def display_map_coot(inp1, inp2):
''' display map by coordinate & SF file.
'''
mtz, xyz_inp, sf_inp = get_file_type(inp1, inp2)
if not xyz_inp or not sf_inp:
print 'Error: File must be in MTZ or a mmcif file having _refln.pdbx_FWT\n'
sys.exit()
fp = open(sf_inp, 'r')
sf_new = sf_inp + '__new'
fw = open(sf_new, 'w')
n = 0
for x in fp:
if '_refln.pdbx_r_free_flag' in x: #change it to bypass a bug in CAD.
fw.write('%s_x\n' % (x.rstrip()))
else:
if '_refln.pdbx_FWT' in x: n = n + 1
fw.write(x)
fw.close()
add = ''
if n > 0: # a cif file with pdbx_FWT
sf = prog.sf_convertor(xyz_inp, sf_new, 'mtz', add)
arg = 'coot --pdb %s --mtz %s' % (xyz_inp, sf)
os.system(arg)
else:
print 'Error: SF file should be the mmcif having _refln.pdbx_FWT.'
util.delete_file(sf_new, sf_new + '.mtz', 'sf_information.cif',
'sf_format_guess.text')
def cut_map_around_xyz(mapfile, peppdb_in, pepid):
'''using several CCP4 until to cut map around the selected molecule
color: [x800080] [xc00000] [xb0b0b0]
'''
mapout = pepid + '_cut.map'
util.delete_file(mapout)
'''
xyzlim,xyzcomp=find_xyzlim_compound(pepid, peppdb_in)
mapscr=cut_map_bylimit(xyzlim)
arg = mapfile + ' ' + ' ' + mapout
command="chmod +x %s ; ./%s " %(mapscr, mapscr) + arg
os.system(command)
return mapout
'''
peppdb = peppdb_in
if util.is_cif(peppdb_in): peppdb = cif.cif2pdb(peppdb_in)
mapscr = cut_map_scr()
arg = mapfile + ' ' + peppdb + ' ' + mapout
command = "chmod +x %s ; ./%s " % (mapscr, mapscr) + arg
os.system(command)
if util.is_cif(peppdb_in):
util.delete_file('%s.PDB' % peppdb_in)
peppdb = peppdb_in
return mapout
def map_info(mapfile):
'''get the min, max, mean, sigma from the map
'''
min, max, mean, sigma = '-1', '-1', '-1', '-1'
log = mapfile + '_header'
scr = mapfile + '.sh'
arg = 'mapdump mapin %s <<eof >%s \neof\n' % (mapfile, log)
fw = open(scr, 'w')
fw.write(arg)
fw.close()
os.system('chmod +x %s ; ./%s' % (scr, scr))
if not util.check_file(10, log): return min, max, mean, sigma
fp = open(log, 'r')
for x in fp:
if 'Minimum density ...' in x:
min = x.rstrip().split(' ')[-1]
elif 'Maximum density ...' in x:
max = x.rstrip().split(' ')[-1]
elif ' Mean density ..' in x:
mean = x.rstrip().split(' ')[-1]
elif 'deviation from mean density ..' in x:
sigma = x.rstrip().split(' ')[-1]
util.delete_file(scr, log)
return min, max, mean, sigma
def zip_one_file(dir, to_pack, zip_name):
verify_path_exists(dir)
# for the benefit of pigz, we have to cd to the directory, because
# we don't control the name of the file inside created zip file - it's
# the same as path of the file we're compressing
curr_dir = os.getcwd()
os.chdir(dir)
verify_path_exists(to_pack)
util.delete_file(zip_name) # ensure destination doesn't exist
try:
# -11 for zopfil compression
# --keep to not delete the source file
# --zip to create a single-file zip archive
# we can't control the name of the file pigz will create, so rename
# to desired name after it's created
pigz_dst = to_pack + ".zip"
util.delete_file(pigz_dst)
run_cmd_throw("pigz", "-11", "--keep", "--zip", to_pack)
print("Compressed using pigz.exe")
if pigz_dst != zip_name:
print("moving %s => %s" % (pigz_dst, zip_name))
shutil.move(pigz_dst, zip_name)
except:
# if pigz.exe is not in path, use regular zip compression
zip_file(zip_name, to_pack, to_pack, compress=True)
print("Compressed using regular zip")
verify_path_exists(zip_name)
os.chdir(curr_dir)
def delete_question(question_id=None):
try:
user_id = data_manager.get_userid_by_username(session['username'])
except KeyError:
return redirect('/')
if user_id == data_manager.get_foreign_key_by_id(
data_manager.question_db, 'users_id', question_id)[0]['users_id']:
data_manager.delete_line_by_foreign_id(data_manager.comment_db,
'question_id', question_id)
filename = 'static/image_for_question' + str(question_id) + '.png'
if util.check_file(filename):
util.delete_file(filename)
answer_ids_to_delete = data_manager.get_ids_by_foreign_id(
data_manager.answer_db, 'question_id', question_id)
for answer_id in answer_ids_to_delete:
data_manager.delete_line_by_foreign_id(data_manager.comment_db,
'answer_id',
answer_id['id'])
