def make_zip(filelist):
"""
:type filelist: list
"""
# Main path in tarfile:
maindir = 'DSR-{}/'.format(VERSION)
# tmpdir for file collection:
tmpdir = tempfile.mkdtemp()
# full directory in temp:
full_tmp_dir = os.path.abspath(os.path.join(tmpdir, maindir))
os.makedirs(full_tmp_dir)
# Tar output file
zipfilename = os.path.abspath('setup/Output/DSR-{}.tar.gz'.format(VERSION))
remove_file(zipfilename)
# Go through DSR path and add files from list:
for f in filelist:
# Also add recoursive dirs:
for filen in walkdir(f, exclude=['.pyc', '.DS_Store']):
print(filen)
# need path without filename to create target directories:
path, _ = os.path.split(filen)
target_tmp_dir = os.path.join(full_tmp_dir, path)
if not os.path.exists(target_tmp_dir):
os.makedirs(target_tmp_dir)
copy_file(filen, target_tmp_dir)
dos2unix(os.path.join(target_tmp_dir, os.path.split(filen)[1])) # dos2unix only in target tmp
with tarfile.open(zipfilename, mode='w:gz') as archive:
archive.add(full_tmp_dir, arcname=maindir, recursive=True)
# copy_file(zipfilen, 'StructureFinder/scripts/Output/')
print("\nFile written to {}".format(zipfilename))
shutil.rmtree(tmpdir)
make_shasum(zipfilename)
def make_shasum(filename):
sha = sha512_checksum(filename)
shafile = os.path.abspath('setup/Output/DSR-{}-sha512.sha'.format(VERSION))
remove_file(shafile)
with open(shafile, 'w') as f:
f.write(sha)
print("SHA512: {}".format(sha))
def setUp(self):
import db
self.maxDiff = None
self.res_file = 'p21c.res'
testresfile = './p21c.res'
invert = True
class OptionsParser():
rigid_group = False
target_coords = False
self.options = OptionsParser()
self.rl = ResList(testresfile)
self.reslist = self.rl.get_res_list()
self.dsrp = DSRParser(self.reslist)
self.find_atoms = FindAtoms(self.reslist)
self.gdb = dbfile.ParseDB()
fragment = 'OC(CF3)3'
self.dbatoms = self.gdb.get_atoms(fragment) # only the atoms of the dbentry as list
self.dbhead = self.gdb.get_restraints(fragment) # this is only executed once
self.resi = Resi(self.dsrp, 'CF3', self.find_atoms)
self.dbtypes = get_atomtypes(self.dbatoms)
with open('./intern.TXT') as txt:
self.intern = txt.read()
with open('./extern.TXT') as txt2:
self.extern = txt2.read()
misc.remove_file('./dsr_CF3_4_dsr_CF3_p21c.dfix')
self.sf = SfacTable(self.reslist, self.dbtypes)
self.sfac_table = self.sf.set_sfac_table()
self.num = NumberScheme(self.reslist, self.dbatoms, self.dsrp)
self.numberscheme = self.num.get_fragment_number_scheme()
self.db_testhead = db.db_testhead
def artwork_set_image(self, filename, artist, album, path, info_img_only=False):
# Note: filename arrives here is in FILESYSTEM_CHARSET, not UTF-8!
if (self.status_is_play_or_pause() and
self.songinfo and
self.songinfo.get('artist') == artist and
self.songinfo.get('album') == album):
if os.path.exists(filename):
# We use try here because the file might exist, but might
# still be downloading or corrupt:
try:
pix = gtk.gdk.pixbuf_new_from_file(filename)
except:
