# shelx.py # BL python adaption of shelx.scm by Paul Emsley # # Copyright (C) 2005, 2006, 2007 by Bernhard Lohkamp # Copyright (C) 2007, 2008 by Bernhard Lohkamp, The University of York # # This program is free software: you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by # the Free Software Foundation, either version 3 of the License, or # (at your option) any later version. # # This program is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # GNU General Public License for more details. # # You should have received a copy of the GNU General Public License # along with this program. If not, see . # Provide functions to handle shelx fcf file (which I believe to be old-style # cif rather than mmCIF). # # So, in Coot, if it sees the extention of .fcf then it calls the # fcf handler and the handler does the conversion, writes a new # mmCIF file and then reads it. # import coot from types import * import numbers def handle_shelx_fcf_file_old(filename): import os filename = os.path.normpath(filename) # OK, so we have been passed a shelx fcf file. # We need to run this through the awk filter. # BL says: I guess in python it's easier to do it within python output_mmCIF_file_name = filename + ".cif" convert_shelx_fcf_to_cif(filename,output_mmCIF_file_name) ret = coot.auto_read_cif_data_with_phases(output_mmCIF_file_name) return ret # read_cif_data_with_phases(output_mmCIF_file_name) # coot.read_cif_data_with_phases_fo_fc(output_mmCIF_file_name) def handle_shelx_fcf_file(filename): return coot.read_small_molecule_data_cif(filename) def convert_shelx_fcf_to_cif(fcf_filename,cif_filename): import string, math fin = False fout = False intable = 0 try: fin = open(fcf_filename,'r') except IOError: print("BL ERROR:: Cannot read ", fcf_filename) try: fout = file(cif_filename,"w") except IOError: print("BL ERROR:: Cannot write ", cif_filename) if (fin and fout): lines = fin.readlines() for line in lines: if "_shelx_title" in line: # dont write pass elif "_shelx_refln_list_code" in line: # dont write pass elif "_shelx_F_calc_maximum" in line: # dont write pass elif "_exptl_crystal_F_000" in line: # dont write pass elif "_reflns_d_resolution_high" in line: # dont write pass elif "_shelx_refln_list_code" in line: # dont write pass elif "_shelx_F_calc_maximum" in line: # dont write pass elif "_exptl_crystal_F_000" in line: # dont write pass elif "_reflns_d_resolution_high" in line: # dont write pass else: if "_refln_F_squared_meas" in line: line = line.replace("_refln_F_squared_meas"," _refln.F_meas") if "_refln_F_squared_sigma" in line: line = line.replace("_refln_F_squared_sigma"," _refln.F_meas_sigma") # symm equivs: if " _symmetry_equiv_pos_as_xyz" in line: line = line.replace(" _symmetry_equiv_pos_as_xyz","_symmetry_equiv.pos_as_xyz") if "_cell_length_a" in line: line = line.replace("_cell_length_a","_cell.length_a ") if "_refln_F_squared_meas" in line: line = line.replace("_refln_F_squared_meas"," _refln.F_meas") if "_refln_F_squared_sigma" in line: line = line.replace("_refln_F_squared_sigma"," _refln.F_meas_sigma") # symm equivs: if "_symmetry_equiv_pos_as_xyz" in line: line = line.replace("_symmetry_equiv_pos_as_xyz","_symmetry_equiv.pos_as_xyz") if "_cell_length_a" in line: line = line.replace("_cell_length_a","_cell.length_a ") if "_cell_length_b" in line: line = line.replace("_cell_length_b","_cell.length_b ") if "_cell_length_c" in line: line = line.replace("_cell_length_c","_cell.length_c ") if "_cell_angle_alpha" in line: line = line.replace("_cell_angle_alpha","_cell.angle_alpha ") if "_cell_angle_beta" in line: line = line.replace("_cell_angle_beta","_cell.angle_beta ") if "_cell_angle_gamma" in line: line = line.replace("_cell_angle_gamma","_cell.angle_gamma ") if "_refln_index_h" in line: line = line.replace("_refln_index_h"," _refln.index_h") if "_cell_length_b" in line: line = line.replace("_cell_length_b","_cell.length_b ") if "_cell_length_c" in