filename = 'static/image_for_answer' + str(
answer_id['id']) + '.png'
if util.check_file(filename):
util.delete_file(filename)
data_manager.delete_answer_by_question_id(question_id)
data_manager.delete_question(question_id)
else:
flash('Invalid user')
return redirect('/list')
def decode(self, message):
mask = int(message[0]) #mascara
filename = message[2] #nome do arquivo
path = message[3] #caminho
if mask == notify.CREATE_DIR: #se for uma mensagem de criar pasta, chama a função que cria pasta, e assim por diante, para todas as máscaras
util.create_folder(path, filename)
elif mask == notify.DELETE_DIR:
util.delete_folder(path, filename)
elif mask == notify.CREATE_FILE:
util.create_file(path, filename)
elif mask == notify.DELETE_FILE:
util.delete_file(path, filename)
elif mask == notify.MODIFY_FILE:
BkpSync.flag_send = 1
time.sleep(0.5)
util.modify_file(path, filename, self.conn)
time.sleep(1)
BkpSync.flag_send = 0
elif mask == notify.DIR_MOVED_FROM:
util.delete_folder(path, filename)
elif mask == notify.DIR_MOVED_TO:
util.create_folder(path, filename)
elif mask == notify.FILE_MOVED_FROM:
util.delete_file(path, filename)
elif mask == notify.FILE_MOVE_TO:
BkpSync.flag_send = 1
time.sleep(0.5)
util.modify_file(path, filename, self.conn)
time.sleep(1)
BkpSync.flag_send = 0
def zip_one_file(dir, to_pack, zip_name):
verify_path_exists(dir)
# for the benefit of pigz, we have to cd to the directory, because
# we don't control the name of the file inside created zip file - it's
# the same as path of the file we're compressing
curr_dir = os.getcwd()
os.chdir(dir)
verify_path_exists(to_pack)
util.delete_file(zip_name) # ensure destination doesn't exist
try:
# -11 for zopfil compression
# --keep to not delete the source file
# --zip to create a single-file zip archive
# we can't control the name of the file pigz will create, so rename
# to desired name after it's created
pigz_dst = to_pack + ".zip"
util.delete_file(pigz_dst)
run_cmd_throw("pigz", "-11", "--keep", "--zip", to_pack)
print("Compressed using pigz.exe")
if pigz_dst != zip_name:
print("moving %s => %s" % (pigz_dst, zip_name))
shutil.move(pigz_dst, zip_name)
except:
# if pigz.exe is not in path, use regular zip compression
zip_file(zip_name, to_pack, to_pack, compress=True)
print("Compressed using regular zip")
verify_path_exists(zip_name)
os.chdir(curr_dir)
def isolate_connect_ligand(pdb, k, v):
'''separate isolated and connected ligands
pdb: the list of coordinate (all atoms)
k: the chainID; v: the list of residue numbers.
'''
if len(v) == 1: return [v]
idd = '%s_%s_all' % (k, v[0])
natom, pdb_lig = get_subpdb(pdb, k, v, idd)
tmp = [v[0]]
for i, x in enumerate(v):
if i == 0: continue
n1, n2 = i - 1, i
nc = connect(pdb_lig, n1, n2, k, v)
if not nc: tmp.append(99999)
tmp.append(x)
ss = ''
for x in tmp:
ss = ss + ' %d' % x
t1 = (ss.split('99999'))
nres_list = []
for x in t1:
tt = x.split()
nres_list.append([int(i) for i in tt])
util.delete_file(pdb_lig)
# print(nres_list)
return nres_list
def map_around_compound(mapfile, coord, compid):
'''cut the ASU map to the residue level.
compid: model_compound_chainID_resnumber_alt_insertion.
mapfile: the CCP4 map in ASU.
coord: the coordinate file for the map (in cif/pdb)
'''
if (not util.check_file(100, mapfile) or not util.check_file(100, coord)):
err = 'Error: Either mapfile or coordinate file does not exist.'
config.ERRLOG.append(err)
print(err)
return
xyzlim, xyzcomp = find_xyzlim_compound(compid, coord)
if (len(xyzlim.strip()) < 2):
err = 'Error: compound boundary in fraction not found. check with compound ID'
config.ERRLOG.append(err)
print(err)
return
# below is cut map and get jmol
t = compid.split('_')
comp = '_'.join([t[0], t[1], t[2]])
mapout = comp + '_cut.map'
maphtml = comp + '.html'
mapscr = cut_map_bylimit(xyzlim)
util.delete_file(mapout)
arg = mapfile + ' ' + ' ' + mapout
command = "chmod +x %s ; ./%s " % (mapscr, mapscr) + arg
os.system(command)
min, max, mean, sigma = map_info(mapfile)
min1, max1, mean1, sigma1 = map_info(mapout)
cont = {
'0.5': 0.5,
'0.7': 0.7,
'1.0': 1.0,
'1.5': 1.5,
'2.0': 2.0
} #contour 4 map in asu.
