def get_surrounding_unit_cells_2d(unit_cell_sym_mates, uc_dimensions):
all_surrounding_unit_cells = []
asu_bb_atom_template = unit_cell_sym_mates[0].get_backbone_atoms()
unit_cell_sym_mates_len = len(unit_cell_sym_mates)
central_uc_bb_cart_coords = []
for unit_cell_sym_mate_pdb in unit_cell_sym_mates:
central_uc_bb_cart_coords.extend(
unit_cell_sym_mate_pdb.extract_backbone_coords())
central_uc_bb_frac_coords = cart_to_frac(central_uc_bb_cart_coords,
uc_dimensions)
all_surrounding_uc_bb_frac_coords = []
for x_shift in [-1, 0, 1]:
for y_shift in [-1, 0, 1]:
if [x_shift, y_shift] != [0, 0]:
shifted_uc_bb_frac_coords = central_uc_bb_frac_coords + [
x_shift, y_shift, 0
]
all_surrounding_uc_bb_frac_coords.extend(
shifted_uc_bb_frac_coords)
all_surrounding_uc_bb_cart_coords = frac_to_cart(
all_surrounding_uc_bb_frac_coords, uc_dimensions)
all_surrounding_uc_bb_cart_coords = np.split(
all_surrounding_uc_bb_cart_coords, 8)
for surrounding_uc_bb_cart_coords in all_surrounding_uc_bb_cart_coords:
all_uc_sym_mates_bb_cart_coords = np.split(
surrounding_uc_bb_cart_coords, unit_cell_sym_mates_len)
one_surrounding_unit_cell = []
for uc_sym_mate_bb_cart_coords in all_uc_sym_mates_bb_cart_coords:
uc_sym_mate_bb_pdb = PDB()
uc_sym_mate_bb_atoms = []
atom_count = 0
for atom in asu_bb_atom_template:
x_transformed = uc_sym_mate_bb_cart_coords[atom_count][0]
y_transformed = uc_sym_mate_bb_cart_coords[atom_count][1]
z_transformed = uc_sym_mate_bb_cart_coords[atom_count][2]
atom_transformed = Atom(atom.get_number(), atom.get_type(),
atom.get_alt_location(),
atom.get_residue_type(),
atom.get_chain(),
atom.get_residue_number(),
atom.get_code_for_insertion(),
x_transformed, y_transformed,
z_transformed, atom.get_occ(),
atom.get_temp_fact(),
atom.get_element_symbol(),
atom.get_atom_charge())
uc_sym_mate_bb_atoms.append(atom_transformed)
atom_count += 1
uc_sym_mate_bb_pdb.set_all_atoms(uc_sym_mate_bb_atoms)
one_surrounding_unit_cell.append(uc_sym_mate_bb_pdb)
all_surrounding_unit_cells.append(one_surrounding_unit_cell)
return all_surrounding_unit_cells
def get_central_asu_pdb_2d(pdb1, pdb2, uc_dimensions):
pdb_asu = PDB()
pdb_asu.read_atom_list(pdb1.get_all_atoms() + pdb2.get_all_atoms())
pdb_asu_coords_cart = pdb_asu.extract_all_coords()
asu_com_cart = center_of_mass_3d(pdb_asu_coords_cart)
asu_com_frac = cart_to_frac(asu_com_cart, uc_dimensions)
asu_com_x_min_cart = sys.maxint
x_min_shift_vec_frac = None
for x in range(-10, 11):
asu_com_x_shifted_coords_frac = asu_com_frac + [x, 0, 0]
asu_com_x_shifted_coords_cart = frac_to_cart(
asu_com_x_shifted_coords_frac, uc_dimensions)
if abs(asu_com_x_shifted_coords_cart[0]) < abs(asu_com_x_min_cart):
asu_com_x_min_cart = asu_com_x_shifted_coords_cart[0]
x_min_shift_vec_frac = [x, 0, 0]
asu_com_y_min_cart = sys.maxint
y_min_shift_vec_frac = None
for y in range(-10, 11):
asu_com_y_shifted_coords_frac = asu_com_frac + [0, y, 0]
asu_com_y_shifted_coords_cart = frac_to_cart(
asu_com_y_shifted_coords_frac, uc_dimensions)
if abs(asu_com_y_shifted_coords_cart[1]) < abs(asu_com_y_min_cart):
asu_com_y_min_cart = asu_com_y_shifted_coords_cart[1]
y_min_shift_vec_frac = [0, y, 0]
if x_min_shift_vec_frac is not None and y_min_shift_vec_frac is not None:
xyz_min_shift_vec_frac = [
x_min_shift_vec_frac[0], y_min_shift_vec_frac[1], 0
]
if xyz_min_shift_vec_frac == [0, 0, 0]:
return pdb_asu
else:
pdb_asu_coords_frac = cart_to_frac(pdb_asu_coords_cart,
uc_dimensions)
xyz_min_shifted_pdb_asu_coords_frac = pdb_asu_coords_frac + xyz_min_shift_vec_frac
xyz_min_shifted_pdb_asu_coords_cart = frac_to_cart(
xyz_min_shifted_pdb_asu_coords_frac, uc_dimensions)
xyz_min_shifted_asu_pdb = copy.deepcopy(pdb_asu)
xyz_min_shifted_asu_pdb.replace_coords(
xyz_min_shifted_pdb_asu_coords_cart)
return xyz_min_shifted_asu_pdb
else:
return pdb_asu
def get_unit_cell_sym_mates(pdb_asu, expand_matrices, uc_dimensions):
unit_cell_sym_mates = [pdb_asu]
asu_cart_coords = pdb_asu.extract_all_coords()
asu_frac_coords = cart_to_frac(asu_cart_coords, uc_dimensions)
for r, t in expand_matrices:
