def get_NGL_selection_from_AtomID(pose: pyrosetta.Pose,
atom_id: pyrosetta.AtomID):
pose_resi = atom_id.rsd()
residue = pose.residue(pose_resi)
atom_name = residue.atom_name(atom_id.atomno()).strip()
pdb_resi, chain = pose.pdb_info().pose2pdb(pose_resi).strip().split()
return f'[{residue.name3().strip()}]{pdb_resi}:{chain}.{atom_name}'
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 name2aid(pose, ires, aname):
return AtomID(pose.residue(ires).atom_index(aname.strip()), ires)
print(pose.residue(500).name())
print(pose.pdb_info().chain(500))
print(pose.pdb_info().number(500))
print(pose.pdb_info().pdb2pose("A", 100))
print(pose.pdb_info().pose2pdb(25))
pose.display_secstruct()
# Protein Geometry
print(pose.phi(5))
print(pose.psi(5))
print(pose.chi(1, 5))
R5N = AtomID(1, 5)
R5CA = AtomID(2, 5)
R5C = AtomID(3, 5)
print(pose.conformation().bond_length(R5N, R5CA))
print(pose.conformation().bond_length(R5CA, R5C))
N_xyz = pose.residue(5).xyz("N")
CA_xyz = pose.residue(5).xyz("CA")
N_CA_vector = CA_xyz - N_xyz
print(N_CA_vector.norm)
print(pose.conformation().bond_angle(R5N, R5CA, R5C))
pose.set_phi(5, -60)
pose.set_psi(5, -43)
pose.set_chi(1, 5, 180)
pose.conformation().set_bond_length(R5N, R5CA, 1.5)
def xtal_build(
pdb_name,
xspec,
aa1,
aa2,
pose,
peptide_sym,
peptide_orig,
peptide_axis,
metal_sym,
metal_origin,
metal_sym_axis,
rpxbody,
tag,
clash_dis,
contact_dis,
min_contacts,
max_sym_score,
debug=False,
**kw,
):
kw = rp.Bunch(kw)
if not kw.timer: kw.timer = rp.Timer().start()
lj_sfxn = get_sfxn('sterics')
sym1 = xspec.sym1
orig1 = xspec.orig1
axis1 = xspec.axis1
axis1d = xspec.axis1d
sym2 = xspec.sym2
orig2 = xspec.orig2
axis2 = xspec.axis2
axis2d = xspec.axis2d
dihedral = xspec.dihedral
if np.allclose(orig2, [0, 0, 0, 1]):
sym1, sym2 = sym2, sym1
orig1, orig2 = orig2, orig1
axis1, axis2 = axis2, axis1
axis1d, axis2d = axis2d, axis1d
swapped = True # hopefully won't need this
assert sym1 == metal_sym
assert sym2 == peptide_sym
# axis2 = np.array([0.57735, 0.57735, 0.57735, 0])
# axis1 = np.array([1, 0, 0, 0])
# orig2 = np.array([0.5, 0.5, 0, 1])
elif np.allclose(orig1, [0, 0, 0, 1]):
# assert np.allclose(orig1, [0, 0, 0, 1])
assert sym1 == peptide_sym
assert sym2 == metal_sym
swapped = False
# axis1 = np.array([0.57735, 0.57735, 0.57735, 0])
# assert 0, 'maybe ok, check this new branch'
else:
# print('both sym elements not at origin')
pass
# raise NotImplementedError('both sym elements not at origin')
if sym1 == peptide_sym:
pt1, ax1 = peptide_orig, peptide_axis
pt2, ax2 = metal_origin, metal_sym_axis
first_is_peptide = True
else:
pt1, ax1 = metal_origin, metal_sym_axis
pt2, ax2 = peptide_orig, peptide_axis
first_is_peptide = False
nfold1 = float(str(sym1)[1])
nfold2 = float(str(sym2)[1])
ax1 = ax1 / np.linalg.norm(ax1)
ax2 = ax2 / np.linalg.norm(ax2)
# print(rp.homog.line_angle(metal_sym_axis, peptide_axis), np.radians(dihedral))
assert np.allclose(rp.homog.line_angle(metal_sym_axis, peptide_axis), np.radians(dihedral),
atol=1e-3)
assert np.allclose(rp.homog.line_angle(ax1, ax2), np.radians(dihedral), atol=1e-3)
# print(rp.homog.line_angle(ax1, ax2), np.radians(dihedral), dihedral)
# print('sym1', sym1, orig1, axis1, ax1)
# print('sym2', sym2, orig2, axis2, ax2)
#
# print('== xtal_build ==')
# Xalign, _ = rp.homog.align_lines_isect_axis2(pt1, ax1, pt2, ax2, axis1, orig1, axis2, orig2)
Xalign, scale = rp.homog.scale_translate_lines_isect_lines(pt1, ax1, pt2, ax2, orig1, axis1,
orig2, axis2)
xpt1, xax1 = Xalign @ pt1, Xalign @ ax1
xpt2, xax2 = Xalign @ pt2, Xalign @ ax2
# print('aligned1', xpt1, xax1)
# print('aligned2', xpt2, xax2)
assert np.allclose(rp.homog.line_angle(xax1, axis1), 0.0, atol=0.001)
assert np.allclose(rp.homog.line_angle(xax2, axis2), 0.0, atol=0.001)
