def xform_pose(pose, xform):
for ir in range(1, len(pose.residues) + 1):
res = pose.residue(ir)
for ia in range(1, res.natoms() + 1):
old = res.xyz(ia)
old = np.array([old[0], old[1], old[2], 1])
new = xform @ old
pose.set_xyz(AtomID(ia, ir), rVec(new[0], new[1], new[2]))
def hokey_position_atoms(pose, ires1, ires2, metal_pos, metalaxispos):
znres1, znres2 = None, None
# if pose.residue(ires1).name() == 'HZD':
# znres1 = ires1
# znatom1 = 'VZN'
# axisatom1 = 'HZ'
# elif pose.residue(ires1).name3() == 'CYS':
# znres1 = ires1
# znatom1 = 'HG'
# axisatom1 = '2HB'
# elif pose.residue(ires1).name3() == 'ASP':
# znres1 = ires1
# znatom1 = '1HB'
# axisatom1 = '2HB'
# elif pose.residue(ires1).name3() == 'GLU':
# znres1 = ires1
# znatom1 = '1HG'
# axisatom1 = '2HG'
#
# if pose.residue(ires2).name3() == 'HZD':
# znres2 = ires2
# znatom2 = 'VZN'
# axisatom2 = 'HZ'
# elif pose.residue(ires2).name3() == 'CYS':
# znres2 = ires2
# znatom2 = 'HG'
# axisatom2 = '2HB'
# elif pose.residue(ires2).name3() == 'ASP':
# znres2 = ires2
# znatom2 = '1HB'
# axisatom2 = '2HB'
# elif pose.residue(ires2).name3() == 'GLU':
# znres2 = ires2
# znatom2 = '1HG'
# axisatom2 = '2HG'
znres1 = ires1
znres2 = ires2
znatom1 = '1HB'
znatom2 = '1HB'
axisatom1 = '2HB'
axisatom2 = '2HB'
for znres, znatom, axisatom in [(znres1, znatom1, axisatom1), (znres2, znatom2, axisatom2)]:
pose.set_xyz(AtomID(pose.residue(znres).atom_index(znatom), znres),
rVec(metal_pos[0], metal_pos[1], metal_pos[2]))
pose.set_xyz(AtomID(pose.residue(znres).atom_index(axisatom), znres),
rVec(metalaxispos[0], metalaxispos[1], metalaxispos[2]))
def xtal_search_single_residue(search_spec, pose, **kw):
raise NotImplemntedError('xtal_search_single_residue needs updating')
kw = rp.Bunch(kw)
spec = search_spec
xspec = spec.xtal_spec
results = list()
p_n = pose.pdb_info().name().split('/')[-1]
# gets rid of the ".pdb" at the end of the pdb name
pdb_name = p_n[:-4]
print(f'{pdb_name} searching')
# check the symmetry type of the pdb
last_res = rt.core.pose.chain_end_res(pose).pop()
total_res = int(last_res)
sym_num = pose.chain(last_res)
if sym_num < 2:
print('bad pdb', p_n)
return list()
sym = int(sym_num)
peptide_sym = "C%i" % sym_num
for ires in range(1, int(total_res / sym) + 1):
if pose.residue_type(ires) not in (spec.rts.name_map('GLY'), spec.rts.name_map('ALA'),
spec.rts.name_map('DALA')):
continue
lig_poses = util.mut_to_ligand(pose, ires, spec.ligands, spec.sym_of_ligand)
bad_rots = 0
for ilig, lig_pose in enumerate(lig_poses):
mut_res_name, lig_sym = lig_poses[lig_pose]
rotamers = lig_pose.residue(ires).get_rotamers()
rotamers = util.extra_rotamers(rotamers, lb=-20, ub=21, bs=20)
pose_num = 1
for irot, rotamer in enumerate(rotamers):
#for i in range(1, len(rotamer)+1): # if I want to sample the metal-axis too
for i in range(len(rotamer)):
lig_pose.residue(ires).set_chi(i + 1, rotamer[i])
rot_pose = rt.protocols.grafting.return_region(lig_pose, 1, lig_pose.size())
if kw.debug:
rot_pose.set_xyz(AtomID(rot_pose.residue(ires).atom_index('1HB'), ires),
rVec(0, 0, -2))
rot_pose.set_xyz(AtomID(rot_pose.residue(ires).atom_index('CB'), ires),
rVec(0, 0, +0.0))
rot_pose.set_xyz(AtomID(rot_pose.residue(ires).atom_index('2HB'), ires),
rVec(0, 0, +2))
spec.sfxn_rotamer(rot_pose)
dun_score = rot_pose.energies().residue_total_energy(ires)
if dun_score >= spec.max_dun_score:
bad_rots += 1
continue
rpxbody = rp.Body(rot_pose)
############ fix this
metal_orig = hm.hpoint(util.coord_find(rot_pose, ires, 'VZN'))
hz = hm.hpoint(util.coord_find(rot_pose, ires, 'HZ'))
ne = hm.hpoint(util.coord_find(rot_pose, ires, 'VNE'))
metal_his_bond = hm.hnormalized(metal_orig - ne)
metal_sym_axis0 = hm.hnormalized(hz - metal_orig)
dihedral = xspec.dihedral
############# ...
