# libcheck.py # # Copyright 2004, 2005, 2006 by Paul Emsley, The University of York # Copyright 2005, 2006 by Bernhard Lohkamp # Copyright (C) 2007, 2008, 2009 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 . # BL to do: # coot_utils.debug with given ccp4i_dir and lib file # else if refmac doesnt exist # # this is override-able by the user in their .coot file (for example). libcheck_exe = "libcheck" # This files provides an interface to libcheck # Where @var{code} is @emph{e.g.} "3GP" and @var{ccp4i-project-dir} # is an optional arg which is the directory to which the libcheck log # files and pdb file will go. # # Return -2 on @var{code} is not a string # Return -3 on libcheck failure # Return -4 on refmac failure # Return @var{imol} on success # Return @code{handle-read-draw-molecule} error code on failure to # read resultant pdb file # # Actually, it would be nice to know if this code represented a full # description - or a minimal one... perhaps we can parse the log # file and call a pop-up that will tell us. # # @var{dict_cif_libin should be a string}. If it is "" then it is # ignored. If it is not "" then it is used to create input to # libcheck (not a command line argument) so that bespoke dictionary # libraries can produce coords using "Get Monomer". # # might not do all above mentioned things in python, yet # def monomer_molecule_from_3_let_code(code, dict_cif_libin, ccp4i_project_dir = ""): import os, stat, shutil # return True if log file has "has the minimal description" in it. # else return False # def libcheck_minimal_qm(filename): # BL says: a quick fix for now, maybe we want to use something like # Paul's call_with_input_file funcn at some point ret = False try: f = open(filename, 'r') lines = f.readlines() for line in lines: if "has the minimal description" in line: ret = True break f.close() except: print("BL WARNING: couldnt open file ", filename) return ret # move file_name to some file name with a date extension # def move_aside(file_name): import time if (os.path.isfile(file_name)): # we use - and not : to avoid hazzle in windows extension = time.strftime('%d-%m-%Y-%H-%M-%S') new_file_name = file_name + "-" + extension try: os.rename(file_name, new_file_name) except: print("BL WARNING:: could not rename file %s to %s" %(file_name, new_file_name)) # the exe and log_file_name (and command_lines_args perhaps) # relative to dir (not the calling dir) # BL says:: maybe this should be in coot_utils.py def run_command_in_dir(run_dir, exe_name, command_line_args, data_lines, log_file_name, to_screen_flag): import os print(("BL INFO:: run_command_in_dir dir:" "%s exe: %s cl_args: %s data_lines: %s log_file: %s" %(run_dir, exe_name, command_line_args, data_lines, log_file_name))) current = os.getcwd() norm_dir = os.path.normpath(run_dir) os.chdir(norm_dir) status = coot_utils.popen_command(exe_name, command_line_args, data_lines, log_file_name, to_screen_flag) os.chdir(current) return status def log_file2text(log_file_name, dir): f = os.path.join(dir, log_file_name) return coot_utils.file2string(f) # This gets called in non-graphics mode too. # def libcheck_monomer_gui(dir_prefix, code_str, cif_file_name, pdb_file_name, post_refmac_pdb_file_name): # print "================= coot_utils.debug: libcheck_monomer_gui: dir_prefix: %s code_str: %s cif_file_name: %s pdb_file_name: %s post_refmac_pdb_file_name: %s" %(dir_prefix, code_str, cif_file_name, pdb_file_name, post_refmac_pdb_file_name) if (len(dict_cif_libin) == 0): libcheck_input = ["N", "MON " + code_str[0:3], ""] else: # BL says:: Paul's code says FILE_CIF as argument, but I beleave this should be # FILE_L. FILE_CIF is for coordinate cif files and not dictionary cif file (which is # what we have here, I think) # libcheck_input = ["N","FILE_CIF " + dict_cif_libin,"MON " + code_str,""] libcheck_input = ["N", "FILE_L " + dict_cif_libin, "MON " + code_str, ""] log_file_name = "coot-libcheck-" + code_str + ".log" log_file_name_in_dir = os.path.join(dir_prefix, log_file_name) refmac_input = ["MODE NEWENTRY", "END"] refmac_log_file_name = os.path.join(dir_prefix, "coot-libcheck-refmac-" + code_str + ".log") refmac_command_line = ["LIBIN", cif_file_name, "XYZIN", pdb_file_name, "XYZOUT", post_refmac_pdb_file_name] move_aside(os.path.join(dir_prefix, "libcheck.lib")) #print "passing libcheck these data lines:", libcheck_input libcheck_exe_file = coot_utils.find_exe(libcheck_exe, "CBIN", "CCP4_BIN", "PATH") if (libcheck_exe_file): libstatus = run_command_in_dir(dir_prefix, libcheck_exe_file, [], libcheck_input, log_file_name, True) print("BL INFO:: libcheck status:", libstatus) if (not coot_utils.isNumber(libstatus)): log_text = log_file2text(log_file_name, dir_prefix) if (isinstance(log_text, str)): coot.simple_text_dialog("Libcheck log", log_text, 200, 400) return -1 else: if (libstatus != 0): log_text = log_file2text(log_file_name, dir_prefix) if isinstance(log_text, str): coot.simple_text_dialog("Libcheck log", log_text, 400, 400) return -1 else: # we assume libcheck run ok # # But I now find that libcheck can run OK, but # not produce an output file (using dict .cif # file from PRODRG). # # So we first need to check that the output of # libcheck exists. # if (not os.path.isfile(cif_file_name)): print("libcheck failed to write the output cif file", cif_file_name) log_text = log_file2text(log_file_name, dir_prefix) if isinstance(log_text, str): coot.simple_text_dialog("Libcheck log", log_text, 400, 400) return -1 else: # OK, now let's run refmac: # libcheck_minimal_desc_status = libcheck_minimal_qm(log_file_name_in_dir) refmac_exe = coot_utils.find_exe("refmac5", "CBIN", "CCP4_BIN", "PATH") refmac_status = coot_utils.popen_command(refmac_exe, refmac_command_line, refmac_input, refmac_log_file_name) print("INFO:: libcheck-minimal? is ", libcheck_minimal_desc_status) if (not coot_utils.isNumber(refmac_status)): return -4 # refmac fails else: if (not refmac_status == 0): return -4 # refmac fails elsewhere else: # refmac run ok # # if there was a minimal description, # we get the real cif file in # libcheck.lib. libcheck_lib = os.path.join(dir_prefix, "libcheck.lib") #print "------------- about to copy file %s to %s in dir %s" %(libcheck_lib, cif_file_name, os.getcwd()) if (os.path.isfile(libcheck_lib)): shutil.copyfile(libcheck_lib, cif_file_name) return handle_libcheck_cif_and_pdb(cif_file_name, pdb_file_name, post_refmac_pdb_file_name) def handle_libcheck_cif_and_pdb(cif_file_name, pdb_file_name, post_refmac_pdb_file_name): #print "================= coot_utils.debug:: handle-libcheck-cif-and-pdb: cif-file-name: %s pdb-file-name: %s post-refmac-pdb-file-name: %s" %(cif_file_name, pdb_file_name, post_refmac_pdb_file_name) if (os.path.isfile(post_refmac_pdb_file_name) and os.path.isfile(cif_file_name)): pdb_status = coot.handle_read_draw_molecule_with_recentre( post_refmac_pdb_file_name, 0) if (coot_utils.valid_model_molecule_qm(pdb_status)): coot.assign_hetatms(pdb_status) move_molecule_here(pdb_status) coot.read_cif_dictionary(cif_file_name) return pdb_status # return imol of the ligand return -1 # on fail # main body if not isinstance(code, str): print("WARNING:: Oops code %s was not a string " %code) return -2 else: # do the files exist already? If so, just read them in. if (ccp4i_project_dir == ""): target_dir_name = "coot-ccp4" dir_name = coot_utils.get_directory(target_dir_name) dir_prefix = os.path.normpath(dir_name) else: dir_prefix = os.path.normpath(ccp4i_project_dir) #print "BL DEBUG:: dir prefix", dir_prefix code_str = str(code) pdb_file_name = os.path.join(dir_prefix, "libcheck_" + code_str + ".pdb") cif_file_name = os.path.join(dir_prefix, "libcheck_" + code_str + ".cif") post_refmac_pdb_file_name = os.path.join(dir_prefix, "monomer-" + code_str + ".pdb") if (os.path.isfile(post_refmac_pdb_file_name) and os.path.isfile(cif_file_name)): return handle_libcheck_cif_and_pdb(cif_file_name, pdb_file_name, post_refmac_pdb_file_name) else: libcheck_exe_file = coot_utils.find_exe(libcheck_exe, "CBIN", "CCP4_BIN", "PATH") if (not libcheck_exe_file): coot.info_dialog("You need to setup CCP4 (specifically LIBCHECK) first.") return -2 else: v = libcheck_monomer_gui(dir_prefix, code_str, cif_file_name, pdb_file_name, post_refmac_pdb_file_name) # somehow this can be none?! shouldnt if (not coot_utils.isNumber(v)): v = -1 return v #monomer_molecule_from_3_let_code("3GP","")