# If we have a 0-byte file, it should mean that
# sonata reset the image file. Otherwise, it's a
# bad file and should be removed.
if os.stat(filename).st_size != 0:
misc.remove_file(filename)
return
self.currentpb = pix
if not info_img_only:
# Store in cache
cache_key = library_set_data(artist=artist, album=album, path=path)
self.set_library_artwork_cached_filename(cache_key, filename)
# Artwork for tooltip, left-top of player:
(pix1, w, h) = img.get_pixbuf_of_size(pix, 75)
pix1 = self.artwork_apply_composite_case(pix1, w, h)
pix1 = img.pixbuf_add_border(pix1)
pix1 = img.pixbuf_pad(pix1, 77, 77)
self.albumimage.set_from_pixbuf(pix1)
self.artwork_set_tooltip_art(pix1)
del pix1
# Artwork for library, if current song matches:
self.library_set_image_for_current_song(cache_key)
# Artwork for fullscreen
self.fullscreen_cover_art_set_image()
# Artwork for info tab:
if self.info_imagebox_get_size_request()[0] == -1:
fullwidth = self.notebook_get_allocation()[2] - 50
(pix2, w, h) = img.get_pixbuf_of_size(pix, fullwidth)
else:
(pix2, w, h) = img.get_pixbuf_of_size(pix, 150)
pix2 = self.artwork_apply_composite_case(pix2, w, h)
pix2 = img.pixbuf_add_border(pix2)
self.info_image.set_from_pixbuf(pix2)
del pix2
del pix
self.lastalbumart = filename
self.schedule_gc_collect()
def artwork_set_image(self, filename, artist, album, path, info_img_only=False):
# Note: filename arrives here is in FILESYSTEM_CHARSET, not UTF-8!
if self.artwork_is_for_playing_song(filename):
if os.path.exists(filename):
# We use try here because the file might exist, but might
# still be downloading or corrupt:
try:
pix = gtk.gdk.pixbuf_new_from_file(filename)
except:
# If we have a 0-byte file, it should mean that
# sonata reset the image file. Otherwise, it's a
# bad file and should be removed.
if os.stat(filename).st_size != 0:
misc.remove_file(filename)
return
self.currentpb = pix
if not info_img_only:
# Store in cache
cache_key = library_set_data(artist=artist, album=album, path=path)
self.set_library_artwork_cached_filename(cache_key, filename)
# Artwork for tooltip, left-top of player:
(pix1, w, h) = img.get_pixbuf_of_size(pix, 75)
pix1 = self.artwork_apply_composite_case(pix1, w, h)
pix1 = img.pixbuf_add_border(pix1)
pix1 = img.pixbuf_pad(pix1, 77, 77)
self.albumimage.set_from_pixbuf(pix1)
self.artwork_set_tooltip_art(pix1)
del pix1
# Artwork for library, if current song matches:
self.library_set_image_for_current_song(cache_key)
# Artwork for fullscreen
self.fullscreen_cover_art_set_image()
# Artwork for info tab:
if self.info_imagebox_get_size_request()[0] == -1:
fullwidth = self.notebook_get_allocation()[2] - 50
(pix2, w, h) = img.get_pixbuf_of_size(pix, fullwidth)
else:
(pix2, w, h) = img.get_pixbuf_of_size(pix, 150)
pix2 = self.artwork_apply_composite_case(pix2, w, h)
pix2 = img.pixbuf_add_border(pix2)
self.info_image.set_from_pixbuf(pix2)
del pix2
del pix
self.lastalbumart = filename
self.schedule_gc_collect()
def library_get_album_cover(self, dirname, artist, album, pb_size):
_tmp, coverfile = self.artwork_get_local_image(dirname, artist, album)
if coverfile:
try:
coverpb = gtk.gdk.pixbuf_new_from_file_at_size(coverfile, pb_size, pb_size)
except:
# Delete bad image:
misc.remove_file(coverfile)
return (None, None)
w = coverpb.get_width()
h = coverpb.get_height()
coverpb = self.artwork_apply_composite_case(coverpb, w, h)
return (coverpb, coverfile)
return (None, None)
def restore_shx_file(self):
"""
restores filename from backup
"""
resfile = os.path.abspath(str(self.resfile_name + '.res'))
try:
print('*** Restoring previous res file. ***')
shutil.copyfile(self.backup_file, resfile)
except IOError:
print('Unable to restore res file from {}.'.format(self.backup_file))
try:
misc.remove_file(self.backup_file)
except IOError:
print('Unable to delete backup file {}.'.format(self.backup_file))
def library_get_album_cover(self, dirname, artist, album, pb_size): _tmp, coverfile = self.artwork_get_local_image(dirname, artist, album) if coverfile: try: coverpb = gtk.gdk.pixbuf_new_from_file_at_size(coverfile, pb_size, pb_size) except: # Delete bad image: misc.remove_file(coverfile) return (None, None) w = coverpb.get_width() h = coverpb.get_height() coverpb = self.artwork_apply_composite_case(coverpb, w, h) return (coverpb, coverfile) return (None, None)
def get_lyrics_start(self, search_artist, search_title, filename_artist,
filename_title, song_dir):
filename_artist = misc.strip_all_slashes(filename_artist)
filename_title = misc.strip_all_slashes(filename_title)
filename = self._check_for_local_lyrics(filename_artist,
filename_title, song_dir)
lyrics = ""
if filename:
# If the lyrics only contain "not found", delete the file and try
# to fetch new lyrics. If there is a bug in Sonata/SZI/LyricWiki
# that prevents lyrics from being found, storing the "not found"
# will prevent a future release from correctly fetching the lyrics.
try:
with open(filename, 'r') as f:
lyrics = f.read()
except IOError:
pass
if lyrics == _("Lyrics not found"):
misc.remove_file(filename)
filename = self._check_for_local_lyrics(filename_artist,
filename_title,
song_dir)
if filename:
# Re-use lyrics from file:
try:
with open(filename, 'r') as f:
lyrics = f.read()
except IOError:
pass
# Strip artist - title line from file if it exists, since we
# now have that information visible elsewhere.
header = "%s - %s\n\n" % (filename_artist, filename_title)
if lyrics[:len(header)] == header:
lyrics = lyrics[len(header):]
self._show_lyrics(filename_artist, filename_title, lyrics=lyrics)
else:
# Fetch lyrics from lyricwiki.org etc.
lyrics_fetchers = pluginsystem.get('lyrics_fetching')
callback = lambda * args: self.get_lyrics_response(
filename_artist, filename_title, song_dir, *args)
if lyrics_fetchers:
msg = _("Fetching lyrics...")
for _plugin, cb in lyrics_fetchers:
cb(callback, search_artist, search_title)
else:
msg = _("No lyrics plug-in enabled.")
self._show_lyrics(filename_artist, filename_title,
lyrics=msg)
def get_lyrics_start(self, search_artist, search_title, filename_artist,
filename_title, song_dir):
filename_artist = misc.strip_all_slashes(filename_artist)
filename_title = misc.strip_all_slashes(filename_title)
filename = self._check_for_local_lyrics(filename_artist,
filename_title, song_dir)
lyrics = ''
if filename:
# If the lyrics only contain "not found", delete the file and try to
# fetch new lyrics. If there is a bug in Sonata/SZI/LyricWiki that
# prevents lyrics from being found, storing the "not found" will
# prevent a future release from correctly fetching the lyrics.
try:
with open(filename, 'r') as f:
lyrics = f.read()
except IOError:
pass
if lyrics == _('Lyrics not found'):
misc.remove_file(filename)
filename = self._check_for_local_lyrics(
filename_artist, filename_title, song_dir)
if filename:
# Re-use lyrics from file:
try:
with open(filename, 'r') as f:
lyrics = f.read()
except IOError:
pass
# Strip artist - title line from file if it exists, since we
# now have that information visible elsewhere.
header = '%s - %s\n\n' % (filename_artist, filename_title)
if lyrics[:len(header)] == header:
lyrics = lyrics[len(header):]
self._show_lyrics(filename_artist, filename_title, lyrics=lyrics)
else:
# Fetch lyrics from lyrics.wikia.org etc.
lyrics_fetchers = pluginsystem.get('lyrics_fetching')
callback = lambda *args: self.get_lyrics_response(
filename_artist, filename_title, song_dir, *args)
if lyrics_fetchers:
msg = _('Fetching lyrics...')
for _plugin, cb in lyrics_fetchers:
cb(callback, search_artist, search_title)
else:
msg = _('No lyrics plug-in enabled.')
