def main(path):
print "parsing %s" % (path)
cif_file = mmCIFFile()
cif_file.load_file(path)
os.mkdir("Monomers")
for cif_data in cif_file:
mkdir_path = os.path.join("Monomers", cif_data.name[0])
if not os.path.isdir(mkdir_path):
os.mkdir(mkdir_path)
save_path = os.path.join(mkdir_path, "%s.cif" % (cif_data.name))
print "saving %s" % (save_path)
cf = mmCIFFile()
cf.append(copy.deepcopy(cif_data))
cf.save_file(save_path)
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)
def main(path):
print "parsing %s" % (path)
cif_file = mmCIFFile()
cif_file.load_file(path)
os.mkdir("Monomers")
for cif_data in cif_file:
mkdir_path = os.path.join("Monomers", cif_data.name[0])
if not os.path.isdir(mkdir_path):
os.mkdir(mkdir_path)
save_path = os.path.join(mkdir_path, "%s.cif" % (cif_data.name))
print "saving %s" % (save_path)
cf = mmCIFFile()
cf.append(copy.deepcopy(cif_data))
cf.save_file(save_path)
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)
def cif_merge(merge_paths, output_path, entry_id):
"""Merge the mmCIF files in merge_paths into a mmCIF file which will be
written to the output_path. This merging is configured for a
crystallographic structure, and the entry_ids of all tables are
overridden with the given entry_id.
"""
output_cif_file = mmCIF.mmCIFFile()
output_cif_data = output_cif_file.new_data(entry_id)
## add the entry table to the output mmCIFFile
entry = output_cif_data.new_table("entry", ["id"])
row = entry.new_row()
row["id"] = entry_id
## merge in mmCIF files
for mpath in merge_paths:
merge_cif_file = mmCIF.mmCIFFile()
merge_cif_file.load_file(mpath)
for src_data in merge_cif_file:
for src_table in src_data:
## don't merge the entry table
if src_table.name == "entry":
continue
vet_merge_cif_table_entry_id(src_table, entry_id)
default_table_merge(output_cif_data, src_table)
## post-process merged mmCIF file
## make sure the entry_id fields are filled in
for cif_table in output_cif_data:
add_entry_id(cif_table, entry_id)
## report missing items
rcsb_report_missing(output_cif_data)
output_cif_file.save_file(output_path)
def cif_merge(merge_paths, output_path, entry_id):
"""Merge the mmCIF files in merge_paths into a mmCIF file which will be
written to the output_path. This merging is configured for a
crystallographic structure, and the entry_ids of all tables are
overridden with the given entry_id.
"""
output_cif_file = mmCIF.mmCIFFile()
output_cif_data = output_cif_file.new_data(entry_id)
## add the entry table to the output mmCIFFile
entry = output_cif_data.new_table("entry", ["id"])
row = entry.new_row()
row["id"] = entry_id
## merge in mmCIF files
for mpath in merge_paths:
merge_cif_file = mmCIF.mmCIFFile()
merge_cif_file.load_file(mpath)
for src_data in merge_cif_file:
for src_table in src_data:
## don't merge the entry table
if src_table.name == "entry":
continue
vet_merge_cif_table_entry_id(src_table, entry_id)
default_table_merge(output_cif_data, src_table)
## post-process merged mmCIF file
## make sure the entry_id fields are filled in
for cif_table in output_cif_data:
add_entry_id(cif_table, entry_id)
## report missing items
rcsb_report_missing(output_cif_data)
output_cif_file.save_file(output_path)