from __future__ import absolute_import, division, print_function import os, sys cif_keyword_dictionary = { "_chem_comp" : {"id" : str, "name" : str, "type" : str, "pdbx_type" : str, "formula" : str, "mon_nstd_parent_comp_id" : str, "pdbx_synonyms" : str, "pdbx_formal_charge" : int, "pdbx_initial_date" : str, "pdbx_modified_date" : str, "pdbx_ambiguous_flag" : str, "pdbx_release_status" : str, "pdbx_replaced_by" : str, "pdbx_replaces" : str, "formula_weight" : float, "one_letter_code" : str, "three_letter_code" : str, "pdbx_model_coordinates_details" : str, "pdbx_model_coordinates_missing_flag" : str, "pdbx_ideal_coordinates_details" : str, "pdbx_ideal_coordinates_missing_flag" : str, "pdbx_model_coordinates_db_code" : str, "pdbx_processing_site" : str, # added 11/2008 "pdbx_subcomponent_list" : str, }, "_chem_comp_atom" : {"comp_id": str, "atom_id": str, "alt_atom_id": str, "type_symbol": str, "charge" : int, "pdbx_align": int, "pdbx_aromatic_flag": str, "pdbx_leaving_atom_flag": str, "pdbx_stereo_config": str, "model_Cartn_x": float, "model_Cartn_y": float, "model_Cartn_z": float, "pdbx_model_Cartn_x_ideal": float, "pdbx_model_Cartn_y_ideal": float, "pdbx_model_Cartn_z_ideal": float, "pdbx_ordinal" : int, # added 11/2008 "pdbx_component_atom_id" : str, "pdbx_component_comp_id" : str, }, "_chem_comp_bond" : {"comp_id": str, "atom_id_1": str, "atom_id_2": str, "value_order": str, "pdbx_aromatic_flag": str, "pdbx_stereo_config": str, "pdbx_ordinal": int, }, "_pdbx_chem_comp_descriptor" : {"comp_id" : str, "type" : str, "program" : str, "program_version" : str, "descriptor" : str, }, "_pdbx_chem_comp_identifier" : {"comp_id" : str, "type" : str, "program" : str, "program_version" : str, "identifier" : str, }, } class empty(object): def __repr__(self): outl = "\nObject" for attr in self.__dict__: outl += "\n %s : %s %s" % (attr, getattr(self, attr), type(getattr(self, attr))) return outl def __len__(self): return len(self.__dict__) def smart_split_cif_line(line): line = " %s " % line tmp = [] delimiters = [" ", "'", '"'] while line: delimiter=" " if line[0] in delimiters: delimiter=line[0] start = line.find(delimiter) finish = line.find(delimiter, start+1) items = line.split(delimiter) items = list(filter(None, items)) if not items: break item=items[0] tmp.append(item) if finish==-1: if len(items)==2: tmp.append(items[1]) break if delimiter==" ": line = line[len(item)+1:].strip() else: line = line[len(item)+3:].strip() return tmp def run2(filename): if not os.path.exists(filename): return None lines = [] with open(filename) as f: lines = f.read().splitlines() merge = True while merge: merge = [] for i, line in enumerate(lines): if line.find(";")==0: if i not in merge: merge.append(i) elif line.find('"')==0: if i not in merge: merge.append(i) elif line.find("_chem_comp.name")==0: if len(line.split())==1: if i+1 not in merge: merge.append(i+1) elif line.find("_chem_comp.pdbx_synonyms")==0: if len(line.split())==1: if i+1 not in merge: merge.append(i+1) if merge: merge.reverse() for i in merge: if lines[i][1:].strip(): if lines[i][0] in [";"]: lines[i-1] += ' "%s"' % lines[i][1:].strip() else: lines[i-1] += ' "%s"' % lines[i].strip() del lines[i] line_iter = iter(lines) complete_cif_data = {} loop_list = [] non_loop = {} code = "" pdbx_reading = False remove_loop_fields = {} loop_index = 0 for line in line_iter: line = line.replace("\t", " "*8) if line.find("#")==0: continue if line.find("_pdbx")==0: pdbx_reading = True line = "%s " % line if False: while line.find('"')>-1: start = line.find('"') finish = line.find('"', start+1) if finish==-1: break line = "%s%s%s" % (line[:start], line[start+1:finish].replace(" ", "_space_"), line[finish+1:]) if pdbx_reading: while line.find("'")>-1: start = line.find("'") finish = line.find("'", start+1) if finish==-1: break line = "%s%s%s" % (line[:start], line[start+1:finish].replace(" ", "_space_"), line[finish+1:]) if line.find("loop_")==0: loop_list = [] loop_index = 0 continue if line.find(";")==0: continue if line.find("_")==0: for cif_key in cif_keyword_dictionary: if line.find(cif_key)==-1: continue for attr in cif_keyword_dictionary[cif_key]: test = "%s.%s " % (cif_key, attr) if line.find(test)>-1: loop_list.append(attr) if len(line.split())>1: non_loop[test] = line.split()[1:] break if line.find(test)>-1: break else: tmp = line.split()[0] cif_key, attr = tmp.split(".") remove_loop_fields.setdefault(cif_key, []) remove_loop_fields[cif_key].append(loop_index) loop_index+=1 else: if loop_list: if code and line.find(code)!=0: continue obj = empty() i=0 #for ptr, item in enumerate(line.split()): for ptr, item in enumerate(smart_split_cif_line(line)): if ptr in remove_loop_fields.get(cif_key, []): continue if len(loop_list)<=i: print('Problem with CIF line parsing') print(line) print(loop_list) continue if loop_list[i]=="comp_id": code = item if item not in ["?", "."]: item = cif_keyword_dictionary[cif_key][loop_list[i]](item) if type(item)==type(""): if item[0]=='"' and item[-1]=='"': item = item[1:-1] item = item.replace("_space_", " ") setattr(obj, loop_list[i], item) i+=1 complete_cif_data.setdefault(cif_key, []) if hasattr(obj, "alt_atom_id"): if len(obj.alt_atom_id)>5: assert 0 complete_cif_data[cif_key].append(obj) # non loop parsing for cif_key in cif_keyword_dictionary: obj = empty() for key in non_loop: if key.find("%s." % cif_key)==0: if len(non_loop[key])==1: item = non_loop[key][0] else: item = " ".join(non_loop[key]) sk = key.split(".")[1].strip() if item not in ["?", "."]: try: item = cif_keyword_dictionary[cif_key][sk](item) except Exception: print(key) print(sk) print(cif_key) print(list(cif_keyword_dictionary[cif_key].keys())) raise setattr(obj, sk, item) if len(obj): complete_cif_data[cif_key] = [obj] return complete_cif_data def get_func(cif_key, sk): func = None if cif_key in cif_keyword_dictionary: func = cif_keyword_dictionary[cif_key].get(sk, None) return func def get_typed_field(cif_key, sk, field, func=None): if func is None: func = get_func(cif_key, sk) if field not in ["?", "."] and func not in [None, str]: field = func(field) return field def run(filename): from iotbx import cif if not os.path.exists(filename): return None complete_cif_data = {} cm = cif.reader(filename, strict=False, raise_if_errors=False).model() for code, rc in cm.items(): for key, item in rc.items(): cif_key = key.split('.')[0] sk = key.split(".")[1].strip() complete_cif_data.setdefault(cif_key, []) if type(item)==type(''): item=[item] else: continue for i, row in enumerate(item): if len(complete_cif_data[cif_key])