t_vec = np.array(t)
r_mat = np.transpose(np.array(r))
r_asu_frac_coords = np.matmul(asu_frac_coords, r_mat)
tr_asu_frac_coords = r_asu_frac_coords + t_vec
tr_asu_cart_coords = frac_to_cart(tr_asu_frac_coords,
uc_dimensions).tolist()
unit_cell_sym_mate_pdb = PDB()
unit_cell_sym_mate_pdb_atom_list = []
atom_count = 0
for atom in pdb_asu.get_all_atoms():
x_transformed = tr_asu_cart_coords[atom_count][0]
y_transformed = tr_asu_cart_coords[atom_count][1]
z_transformed = tr_asu_cart_coords[atom_count][2]
atom_transformed = Atom(atom_count, atom.get_type(),
atom.get_alt_location(),
atom.get_residue_type(), atom.get_chain(),
atom.get_residue_number(),
atom.get_code_for_insertion(),
x_transformed, y_transformed,
z_transformed, atom.get_occ(),
atom.get_temp_fact(),
atom.get_element_symbol(),
atom.get_atom_charge())
atom_count += 1
unit_cell_sym_mate_pdb_atom_list.append(atom_transformed)
unit_cell_sym_mate_pdb.set_all_atoms(unit_cell_sym_mate_pdb_atom_list)
unit_cell_sym_mates.append(unit_cell_sym_mate_pdb)
return unit_cell_sym_mates
def get_expanded_ptgrp_pdbs(pdb1_asu, pdb2_asu, expand_matrices):
asu_symm_mates = []
pdb_asu = PDB()
pdb_asu.set_all_atoms(pdb1_asu.get_all_atoms() + pdb2_asu.get_all_atoms())
asu_coords = pdb_asu.extract_all_coords()
for r in expand_matrices:
r_mat = np.transpose(np.array(r))
r_asu_coords = np.matmul(asu_coords, r_mat)
asu_sym_mate_pdb = PDB()
asu_sym_mate_pdb_atom_list = []
atom_count = 0
for atom in pdb_asu.get_all_atoms():
x_transformed = r_asu_coords[atom_count][0]
y_transformed = r_asu_coords[atom_count][1]
z_transformed = r_asu_coords[atom_count][2]
atom_transformed = Atom(atom_count, atom.get_type(),
atom.get_alt_location(),
atom.get_residue_type(), atom.get_chain(),
atom.get_residue_number(),
atom.get_code_for_insertion(),
x_transformed, y_transformed,
z_transformed, atom.get_occ(),
atom.get_temp_fact(),
atom.get_element_symbol(),
atom.get_atom_charge())
atom_count += 1
asu_sym_mate_pdb_atom_list.append(atom_transformed)
asu_sym_mate_pdb.set_all_atoms(asu_sym_mate_pdb_atom_list)
asu_symm_mates.append(asu_sym_mate_pdb)
return asu_symm_mates
def biopdb_aligned_chain(pdb_fixed, chain_id_fixed, pdb_moving,
chain_id_moving):
biopdb_atom_fixed = []
biopdb_atom_moving = []
for atom in pdb_fixed.get_CA_atoms():
if atom.chain == chain_id_fixed:
biopdb_atom_fixed.append(
BioPDBAtom(atom.type, (atom.x, atom.y, atom.z),
atom.temp_fact,
atom.occ,
atom.alt_location,
" %s " % atom.type,
atom.number,
element=atom.element_symbol))
pdb_moving_coords = []
for atom in pdb_moving.get_all_atoms():
pdb_moving_coords.append([atom.get_x(), atom.get_y(), atom.get_z()])
if atom.is_CA():
if atom.chain == chain_id_moving:
biopdb_atom_moving.append(
BioPDBAtom(atom.type, (atom.x, atom.y, atom.z),
atom.temp_fact,
atom.occ,
atom.alt_location,
" %s " % atom.type,
atom.number,
element=atom.element_symbol))
sup = Bio.PDB.Superimposer()
sup.set_atoms(biopdb_atom_fixed, biopdb_atom_moving)
# no need to transpose rotation matrix as Bio.PDB.Superimposer() generates correct matrix to rotate using np.matmul
rot, tr = sup.rotran[0], sup.rotran[1]
pdb_moving_coords_rot = np.matmul(pdb_moving_coords, rot)
pdb_moving_coords_rot_tx = pdb_moving_coords_rot + tr
pdb_moving_copy = PDB()
pdb_moving_copy.set_chain_id_list(pdb_moving.get_chain_id_list())
pdb_moving_copy_atom_list = []
atom_count = 0
for atom in pdb_moving.get_all_atoms():
x_transformed = pdb_moving_coords_rot_tx[atom_count][0]
y_transformed = pdb_moving_coords_rot_tx[atom_count][1]
z_transformed = pdb_moving_coords_rot_tx[atom_count][2]
atom_transformed = Atom(atom.get_number(), atom.get_type(),
atom.get_alt_location(),
atom.get_residue_type(), atom.get_chain(),
atom.get_residue_number(),
atom.get_code_for_insertion(),
x_transformed, y_transformed, z_transformed,
atom.get_occ(), atom.get_temp_fact(),
atom.get_element_symbol(),
atom.get_atom_charge())
pdb_moving_copy_atom_list.append(atom_transformed)
atom_count += 1
pdb_moving_copy.set_all_atoms(pdb_moving_copy_atom_list)
return pdb_moving_copy