# from previous req that ax1 isect the origin??
# assert np.allclose(rp.homog.line_angle(xpt1, axis1), 0.0, atol=0.001)
isect_error2 = rp.homog.line_line_distance_pa(xpt2, xax2, [0, 0, 0, 1], orig2)
assert np.allclose(isect_error2, 0, atol=0.001)
# isect = rp.homog.line_line_closest_points_pa(xpt2, xax2, [0, 0, 0, 1], orig2)
# isect = (isect[0] + isect[1]) / 2
# orig = orig2 # not always??
# celldims = [isect[i] / o for i, o in enumerate(orig[:3]) if abs(o) > 0.001]
celldims = scale[:3]
assert np.allclose(min(celldims), max(celldims), atol=0.001)
celldim = abs(min(celldims))
if not (kw.min_cell_size <= celldim <= kw.max_cell_size):
print(' ', xspec.spacegroup, pdb_name, aa1, aa2, 'Fail on cell_size', celldim)
return []
nsym = int(peptide_sym[1])
assert pose.size() % nsym == 0
nres_asym = pose.size() // nsym
xtal_pose = rt.protocols.grafting.return_region(pose, 1, nres_asym)
solv_frac = mof.filters.approx_solvent_fraction(xtal_pose, xspec, celldim)
if kw.max_solv_frac < solv_frac:
print(' ', xspec.spacegroup, pdb_name, aa1, aa2, 'Fail on solv_frac', solv_frac)
return []
# rt.numeric.xyzVec(hz[0], hz[1], hz[2]))
xtal_pose.apply_transform_Rx_plus_v(
xyzMat.cols(Xalign[0, 0], Xalign[1, 0], Xalign[2, 0], Xalign[0, 1], Xalign[1, 1],
Xalign[2, 1], Xalign[0, 2], Xalign[1, 2], Xalign[2, 2]),
xyzVec(Xalign[0, 3], Xalign[1, 3], Xalign[2, 3]))
# check ZN sym center location vs zn position?????????
# print('--------------')
# print(celldim, orig1[:3], orig2[:3])
# print('--------------')
if xspec.frames is None:
# raise NotImplementedError('no sym frames for', xspec.spacegroup)
print(f'{f" generate sym frames for {spec.spacegroup} ":}')
dummy_scale = 100.0
if sym1 == peptide_sym:
redundant_point = rp.homog.hpoint(dummy_scale * orig1[:3] + 10 * axis1[:3])
else:
redundant_point = rp.homog.hpoint(dummy_scale * orig2[:3] + 10 * axis2[:3])
# redundant_point = rp.homog.rand_point()
# redundant_point[:3] *= dummy_scale
print('redundant_point', redundant_point)
print(Xalign @ redundant_point)
g1 = rp.homog.hrot(axis1, (2 * np.pi / nfold1) * np.arange(nfold1), dummy_scale * orig1[:3])
g2 = rp.homog.hrot(axis2, (2 * np.pi / nfold2) * np.arange(nfold2), dummy_scale * orig2[:3])
g = np.concatenate([g1, g2])
symxforms = list()
count = 0
for x in rp.homog.expand_xforms(g, redundant_point=redundant_point, N=12,
maxrad=3.0 * dummy_scale):
symxforms.append(x)
print(count)
count += 1
# rp.dump(list(symxforms), 'i213_redundant111_n16_maxrad2.pickle')
# symxforms = rp.load('i213_redundant111_n16_maxrad2_ORIG.pickle')
print('num symframes', len(symxforms), type(symxforms[0]))
symxforms = np.stack(symxforms, axis=0)
