def parse_ins(fpath_ins):
"""Parses .ins file and returns information relevant for creation
of .inflip file"""
def dispatcher(list_matched_objects):
"""fills parsing_dict with key-value pairs"""
parsing_dict = dict()
for line in list_matched_objects:
match_obj = line.pop()
if match_obj.group('tag') in parsing_dict:
parsing_dict[match_obj.group('tag')] += \
"\n{}".format(match_obj.group('value'))
else:
parsing_dict[match_obj.group('tag')] = match_obj.group('value')
return parsing_dict
tags = ['CELL', 'SYMM', 'LATT', 'LIST']
re_compile_objs = map(lambda tag: \
re.compile("(?P<tag>{})\\s+(?P<value>\\S+.*)".format(tag)), tags)
filenames = generators.gen_find(os.path.basename(fpath_ins),
os.path.dirname(fpath_ins))
fobjects = generators.gen_open(filenames)
lines = generators.gen_cat(fobjects)
list_matched_objects = generators.gen_grep(lines, re_compile_objs,
yield_line = False)
parsing_dict = dispatcher(list_matched_objects)
return parsing_dict
def symops_from_cif():
yield "loop_\n"
yield "_symmetry_equiv_pos_as_xyz\n"
filenames = generators.gen_find(
os.path.basename(fpath_res).rsplit(".res")[0] + ".cif",
os.path.dirname(fpath_res))
fobjects = generators.gen_open(filenames)
lines = generators.gen_cat(fobjects)
patt = patt =re.compile(r"('[^,'()]+,[^,'()]+,[^,'()]+')")
for line in lines:
mobj = re.search(patt, line)
if mobj:
yield line
def difference_peaks(fpath_res):
"""Saves peaks from difference Fourier(liested in .res) into peaks.cif"""
def cell():
cell_str = "_cell_length_a {}\n"\
"_cell_length_b {}\n"\
"_cell_length_c {}\n"\
"_cell_angle_alpha {}\n"\
"_cell_angle_beta {}\n"\
"_cell_angle_gamma {}".format(
*parsing_dict["CELL"].strip().split()[1:])
for line in cell_str.split("\n"):
yield line
#def group_HM():
# yield "_symmetry_space_group_name_H-M '{}'\n".format(
# sgnr)
# #groupsHM.table[sgnr])
# #yield "_symmetry_Int_Tables_number {}\n".format(sgnr)
def symops_from_cif():
yield "loop_\n"
yield "_symmetry_equiv_pos_as_xyz\n"
filenames = generators.gen_find(
os.path.basename(fpath_res).rsplit(".res")[0] + ".cif",
os.path.dirname(fpath_res))
fobjects = generators.gen_open(filenames)
lines = generators.gen_cat(fobjects)
patt = patt =re.compile(r"('[^,'()]+,[^,'()]+,[^,'()]+')")
for line in lines:
mobj = re.search(patt, line)
if mobj:
yield line
def loop_atom():
yield "loop_\n"
yield "_atom_site_label\n"
yield "_atom_site_type_symbol\n"
yield "_atom_site_fract_x\n"
yield "_atom_site_fract_y\n"
yield "_atom_site_fract_z\n"
def density_peaks():
for matchobj in parsing_dict["PEAKS"]:
yield " {} {} {} {} {}\n".format(
matchobj.group(1),
'He',
matchobj.group(3),
matchobj.group(4),
matchobj.group(5),
matchobj.group(6))
re_compile_objs = (
re.compile("\s*(CELL)(.*)"),
re.compile(
r'\s*(Q\d+)\s+(\d+)'\
r'\s+(-?\d+\.\d+)\s+(-?\d+\.\d+)\s+(-?\d+\.\d+)'\
r'\s+(\d+\.\d+)\s+(\d+\.\d+)\s+(\d+\.\d+)\s*'))
parsing_dict = dict()
filenames = generators.gen_find(os.path.basename(fpath_res),
os.path.dirname(fpath_res))
fobjects = generators.gen_open(filenames)
lines = generators.gen_cat(fobjects)
list_matched_objects = generators.gen_grep(lines, re_compile_objs,
yield_line = False)
poped_objs = generators.pop_it_fromlist(list_matched_objects)
for obj in poped_objs:
if obj.group(1) == "CELL":
parsing_dict["CELL"] = obj.group(2)
else:
parsing_dict.setdefault("PEAKS", []).append(obj)
peaks_fpath = os.path.join(os.path.dirname(fpath_res), "peaks.cif")
with open(peaks_fpath, 'w') as f:
f.write("data_{}\n".format(os.path.basename(fpath_res)))
for line in cell():
f.write(line + "\n")
for line in symops_from_cif():
f.write(line)
for line in loop_atom():
f.write(line)
for line in density_peaks():
f.write(line)
def gen_inflip_from_ins(fpath_ins, fpath_inflip, purpose, voxel = 'AUTO'):
"""generates .inflip file from .ins file"""
def commands_inflip():
inflip_inp = "{fname}\noutputfile {fname}_{job}.xplor\n"\
"outputformat xplor\nexpandedlog yes\n"\
"#coverage no\nperform fourier\ncell {cell}\n"\
"dimension 3\nrealdimension 3\nvoxel {voxel}\ncenters\n"\
"{centers}\nendcenters\nsymmetry\n{symmetry}\n"\
"endsymmetry\n#Keywords for charge flipping\n"\
"#delta AUTO\n#weakratio 0.000\n#Biso 0.000\n"\
"#polish yes 200\n#randomseed AUTO\n#derivesymmetry no\n"\
"#searchsymmetry average\n"\
"dataformat amplitude phase\n".format(**inflip_dict)
for line in inflip_inp.split("\n"):
yield line
def reflections_inflip():
yield "fbegin\n"
for line in purposes[purpose](fpath_fcf):
yield line
yield "endf\n"
def centers():
return centering_vecs(abs(eval(parsing_dict['LATT'])))
def symmetry():
"""Generates centers and symmetry for inflip"""
hasinversion = lambda parsing_dict: eval(parsing_dict['LATT']) > 0
symmops = 'x,y,z\n' + parsing_dict["SYMM"]
#this adds inverted symmetry operations in case LATT is less than 0
if hasinversion(parsing_dict):
symmops += "\n{}".format(
"\n".join(map(symmath.invert_symop, symmops.split("\n"))))
return symmops
def cell():
return "{} {} {} {} {} {}".format(
*parsing_dict["CELL"].strip().split()[1:]
)
def dispatcher(list_matched_objects):
"""fills parsed_dict with key-value pairs"""
parsing_dict = dict()
for line in list_matched_objects:
match_obj = line.pop()
if match_obj.group('tag') in parsing_dict:
parsing_dict[match_obj.group('tag')] += \
"\n{}".format(match_obj.group('value'))
else:
parsing_dict[match_obj.group('tag')] = match_obj.group('value')
return parsing_dict
def check_list():
return parsing_dict['LIST'] == 5
inflip_dict = dict()
purposes = {
'Fo': gen_fo4sflip,
'Fc': gen_fc4sflip,
'dF': gen_df_4sflip
}
assert purpose in purposes.keys()
fpath_fcf = fpath_ins.rsplit(".ins")[0] + ".fcf"
tags = ['CELL', 'SYMM', 'LATT', 'LIST']
re_compile_objs = map(lambda tag: \
re.compile("(?P<tag>{})\\s+(?P<value>\\S+.*)".format(tag)), tags)
filenames = generators.gen_find(os.path.basename(fpath_ins),
os.path.dirname(fpath_ins))
fobjects = generators.gen_open(filenames)
lines = generators.gen_cat(fobjects)
list_matched_objects = generators.gen_grep(lines, re_compile_objs,
yield_line = False)
parsing_dict = dispatcher(list_matched_objects)
inflip_dict['job'] = purpose
inflip_dict['fname'] = os.path.basename(fpath_ins).rsplit(".ins")[0]
inflip_dict['cell'] = cell()
inflip_dict['centers'] = centers()
inflip_dict['symmetry'] = symmetry()
inflip_dict['voxel'] = voxel
with open(fpath_inflip, 'w') as f:
for line in commands_inflip():
f.write(line + "\n")
for line in reflections_inflip():
f.write(line)