def refmac_pure_tls_prep(xyzin, tlsin_list, wilson, xyzout, tlsout):
"""Use TLS model (without Uiso) for each atom. Output xyzout with the
B-factors reset to either the Bmean or the Wilson B value.
"""
## load structure
struct = FileIO.LoadStructure(fil=xyzin)
## load and construct TLS groups
tls_group_list = []
tls_file = TLS.TLSFile()
tls_file.set_file_format(TLS.TLSFileFormatPureTLSOUT())
tls_file_format = TLS.TLSFileFormatPureTLSOUT()
for tlsin in tlsin_list:
tls_desc_list = tls_file_format.load(open(tlsin, "r"))
for tls_desc in tls_desc_list:
tls_file.tls_desc_list.append(tls_desc)
tls_group = tls_desc.construct_tls_group_with_atoms(struct)
tls_group.tls_desc = tls_desc
tls_group_list.append(tls_group)
## set the extra Uiso for each atom
for tls_group in tls_group_list:
Bmean = 0.0
sum_Biso = 0.0
num_atms = 0
for atm, Utls in tls_group.iter_atm_Utls():
num_atms += 1
sum_Biso += atm.temp_factor
## EAM Aug 2011: num_atms goes to zero if there are atom selection problems.
## The output files will contain empty groups, but at least it doesn't crash.
if num_atms > 0:
Bmean = sum_Biso / num_atms
## reset the TLS tensor values in the TLSDesc object so they can be
## saved
tls_group.tls_desc.set_tls_group(tls_group)
## reset atm.temp_factor to the Bmean for this TLS group
for atm, Utls in tls_group.iter_atm_Utls():
atm.temp_factor = Bmean
atm.temp_factor = wilson
## save the new xyzout file with temp_factors reset to "wilson" value
FileIO.SaveStructure(fil=xyzout, struct=struct)
## save the REFMAC-format file, but without T, L, S, and ORIGIN values
tls_file.save(open(tlsout, "w"))