print('symframes shape', symxforms.shape)
symxforms[:, :3, 3] /= dummy_scale
# print(np.around(symxforms[:, :3, 3], 3))
rp.dump(symxforms, 'new_symframes.pickle')
symxforms[:, :3, 3] *= celldim
rpxbody.move_to(Xalign)
rpxbody.dump_pdb('body_I.pdb')
for i, x in enumerate(symxforms):
rpxbody.move_to(x @ Xalign)
rpxbody.dump_pdb('body_%i.pdb' % i)
assert 0, "must rerun with newly genrated symframes"
symxforms = xspec.frames.copy()
symxforms[:, :3, 3] *= celldim
# g1 = rp.homog.hrot(axis1, (2 * np.pi / nfold1) * np.arange(0, nfold1), celldim * orig1[:3])
# g2 = rp.homog.hrot(axis2, (2 * np.pi / nfold2) * np.arange(0, nfold2), celldim * orig2[:3])
# # # print('g1', axis1.round(3), 360 / nfold1, (celldim * orig1[:3]).round(3))
# # # print('g2', axis2.round(3), 360 / nfold2, (celldim * orig2[:3]).round(3))
# if swapped: g1, g2 = g2, g1
# g = np.concatenate([g1, g2])
# # print('swapped', swapped)
# redundant_point = (xpt1 + xax1) if first_is_peptide else (xpt2 + xax2)
# # redundant_point = xpt1 if first_is_peptide else xpt2
# # print('redundancy point', redundant_point)
# # # rpxbody.move_to(np.eye(4))
# # # rpxbody.dump_pdb('a_body.pdb')
# rpxbody.move_to(Xalign)
# # # print(0, Xalign @ rp.homog.hpoint([1, 2, 3]))
# # rpxbody.dump_pdb('a_body_xalign.pdb')
kw.timer.checkpoint()
clash, tot_ncontact = False, 0
rpxbody_pdb, ir_ic = rpxbody.str_pdb(warn_on_chain_overflow=False, use_orig_coords=False)
body_xalign = rpxbody.copy()
body_xalign.move_to(Xalign)
# body_xalign.dump_pdb('body_xalign.pdb')
prev = [np.eye(4)]
for i, x in enumerate(symxforms):
# rp.homog.expand_xforms(g, redundant_point=redundant_point, N=6, maxrad=30)):
if np.allclose(x, np.eye(4), atol=1e-4): assert 0
rpxbody.move_to(x @ Xalign)
# rpxbody.dump_pdb('clashcheck%02i.pdb' % i)
if debug:
pdbstr, ir_ic = rpxbody.str_pdb(start=ir_ic, warn_on_chain_overflow=False,
use_orig_coords=False)
rpxbody_pdb += pdbstr
if np.any(rpxbody.intersect(rpxbody,
np.stack(prev) @ Xalign, x @ Xalign, mindis=clash_dis)):
clash = True
print(' ', xspec.spacegroup, pdb_name, aa1, aa2, 'Fail on xtal clash', f'sub{i+1}')
return []
ncontact = rpxbody.contact_count(body_xalign, maxdis=contact_dis)
tot_ncontact += ncontact
prev.append(x)
# if clash and debug:
# for xprev in prev:
# # print(xprev.shape, (xprev @ Xalign).shape, (x @ Xalign).shape)
# if rpxbody.intersect(rpxbody, xprev @ Xalign, x @ Xalign, mindis=3.0):
# show_body_isect(rpxbody, Xalign, maxdis=3.0)
# rp.util.dump_str(rpxbody_pdb, 'sym_bodies.pdb')
# assert 0
if tot_ncontact < min_contacts:
print(' ', xspec.spacegroup, pdb_name, aa1, aa2, 'Fail on ncontact', tot_ncontact)
return []
kw.timer.checkpoint('clash_check')
