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# 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 <http://www.gnu.org/licenses/>.
# 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","")
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