cont1 = cont #contour 4 sub map.
scale = 1.0
if (float(sigma1) > 0):
scale = float(sigma) / float(sigma1)
for z in list(cont.keys()):
cont1[z] = cont[z] * scale
maphtml = get_html4jmol(comp, xyzcomp, mapout, cont1)
return maphtml, mapout
def build_installer_data(dir):
src = os.path.join("mupdf", "fonts", "droid", "DroidSansFallback.ttf")
dst = os.path.join(dir, "DroidSansFallback.ttf")
if not os.path.exists(dst) or is_more_recent(src, dst):
copy_to_dst_dir(src, dir)
files = [["SumatraPDF-no-MuPDF.exe", "SumatraPDF.exe"],
"DroidSansFallback.ttf", "libmupdf.dll", "npPdfViewer.dll",
"PdfFilter.dll", "PdfPreview.dll", "uninstall.exe"]
create_lzma_archive(dir, "InstallerData.dat", files)
installer_res = os.path.join(dir, "sumatrapdf", "Installer.res")
util.delete_file(installer_res)
def md_to_html(src, dst):
s = read_file_utf8(src)
md_info = parse_md(s)
body = markdown.markdown(md_info.s)
tmpl = tmpl_for_src_path(src)
#print("Found template: %s" % mdtmpl)
title = md_info.meta_data["title"]
#print(vars.keys())
html = str(tmpl(title, body))
util.delete_file(dst)
print("wrote %s" % dst)
write_file_utf8(dst, html)
def run_phenix(pdbfile, sffile, type1):
'''run sub-programs of phenix
'''
outfile = 'phenix__%s.log' %type1
util.delete_file(outfile)
print ('\nDoing PHENIX calculation for (%s) ...' %type1)
if type1 == 'xtriage' :
arg="phenix.xtriage %s log=%s >/dev/null" %(sffile, outfile)
os.system(arg)
return outfile
def md_to_html(src, dst):
s = read_file_utf8(src)
md_info = parse_md(s)
body = markdown.markdown(md_info.s)
tmpl = tmpl_for_src_path(src)
# print("Found template: %s" % mdtmpl)
title = md_info.meta_data["title"]
# print(vars.keys())
html = str(tmpl(title, body))
util.delete_file(dst)
print("wrote %s" % dst)
write_file_utf8(dst, html)
def build_installer_data(dir):
src = os.path.join("mupdf", "fonts", "droid", "DroidSansFallback.ttf")
dst = os.path.join(dir, "DroidSansFallback.ttf")
if not os.path.exists(dst) or is_more_recent(src, dst):
copy_to_dst_dir(src, dir)
files = [ ["SumatraPDF-no-MuPDF.exe", "SumatraPDF.exe"], "DroidSansFallback.ttf",
"libmupdf.dll", "npPdfViewer.dll", "PdfFilter.dll", "PdfPreview.dll",
"uninstall.exe"]
create_lzma_archive(dir, "InstallerData.dat", files)
installer_res = os.path.join(dir, "sumatrapdf", "Installer.res")
util.delete_file(installer_res)
def compare_r_tls_water(pdbfile_inp, sffile):
''' compare the R factors with/without TLS correction for waters.
Remove all the ANISOU and apply TLS again with/without water.