# for i, x in enumerate(symxforms):
# # print('sym xform %02i' % i, rp.homog.axis_ang_cen_of(x)
# rpxbody.move_to(x @ Xalign)
# rpxbody.dump_pdb('clashframe_%02i.pdb' % i)
# assert 0
# print('!!!!!!!!!!!!!!!! debug clash check !!!!!!!!!!!!!!!!!!!!!!!!!')
# rpxbody.move_to(Xalign)
# rpxbody.dump_pdb('body.pdb')
# symxforms = rp.homog.expand_xforms(g, redundant_point=redundant_point, N=8, maxrad=30)
# for i, x in enumerate(symxforms):
# # print('sym xform %02i' % i, rp.homog.axis_ang_cen_of(x))
# rpxbody.move_to(x @ Xalign)
# rpxbody.dump_pdb('clashcheck%02i.pdb' % i)
# if rpxbody.intersect(rpxbody, Xalign, x @ Xalign, mindis=3.0):
# util.show_body_isect(rpxbody, Xalign, maxdis=3.0)
# rp.util.dump_str(rpxbody_pdb, 'sym_bodies.pdb')
# assert 0
# assert 0, 'xtal build after clashcheck'
# fname = f'{tag}_body_xtal.pdb'
# print('dumping checked bodies', fname)
ci = rt.core.io.CrystInfo()
ci.A(celldim) # cell dimensions
ci.B(celldim)
ci.C(celldim)
ci.alpha(90) # cell angles
ci.beta(90)
ci.gamma(90)
ci.spacegroup(xspec.spacegroup) # sace group
pi = rt.core.pose.PDBInfo(xtal_pose)
pi.set_crystinfo(ci)
xtal_pose.pdb_info(pi)
nonbonded_energy = 0
if max_sym_score < 1000:
sympose = xtal_pose.clone()
rt.protocols.cryst.MakeLatticeMover().apply(sympose)
syminfo = rt.core.pose.symmetry.symmetry_info(sympose)
# rp.util.dump_str(rpxbody_pdb, 'symbodies.pdb')
lj_sfxn(sympose)
nasym = len(xtal_pose.residues)
nchain = syminfo.subunits() # sympose.num_chains()
bonded_subunits = []
nterm = sympose.residue(1).xyz('N')
cterm = sympose.residue(nasym).xyz('C')
for i in range(1, nchain):
nres = i * nasym + 1
cres = i * nasym + nasym
if 2 > cterm.distance(sympose.residue(nres).xyz('N')):
bonded_subunits.append(i + 1)
if 2 > nterm.distance(sympose.residue(cres).xyz('C')):
bonded_subunits.append(i + 1)
energy_graph = sympose.energies().energy_graph()
eweights = sympose.energies().weights()
nonbonded_energy = 0
for ichain in range(1, nchain):
if ichain + 1 in bonded_subunits: continue
for i in range(nasym):
ir = ichain + i + 1
for j in range(nasym):
jr = j + 1
edge = energy_graph.find_edge(ir, jr)
if not edge:
continue
nonbonded_energy += edge.dot(eweights)
# print('nonbonded_energy', nonbonded_energy)
if nonbonded_energy > max_sym_score:
print(' ', xspec.spacegroup, pdb_name, aa1, aa2,
'Fail on nonbonded_energy(max_sym_score)', nonbonded_energy)
return []
kw.timer.checkpoint('make sympose and "nonbonded" score')
znpos = Xalign @ metal_origin
znres = make_residue('VZN')
xtal_pose.append_residue_by_jump(znres, 1)
znresi = len(xtal_pose.residues)
znpos = xyzVec(*znpos[:3])
zndelta = znpos - xtal_pose.residue(znresi).xyz(1)
for ia in range(1, xtal_pose.residue(znresi).natoms() + 1):
newxyz = zndelta + xtal_pose.residue(znresi).xyz(ia)
# print(xtal_pose.residue(znresi).name(), ia, xtal_pose.residue(znresi).atom_name(ia), newxyz)
xtal_pose.set_xyz(AtomID(ia, znresi), newxyz)
# xtal_pose.dump_pdb('a_xtal_pose.pdb')
# assert 0
# rp.util.dump_str(rpxbody_pdb, 'a_symframes.pdb')
# assert 0
return [(Xalign, xtal_pose, rpxbody_pdb, tot_ncontact, nonbonded_energy, solv_frac)]
def load(pose):
"""
Load a :class:`Pose` object and return a populated :class:`Structure`
instance
Parameters
----------
pose : :class:`Pose`
PyRosetta :class:`Pose` object to convert
"""
if not Pose or not AtomID:
raise ImportError('Could not load the PyRosetta module.')
if not isinstance(pose, Pose):
raise TypeError('Object is not a PyRosetta Pose object.')
struct = Structure()
atnum = 1
conf = pose.conformation()
for resid in range(1, pose.total_residue() + 1):
res = pose.residue(resid)
resname = res.name3().strip()
chain = chr(res.chain() + ord('A') - 1)
for atno, at in enumerate(res.atoms(), start=1):
try:
atinfo = res.atom_type(atno)
atname = res.atom_name(atno).strip()
if atinfo.is_virtual():
atsym = 'EP'
else:
atsym = atinfo.element()
rmin = atinfo.lj_radius()
epsilon = atinfo.lj_wdepth()
atomic_number = AtomicNum[atsym]
mass = Mass[atsym]
except KeyError:
raise RosettaError('Could not recognize element: %s.' %
atsym)
params = dict(atomic_number=atomic_number,
name=atname,
charge=0.0,
mass=mass,
occupancy=0.0,
bfactor=0.0,
altloc='',
number=atnum,
rmin=rmin,
epsilon=epsilon)
if atinfo.is_virtual():
atom = ExtraPoint(**params)
else:
atom = Atom(**params)
atom.xx, atom.xy, atom.xz = (at.xyz()[0], at.xyz()[1],
at.xyz()[2])
struct.add_atom(atom, resname, resid, chain, '')
atnum += 1
try:
for nbr in conf.bonded_neighbor_all_res(AtomID(
atno, resid)):
if nbr.rsd() < resid or (nbr.rsd() == resid
and nbr.atomno() < atno):
struct.bonds.append(
Bond(struct.atoms[_n_prior(pose, nbr)], atom))
except:
raise RosettaError('Could not add bonds.')
