.dimensions[:3]
for s, vr in zip(sel, vref):
v0 = vft.pbc_pos(s.positions.T, box)
v1 = vft.principle_axis_MOI(v0)[:, 0]
v.append(v1 * np.sign(np.dot(v1, vr)))
return np.array(v).T
return sub
def MOIbeta(molecule,
sel,
sel1=None,
sel2=None,
Nuc=None,
index=None,
resids=None,
segids=None,
filter_str=None):
"""
Separates out rotation within the moment of inertia frame (should be used in
conjunction with MOIz). That is, we identify rotational motion, where the z-axis
is the direction of the Moment of Inertia vector.
The user must provide one or more selections to define the moment of inertia
(sel). The user must also provide the selections to which the MOI is applied
(sel1 and sel2, or Nuc). Additional filters will be used as normal, applied
to all selections (resids,segids,filter_str). In case multiple MOI selections
are provided (in a list), the user must provide an index, to specifify which
bond goes with which MOI selection. This should usually be the same variable
as provided for the frame_index when using MOIz (and one will usually not
use a frame_index when setting up this frame)
MOIxy(sel,sel1=None,sel2=None,Nuc=None,index=None,resids=None,segids=None,filter_str=None)
"""
sel = selt.sel_lists(molecule, sel, resids, segids, filter_str)
if Nuc is not None:
sel1, sel2 = selt.protein_defaults(Nuc, molecule, resids, segids,
filter_str)
else:
sel1 = selt.sel_simple(molecule, sel1, resids, segids, filter_str)
sel2 = selt.sel_simple(molecule, sel2, resids, segids, filter_str)
uni = molecule.mda_object
uni.trajectory[0]
sel = selt.sel_lists(molecule, sel, resids, segids, filter_str)
uni = molecule.mda_object
uni.trajectory[0]
box = uni.dimensions[:3]
for k, s in enumerate(sel):
vr = s.positions
i0 = vft.sort_by_dist(vr)
sel[k] = sel[k][i0]
vref = list()
for s in sel:
v0 = vft.pbc_pos(s.positions.T, box)
vref.append(vft.principle_axis_MOI(v0)[:, 0])
def MOIsub():
v = list()
box = uni.dimensions[:3]
for s, vr in zip(sel, vref):
v0 = vft.pbc_pos(s.positions.T, box)
v1 = vft.principle_axis_MOI(v0)[:, 0]
v.append(v1 * np.sign(np.dot(v1, vr)))
return np.array(v).T
# for k,s in enumerate(sel):
# vr=s.positions
# i0=vft.sort_by_dist(vr)
# sel[k]=sel[k][i0]
if index is None:
if len(sel) == 1:
index = np.zeros(sel1.n_atoms, dtype=int)
elif len(sel) == sel1.n_atoms:
index = np.arange(sel1.n_atoms, dtype=int)
else:
print('index must be defined')
return
# vref=list()
# box=uni.dimensions[:3]
# for s in sel:
# v0=vft.pbc_pos(s.positions.T,box)
# vref.append(vft.principle_axis_MOI(v0)[:,0])
def sub():
vnorm = MOIsub()
#Pre-allocate output vector, to point along z
vZ = np.zeros([3, sel1.n_atoms])
vZ[2] = 1 #If a bond not in index, then vZ just on Z
# vXZ=np.zeros([3,sel1.n_atoms])
# vXZ[0]=1 #If a bond not in index, then vXZ just along x
sc = np.array(vft.getFrame(vnorm)).T
v00 = vft.norm(vft.pbc_corr((sel1.positions - sel2.positions).T, box))
for k, (vn, sc0) in enumerate(zip(vnorm.T, sc)):
v0 = v00[:, k == index]
cb = v0[0] * vn[0] + v0[1] * vn[1] + v0[2] * vn[
2] #Angle between MOI and bond
cb[cb > 1] = 1.0
sb = np.sqrt(1 - cb**2)
v0 = np.concatenate(([sb], [np.zeros(sb.shape)], [cb]), axis=0)
"Here, we keep the vector fixed in the xz plane of the MOI frame"
vZ[:, k == index] = vft.R(v0, *sc0)
# vZ[:,k==index]=v0
# vXZ[:,k==index]=np.atleast_2d(vn).T.repeat(v0.shape[1],1)
return vZ
return sub