'''
pdbfile = rid_of_anisou(pdbfile_inp)
pdbfile_new = find_tls_water(pdbfile)
out2 = prog.run_dcc(pdbfile_new, sffile, '')
util.delete_file(pdbfile)
return
def delete_question_image(question_id):
try:
user_id = data_manager.get_userid_by_username(session['username'])
except KeyError:
return redirect('/')
if user_id == data_manager.get_foreign_key_by_id(
data_manager.question_db, 'users_id', question_id)[0]['users_id']:
filename = 'static/image_for_question' + str(question_id) + '.png'
util.delete_file(filename)
data_manager.update_image_data_by_id(data_manager.question_db,
question_id, 'no image')
else:
flash('Invalid user')
return redirect('/question/{}'.format(question_id))
def build_installer_data(dir):
src = os.path.join("mupdf", "resources", "fonts", "droid", "DroidSansFallback.ttf")
if not os.path.exists(src):
# location before https://code.google.com/p/sumatrapdf/source/detail?r=8266
src = os.path.join("mupdf", "fonts", "droid", "DroidSansFallback.ttf")
assert os.path.exists(src)
dst = os.path.join(dir, "DroidSansFallback.ttf")
if not os.path.exists(dst) or is_more_recent(src, dst):
copy_to_dst_dir(src, dir)
files = [ ["SumatraPDF-no-MuPDF.exe", "SumatraPDF.exe"], "DroidSansFallback.ttf",
"libmupdf.dll", "npPdfViewer.dll", "PdfFilter.dll", "PdfPreview.dll",
"uninstall.exe"]
create_lzma_archive(dir, "InstallerData.dat", files)
installer_res = os.path.join(dir, "sumatrapdf", "Installer.res")
util.delete_file(installer_res)
def build_installer_data(dir):
src = os.path.join("mupdf", "resources", "fonts", "droid", "DroidSansFallback.ttf")
if not os.path.exists(src):
# location before https://code.google.com/p/sumatrapdf/source/detail?r=8266
src = os.path.join("mupdf", "fonts", "droid", "DroidSansFallback.ttf")
assert os.path.exists(src)
dst = os.path.join(dir, "DroidSansFallback.ttf")
if not os.path.exists(dst) or is_more_recent(src, dst):
copy_to_dst_dir(src, dir)
files = [ ["SumatraPDF-no-MuPDF.exe", "SumatraPDF.exe"], "DroidSansFallback.ttf",
"libmupdf.dll", "npPdfViewer.dll", "PdfFilter.dll", "PdfPreview.dll",
"uninstall.exe"]
create_lzma_archive(dir, "InstallerData.dat", files)
installer_res = os.path.join(dir, "sumatrapdf", "Installer.res")
util.delete_file(installer_res)
def sf_symmetry(sffile, pdbfile):
''' get the best space group by pointless.
'''
sfmtz = prog.sf_convertor(pdbfile, sffile, 'mtz', '')
if not util.check_file(500, sfmtz):
print("Error: MTZ file not generated, check symmetry/cell in sf file.")
sys.exit()
print('Getting the best space group by pointless...')
out = prog.run_ccp4(pdbfile, sfmtz, 'pointless')
print('For details, please see the output file =%s' % out)
util.delete_file(sfmtz, 'sf_format_guess.text', 'sf_information.txt')
def run_ccp4(pdbfile, sffile, type1):
'''run sub-programs of CCP4
'''
outfile = 'ccp4__%s.log' %type1
util.delete_file(outfile)
print ('\nDoing %s ...' %type1)
if type1 == 'ctruncate' :
arg='ctruncate -hklin %s -amplitudes -colin "/*/*/[FP,SIGFP]" -hklout ctruncate-SF.mtz>& %s' %(sffile,outfile)
# arg='ctruncate -hklin %s -amplitudes -colano "/*/*/[I(+),SIGI(+),I(-),SIGI(-)]" -hklout ctruncate-SF.mtz>& %s' %(sffile,outfile)
os.system(arg)
elif type1 == 'pointless' :
arg='pointless hklin %s > %s' %(sffile, outfile)
os.system(arg)
os.system('grep "Best Solution" %s ' %outfile)
return outfile
def get_subpdb(pdb, k, v, idd):
'''pick the atoms in pdb (a list) for chain k in residue number v (a list)
'''
peppdb = '%s.pdb' % (idd)
fwt = open(peppdb, 'w')
natom = 0
for x in pdb:
if ('CRYST1' in x[:6] or 'SCALE' in x[:5]):
fwt.write(x)
elif (('ATOM' in x[:6] or 'HETATM' in x[:6]) and k == x[20:22].strip()
and int(x[22:26]) in v):
fwt.write(x)
natom = natom + 1
fwt.close()
if natom < 2: util.delete_file(peppdb) # ion
return natom, peppdb
def get_freer_flag(inp1, inp2):
''' find the correct free set in the mtz or mmcif file by exaustive test.
