def crystal_symmetry_from_comments(self):
for comment in self.comments:
m = re.match(r'\{\s+' + re_sg_uc, comment)
if (m is None): continue
result = crystal_symmetry_from_re_match(m=m)
if (result is not None): return result
return None
def crystal_symmetry_from_comments(self):
for comment in self.comments:
m = re.match(r'\{\s+' + re_sg_uc, comment)
if (m is None): continue
result = crystal_symmetry_from_re_match(m=m)
if (result is not None): return result
return None
def multi_sdb_parser(lines, file_name=None, max_characters=1000000):
# Parser for one or more cns sdb files.
# Lines interpreted:
# {+ file: heavy_search_1.sdb +}
# sg= P6 a= 116.097 b= 116.097 c= 44.175 alpha= 90 beta= 90 gamma= 120
# {===>} site.action_1="refine";
# {===>} site.segid_1="SITE"; site.type_1="SE";
# {===>} site.x_1=18.7869; site.y_1=12.1257; site.z_1=0.163635;
# {===>} site.b_1=65.6408; site.q_1=1; site.g_1="";
# Sites must be sorted.
sdb_files = []
block_name = None
current_symmetry = None
n_characters = 0
p = 0
for line in lines:
if (max_characters != 0):
n_characters += len(line)
if (n_characters > max_characters): break
m = re.search(r'\{\+\s+file:\s*(\S*)', line)
if (m):
block_name = m.group(1)
m = re.match(re_sg_uc, line)
if (m):
current_symmetry = crystal_symmetry_from_re_match(m=m)
m = re.search(
r'\{\-\s+begin\s+block\s+parameter\s+definition\s+\-\}', line)
if (m):
if (block_name is None):
i = len(sdb_files) + 1
if (p): i += 1
if (file_name is None):
block_name = "block_%d" % i
else:
block_name = file_name + "_%d" % i
if (p): sdb_files.append(p.as_sdb_sites())
p = raw_parameters(block_name)
if (current_symmetry is None):
p.unit_cell = None
p.space_group_info = None
else:
p.unit_cell = current_symmetry.unit_cell()
p.space_group_info = current_symmetry.space_group_info()
current_symmetry = None
block_name = None
if (not p): continue
m = re.match(r'\{===>\}\s*sg=\s*"(\S+)"\s*;', line)
if (m):
p.space_group_info = sgtbx.space_group_info(m.group(1))
p.add_action(re.search(r'site\.action_(\d+)\s*=\s*"([^"]*)"', line))
p.add_segid(re.search(r'site\.segid_(\d+)\s*=\s*"([^"]*)"', line))
p.add_type(re.search(r'site\.type_(\d+)\s*=\s*"([^"]*)"', line))
p.add_x(re.search(r'site\.x_(\d+)\s*=\s*([^\s;]*)', line))
p.add_y(re.search(r'site\.y_(\d+)\s*=\s*([^\s;]*)', line))
p.add_z(re.search(r'site\.z_(\d+)\s*=\s*([^\s;]*)', line))
p.add_b(re.search(r'site\.b_(\d+)\s*=\s*([^\s;]*)', line))
p.add_q(re.search(r'site\.q_(\d+)\s*=\s*([^\s;]*)', line))
p.add_g(re.search(r'site\.g_(\d+)\s*=\s*"([^"]*)"', line))
if (p): sdb_files.append(p.as_sdb_sites())
return sdb_files
def crystal_symmetry_from_remark_uc_sg(self):
sg = self.space_group_from_remark_symop()
for remark in self.remarks:
remark = remark.lstrip()[6:].strip()
m = re.match(re_uc_sg, remark)
if (m is None): continue
result = crystal_symmetry_from_re_match(m=m, i_uc=1, i_sg=7)
if (result is not None):
if (sg is not None):
result = crystal.symmetry(
unit_cell=result.unit_cell(),
space_group=sg)
return result
return None
def crystal_symmetry_from_remark_uc_sg(self):
sg = self.space_group_from_remark_symop()
for remark in self.remarks:
remark = remark.lstrip()[6:].strip()
m = re.match(re_uc_sg, remark)
if (m is None): continue
result = crystal_symmetry_from_re_match(m=m, i_uc=1, i_sg=7)
if (result is not None):
if (sg is not None):
result = crystal.symmetry(
unit_cell=result.unit_cell(),
space_group=sg)
return result
return None
def extract_symmetry(pdb_record): m = re.match(r'REMARK\s+' + re_sg_uc , pdb_record) if (not m): return None return crystal_symmetry_from_re_match(m=m)