line: line = line.replace("_cell_length_c","_cell.length_c ") if "_cell_angle_alpha" in line: line = line.replace("_cell_angle_alpha","_cell.angle_alpha ") if "_cell_angle_beta" in line: line = line.replace("_cell_angle_beta","_cell.angle_beta ") if "_cell_angle_gamma" in line: line = line.replace("_cell_angle_gamma","_cell.angle_gamma ") if "_refln_index_h" in line: line = line.replace("_refln_index_h"," _refln.index_h") if "_refln_index_k" in line: line = line.replace("_refln_index_k"," _refln.index_k") if "_refln_index_l" in line: line = line.replace("_refln_index_l"," _refln.index_l") if "_refln_F_calc" in line: line = line.replace("_refln_F_calc"," _refln.F_calc") if "_refln_phase_calc" in line: line = line.replace("_refln_phase_calc"," _refln.phase_calc") intable = 1 if (intable == 1 and len(string.split(line))>5): col = string.split(line) col[3] = str(math.sqrt(float(col[3]))) if (float(col[3]) > 0.0): col[4] = str(0.5 * (float(col[4]) + 0.0) / float(col[3])) line = string.join(col) + "\n" fout.write(line) fin.close() fout.close() else: print("BL ERROR:: IO error in conversion!") global coot_shelxl_dir coot_shelxl_dir = "coot-shelxl" def remove_time_extensions(str): # e.g. remove -2007-04-27_1326.24 from 03srv164-2007-04-27_1326.24 import re pattern = "-20[0-9][0-9]-[01][0-9]-[0-3][0-9]_[0-2][0-9][0-5][-0-9].[0-5][-0-9]" # we replace pattern with '' result = re.sub(pattern,"",str) return result # BL says: shelxl_refine can have 3 arguments here: # # first: imol # # second: orig hkl file # # third: shelxh_flag , i.e. use shelxh instead of shelxl (in absenc of hkl # inputfile this has to be written as: shelxh_flag=YOURSETTING # True: use shelxh # False: use shelxl (default) # def shelxl_refine(imol, hkl_file_in_maybe=False, shelxh_flag=False): func = lambda ins_file_name: coot.write_shelx_ins_file(imol, ins_file_name) shelxl_refine_inner(imol, hkl_file_in_maybe, func, shelxh_flag) # shelxl refinement with input text # def shelxl_refine_primitive(imol, ins_text, hkl_file_in_maybe=False, shelxh_flag=False): func = lambda ins_file_name: coot_utils.save_string_to_file(ins_text, ins_file_name, True) shelxl_refine_inner(imol, hkl_file_in_maybe, func, shelxh_flag) def shelxl_refine_inner(imol, hkl_file_in_maybe, func, shelxh_flag): import os import shutil global coot_shelxl_dir # First write out the imol-th molecule in shelx format. # What should the filename be? # Let's say that we read "abc.res" # We want to create "abc-coot.ins". Ah, but what about the data file? # Urg. # # This, as it stands, doesn't properly deal with incrementing the # filenames. if (shelxh_flag): shelxl_exe = coot_utils.find_exe("shelxh", "PATH") else: shelxl_exe = coot_utils.find_exe("shelxl", "PATH") if (not shelxl_exe): print("WARNING:: can't find executable shelxl/h") else: orig_hkl_file = False if (hkl_file_in_maybe and os.path.isfile(hkl_file_in_maybe)): orig_hkl_file = hkl_file_in_maybe dir = os.path.join(os.path.abspath("."), coot_shelxl_dir) if (not os.path.isdir(dir)): try: os.mkdir(dir) except: pass if (not os.path.isdir(dir)): # We dont have shelxl dir and couldnt make it so exit! print("Failed to make shelxl directory ", dir) else: # run shelx stub = os.path.join(dir,(coot_utils.strip_path(coot_utils.strip_extension(coot.molecule_name(imol))) + "-" + coot_utils.unique_date_time_str())) # BL says: shelxl only excepts filename <= 80 char, so check it before if (len(stub) > 80): print("BL WARNING:: filename %s too long! Has %s characters, only 80 are allowed!" %(stub, len(stub))) else: ins_filename = stub + ".ins" res_filename = stub + ".res" lst_filename = stub + ".lst" fcf_filename = stub + ".fcf" log_filename = stub + ".log" hkl_filename = stub + ".hkl" # BL says: non-unix OS python cant make a link. grr! # So we have to make a copy of the passed hkl-file-in # if we cannot create a link # If we copied the file we maybe we should remove the # copied file after use since it's