'''
idd, xyz_inp, sf_inp = get_file_type(inp1, inp2)
if not xyz_inp or not sf_inp:
print 'Error: Stopped searching the free set. '
print ' File must be in MTZ or a mmcif file having _refln.pdbx_r_free_flag\n'
sys.exit()
flist = open(sf_inp, 'r').readlines()
out = xyz_inp + '_test_Rf'
fw = open(out, 'w')
tmp = 'set reso R_rep Rf_rep CC_rep R_cal Rf_cal CC_cal \n'
print(tmp)
fw.write(tmp)
mark = ' '
for i in range(20):
if idd == 1: #sf is mtz
add = ' -freer %d' % i
sf = prog.sf_convertor(xyz_inp, sf_inp, 'mmcif', add)
else:
sf = cif2cif_sf(flist, i)
dcc_out = prog.run_dcc(xyz_inp, sf, ' -one -no_xtriage ')
val, rep, notls, tls, bstat, prog_rep = parse.values_from_dcc(dcc_out)
if (notls[3] - notls[2]) > 0.02: mark = '*'
arg = ' %2d %s %s\n' % (i, val, mark)
print(arg)
fw.write(arg)
if mark == '*': break
util.delete_file(sf)
fw.close()
print('The statistics output file is =%s' % out)
if mark == '*':
print('The matched SF file is =%s\n' % sf)
else:
print('Warning: No proper free set is found! \n')
def delete_answer(answer_id=None):
try:
user_id = data_manager.get_userid_by_username(session['username'])
except KeyError:
return redirect('/')
question_id = data_manager.get_foreign_key_by_id(
data_manager.answer_db, 'question_id', answer_id)[0]['question_id']
if user_id == data_manager.get_foreign_key_by_id(data_manager.answer_db,
'users_id',
answer_id)[0]['users_id']:
data_manager.delete_line_by_foreign_id(data_manager.comment_db,
'answer_id', answer_id)
question_id = data_manager.delete_answer_by_id(
answer_id)['question_id']
filename = 'static/image_for_answer' + str(answer_id) + '.png'
if util.check_file(filename):
util.delete_file(filename)
else:
flash('Invalid user')
return redirect('/question/{}'.format(question_id))
def run_async(command, exec_time_in_seconds):
if util.valid_ip():
try:
temp_out_file_name = tempfile.NamedTemporaryFile().name
with open(temp_out_file_name, "w") as fout:
proc = subprocess.Popen(command, shell=True, stdout=fout)
# wait for a few seconds
time.sleep(exec_time_in_seconds)
# stop the process
proc.kill()
# read contents of the file
with open(temp_out_file_name, "rb") as fin:
output = fin.read()
# remove the temp file
util.delete_file(temp_out_file_name)
return util.replace_all(output, util.get_replace_dic())
except subprocess.SubprocessError:
proc.kill()
outs, errs = proc.communicate()
return errs
else:
return message.error_404_msg
def build_one_output(name, input_fn):
output_fn = change_extension(input_fn, 'sol')
delete_file(output_fn)
result = run_solution(reference_solution(name), input_fn, output_fn)
return result.status == 'OK'
def test_delete_file():
util.delete_file('z.txt')
def run_solution(sol_fn,
input_fn,
output_fn=None,
reference_fn=None,
time_limit=20,
mem_limit=1024,
file_limit=1024):
if reference_fn is None:
if output_fn is None:
output_fn = '/dev/null'
else:
assert output_fn is None
output_file = NamedTemporaryFile(delete=False)
output_fn = output_file.name
mem_limit = mem_limit * 1024 * 1024
file_limit = file_limit * 1024
pid = os.fork()
if pid == 0:
resource.setrlimit(resource.RLIMIT_CPU,
(time_limit + 1, time_limit + 1))
resource.setrlimit(resource.RLIMIT_DATA, (mem_limit, mem_limit))
resource.setrlimit(resource.RLIMIT_FSIZE, (file_limit, file_limit))
with open(input_fn, 'r') as in_file:
os.dup2(in_file.fileno(), 0)
with open(output_fn, 'w') as out_file:
os.dup2(out_file.fileno(), 1)
with open('/dev/null', 'w') as err_file:
os.dup2(err_file.fileno(), 2)
os.execl(sol_fn, sol_fn)
(pid, status, rusage) = os.wait4(pid, 0)
# ranido changed
#result = Result(running_time = rusage.ru_utime)
result = Result(running_time=rusage.ru_utime + rusage.ru_stime)
# ranido changed
#if os.WIFSIGNALED(status) and os.WTERMSIG(status) == signal.SIGXCPU:
if result.running_time > time_limit:
result.status = 'TLE'
elif os.WEXITSTATUS(status) != 0:
result.status = 'RE'
result.detail = 'failed'
hints.give_hint('solution-failed')
if os.WIFSIGNALED(status) and os.WTERMSIG(status) == signal.SIGSEGV:
hints.give_hint('solution-SIGSEGV')
result.detail = 'SIGSEGV'
elif os.WIFSIGNALED(status) and os.WTERMSIG(status) == signal.SIGABRT:
hints.give_hint('solution-SIGABRT')
result.detail = 'SIGABRT'
elif reference_fn:
if subprocess.call(['diff', reference_fn, output_fn],
stdout=NamedTemporaryFile(),
stderr=NamedTemporaryFile()) == 0:
result.status = 'AC'
else:
result.status = 'WA'
else:
result.status = 'OK'
if reference_fn:
delete_file(output_fn)
return result
def clean_backups(name):
u"Delete backup files from problem `name`'s tree."