struct.unchange()
return struct
print('accessing atoms from residue 5')
at5N = res5.atom('N')
at5CA = res5.atom("CA")
at5C = res5.atom("C")
print(at5N)
# TODO: above should print atom type key not magic number
# 2/23/9: hm, not sure this is possible b/c atom does not know which AtomTypeSet to use!
print('xyz of at5N:', at5N.xyz().x, at5N.xyz().y, at5N.xyz().z)
print('norm of xyz at5N:', at5N.xyz().norm)
print(res5.atoms()) # <-- Still missing
atomN = AtomID(1, 5)
atomCA = AtomID(2, 5)
atomC = AtomID(3, 5)
print('bond length of N-CA in residue 5 is ')
print(pose.conformation().bond_length(atomN, atomCA))
print('bond angle of N-CA-C in residue 5 is ')
print(pose.conformation().bond_angle(atomN, atomCA, atomC))
print('setting bond length of N-CA in residue 5 to 1.5A ')
pose.conformation().set_bond_length(atomN, atomCA, 1.5)
print('setting bond angle of N-CA-C in residue 5 to 90 ')
pose.conformation().set_bond_angle(atomN, atomCA, atomC, 90)
# TODO: make the above work with atom objects instead of atomIDs
print('pose was generated from this pdb file: ', pose.pdb_info().name())
print('pose numbering for chain A, residue 5, is ',
pose.pdb_info().pdb2pose('A', 5))
def minimize_mof_xtal(sfxn, xspec, pose, debug=False, **kw):
kw = rp.Bunch(kw)
# try:
# print('''
# minimize.py score initial.................... 687.825
# minimize.py: score before chem bonds......... 687.825
# minimize.py: score after chem bonds.......... 166.551
# minimize.py: score after chainbreaks......... 166.551
# minimize.py: score after metal olap ......... 166.551
# minimize.py: score after metal dist ......... 176.766
# minimize.py: score after metal dir........... 275.546
# minimize.py: score after lig angle added..... 290.724
# minimize.py: score after min no scale........ 111.465
# ==========================================================
# '''.strip())
# os.remove('before.pdb')
# os.remove('zafter.pdb')
# except:
# pass
nresasym = pose.size()
beg = 1
end = nresasym - 1
metalres = rts.name_map('ZN')
metalname = 'ZN'
metalresnos = [nresasym, 2 * nresasym] # TODO.. make not stupid
metalnbonds = 4
metalaid = AtomID(1, metalresnos[0])
# cst_ang_metal = 109.47
# cst_dis_metal = 2.2
# cst_sd_metal_olap = 0.01
# cst_sd_metal_dir = 0.4
# cst_sd_metal_lig_dist = 0.2
# cst_sd_metal_lig_ang = 0.4
# cst_sd_metal_coo = 0.5
# cst_sd_cut_dis = 0.01
# cst_sd_cut_ang = 0.01
# cst_sd_cut_dih = 0.1
pose = pose.clone()
r.core.pose.remove_lower_terminus_type_from_pose_residue(pose, beg)
r.core.pose.remove_upper_terminus_type_from_pose_residue(pose, end)
for ir in range(1, pose.size() + 1):
if 'HIS' in pose.residue(ir).name():
newname = pose.residue(ir).name().replace('HIS', 'HIS_D')
newname = newname.replace('_D_D', '')
r.core.pose.replace_pose_residue_copying_existing_coordinates(
pose, ir, rts.name_map(newname))
if False:
tmp = pose.clone()
r.core.pose.replace_pose_residue_copying_existing_coordinates(
tmp, metalresnos[0], metalres)
makelattice(tmp)
tmp.dump_pdb('before.pdb')
makelattice(pose)
if debug:
print(
f'minimize.py score initial.................... {sfxn(pose):10.3f}'
)
# print_nonzero_energies(sfxn, pose)
syminfo = r.core.pose.symmetry.symmetry_info(pose)
symdofs = syminfo.get_dofs()
allowed_jumps = list()
# for jid, dofinfo in symdofs.items():
# # if dofinfo.allow_dof(1) and not any(dofinfo.allow_dof(i) for i in range(2, 7)):
# allowed_jumps.append(jid)
# print('minimize_mof_xtal allowed jumps:', allowed_jumps)
nxyz = pose.residue(beg).xyz('N')
cxyz = pose.residue(end).xyz('C')
nac, cac = None, None # (N/C)-(a)djacent (c)hain
for isub in range(1, syminfo.subunits()):
othern = pose.residue((isub + 0) * nresasym + 1).xyz('N')
otherc = pose.residue((isub + 1) * nresasym - 1).xyz('C')
if nxyz.distance(otherc) < 2.0: cac = (isub + 1) * nresasym - 1
if cxyz.distance(othern) < 2.0: nac = (isub + 0) * nresasym + 1
assert nac and cac, 'backbone is weird?'
