def find_rotation_rest(fxyz, ligidx0, atomnames='CA', rcutoff=0.6, alpha=1.0, rest_rotbond=False, rotbond_only=False):
try:
t = md.load_arc(fxyz)
except IOError:
t = md.load(fxyz)
if rest_rotbond:
get_rottors(t, ligidx0)
if rotbond_only:
return
nbr = get_tab_branch(t.topology)
ligidx = np.array(sorted(list(set(ligidx0) - set(t.topology.select('name H')))))
if len(ligidx) == 0:
error_exit("No ligand heavy atoms found")
protidx0 = t.topology.select('name %s'%(atomnames))
protidx0 = np.array(sorted(set(protidx0) - set(ligidx)))
if len(protidx0) == 0:
error_exit("No ligand atoms within %.3f nm of protein %s atoms"%(rcutoff, atomnames))
int_idxs, r0s = get_idx_pocket(t, protidx0, ligidx)
RAD_IN_DEG = 180/np.pi
k0s = np.zeros_like(r0s) + 10.0/(RAD_IN_DEG)**2.0
k0s[0] = 10.0
print(write_rest(int_idxs, r0s, k0s))
RT = 8.314 * 298 / 4184
# https://doi.org/10.1021/jp0217839
# Eq. (14)
assert len(k0s) == 6
dgrest = RT*np.log(1662*8*np.pi**2.0*np.sqrt(np.prod(k0s)*RAD_IN_DEG**10.0) \
/(r0s[0]**2.0*np.sin(r0s[1]/RAD_IN_DEG)*np.sin(r0s[2]/RAD_IN_DEG)*(2*np.pi*RT)**3))
print("#dGrest(kcal/mol) %.5f"%dgrest)
def find_rotation_rest(annihilator,
fxyz,
ligidx0,
atomnames='CA',
rcutoff=0.6,
alpha=1.0,
rest_rotbond=False,
rotbond_only=False):
try:
t = md.load_arc(fxyz)
except IOError:
t = md.load(fxyz)
if rest_rotbond:
get_rottors(t, ligidx0)
if rotbond_only:
return
nbr = get_tab_branch(t.topology)
ligidx = np.array(
sorted(list(set(ligidx0) - set(t.topology.select('name H')))))
if len(ligidx) == 0:
error_exit("No ligand heavy atoms found")
protidx0 = t.topology.select('name %s' % (atomnames))
protidx0 = np.array(sorted(set(protidx0) - set(ligidx)))
if len(protidx0) == 0:
error_exit("No ligand atoms within %.3f nm of protein %s atoms" %
(rcutoff, atomnames))
annihilator.int_idxs = get_idx_pocket(t, protidx0, ligidx)
r0s = [calc_coord(t, _)[-1] for _ in annihilator.int_idxs] # last frame
RAD_IN_DEG = 180 / np.pi
k0s = np.zeros_like(r0s) + annihilator.anglerestraintconstant
k0s[0] = annihilator.distancerestraintconstant
restraintstrings = write_rest(annihilator.int_idxs, r0s, k0s)
keymods.RemoveKeyWord(annihilator, annihilator.configkeyfilename,
'restrain')
for string in restraintstrings:
keymods.AddKeyWord(annihilator, annihilator.configkeyfilename,
string + '\n')
RT = 8.314 * 298 / 4184
# https://doi.org/10.1021/jp0217839
# Eq. (14)
assert len(k0s) == 6
dgrest = -RT * np.log(
1662 * 8 * np.pi**2.0 * np.sqrt(np.prod(k0s) * RAD_IN_DEG**10.0) /
(r0s[0]**2.0 * np.sin(r0s[1] / RAD_IN_DEG) *
np.sin(r0s[2] / RAD_IN_DEG) * (2 * np.pi * RT)**3))
annihilator.rescorrection = dgrest
def AverageCOMGroups(annihilator, filename):
annihilator.WriteToLog('Averaging COM groups from ' + filename, prin=True)
try:
t = md.load_arc(filename)
except IOError:
t = md.load(filename)
g1COMtog2COMdistarray = []
g1atomidxtovecdic = {}
g1atomidxtomassdic = {}
g2atomidxtovecdic = {}
g2atomidxtomassdic = {}
for framecount in range(t.n_frames):
for a in t.topology.atoms:
zeroindex = a.index
atomidx = zeroindex + 1
atomsymb = a.element.symbol
mass = annihilator.elementsymtomass[atomsymb]
vec = t.xyz[framecount, zeroindex, :]