for dirpath, _, backup_fns in os.walk('%s/' % name):
for backup_fn in backup_fns:
if backup_fn.endswith('~'):
delete_file(os.path.join(dirpath, backup_fn))
def set_file(path):
util.delete_file(path)
logging.basicConfig(format='%(levelname)s:%(message)s',
filename=path,
level=logging.DEBUG)
def drop(self):
path = util.path_join("pages", self.name + ".json")
util.delete_file(path)
self.logger.info("delete page %s successfully" % self.name)
for file in [
"LICENSE", "Makefile", "pkginfo.in", "prototype.in", "icon.desktop",
"start.sh", "vmoptions.README"
]:
if not util.check_file_exists(os.path.join(util.get_script_path(), "data", args.ide, file)) and not \
util.check_file_readable(os.path.join(util.get_script_path(), "data", args.ide, file)):
logger.error("%s does not exist or is not readable." % file)
cleanup(-1, logger)
# Download URL
if util.check_file_exists(
os.path.join(util.get_script_path(), "tmp",
link.split("/")[-1])):
if not util.delete_file(
os.path.join(util.get_script_path(), "tmp",
link.split("/")[-1]), logger, False):
cleanup(-1, logger)
resp = urllib.request.urlretrieve(
link, os.path.join(util.get_script_path(), "tmp",
link.split("/")[-1]), util.progress_hook)
if resp is None or resp[1]["Connection"] != "close" or int(
resp[1]["Content-Length"]) < 100000:
logger.error("Error while downloading '%s'." %
os.path.join(util.get_script_path(), "tmp",
link.split("/")[-1]))
cleanup(-1, logger)
if not util.run_cmd(
"tar --strip-components 1 -C %s -zxf %s" %
# Checking files
for file in ["control.in", "postinst", "sysctl-99.conf"]:
if not util.check_file_exists(os.path.join(util.get_script_path(), "data", args.ide, "debian", file)) and not \
util.check_file_readable(os.path.join(util.get_script_path(), "data", args.ide, "debian", file)):
logger.error("%s does not exist or is not readable." % file)
cleanup(-1, logger)
for file in ["LICENSE", "Makefile", "pkginfo.in", "prototype.in", "icon.desktop", "start.sh", "vmoptions.README"]:
if not util.check_file_exists(os.path.join(util.get_script_path(), "data", args.ide, file)) and not \
util.check_file_readable(os.path.join(util.get_script_path(), "data", args.ide, file)):
logger.error("%s does not exist or is not readable." % file)
cleanup(-1, logger)
# Download URL
if util.check_file_exists(os.path.join(util.get_script_path(), "tmp", link.split("/")[-1])):
if not util.delete_file(os.path.join(util.get_script_path(), "tmp", link.split("/")[-1]), logger, False):
cleanup(-1, logger)
resp = urllib.request.urlretrieve(link, os.path.join(util.get_script_path(), "tmp", link.split("/")[-1]), util.progress_hook)
if resp is None or resp[1]["Connection"] != "close" or int(resp[1]["Content-Length"]) < 100000:
logger.error("Error while downloading '%s'." % os.path.join(util.get_script_path(), "tmp", link.split("/")[-1]))
cleanup(-1, logger)
if not util.run_cmd("tar --strip-components 1 -C %s -zxf %s" %
(os.path.join(util.get_script_path(), "tmp", "root", "usr", "share", "jetbrains", args.ide),
os.path.join(util.get_script_path(), "tmp", link.split("/")[-1])), logger, False):
logger.error("Error while unpacking '%s' to '%s'." %
(os.path.join(util.get_script_path(), "tmp", link.split("/")[-1])),
os.path.join(util.get_script_path(), "tmp", "root", "usr", "share", "jetbrains", args.ide))
cleanup(-1, logger)
def sf_quality(sffile, pdbfile):
'''run ctruncate and analysis the result
'''
sf_tmp = sffile + '.mtz'
sf_tmp1 = prog.sf_convertor(pdbfile, sffile, 'mmcif', '')
sf_tmp = prog.sf_convertor(pdbfile, 'SF_4_validate.cif', 'mtz', '')
if not util.check_file(500, sf_tmp):
print(
"Error: Conversion failed! Maybe your sf file has no symmetry/cell."