self._show_lyrics(filename_artist, filename_title, lyrics=msg)
def on_reset_image(self, _action): if self.songinfo: if 'name' in self.songinfo: # Stream, remove file: misc.remove_file(self.artwork_stream_filename(mpdh.get(self.songinfo, 'name'))) else: # Normal song: misc.remove_file(self.target_image_filename()) misc.remove_file(self.target_image_filename(consts.ART_LOCATION_HOMECOVERS)) # Use blank cover as the artwork dest_filename = self.target_image_filename(consts.ART_LOCATION_HOMECOVERS) emptyfile = open(dest_filename, 'w') emptyfile.close() self.artwork_update(True)
def on_reset_image(self, _action): if self.songinfo: if 'name' in self.songinfo: # Stream, remove file: misc.remove_file(self.artwork_stream_filename(mpdh.get(self.songinfo, 'name'))) else: # Normal song: misc.remove_file(self.target_image_filename()) misc.remove_file(self.target_image_filename(consts.ART_LOCATION_HOMECOVERS)) # Use blank cover as the artwork dest_filename = self.target_image_filename(consts.ART_LOCATION_HOMECOVERS) emptyfile = open(dest_filename, 'w') emptyfile.close() self.artwork_update(True)
def on_reset_image(self, _action):
if self.songinfo:
if "name" in self.songinfo:
# Stream, remove file:
misc.remove_file(self.artwork_stream_filename(mpdh.get(self.songinfo, "name")))
else:
# Normal song:
misc.remove_file(self.target_image_filename())
misc.remove_file(self.target_image_filename(consts.ART_LOCATION_HOMECOVERS))
# Use blank cover as the artwork
dest_filename = self.target_image_filename(consts.ART_LOCATION_HOMECOVERS)
try:
emptyfile = open(dest_filename, "w")
emptyfile.close()
except IOError:
pass
self.artwork_update(True)
# Clean temporary image:
misc.remove_file(finaltmpdmg)
sys.exit()
"""
# use instead of webserver stuff above
tmpdir = tempfile.mkdtemp() # a temporary directory
misc.extract_tarfile(inputfile, tmpdir)
selfupdate.move_dir(os.path.join(tmpdir, "DSR-{}".format(version)), '/Volumes/DSR-install/DSR/')
# end
#########################################################
# Do modification stuff here:
misc.copy_file("/Volumes/DSR-install/DSR/setup/dsr-mac", "/Volumes/DSR-install/DSR/dsr")
subprocess.call(["chmod", "755", "/Volumes/DSR-install/DSR/dsr"])
# Rename the volume:
renamecommand = ["diskutil", "rename", "DSR-install", "DSR-{}".format(version)]
subprocess.call(renamecommand)
#########################################################
subprocess.call(unmountcommmand)
#time.sleep(1)
# convert to compressed image:
misc.remove_file(dmgname)
subprocess.call(convert_to_compressed)
# Clean temporary image:
misc.remove_file(finaltmpdmg)
def get_lyrics_thread(self, search_artist, search_title, filename_artist,
filename_title, song_dir):
filename_artist = misc.strip_all_slashes(filename_artist)
filename_title = misc.strip_all_slashes(filename_title)
filename = self.info_check_for_local_lyrics(filename_artist,
filename_title, song_dir)
search_str = misc.link_markup(_("search"), True, True, self.linkcolor)
edit_str = misc.link_markup(_("edit"), True, True, self.linkcolor)
if filename:
# If the lyrics only contain "not found", delete the file and try to
# fetch new lyrics. If there is a bug in Sonata/SZI/LyricWiki that
# prevents lyrics from being found, storing the "not found" will
# prevent a future release from correctly fetching the lyrics.
f = open(filename, 'r')
lyrics = f.read()
f.close()
if lyrics == _("Lyrics not found"):
misc.remove_file(filename)
filename = self.info_check_for_local_lyrics(
filename_artist, filename_title, song_dir)
if filename:
# Re-use lyrics from file:
f = open(filename, 'r')
lyrics = f.read()
f.close()