if atomidx in annihilator.restrainatomgroup1:
g1atomidxtovecdic[atomidx] = vec
g1atomidxtomassdic[atomidx] = mass
elif atomidx in annihilator.restrainatomgroup2:
g2atomidxtovecdic[atomidx] = vec
g2atomidxtomassdic[atomidx] = mass
if len(g1atomidxtovecdic.keys()) == len(
annihilator.restrainatomgroup1) and len(
g2atomidxtovecdic.keys()) == len(
annihilator.restrainatomgroup2):
g1COM = ComputeCOM(annihilator, g1atomidxtovecdic,
g1atomidxtomassdic)
g2COM = ComputeCOM(annihilator, g2atomidxtovecdic,
g2atomidxtomassdic)
dispx = g1COM[0] - g2COM[0]
dispx = ShiftDisplacementByPBC(annihilator, dispx)
dispy = g1COM[1] - g2COM[1]
dispy = ShiftDisplacementByPBC(annihilator, dispy)
dispz = g1COM[2] - g2COM[2]
dispz = ShiftDisplacementByPBC(annihilator, dispz)
dist = np.sqrt(dispx**2 + dispy**2 + dispz**2)
g1COMtog2COMdistarray.append(dist)
atomidxtovecdic = {}
atomidxtomassdic = {}
return round(np.mean(g1COMtog2COMdistarray), 2)
def find_grp_idx(fxyz, ligidx0, atomnames='CA', rcutoff=1.2, alpha=1.0):
try:
t = md.load_arc(fxyz)
except IOError:
t = md.load(fxyz)
ligidx = np.array(sorted(list(set(ligidx0) - set(t.topology.select('name H')))))
if len(ligidx) == 0:
error_exit("No ligand heavy atoms found")
protidx0 = t.topology.select('name %s'%(atomnames))
protidx0 = np.array(sorted(set(protidx0) - set(ligidx)))
distmat = distance_matrix(t.xyz[0, ligidx, :], t.xyz[0, protidx0, :])
distpro = np.min(distmat, axis=0)
protidx = protidx0[distpro <= rcutoff]
if len(protidx) == 0:
return
imindist = np.argmin(distmat)
iminlig = ligidx[imindist // len(protidx0)]
com_lig = np.mean(t.xyz[0, list(ligidx), :], axis=0)
com_lig = t.xyz[0, [iminlig], :]
wts0 = np.ones(len(protidx))
xyz_prot = t.xyz[0, protidx, :]
xyz1_prot = xyz_prot - com_lig.reshape((1, -1))
res = scipy.optimize.minimize(target_disp, wts0, args=(xyz1_prot, alpha))
wts1 = np.array(res.x)
wts1 = np.maximum(0, wts1)
wts1 *= 1.0/np.sum(wts1)
wtm = np.mean(wts1[wts1 > 0])
mask1 = wts1 > 0.4*wtm
#print(wts1)
#print(np.mean(wts1))
#print(mask1)
com_p1 = (np.mean(t.xyz[0, protidx[mask1], :], axis=0)).reshape((1, -1))
xyz_lig = t.xyz[0, ligidx, :]
dists = np.linalg.norm(xyz_lig - com_p1, axis=1)
#print('DIST', dists)
imin = np.argmin(dists)
dcom = np.linalg.norm(com_lig - com_p1)
dmin = np.linalg.norm(xyz_lig[imin] - com_p1)
idx_tinker = write_tinker_idx([_+1 for _ in protidx[mask1]])
#print('#', (' '.join(['%5d'%(_) for _ in protidx[mask1]])))
outp = ''
sgrp = ''
for n in idx_tinker:
sgrp += ' %5d'%n
if len(sgrp) > 50 and n > 0:
#print('group 1 %s'%sgrp)
outp += ('group 1 %s\n'%sgrp)
sgrp = ''
outp += ('group 2 %s\n'%(' '.join(['%5d'%(_) for _ in [ligidx[imin] + 1]])))
outp += ("#r_0=%.3f"%(dmin*10))
#print('group 2 %s'%(' '.join(['%5d'%(_) for _ in [ligidx[imin] + 1]])))
#print("#r_0=%.3f"%(dmin*10))
return dmin*10, outp
def __init__(self,arcname):
"""Reads in Tinker trajectory arcname."""
self.traj = md.load_arc(arcname)
def __init__(self,uindname):
"""Reads in Tinker uind file uindname."""
self.traj = md.load_arc(uindname)
# Convert units - mdtraj reads in as distance in nm!
self.traj.xyz = self.traj.xyz *10