if debug: print('peptide connection 1:', cac, beg)
if debug: print('peptide_connection 2:', end, nac)
# pose.dump_pdb('check_cuts.pdb')
# assert 0
f_metal_lig_dist = r.core.scoring.func.HarmonicFunc(
kw.cst_dis_metal, kw.cst_sd_metal_lig_dist)
f_metal_lig_ang = r.core.scoring.func.HarmonicFunc(
np.radians(kw.cst_ang_metal), kw.cst_sd_metal_lig_ang)
f_metal_olap = r.core.scoring.func.HarmonicFunc(0.0, kw.cst_sd_metal_olap)
f_point_at_metal = r.core.scoring.func.HarmonicFunc(
0.0, kw.cst_sd_metal_dir)
f_metal_coo = r.core.scoring.func.CircularHarmonicFunc(
0.0, kw.cst_sd_metal_coo)
f_cut_dis = r.core.scoring.func.HarmonicFunc(1.328685, kw.cst_sd_cut_dis)
f_cut_ang_cacn = r.core.scoring.func.HarmonicFunc(2.028, kw.cst_sd_cut_ang)
f_cut_ang_cnca = r.core.scoring.func.HarmonicFunc(2.124, kw.cst_sd_cut_ang)
f_cut_dih = r.core.scoring.func.CircularHarmonicFunc(
np.pi, kw.cst_sd_cut_dih)
f_cut_dihO = r.core.scoring.func.CircularHarmonicFunc(
0.00, kw.cst_sd_cut_dih)
################### check cutpoint ##################
conf = pose.conformation().clone()
assert r.core.conformation.symmetry.is_symmetric(conf)
# print(pose.pdb_info().crystinfo())
pi = pose.pdb_info()
# conf.detect_bonds()
conf.declare_chemical_bond(cac, 'C', beg, 'N')
# conf.declare_chemical_bond(end, 'N', nac, 'N')
pose.set_new_conformation(conf)
pose.set_new_energies_object(r.core.scoring.symmetry.SymmetricEnergies())
pose.pdb_info(pi)
if debug:
print(
f'minimize.py: score after chem bonds.......... {sfxn(pose):10.3f}'
)
#############################################3
cst_cut, cst_lig_dis, cst_lig_ang, cst_lig_ori = list(), list(), list(
), list()
############### chainbreaks ################3
# this doesn't behave well...
# # 39 C / 1 OVU1
# # 39 OVL1 / 1 N
# # 29 OVL2 / CA
# r.core.pose.add_variant_type_to_pose_residue(pose, 'CUTPOINT_UPPER', beg)
# r.core.pose.add_variant_type_to_pose_residue(pose, 'CUTPOINT_LOWER', end)
# cres1 = pose.residue(cac)
# nres1 = pose.residue(1)
# cres2 = pose.residue(end)
# nres2 = pose.residue(nac)
# # Apc = r.core.scoring.constraints.AtomPairConstraint
# # getaid = lambda p, n, i: AtomID(p.residue(i).atom_index(n.strip()), i)
# for cst in [
# Apc(getaid(pose, 'C ', cac), getaid(pose, 'OVU1', beg), f_cut),
# Apc(getaid(pose, 'OVL1', cac), getaid(pose, 'N ', beg), f_cut),
# Apc(getaid(pose, 'OVL2', cac), getaid(pose, 'CA ', beg), f_cut),
# Apc(getaid(pose, 'C ', end), getaid(pose, 'OVU1', nac), f_cut),
# Apc(getaid(pose, 'OVL1', end), getaid(pose, 'N ', nac), f_cut),
# Apc(getaid(pose, 'OVL2', end), getaid(pose, 'CA ', nac), f_cut),
# ]:
# pose.add_constraint(cst)
cst_cut.append(addcst_dis(pose, cac, 'C ', beg, 'N', f_cut_dis))
cst_cut.append(addcst_dis(pose, end, 'C ', nac, 'N', f_cut_dis))
if debug:
print(
f'minimize.py: score after chainbreak dis...... {sfxn(pose):10.3f}'
)
cst_cut.append(
addcst_ang(pose, cac, 'CA', cac, 'C', beg, 'N ', f_cut_ang_cacn))
cst_cut.append(
addcst_ang(pose, cac, 'C ', beg, 'N', beg, 'CA', f_cut_ang_cnca))
cst_cut.append(
addcst_ang(pose, end, 'CA', end, 'C', nac, 'N ', f_cut_ang_cacn))
cst_cut.append(
addcst_ang(pose, end, 'C ', nac, 'N', nac, 'CA', f_cut_ang_cnca))
if debug:
print(
f'minimize.py: score after chainbreak ang...... {sfxn(pose):10.3f}'
)
# print(r.numeric.dihedral(
# pose.residue(cac).xyz('CA'),
# pose.residue(cac).xyz('C'),
# pose.residue(beg).xyz('N'),
# pose.residue(beg).xyz('CA'),
# ))
cst_cut.append(
addcst_dih(pose, cac, 'CA', cac, 'C', beg, 'N ', beg, 'CA', f_cut_dih))
cst_cut.append(
addcst_dih(pose, end, 'CA', end, 'C', nac, 'N ', nac, 'CA', f_cut_dih))
cst_cut.append(