large?! # # helper function to either link or copy file # return True on sucess, False otherwise def make_symlink(src_file, dst_file): try: print("make link from %s to %s" %(dst_file, src_file)) os.symlink(src_file, dst_file) return True except: # failed to create link, try so copy try: print("copy %s to %s" %(src_file, dst_file)) shutil.copyfile(src_file, dst_file) return True except: return False # make a link to the passed hkl-file-in, if it was passed. # (if not, we presume that this file (or the link) exists # already. (Let's check that, and stop early if it doesn't # exist) if (orig_hkl_file): symlink_target = False if (len(orig_hkl_file) == 0): # shouldnt happen!? symlink_target = False elif (hkl_filename[0:1] == "/" or hkl_filename[0:1] == "\\"): # BL nore: maybe we shoudl use coot_utils.slash_start_qm here too?! symlink_target = orig_hkl_file else: if (coot_utils.slash_start_qm(orig_hkl_file)): symlink_target = orig_hkl_file else: symlink_target = "../" + orig_hkl_file if symlink_target: make_symlink(symlink_target, hkl_filename) else: # no input hklin or it wasnt an accessible file # # hklin was not given, let's generate a filename # from the filename of the coordinates molecule # imol, trial names are derived from the name of # the coordinates molecule trial_file_stub = coot_utils.strip_extension(coot.molecule_name(imol)) trial_hkl_file_name = trial_file_stub + ".hkl" print("BL DEBUG:: looking for", trial_hkl_file_name) if (os.path.isfile(trial_hkl_file_name)): print("INFO:: hkl file %s found" %trial_hkl_file_name) # BL says: I dont understand the following but I gues # I have tp believe Paul (at least for now) # if trial-hkl-file-name and hkl-filename # are in the same directory (e.g # shelx-coot), then (strange as it may # seem) we *don't* put the directory name # in the "file that exists" (the first # argument - ie. the target). Bizarre but true. hkl_filename_dir = os.path.abspath(hkl_filename) trial_hkl_file_name_dir = os.path.abspath(trial_hkl_file_name) print("BL DEBUG:: comparing path", hkl_filename_dir, trial_hkl_file_name_dir) if (hkl_filename_dir == trial_hkl_file_name_dir): # same dirs # so lets strip off the dir of the target: new_target = coot_utils.strip_path(trial_hkl_file_name) make_symlink(new_target, hkl_filename) else: # different dirs, keep the dirs: make_symlink(trial_hkl_file_name, hkl_filename) else: print("INFO:: hkl file %s does not exist!" %trial_hkl_file_name) if (not os.path.isfile(hkl_filename)): print("data (hkl) file %s not found - not running shelxl!" %hkl_filename) else: func(ins_filename) # running shelxl creates stub.res print("BL INFO:: Running shelxl as: ", shelxl_exe + " " + stub + " > " + log_filename) shelx_status = coot_utils.popen_command(shelxl_exe, [stub], [], log_filename) if (not shelx_status and os.path.isfile(res_filename) and os.path.isfile(fcf_filename)): # it isn't a pdb file, but Coot knows what to do. imol_res = coot.handle_read_draw_molecule_with_recentre(res_filename, 0) handle_shelx_fcf_file(fcf_filename) read_shelx_lst_file(lst_filename, imol_res) else: print("BL WARNING:: shelxl didnt run ok! No output files found!") #handle_shelx_fcf_file("test.fcf") #shelxl_refine(0,"./shelx_tut/lyso-tet.hkl") # do-shelx-lst-file # # ie. create a interesting-things GUI for split (and other things?) # in a shelx .lst file. # def read_shelx_lst_file(file_name, imol): import os import operator # turn interesting-list into a GUI: # def gui_interesting_list(interesting_list): if (interesting_list): coot_gui.interesting_things_gui("Interesting Things from SHELX", interesting_list) else: print("INFO:: Nothing Interesting from LST file") coot.add_status_bar_text("Nothing Interesting from LST file") # chop off last char of string def chop_end(s): return s[:-1] # return last char of string: def last_char(s): return s[-1] # return a chain resno inscode atom-name altconf list # def make_atom_parts(atom_id): list = [] ls = atom_id.rsplit("_",1) if (len(ls)==2): # chain resno inscode atom-name altconf # The resno part can contain an alt conf specifier # e.g.: 34 or 34a. So let's try to make it a number # simply. If that fails, then strip off the last char # and try again. If *that* is successful, return the # resno and the last char is the altconf specifier. # BL says:: we try to make it to integer, otherwise exception!? resno = ls[1] try: resno = int(resno) chain_id = chain_id_for_shelxl_residue_number(imol, resno) if (not chain_id): print("couldn't find chain id for resno ", resno) return ["", resno, "", ls[0], ""] else: return [chain_id, resno, "", ls[0], ""] except: # handle the alt conf s = ls[1] p = chop_end(s) alt_conf = last_char(s) try: n = int(p) except: return ["", 1, "", "blank", ""] # failure chain_id = chain_id_for_shelxl_residue_number(imol,n) if (not chain_id): print("couldn't find chain id for resno ", resno) return ["", n, "", ls[0], alt_conf] else: return [chain_id, n, "", ls[0], alt_conf] # So we have a line in a table something like these: # # " 2.7499 2.5580 0.1919 0.0400 DANG CN_2011 C_2011" # " 1.5156 0.5000 FLAT O_1012 CA_1012 N_1013 CA_1013" # # It seems that there are either 4 leading numbers or 2 leading # numbers. Let's parse up the line here and return (list # observed target error sigma restraint) where observed and # target are #f if there number is missing (e.g. a "FLAT" # restraint). # # There are 2 regimes we understand, either # number number number number restraint-descr atom-1-desc atom-2-desc # or # number number restraint-descr atom-stuff [.. atom-stuff] # # Actually here we will just make a string list of the # atom-stuffs (after the restraint-descr) and parse that # elsewhere (in do-gui) to find the atoms. The actual # meaning of the atom-stuffs depends on the restraint-descr. # # return #f on something we don't understand # def parse_dr_line(line): import string bits = line.split() if (len(bits) <=3): return False # failed to understand else: try: n0 = float(bits[0]) except: n0 = False try: n1 = float(bits[1]) except: n1 = False try: n2 = float(bits[2]) except: n2 = False try: n3 = float(bits[3]) except: n3 = False if (not n0 and not n1): return False # failed to understand else: if (n2 and n3): # a 4 number line if (len(bits)<=6): return False # failed to understand else: lst = [n0, n1, n2, n3, bits[4], bits[5:]] return lst else: # a 2 number line if (len(bits)<=3): # shouldnt actually happen as we checked earlier!!! Paul!? return False # failed to understand else: lst = [False, False, n0, n1, bits[2], bits[3:]] return lst # def do_gui(disagreeable_restraints_list, interesting_list): #print "BL DEBUG:: DR: ", disagreeable_restraints_list dis_res_button_list = [] for dr_list in disagreeable_restraints_list: restraint_type = dr_list[4] drl_dict = {"BUMP": 0, "DANG": 0, "FLAT": 0, "SIMU": 1, "ISOR": 1} if (restraint_type in drl_dict): drl_index = drl_dict[restraint_type] else: drl_index = 0 atom_parts = make_atom_parts(dr_list[5][drl_index]) stats_string = "not sure what?" n2 = dr_list[2] n3 = dr_list[3] if (isinstance(n2, numbers.Number) and isinstance(n3, numbers.Number) and (n2 != 0)): z = n3 / abs(n2) stats_string = " " + str(n2) + " [Z=" + str(z) +"]" else: stats_string = "" if (drl_index == 0): rt = restraint_type + " " else: rt = restraint_type + " " + dr_list[5][0] button_label = "Disagreeable Restraint " + rt + " " + atom_parts[0] + " " + \ str(atom_parts[1]) + " " + atom_parts[3] + stats_string interesting_thing = [button_label, imol] + atom_parts dis_res_button_list.append(interesting_thing) gui_interesting_list(interesting_list + dis_res_button_list) # main body file_name = os.path.abspath(file_name) if not coot_utils.valid_model_molecule_qm(imol): print("WARNING:: Molecule number %i not valid" %imol) else: if not os.path.isfile(file_name): print("WARNING:: shelx lst file: %s does not exist" %file_name) else: fin = False interesting_list = [] try: fin = open(file_name,'r') except: print("BL ERROR:: Cannot read ", file_name) if (fin): lines = fin.readlines() split_list = [] disagreeable_restraints_list = [] dr_count = 0 for line in lines: if ("may be split into" in line): parts = line.split() if len(parts)>6: atom_id = parts[3] # e.g; atom_id: CD1_1392 atom_parts = make_atom_parts(atom_id) button_label = "Atom " + str(atom_parts[1]) + " " + atom_parts[3] + " may be split?" split_list.append([button_label, imol] + atom_parts) #split_list.append(atom_parts) elif (" Observed Target Error Sigma Restraint" in line): dr_count = 1 elif (dr_count == 1): disagreeable_restraints_list = [] # reset the disagreeable-restraints-list dr_count = 2 elif (dr_count == 2): # OK, in the disagreeable table #print "BL DEBUG:: DR: ", line dr_bits = parse_dr_line(line) #print "BL DEBUG:: dr_bits: ", dr_bits,len(line) if (type(dr_bits) is ListType): disagreeable_restraints_list.append(dr_bits) if (len(line) > 1): dr_count = 2 else: dr_count = 0 else: pass fin.close() # print "BL DEBUG:: now run the gui with ", disagreeable_restraints_list, split_list do_gui(disagreeable_restraints_list, split_list) else: print("BL ERROR:: unknown error opening file ", file_name) #read_shelx_lst_file("test.lst",0) # Read a shelx project (i.e. the .res file, the .lst file and the # .fcf.cif file (if it exists (else read the .fcf file (if it # exists))) # # If the file-name has an extension of .lst .res .ins .fcf .log .hkl # then strip that off before adding new extensions. # def read_shelx_project(file_name): import os file_name = os.path.abspath(file_name) extension = coot_utils.file_name_extension(file_name) if (extension == "lst"): file_stub = coot_utils.file_name_sans_extension(file_name) elif (extension == "ins"): file_stub = coot_utils.file_name_sans_extension(file_name) elif (extension == "insh"): file_stub = coot_utils.file_name_sans_extension(file_name) elif (extension == "log"): file_stub = coot_utils.file_name_sans_extension(file_name) elif (extension == "hkl"): file_stub = coot_utils.file_name_sans_extension(file_name) elif (extension == "res"): file_stub = coot_utils.file_name_sans_extension(file_name) elif (extension == "fcf"): file_stub = coot_utils.file_name_sans_extension(file_name) else: file_stub = file_name res_file_name = file_stub + ".res" lst_file_name = file_stub + ".lst" fcf_file_name = file_stub + ".fcf" fcf_cif_file_name = file_stub + ".fcf.cif" print(" file_name: ", file_name) print(" file_stub: ", file_stub) print(" extension: ", extension) if (os.path.isfile(res_file_name)): print("Read res file ", res_file_name) imol_res = coot.handle_read_draw_molecule_with_recentre(res_file_name, 0) else: print(" No res file ", res_file_name) imol_res = -1 if (not coot_utils.valid_model_molecule_qm(imol_res)): print("WARNING:: Bad molecule from res file read.") else: if (os.path.isfile(fcf_cif_file_name)): if (not os.path.isfile(fcf_file_name)): print(" Read fcf-cif file ", fcf_cif_file_name) coot.auto_read_cif_data_with_phases(fcf_cif_file_name) else: # OK both xxx.fcf and xxx.fcf.cif exist, we # only want to read the xxx.fcf.cif if it is # more recent than xxx.fcf (if it is not, we # want to handle-shelx-fcf-file. from stat import ST_MTIME fcf_date = os.stat(fcf_file_name)[ST_MTIME] fcf_cif_date = os.stat(fcf_cif_file_name)[ST_MTIME] # print " fcf_date %s fcf_cif_date %s" %(time.ctime(fcf_date), time.ctime(fcf_cif_date)) if (fcf_date < fcf_cif_date): coot.auto_read_cif_data_with_phases(fcf_cif_file_name) else: handle_shelx_fcf_file(fcf_file_name) # xxx.fcf.cif did not exist: else: if (os.path.isfile(fcf_file_name)): print(" Read fcf file ", fcf_file_name) handle_chelx_fcf_file(fcf_file_name) else: print("BL WARNING:: no fcf and or cif files found!") if (os.path.isfile(lst_file_name)): print(" ::Read lst file ", lst_file_name) read_shelx_lst_file(lst_file_name, imol_res) else: print(" ::No lst file ", lst_file_name)