def parse_symm_db(args):
"""
:param args:
:return: list of Entry instances that are significant in the CE database
"""
results = []
with open(work_dir + 'ce_symm.xml', 'r') as fin:
xml = fin.read().split('data')
ABC = 'QWERTYUIOPASDFGHJKLZXCVBNM'
for data in xml:
axis = {}
significant = False
for l in data.split('\n'):
if 'isSig' in l:
significant = l.split('>')[1].split('<')[0] == 'true'
if not significant:
break
if '<x>' in l:
axis['x'] = float(l.split('>')[1].split('<')[0])
if '<y>' in l:
axis['y'] = float(l.split('>')[1].split('<')[0])
if '<z>' in l:
axis['z'] = float(l.split('>')[1].split('<')[0])
if 'protodomain' in l:
try:
s = l.split('>')[1].split('<')[0].split(',')
pdb = s[0][:4]
chain = s[0][5]
if len(s) < 2:
continue
segs = []
for s_ in s:
if '_-' not in s_:
start = int(''.join([
a for a in s_.split('_')[1].split('-')[0]
if a not in ABC
]))
end = int(''.join([
a for a in s_.split('_')[1].split('-')[1]
if a not in ABC
]))
if '_-' in s_:
start = int(''.join([
a for a in s_.split('_-')[1].split('-')[0]
if a not in ABC
]))
end = int(''.join([
a for a in s_.split('_-')[1].split('-')[1]
if a not in ABC
]))
segs.append((start, end))
results.append(
Entry(pdb, chain, segs,
mp.XYZ(axis['x'], axis['y'], axis['z'])))
except:
print('SKIPPING', s)
return results
def create_pdb_AA_AA_d_z(aa1: str,
aa2: str,
d: float,
z: float,
res_maker,
path: str = './') -> None:
"""
create a pdb with residues aa1 and aa2 at the XY plane at Z=z and distance d
"""
res1 = res_maker.get_residue(aa1)
res2 = res_maker.get_residue(aa2)
res1.change_chain_name('A')
res2.change_chain_name('B')
# rotate around Z to oppose
axis_z = mp.XYZ(0, 0, 1)
res2.dot_matrix_me(mpf.rotation_matrix_around_vec(axis_z, np.pi))
# translate to get d distance
move_d = mp.XYZ(
0, res1[res_maker.main_residue_atoms[res1.res_type][1]].xyz.y -
res2[res_maker.main_residue_atoms[res2.res_type][1]].xyz.y + d, 0)
res2.translate_xyz(move_d)
# translate all to z
move_z = mp.XYZ(0, 0, z)
res1.translate_xyz(move_z)
res2.translate_xyz(move_z)
# setup in a MyPDB instance, and renumber and write
pdb = mp.MyPDB()
for res in [res1, res2]:
for a in res.values():
pdb.add_atom(a)
pdb.renumber()
mp.write_PDB(
'%s/%s_%s_%.2f_%.2f.pdb' % (path, res1.res_type, res2.res_type, d, z),
pdb)
def translate_and_rotate_res_to_xy_plane(res: mp.Residue,
atom_list: list) -> mp.Residue:
xyz = copy.deepcopy(res[atom_list[0]].xyz)
xyz = xyz.scalar_multi(-1)
res.translate_xyz(xyz)
# rotate a1 to xy plane
proj_a2_xy = copy.deepcopy(res[atom_list[1]].xyz)
proj_a2_xy.z = 0
a2_copy = copy.deepcopy(res[atom_list[1]].xyz)
ang_a2_xy = np.arccos(a2_copy.unit().dot(proj_a2_xy.unit()))
axis_a2_xy = a2_copy.unit().cross(proj_a2_xy.unit()).unit()
rotation_matrix = rotation_matrix_around_vec(axis_a2_xy, ang_a2_xy)
res.dot_matrix_me(rotation_matrix)
# rotate a2 to xy plane
proj_a2_xy = copy.deepcopy(res[atom_list[2]].xyz)
proj_a2_xy.z = 0
a2_copy = copy.deepcopy(res[atom_list[2]].xyz)
ang_a2_xy = np.arccos(a2_copy.unit().dot(proj_a2_xy.unit()))
closest_point = point_on_normed_vec_closest_to_point(
proj_a2_xy.as_nparray(), res[atom_list[1]].xyz.unit().as_nparray())
ang_a2_xy = angle_between_3_XYZs(a2_copy, closest_point, proj_a2_xy)
axis = copy.deepcopy(res[atom_list[1]].xyz)
rotation_matrix = rotation_matrix_around_vec(axis, -ang_a2_xy)
res.dot_matrix_me(rotation_matrix)
# rotate so that a2 and 3 are on both sides of the Y axis
a1_copy = res[atom_list[0]].xyz
a2_copy = res[atom_list[1]].xyz
a3_copy = res[atom_list[2]].xyz
ang_312 = angle_between_3_XYZs(a3_copy, a1_copy, a2_copy)
ang_y12 = angle_between_3_XYZs(mp.XYZ(0, 1, 0), a1_copy, a2_copy)
axis = mp.XYZ(0, 0, 1)
rotation_matrix = rotation_matrix_around_vec(axis,
-(ang_y12 + 0.5 * ang_312))
res.dot_matrix_me(rotation_matrix)
def test_symm_axis_interface(e: Entry, ch: str) -> bool:
print(e)
inter_resi = e.interface[ch]
print(e.symm_segs)
symm_resi = [a for seg in e.symm_segs for a in range(seg[0], seg[1] + 1)]
print('symm_resi', symm_resi)
print(inter_resi)
pdb = mp.parse_PDB(find_pdb(e.pdb), with_non_residue=False)
symm_com = mp.com_residues(chain=pdb[e.chain], residues=symm_resi)
print(symm_resi, symm_com)
pdb.translate_xyz(mp.XYZ(0, 0, 0) - symm_com)
print('pdb translated')
print('writing pdb %s_%s_translated.pdb' % (e.pdb, e.chain))
mp.write_PDB('%s_%s_translated.pdb' % (e.pdb, e.chain), pdb)
print('now symm com is at',
mp.com_residues(chain=pdb[e.chain], residues=symm_resi))
print('symm axis XYZ %r' % (e.symm_axis))
print_pymol_select(e)
def point_on_normed_vec_closest_to_point(p: np.array, v: np.array) -> mp.XYZ:
vec = v * np.dot(p, v)
return mp.XYZ(vec[0], vec[1], vec[2])