addcst_dih(pose, cac, 'O ', cac, 'C', beg, 'N ', beg, 'CA',
f_cut_dihO))
cst_cut.append(
addcst_dih(pose, end, 'O ', end, 'C', nac, 'N ', nac, 'CA',
f_cut_dihO))
if debug:
print(
f'minimize.py: score after chainbreak dihedral. {sfxn(pose):10.3f}'
)
############## metal constraints ################
for i, j in [(i, j) for i in metalresnos for j in metalresnos if i < j]:
addcst_dis(pose, i, metalname, j, metalname, f_metal_olap)
if debug:
print(
f'minimize.py: score after metal olap ......... {sfxn(pose):10.3f}'
)
allowed_elems = 'NOS'
znpos = pose.residue(metalresnos[0]).xyz(1)
znbonded = list()
for ir in range(1, len(pose.residues) + 1):
res = pose.residue(ir)
if not res.is_protein(): continue
for ia in range(5, res.nheavyatoms() + 1):
aid = AtomID(ia, ir)
elem = res.atom_name(ia).strip()[0]
if elem in allowed_elems:
xyz = pose.xyz(aid)
dist = xyz.distance(znpos)
if dist < 3.5:
if res.atom_name(ia) in (
' OD2', ' OE2'): # other COO O sometimes closeish
continue
znbonded.append(aid)
if len(znbonded) != metalnbonds:
print('WRONG NO OF LIGANDING ATOMS', len(znbonded))
for aid in znbonded:
print(
pose.residue(aid.rsd()).name(),
pose.residue(aid.rsd()).atom_name(aid.atomno()))
pose.dump_pdb('WRONG_NO_OF_LIGANDING_ATOMS.pdb')
return None, None
# raise ValueError(f'WRONG NO OF LIGANDING ATOMS {len(znbonded)}')
# metal/lig distance constraints
for i, aid in enumerate(znbonded):
cst = r.core.scoring.constraints.AtomPairConstraint(
metalaid, aid, f_metal_lig_dist)
cst_lig_dis.append(cst)
pose.add_constraint(cst)
if debug:
print(
f'minimize.py: score after metal dist ......... {sfxn(pose):10.3f}'
)
# for aid in znbonded:
# print(aid.rsd(), aid.atomno(),
# pose.residue(aid.rsd()).name(),
# pose.residue(aid.rsd()).atom_name(aid.atomno()))
# assert 0
# lig/metal/lig angle constraints (or dihedral in-place constraint for COO)
# TODO kinda hacky... will need to be more general?
for i, aid in enumerate(znbonded):
ir, res = aid.rsd(), pose.residue(aid.rsd())
if all(_ not in res.name() for _ in 'ASP CYS HIS GLU'.split()):
assert 0, f'unrecognized res {res.name()}'
if any(_ in res.name() for _ in 'ASP GLU'.split()):
# metal comes off of OD1/OE1
ir, coo = aid.rsd(), ('OD1 CG OD2' if 'ASP' in res.name() else
'OE1 CD OE2').split()
cst_lig_ori.append(
addcst_dih(pose, ir, coo[0], ir, coo[1], ir, coo[2],
metalaid.rsd(), metalname, f_metal_coo))
else:
if 'HIS' in res.name(): aname = 'HD1' if res.has('HD1') else 'HE2'
if 'CYS' in res.name(): aname = 'HG'
cst_lig_ori.append(
addcst_ang(pose, ir, res.atom_name(aid.atomno()),
metalaid.rsd(), metalname, ir, aname,
f_point_at_metal))
# cst = r.core.scoring.constraints.AngleConstraint(aid, metalaid, aid2, f_point_at_metal)
# pose.add_constraint(cst)
if debug:
print(
f'minimize.py: score after metal dir........... {sfxn(pose):10.3f}'
)
for i, iaid in enumerate(znbonded):
for j, jaid in enumerate(znbonded[:i]):
# pripnt(i, j)
cst = r.core.scoring.constraints.AngleConstraint(
iaid, metalaid, jaid, f_metal_lig_ang)
cst_lig_ang.append(cst)
pose.add_constraint(cst)
if debug:
print(
f'minimize.py: score after lig angle added..... {sfxn(pose):10.3f}'
)
################ minimization #########################
movemap = r.core.kinematics.MoveMap()
movemap.set_bb(True)
movemap.set_chi(True)
movemap.set_jump(False)
for i in allowed_jumps:
movemap.set_jump(True, i)
minimizer = r.protocols.minimization_packing.symmetry.SymMinMover(
movemap, sfxn, 'lbfgs_armijo_nonmonotone', 0.01, True) # tol, nblist
if sfxn.has_nonzero_weight(r.core.scoring.ScoreType.cart_bonded):
minimizer.cartesian(True)
minimizer.apply(pose)
