def cif_stats(path):
re_atom = re.compile("^(?:ATOM|HETATM)\s+(\d+)\s+.*")
atom_site_ids = {}
start_counting_atoms = False
stats = {"atoms": 0}
for ln in FileIO.OpenFile(path, "r").readlines():
if ln.startswith("_atom_site."):
start_counting_atoms = True
if not start_counting_atoms:
continue
## count atoms
m = re_atom.match(ln)
if m != None:
stats["atoms"] += 1
aid = m.group(1)
if atom_site_ids.has_key(aid):
print "cif_stats() ERROR: CIF DUPLICATE ID"
print "cif_stats() [1]", atom_site_ids[aid]
print "cif_stats() [2]", ln
else:
atom_site_ids[aid] = ln
if stats["atoms"] > 0:
return stats
# Assume that we are looking at plain CIF file
start_counting_atoms = False
for ln in FileIO.OpenFile(path, "r").readlines():
if ln.startswith("_atom_site_label"):
start_counting_atoms = True
if not start_counting_atoms or ln[0] == "_":
continue
fields = ln.split()
if not fields:
break
## count atoms
stats["atoms"] += 1
aid = fields[0]
if atom_site_ids.has_key(aid):
print "CIF DUPLICATE ID"
print "[1]", atom_site_ids[aid]
print "[2]", ln
sys.exit(1)
else:
atom_site_ids[aid] = ln
return stats
def pdb_stats(path):
re_model = re.compile("^MODEL\s+(\d+).*")
re_atom = re.compile("^(?:ATOM|HETATM)\s*(\d+).*")
model = 1
serial_map = {}
stats = {"atoms": 0}
for ln in FileIO.OpenFile(path, "r").readlines():
## change model
m = re_model.match(ln)
if m != None:
model = m.group(1)
continue
## count atoms
m = re_atom.match(ln)
if m != None:
stats["atoms"] += 1
ser = m.group(1)
ser = "%s-%s" % (ser, model)
if serial_map.has_key(ser):
print "pdb_stats() ERROR: PDB DUPLICATE ID"
print "pdb_stats() [1]", serial_map[ser]
print "pdb_stats() [2]", ln
else:
serial_map[ser] = ln
return stats
def cif2html(cif_path, html_path):
fileobj = FileIO.OpenFile(cif_path, "r")
cif_file = mmCIF.mmCIFFile()
print "loading..."
cif_file.load_file(fileobj)
print "converting..."
cif_data = cif_file[0]
c2h_template = kid.Template(file="cif2html.kid")
c2h_template.cif = mmCIFDataKid(cif_data)
c2h_template.write(html_path)