)
sys.exit()
if pdbfile == '-xtriage':
outfile = prog.run_phenix(pdbfile, sf_tmp, 'xtriage')
elif pdbfile == '-ctruncate': #do ctruncate
outfile = prog.run_ccp4(pdbfile, sf_tmp, 'ctruncate')
else: #do ctruncate
outfile = prog.run_ccp4(pdbfile, sf_tmp, 'pointless')
if not util.check_file(500, outfile):
print('Error: The log file (%s) is not generated' % outfile)
sys.exit()
fp = open(outfile, 'r')
flist = fp.readlines()
for i, x in enumerate(flist): #for xtriage/ctruncate
t = x.strip()
if ('<|L|>:' in t[:6] or '<L^2>:' in t[:8]
or 'L-test suggests' in t[:30]
or 'twinning, twin fraction' in t):
print(t)
elif (t == 'Acentric reflections' or t == 'Centric reflections'
or t == 'L test for acentric data'):
print(t)
elif (('<I^2>/<I>^2' in x or '<F>^2/<F^2>' in x or ' <|E^2 - 1|> ' in x
or 'Mean |L| :' in x or 'Mean L^2 :' in x
or 'L statistic = ' in x) and 'untwinned' in x
and ' perfect twin' in x):
print(t)
elif (t == '$TABLE: Acentric moments of E:'
or t == '$TABLE: Centric moments of E:'):
print(x.split(':')[1])
elif '$GRAPHS: 4th moment of E (Expected ' in x or ': 1st & 3rd moments of E (Expected ' in x:
print(x.split(':')[1])
elif 'ML estimate of overall B value of None:' in x:
print('The ML estimate of overall B value = %s' % flist[i + 1])
elif '[MaxAnisoB-MinAnisoB]/[MaxAnisoB' in x:
print('%s' % x)
elif 'pseudo)merohedral twin laws' in x:
print('%s' % x)
elif 'No significant pseudotranslation is detected' in x:
print('No significant pseudotranslation is detected.\n')
fp.seek(0)
law = ''
for x in fp: #for plots
if (' Acentric_theory ' in x and '_perfect_twin ' in x): #Xtriage
fname, start, end = outfile + '_Ltest.data', '$$', '$$'
extract_data4plot(fp, fname, start, end, 'Ltest')
plot_items(fname, 'twin', '', '', '', '')
elif ('H test for possible twin law' in x): #Xtriage
law = x.split('law')[1].strip()
elif ('H ' in x[:5] and 'Observed_S(H)' in x): #Xtriage
fname, start, end = outfile + '_Htest.data', '$$', '$$'
extract_data4plot(fp, fname, start, end, 'Htest')
title = 'H test for Acentric data (twin law =%s)' % law
plot = ''' using 1:2 t "Observed data", '' u 1:3 t "Untwinned by theory" , '' u 1:4 t "Fitted" '''
plot_items(fname, 'twin', title, '|H|', '', plot)
elif ('1/resol^2 <I/sigma_I>;_Signal_to_noise $$' in x): #Xtriage
fname, start, end = outfile + '_I_sigI.data', '$$', '$$'
extract_data4plot(fp, fname, start, end, 'Wilson')
plot_items(fname, 'I/sigI', '', '', '', '')
if (' Expected_untwinned ' in x
and 'Expected_twinned' in x): #Ctruncate
fname, start, end = outfile + '_Ltest.data', '$$', '$$'
extract_data4plot(fp, fname, start, end, 'Ltest')
plot_items(fname, 'twin', '', '', '', '')
elif ('|L| N(|L|) Untwinned Twinned' in x): #Pointless
fname, start, end = outfile + '_Ltest.data', '$$', '$$'
extract_data4plot(fp, fname, start, end, 'Ltest')
plot_items(fname, 'twin', '', '', '', '')
fp.close()
print("\nThe output file = %s\n" % outfile)
util.delete_file('sf_information.txt', 'sf_format_guess.text', sf_tmp,
sf_tmp1)
def matt_coeff(infile, outfile):
'''calculate Matthew_coeff and solven content: file is in pdb format;
'''
if not util.check_file(100, infile):
print('Error: file (%s) not exist' % infile)
return
file = infile
if util.is_cif(infile): file = cif2pdb(infile)
fp = open(file, 'r')
cell = [1, 1, 1, 1, 1, 1]
spt, nop, nmat, sym, res, atom, res = 1, 0, 1, 'X', [], [], []
rmass, amass, armass = 0, 0, 0
hetres, aname, rest = [], [], ''
for x in fp:
if 'REMARK 290 ' in x[:12] and '555' in x and ',' in x[23:32]:
nop = nop + 1
elif 'SEQRES' in x[:6]:
t = x[17:79].split()
res.extend(t)
# elif 'SPLIT' in x[:6] :
# t=x[6:].split()
# spt=len(t)
elif 'MTRIX3' in x[:6] and '1' not in x[55:].strip():
nmat = nmat + 1
elif 'CRYST1' in x[:6]:
c = x[7:54].split()
cell = [float(y) for y in c]
sym = x[54:65].strip()
elif ('ATOM' in x[:4] or 'HETA' in x[:4]):
if ('HOH' in x[17:20] or 'DOD' in x[17:20]): continue
atom.append(x)
occ = float(x[54:60])
amass = amass + atom_mass(x[76:78].strip()) * occ
t = x[17:27] #comp_ch_res_int
aname.append(x[76:78].strip())
if t != rest:
comp = t[:3].strip()
restmp = residue_mass(comp)
if restmp < 1:
hetres.append(comp)
else:
armass = armass + residue_mass(comp)
rest = t
aname = []
elif 'ENDMDL' in x[:6]:
break
fp.close()
cell_vol = cell_volume(cell)
nsym = sg_nsym(sym)
if nsym == -1:
print('Error: space group (%s) is not in the list (%s)' % (sym, file))
nsym = nop
#----------
for x in hetres:
armass = armass + non_standard_res(x, atom)
for x in res:
resm = residue_mass(x)
if resm < 1:
m1 = non_standard_res(x, atom)
rmass = rmass + m1
else:
rmass = rmass + resm
amatt, asolv = calc_matt(cell_vol, amass, nsym, nmat, spt) #by atom, occ
rmatt, rsolv = calc_matt(cell_vol, rmass, nsym, nmat, spt) #by SEQRES
armatt, arsolv = calc_matt(cell_vol, armass, nsym, nmat, spt) #residue
matt, solv = -1, -1
if 2.0 < rmatt < 5:
matt, solv = rmatt, rsolv
elif 2.0 < armatt < 5:
matt, solv = armatt, arsolv
elif 2.0 < amatt < 5:
matt, solv = amatt, asolv
else:
matt, solv = armatt, arsolv
print(
'Warning: packing problem (%s), Matthew_coeff=%.2f; Solvent=%.2f' %
(file, matt, solv))
if util.is_cif(infile): util.delete_file(file)
print('%s : split nsym, nmat= %2d %2d %2d' % (file, spt, nsym, nmat))
print('By ATOM: matt= %6.2f , solvent= %6.2f ' % (amatt, asolv))
print('By SEQRES: matt= %6.2f , solvent= %6.2f ' % (rmatt, rsolv))
print('By residue: matt= %6.2f , solvent= %6.2f ' % (armatt, arsolv))
print('Possible: matt= %6.2f , solvent= %6.2f ' % (matt, solv))
print('\nmass_total_atom=%.1f ; cell_vol=%.1f' % (amass, cell_vol))
error = '?'