if debug:
print(
f'minimize.py: score after min no scale........ {sfxn(pose):10.3f}'
)
# printscores(sfxn, pose)
kw.timer.checkpoint(f'min scale 1.0')
asym = r.core.pose.Pose()
r.core.pose.symmetry.extract_asymmetric_unit(pose, asym, False)
r.core.pose.replace_pose_residue_copying_existing_coordinates(
asym, metalresnos[0], metalres)
# asym.dump_pdb('asym.pdb')
# for ir in metalresnos:
# r.core.pose.replace_pose_residue_copying_existing_coordinates(pose, ir, metalres)
# pose.dump_pdb('zafter.pdb')
if debug: print(kw.timer)
info = rp.Bunch()
info.score = sfxn(pose)
############### score component stuff ################
st = r.core.scoring.ScoreType
etot = pose.energies().total_energies()
info.score_fa_atr = (etot[st.fa_atr])
info.score_fa_rep = (etot[st.fa_rep])
info.score_fa_sol = (etot[st.fa_sol])
info.score_lk_ball = (etot[st.lk_ball] + etot[st.lk_ball_iso] +
etot[st.lk_ball_bridge] +
etot[st.lk_ball_bridge_uncpl])
info.score_fa_elec = (etot[st.fa_elec] + etot[st.fa_intra_elec])
info.score_hbond_sr_bb = (etot[st.hbond_sr_bb] + etot[st.hbond_lr_bb] +
etot[st.hbond_bb_sc] + etot[st.hbond_sc])
info.score_dslf_fa13 = (etot[st.dslf_fa13])
info.score_atom_pair_constraint = (etot[st.atom_pair_constraint])
info.score_angle_constraint = (etot[st.angle_constraint])
info.score_dihedral_constraint = (etot[st.dihedral_constraint])
info.score_omega = (etot[st.omega])
info.score_rotamer = (etot[st.fa_dun] + etot[st.fa_dun_dev] +
etot[st.fa_dun_rot] + etot[st.fa_dun_semi] +
etot[st.fa_intra_elec] + etot[st.fa_intra_rep] +
etot[st.fa_intra_atr_xover4] +
etot[st.fa_intra_rep_xover4] +
etot[st.fa_intra_sol_xover4])
info.score_ref = (etot[st.ref])
info.score_rama_prepro = (etot[st.rama_prepro])
info.score_cart_bonded = (etot[st.cart_bonded])
info.score_gen_bonded = (etot[st.gen_bonded])
############### cst stuff ################
pose.remove_constraints()
info.score_wo_cst = sfxn(pose)
[pose.add_constraint(cst) for cst in cst_cut]
info.score_cst_cut = sfxn(pose) - info.score_wo_cst
pose.remove_constraints()
[pose.add_constraint(cst) for cst in cst_lig_dis]
[pose.add_constraint(cst) for cst in cst_lig_ang]
[pose.add_constraint(cst) for cst in cst_lig_ori]
info.score_cst_lig_ori = sfxn(pose) - info.score_wo_cst
pose.remove_constraints()
[pose.add_constraint(cst) for cst in cst_lig_dis]
info.score_cst_lig_dis = sfxn(pose) - info.score_wo_cst
pose.remove_constraints()
[pose.add_constraint(cst) for cst in cst_lig_ang]
info.score_cst_lig_ang = sfxn(pose) - info.score_wo_cst
pose.remove_constraints()
[pose.add_constraint(cst) for cst in cst_lig_ori]
info.score_cst_lig_ori = sfxn(pose) - info.score_wo_cst
pose.remove_constraints()
return asym, info
import pyrosetta.rosetta as rosetta
from pyrosetta import init, get_fa_scorefxn, AtomID
from pyrosetta.rosetta import core, protocols
init(
extra_options="-constant_seed"
) # WARNING: option '-constant_seed' is for testing only! MAKE SURE TO REMOVE IT IN PRODUCTION RUNS!!!!!
import os
os.chdir('.test.output')
print('constraints ----------------------------------------------')
pose = core.import_pose.pose_from_file("../test/data/test_in.pdb")
scorefxn = get_fa_scorefxn() # create_score_function('standard')
scorefxn.set_weight(core.scoring.atom_pair_constraint, 10)
scorefxn(pose)
print()
print('Score before constraints applied:', scorefxn(pose))
hterm2 = AtomID(1, 55)
gterm2 = AtomID(1, 5)
GF = core.scoring.func.GaussianFunc(4.0, 2.0)
apc = core.scoring.constraints.AtomPairConstraint(hterm2, gterm2, GF)
pose.add_constraint(apc)
print('Score after constraints applied:', scorefxn(pose))