def __init__(self, cif_block, pdb_hierarchy):
self.tls_params = []
self.tls_present = False
self.error_string = None
tls_ids = cif_block.get('_pdbx_refine_tls.id')
T_ijs = [
cif_block.get('_pdbx_refine_tls.T[%s][%s]' % (i, j))
for i, j in ('11', '22', '33', '12', '13', '23')
]
L_ijs = [
cif_block.get('_pdbx_refine_tls.L[%s][%s]' % (i, j))
for i, j in ('11', '22', '33', '12', '13', '23')
]
S_ijs = [
cif_block.get('_pdbx_refine_tls.S[%s][%s]' % (i, j))
for i, j in ('11', '12', '13', '21', '22', '23', '31', '32', '33')
]
origin_xyzs = [
cif_block.get('_pdbx_refine_tls.origin_%s' % x) for x in 'xyz'
]
if isinstance(tls_ids, string_types):
# in case the TLS items are not in a loop
tls_ids = [tls_ids]
T_ijs = [[T_ij] for T_ij in T_ijs]
L_ijs = [[L_ij] for L_ij in L_ijs]
S_ijs = [[S_ij] for S_ij in S_ijs]
origin_xyzs = [[origin_xyz] for origin_xyz in origin_xyzs]
assert T_ijs.count(None) in (0, 6)
assert L_ijs.count(None) in (0, 6)
assert S_ijs.count(None) in (0, 9)
assert origin_xyzs.count(None) in (0, 3)
if T_ijs.count(None) == 6:
return
tls_group_ids = cif_block.get('_pdbx_refine_tls_group.id')
refine_tls_ids = cif_block.get('_pdbx_refine_tls_group.refine_tls_id')
beg_chain_ids = cif_block.get(
'_pdbx_refine_tls_group.beg_auth_asym_id')
beg_seq_ids = cif_block.get('_pdbx_refine_tls_group.beg_auth_seq_id')
end_chain_ids = cif_block.get(
'_pdbx_refine_tls_group.end_auth_asym_id')
end_seq_ids = cif_block.get('_pdbx_refine_tls_group.end_auth_seq_id')
selection_details = cif_block.get(
'_pdbx_refine_tls_group.selection_details')
assert tls_group_ids is not None
if isinstance(tls_group_ids, string_types):
# in case the TLS group items are not in a loop
refine_tls_ids = flex.std_string([refine_tls_ids])
beg_chain_ids = [beg_chain_ids]
beg_seq_ids = [beg_seq_ids]
end_chain_ids = [end_chain_ids]
end_seq_ids = [end_seq_ids]
if selection_details is not None:
selection_details = flex.std_string([selection_details])
selection_cache = pdb_hierarchy.atom_selection_cache()
for i, tls_id in enumerate(tls_ids):
T = [float(T_ij[i]) for T_ij in T_ijs]
L = [float(L_ij[i]) for L_ij in L_ijs]
S = [float(S_ij[i]) for S_ij in S_ijs]
origin = [float(origin_x[i]) for origin_x in origin_xyzs]
i_groups = (refine_tls_ids == tls_id).iselection()
sel_strings = []
for i_group in i_groups:
if selection_details is not None and not selection_details.all_eq(
'?'):
# phenix selection
sel_strings.append(selection_details[i_group].strip())
# check it is a valid selection string
selection_cache.selection(sel_strings[-1])
else:
sel_strings.append(
refmac_range_to_phenix_string_selection(
pdb_hierarchy=pdb_hierarchy,
chain_start=beg_chain_ids[i_group],
resseq_start=beg_seq_ids[i_group],
chain_end=end_chain_ids[i_group],
resseq_end=end_seq_ids[i_group]))
sel_str = " or ".join(sel_strings)
self.tls_params.append(
tls(t=T, l=L, s=S, origin=origin, selection_string=sel_str))
self.tls_present = True
def __init__(self, cif_block, pdb_hierarchy):
self.tls_params = []
self.tls_present = False
self.error_string = None
tls_ids = cif_block.get('_pdbx_refine_tls.id')
T_ijs = [cif_block.get('_pdbx_refine_tls.T[%s][%s]' %(i, j))
for i, j in ('11', '22', '33', '12', '13', '23')]
L_ijs = [cif_block.get('_pdbx_refine_tls.L[%s][%s]' %(i, j))
for i, j in ('11', '22', '33', '12', '13', '23')]
S_ijs = [cif_block.get('_pdbx_refine_tls.S[%s][%s]' %(i, j))
for i, j in ('11', '12', '13', '21', '22', '23', '31', '32', '33')]
origin_xyzs = [cif_block.get('_pdbx_refine_tls.origin_%s' %x) for x in 'xyz']
if isinstance(tls_ids, basestring):
# in case the TLS items are not in a loop
tls_ids = [tls_ids]
T_ijs = [[T_ij] for T_ij in T_ijs]
L_ijs = [[L_ij] for L_ij in L_ijs]
S_ijs = [[S_ij] for S_ij in S_ijs]
origin_xyzs = [[origin_xyz] for origin_xyz in origin_xyzs]
assert T_ijs.count(None) in (0, 6)
assert L_ijs.count(None) in (0, 6)
assert S_ijs.count(None) in (0, 9)
assert origin_xyzs.count(None) in (0, 3)
if T_ijs.count(None) == 6:
return
tls_group_ids = cif_block.get('_pdbx_refine_tls_group.id')
refine_tls_ids = cif_block.get('_pdbx_refine_tls_group.refine_tls_id')
beg_chain_ids = cif_block.get('_pdbx_refine_tls_group.beg_auth_asym_id')
beg_seq_ids = cif_block.get('_pdbx_refine_tls_group.beg_auth_seq_id')
end_chain_ids = cif_block.get('_pdbx_refine_tls_group.end_auth_asym_id')
end_seq_ids = cif_block.get('_pdbx_refine_tls_group.end_auth_seq_id')
selection_details = cif_block.get('_pdbx_refine_tls_group.selection_details')
assert tls_group_ids is not None
if isinstance(tls_group_ids, basestring):
# in case the TLS group items are not in a loop
refine_tls_ids = flex.std_string([refine_tls_ids])
beg_chain_ids = [beg_chain_ids]
beg_seq_ids = [beg_seq_ids]
end_chain_ids = [end_chain_ids]
end_seq_ids = [end_seq_ids]
if selection_details is not None:
selection_details = flex.std_string([selection_details])
selection_cache = pdb_hierarchy.atom_selection_cache()
for i, tls_id in enumerate(tls_ids):
T = [float(T_ij[i]) for T_ij in T_ijs]
L = [float(L_ij[i]) for L_ij in L_ijs]
S = [float(S_ij[i]) for S_ij in S_ijs]
origin = [float(origin_x[i]) for origin_x in origin_xyzs]
i_groups = (refine_tls_ids == tls_id).iselection()
sel_strings = []
for i_group in i_groups:
if selection_details is not None and not selection_details.all_eq('?'):
# phenix selection
sel_strings.append(selection_details[i_group].strip())
# check it is a valid selection string
selection_cache.selection(sel_strings[-1])
else:
sel_strings.append(refmac_range_to_phenix_string_selection(
pdb_hierarchy=pdb_hierarchy,
chain_start=beg_chain_ids[i_group],
resseq_start=beg_seq_ids[i_group],
chain_end=end_chain_ids[i_group],
resseq_end=end_seq_ids[i_group]))
sel_str = " or ".join(sel_strings)
self.tls_params.append(tls(
t=T, l=L, s=S, origin=origin, selection_string=sel_str))
self.tls_present = True