rots_around_nezn = hm.xform_around_dof_for_vector_target_angle(
fix=spec.pept_axis, mov=metal_sym_axis0, dof=metal_his_bond,
target_angle=np.radians(dihedral))
for idof, rot_around_nezn in enumerate(rots_around_nezn):
metal_sym_axis = rot_around_nezn @ metal_sym_axis0
assert np.allclose(hm.line_angle(metal_sym_axis, spec.pept_axis),
np.radians(dihedral))
newhz = util.coord_find(rot_pose, ires, 'VZN') + 2 * metal_sym_axis[:3]
aid = rt.core.id.AtomID(rot_pose.residue(ires).atom_index('HZ'), ires)
xyz = rVec(newhz[0], newhz[1], newhz[2])
rot_pose.set_xyz(aid, xyz)
tag = f'{pdb_name}_{ires}_{lig_poses[lig_pose][0]}_{idof}_{pose_num}'
xtal_poses = mof.xtal_build.xtal_build(
pdb_name,
xspec,
aa1,
aa2,
rot_pose,
peptide_sym,
spec.pept_orig,
spec.pept_axis,
lig_sym,
metal_orig,
metal_sym_axis,
rpxbody,
tag,
)
if False and xtal_poses:
print('hoaktolfhtoia')
print(rot_pose)
print(pdb_name)
print(xspec)
rot_pose.dump_pdb('test_xtal_build_p213.pdb')
print(ires)
print(peptide_sym)
print(spec.pept_orig)
print(spec.pept_axis)
print(lig_sym)
print(metal_orig)
print(metal_sym_axis)
print('rp.Body(pose)')
xalign, xpose, bodypdb = xtal_poses[0]
print(xalign)
xpose.dump_pdb('xtal_pose.pdb')
assert 0
for ixtal, (xalign, xtal_pose, body_pdb) in enumerate(xtal_poses):
celldim = xtal_pose.pdb_info().crystinfo().A()
fname = f"{xspec.spacegroup.replace(' ','_')}_cell{int(celldim):03}_{tag}"
results.append(
mof.result.Result(
xspec,
fname,
xalign,
rpxbody,
xtal_pose,
body_pdb,
))
pose_num += 1
# print(pdb_name, 'res', ires, 'bad rots:', bad_rots)
return results
def xtal_search_two_residues(
search_spec,
pose,
rotcloud1base,
rotcloud2base,
err_tolerance=1.5,
min_dist_to_z_axis=6.0,
sym_axes_angle_tolerance=3.0,
**arg,
):
arg = rp.Bunch(arg)
spec = search_spec
xspec = spec.xtal_spec
results = list()
farep_orig = search_spec.rep_sfxn(pose)
p_n = pose.pdb_info().name().split('/')[-1]
# gets rid of the ".pdb" at the end of the pdb name
pdb_name = p_n[:-4]
print(f'{pdb_name} searching')
# check the symmetry type of the pdb
last_res = rt.core.pose.chain_end_res(pose).pop()
total_res = int(last_res)
sym_num = pose.chain(last_res)
sym = int(sym_num)
if sym_num < 2:
print('bad pdb', p_n)
return list()
asym_nres = int(total_res / sym)
peptide_sym = "C%i" % sym_num
rpxbody = rp.Body(pose)
for ires1 in range(1, asym_nres + 1):
# if pose.residue_type(ires1) not in (spec.rts.name_map('ALA'), spec.rts.name_map('DALA')):
if pose.residue_type(ires1) != spec.rts.name_map('ALA'):
continue
stub1 = rpxbody.stub[ires1 - 1]
rots1ok = min_dist_to_z_axis < np.linalg.norm(
(stub1 @ rotcloud1base.rotframes)[:, :2, 3], axis=1)
if 0 == np.sum(rots1ok): continue
rotcloud1 = rotcloud1base.subset(rots1ok)
rotframes1 = stub1 @ rotcloud1.rotframes
# rotcloud1.dump_pdb(f'cloud_a_{ires1:02}.pdb', position=stub1)
range2 = range(1, int(total_res) + 1)
if rotcloud1base is rotcloud2base:
range2 = range(ires1 + 1, int(total_res) + 1)
for ires2 in range2:
if ires1 == ires2 % asym_nres: continue
if pose.residue_type(ires2) != spec.rts.name_map('ALA'):
continue
stub2 = rpxbody.stub[ires2 - 1]
# rotcloud2.dump_pdb(f'cloud_b_{ires2:02}.pdb', position=stub2)
rots2ok = min_dist_to_z_axis < np.linalg.norm(
(stub2 @ rotcloud2base.rotframes)[:, :2, 3], axis=1)
if 0 == np.sum(rots2ok): continue
