def make_flips_if_necessary_torsion(const_h, flip_h):
""" 3 times faster than other procedure."""
const_h.reset_atom_i_seqs()
flip_h.reset_atom_i_seqs()
assert const_h.atoms().size() == flip_h.atoms().size()
flipped_other_selection = flex.size_t([])
ch_const = const_h.only_model().chains()
ch_flip = flip_h.only_model().chains()
for ch_c, ch_f in zip(ch_const, ch_flip):
for residue, res_flip in zip(ch_c.residues(), ch_f.residues()):
if (residue.resname in flippable_sidechains
and should_be_flipped(residue, res_flip)):
fl_atom_list = flippable_sidechains[residue.resname]
iseqs = [0]*residue.atoms().size()
for i, a in enumerate(residue.atoms()):
try:
ind = fl_atom_list.index(a.name)
if ind == 3 or ind == 5:
iseqs[i+1] = a.i_seq
elif ind == 4 or ind == 6:
iseqs[i-1] = a.i_seq
else:
iseqs[i] = a.i_seq
except ValueError:
iseqs[i] = a.i_seq
for i in iseqs:
flipped_other_selection.append(i)
else:
for a in residue.atoms():
flipped_other_selection.append(a.i_seq)
# print "flipped_other_selection", list(flipped_other_selection)
assert flipped_other_selection.size() == const_h.atoms().size()
return flipped_other_selection
def make_flips_if_necessary_torsion(const_h, flip_h):
""" 3 times faster than other procedure."""
assert len(flip_h.models()) == 1, len(flip_h.models())
assert len(const_h.models()) == 1, len(const_h.models())
# const_h.write_pdb_file(file_name="const.pdb")
# flip_h.write_pdb_file(file_name="flip.pdb")
assert const_h.atoms_size() == flip_h.atoms_size()
original_atoms_size = const_h.atoms_size()
flipped_other_selection = flex.size_t([])
ch_const = const_h.only_model().chains()
ch_flip = flip_h.only_model().chains()
for another_ch in ch_const[1:]:
if another_ch.id == ch_const[0].id:
for rg in another_ch.residue_groups():
ch_const[0].append_residue_group(rg.detached_copy())
for another_ch in ch_flip[1:]:
if another_ch.id == ch_flip[0].id:
for rg in another_ch.residue_groups():
ch_flip[0].append_residue_group(rg.detached_copy())
ch_c = ch_const[0]
ch_f = ch_flip[0]
const_h.reset_atom_i_seqs()
flip_h.reset_atom_i_seqs()
# for ch_c, ch_f in zip(ch_const, ch_flip):
for residue, res_flip in zip(ch_c.residues(), ch_f.residues()):
if (residue.resname in flippable_sidechains
and should_be_flipped(residue, res_flip)):
fl_atom_list = flippable_sidechains[residue.resname]
iseqs = [0]*residue.atoms_size()
for i, a in enumerate(residue.atoms()):
try:
ind = fl_atom_list.index(a.name)
if ind == 3 or ind == 5:
iseqs[i+1] = a.i_seq
elif ind == 4 or ind == 6:
iseqs[i-1] = a.i_seq
else:
iseqs[i] = a.i_seq
except ValueError:
iseqs[i] = a.i_seq
except IndexError:
if i == len(iseqs)-1:
# this is for case where the last atom is not present
iseqs[i] = a.i_seq
for i in iseqs:
flipped_other_selection.append(i)
else:
for a in residue.atoms():
flipped_other_selection.append(a.i_seq)
assert flipped_other_selection.size() == original_atoms_size, "%d %d" % (
flipped_other_selection.size(), original_atoms_size)
# assert flipped_other_selection.size() == const_h.atoms_size()
return flipped_other_selection
def flip_atoms_in_ncs_groups(hierarchy, ncs_restraints_group_list, mon_lib_srv=None):
"""
This function will actually modify hierarchy by making necessary flips
in ncs-related residues. Flip will be made by exchanging atom coordinates.
Will make all copies consistent with master.
"""
if mon_lib_srv is None:
mon_lib_srv = mmtbx.monomer_library.server.server()
for ncs_gr in ncs_restraints_group_list:
master_isel = ncs_gr.master_iselection
chains_master = hierarchy.select(master_isel).only_model().chains()
for copy in ncs_gr.copies:
copy_isel = copy.iselection
chains_copy = hierarchy.select(copy_isel).only_model().chains()
for ch_m, ch_c in zip(chains_master, chains_copy):
for r_m, r_c in zip(ch_m.residues(), ch_c.residues()):
# print "working on ", r_m.id_str(), r_c.id_str()
if should_be_flipped(r_m, r_c):
flip_residue(r_c, mon_lib_srv)
def flip_atoms_in_ncs_groups(hierarchy, ncs_restraints_group_list, mon_lib_srv=None):
"""
This function will actually modify hierarchy by making necessary flips
in ncs-related residues. Flip will be made by exchanging atom coordinates.
Will make all copies consistent with master.
"""
if mon_lib_srv is None:
mon_lib_srv = mmtbx.monomer_library.server.server()
for ncs_gr in ncs_restraints_group_list:
master_isel = ncs_gr.master_iselection
chains_master = hierarchy.select(master_isel).only_model().chains()
for copy in ncs_gr.copies:
copy_isel = copy.iselection
chains_copy = hierarchy.select(copy_isel).only_model().chains()
for ch_m, ch_c in zip(chains_master, chains_copy):
for r_m, r_c in zip(ch_m.residues(), ch_c.residues()):
# print "working on ", r_m.id_str(), r_c.id_str()
if should_be_flipped(r_m, r_c):
flip_residue(r_c, mon_lib_srv)