if (matt > 8.7 or matt < 1.5):
error = 'Warning: Matthew_coefficient(%.2f) is abnormal. Possible incomplete content of ASU (or a split entry).' % matt
if matt == 0.0 and solv == 1.0: error = '?' #space group problem
if outfile:
fw = open(outfile, 'w')
ss = '''data_matt
#
_packing.Matthew_coefficient %6.2f
_packing.solvent_content %6.2f
_packing.error "%s"\n
''' % (matt, solv, error)
fw.write(ss)
fw.close()
print 'The output file = %s\n' % outfile
return matt, solv
def set_file(path):
util.delete_file(path)
logging.basicConfig(format='%(levelname)s:%(message)s',filename=path,level=logging.DEBUG)
def get_subcif(dic, k, v):
'''k is chainID; v is list of residue number
return idd, natom, ciffile name
'''
'''
ciffile=dic['pdbfile']
flist=open(ciffile, 'r').readlines()
cell_items,values = cif.cifparse(flist, '_cell.')
cell=cif.get_rows(cell_items, values)
sym_items,values = cif.cifparse(flist, '_symmetry.')
sym=cif.get_rows(sym_items, values)
items,values = cif.cifparse(flist, '_atom_site.')
comp=cif.parse_values(items,values,"_atom_site.auth_comp_id")
asym=cif.parse_values(items,values,"_atom_site.auth_asym_id")
seq=cif.parse_values(items,values,"_atom_site.auth_seq_id")
alt=cif.parse_values(items,values,"_atom_site.label_alt_id")
ins=cif.parse_values(items,values,"_atom_site.pdbx_PDB_ins_code");
mod=cif.parse_values(items,values,"_atom_site.pdbx_PDB_model_num")
row=cif.get_rows(items, values)
'''
cell_items, cell = dic['cell_items'], dic['lig_cell']
sym_items, sym = dic['sym_items'], dic['lig_sym']
items, comp, asym, seq, alt, ins, mod, row = dic['items'], dic[
'comp1'], dic['asym'], dic['seq'], dic['alt'], dic['ins'], dic[
'mod'], dic['row']
idd, natom, atom = '1_X_X_X__', 0, []
for i in range(len(asym)):
if asym and asym[i] == k and seq and int(seq[i]) in v:
natom = natom + 1
#print(i, natom, k, v[0],asym[i], seq[i], comp[i])
alter, inst = '', ''
if alt and alt[i] != '?' and alt[i] != '.': alter = alt[i]
if ins and ins[i] != '?' and ins[i] != '.': inst = ins[i]
atom.append(row[i])
if natom == 1 and mod and comp:
idd = '_'.join([mod[i], asym[i], comp[i], seq[i], inst, alter])
subpep = '%s.cif' % (idd) #write subcif name
fw = open(subpep, 'w')
fw.write('data_%s\n#\n' % idd)
for i, p in enumerate(cell_items):
if ' ' in cell[0][i]:
fw.write("%s '%s'\n" % (p, cell[0][i]))
else:
fw.write("%s %s\n" % (p, cell[0][i]))
fw.write('#\n')
for i, p in enumerate(sym_items):
if ' ' in sym[0][i]:
fw.write("%s '%s'\n" % (p, sym[0][i]))
else:
fw.write("%s %s\n" % (p, sym[0][i]))
fw.write('\n#\nloop_\n')
for p in items:
fw.write("%s\n" % p)
for x in atom:
for m in x:
fw.write("%s " % m)
fw.write('\n')
fw.close()
if natom < 2: util.delete_file(subpep) # ion
return idd, natom, subpep