def parse_residues_file(self) -> dict:
pdb = mp.parse_PDB(
'/home/labs/fleishman/jonathaw/temp_residue_data/RKDS.txt')
for res in pdb['A'].values():
mpf.translate_and_rotate_res_to_xy_plane(
res, self.main_residue_atoms[res.res_type])
self.residues[res.res_type] = res
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 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 parse_residues_file(self) -> dict:
pdb = mp.parse_PDB("/home/labs/fleishman/jonathaw/temp_residue_data/RKDS.txt")
for res in pdb["A"].values():
mpf.translate_and_rotate_res_to_xy_plane(res, self.main_residue_atoms[res.res_type])
self.residues[res.res_type] = res