rotcloud2 = rotcloud2base.subset(rots2ok)
rotframes2 = stub2 @ rotcloud2.rotframes
dist = rotframes1[:, :, 3].reshape(
-1, 1, 4) - rotframes2[:, :, 3].reshape(1, -1, 4)
dist = np.linalg.norm(dist, axis=2)
# if np.min(dist) < 1.0:
# print(f'{ires1:02} {ires2:02} {np.sort(dist.flat)[:5]}')
dot = np.sum(rotframes1[:, :, 0].reshape(-1, 1, 4) *
rotframes2[:, :, 0].reshape(1, -1, 4),
axis=2)
ang = np.degrees(np.arccos(dot))
angerr = np.abs(ang - 107)
err = angerr / 15.0 + dist
rot1err = np.min(err, axis=1)
bestrot2 = np.argmin(err, axis=1)
hits1 = np.argwhere(rot1err < err_tolerance).reshape(-1)
# hits = (angerr < angle_err_tolerance) * (dist < dist_err_tolerance)
if len(hits1):
# print(rotcloud1.amino_acid, rotcloud2.amino_acid, ires1, ires2)
hits2 = bestrot2[hits1]
hits = np.stack([hits1, hits2], axis=1)
# print(
# f'stats {ires1:2} {ires2:2} {np.sum(angerr < 10):7} {np.sum(dist < 1.0):5} {np.sum(hits):3}'
# )
for ihit, hit in enumerate(hits):
frame1 = rotframes1[hit[0]]
frame2 = rotframes2[hit[1]]
parl = (frame1[:, 0] + frame2[:, 0]) / 2.0
perp = rp.homog.hcross(frame1[:, 0], frame2[:, 0])
metalaxis1 = rp.homog.hrot(parl, +45) @ perp
metalaxis2 = rp.homog.hrot(parl, -45) @ perp
symang1 = rp.homog.line_angle(metalaxis1, spec.pept_axis)
symang2 = rp.homog.line_angle(metalaxis2, spec.pept_axis)
match11 = np.abs(np.degrees(symang1) -
35.26) < sym_axes_angle_tolerance
match12 = np.abs(np.degrees(symang2) -
35.26) < sym_axes_angle_tolerance
match21 = np.abs(np.degrees(symang1) -
54.735) < sym_axes_angle_tolerance
match22 = np.abs(np.degrees(symang2) -
54.735) < sym_axes_angle_tolerance
if not (match11 or match12 or match12 or match22): continue
matchsymang = symang1 if (match11 or match21) else symang2
metalaxis = metalaxis1 if (match11
or match21) else metalaxis2
metal_pos = (rotframes1[hit[0], :3, 3] +
rotframes2[hit[1], :3, 3]) / 2.0
metalaxispos = metal_pos + metalaxis[:3] + metalaxis[:3]
# metal_dist_z = np.sqrt(metal_pos[0]**2 + metal_pos[1]**2)
# if metal_dist_z < 4.0: continue
pose2 = mof.util.mutate_two_res(
pose,
ires1,
rotcloud1.amino_acid,
rotcloud1.rotchi[hit[0]],
ires2,
rotcloud2.amino_acid,
rotcloud2.rotchi[hit[1]],
)
if pose2.residue(ires1).has('VZN'):
pose2.set_xyz(
AtomID(
pose2.residue(ires1).atom_index('VZN'), ires1),
rVec(metal_pos[0], metal_pos[1], metal_pos[2]))
pose2.set_xyz(
AtomID(
pose2.residue(ires1).atom_index('HZ'), ires1),
rVec(metalaxispos[0], metalaxispos[1],
metalaxispos[2]))
elif pose2.residue(ires2).has('VZN'):
pose2.set_xyz(
AtomID(
pose2.residue(ires2).atom_index('VZN'), ires2),
rVec(metal_pos[0], metal_pos[1], metal_pos[2]))
pose2.set_xyz(
AtomID(
pose2.residue(ires2).atom_index('HZ'), ires2),
rVec(metalaxispos[0], metalaxispos[1],
metalaxispos[2]))
farep_delta = search_spec.rep_sfxn(pose2) - farep_orig
if farep_delta > 1.0: continue
print(
"HIT",
rotcloud1.amino_acid,
rotcloud2.amino_acid,
ires1,
ires2,
np.round(np.degrees(matchsymang), 3),
hit,
rotcloud1.rotchi[hit[0]],
rotcloud2.rotchi[hit[1]],
# farep_delta,
np.round(dist[tuple(hit)], 3),
np.round(angerr[tuple(hit)], 3),
)
fn = ('hit_%s_%s_%i_%i_%i.pdb' %
(rotcloud1.amino_acid, rotcloud2.amino_acid, ires1,
ires2, ihit))
rotcloud1.dump_pdb(fn + '_a.pdb', stub1, which=hit[0])
rotcloud2.dump_pdb(fn + '_b.pdb', stub2, which=hit[1])
pose2.dump_pdb(fn)
return results