# Strip artist - title line from file if it exists, since we
# now have that information visible elsewhere.
header = filename_artist + " - " + filename_title + "\n\n"
if lyrics[:len(header)] == header:
lyrics = lyrics[len(header):]
gobject.idle_add(self.info_show_lyrics, lyrics, filename_artist,
filename_title)
gobject.idle_add(self.info_searchlabel.set_markup, search_str)
gobject.idle_add(self.info_editlyricslabel.set_markup, edit_str)
else:
# Use default filename:
filename = self.target_lyrics_filename(filename_artist,
filename_title, song_dir)
# Fetch lyrics from lyricwiki.org
gobject.idle_add(self.info_show_lyrics, _("Fetching lyrics..."),
filename_artist, filename_title)
if self.lyricServer is None:
wsdlFile = "http://lyricwiki.org/server.php?wsdl"
try:
self.lyricServer = True
timeout = socketgettimeout()
socketsettimeout(consts.LYRIC_TIMEOUT)
self.lyricServer = ServiceProxy.ServiceProxy(
wsdlFile,
cachedir=os.path.expanduser("~/.service_proxy_dir"))
except:
socketsettimeout(timeout)
lyrics = _("Couldn't connect to LyricWiki")
gobject.idle_add(self.info_show_lyrics, lyrics,
filename_artist, filename_title)
self.lyricServer = None
gobject.idle_add(self.info_searchlabel.set_markup,
search_str)
gobject.idle_add(self.info_editlyricslabel.set_markup,
edit_str)
return
try:
timeout = socketgettimeout()
socketsettimeout(consts.LYRIC_TIMEOUT)
lyrics = self.lyricServer.getSong(
artist=self.lyricwiki_format(search_artist),
song=self.lyricwiki_format(
search_title))['return']["lyrics"]
if lyrics.lower() != "not found":
lyrics = misc.unescape_html(lyrics)
lyrics = misc.wiki_to_html(lyrics)
lyrics = lyrics.encode("ISO-8859-1")
gobject.idle_add(self.info_show_lyrics, lyrics,
filename_artist, filename_title)
# Save lyrics to file:
misc.create_dir('~/.lyrics/')
f = open(filename, 'w')
lyrics = misc.unescape_html(lyrics)
try:
f.write(lyrics.decode(self.enc).encode('utf8'))
except:
f.write(lyrics)
f.close()
else:
lyrics = _("Lyrics not found")
gobject.idle_add(self.info_show_lyrics, lyrics,
filename_artist, filename_title)
except:
lyrics = _("Fetching lyrics failed")
gobject.idle_add(self.info_show_lyrics, lyrics,
filename_artist, filename_title)
gobject.idle_add(self.info_searchlabel.set_markup, search_str)
gobject.idle_add(self.info_editlyricslabel.set_markup, edit_str)
socketsettimeout(timeout)
def check_refinement_results(self, list_file):
"""
Does some checks if the refinement makes sense e.g. if the data to parameter
ratio is in an acceptable range.
:param list_file: SHELXL listing file
:type list_file: list
"""
is_resfile_there = misc.check_file_exist(self.resfile_name + '.res')
if is_resfile_there and is_resfile_there == 'zero':
print('Something failed in SHELXL. Please check your .ins and .lst file!')
self.restore_shx_file()
try:
misc.remove_file(self.backup_file)
except IOError:
print('Unable to delete backup file {}.'.format(self.backup_file))
sys.exit()
if not is_resfile_there:
print('Something failed in SHELXL. Please check your .ins and .lst file!')
self.restore_shx_file()
try:
misc.remove_file(self.backup_file)
except IOError:
print('Unable to delete backup file {}.'.format(self.backup_file))
sys.exit()
regex_final = r' Final Structure Factor Calculation.*\n'
final_results = find_line(list_file, regex_final)
# find data and parameters:
try:
dataobj = re.search(r'[0-9]+\s+data', list_file[final_results + 4])
data = float(dataobj.group(0).split()[0])
parameterobj = re.search(r'[0-9]+\s+parameters', list_file[final_results + 4])
parameters = float(parameterobj.group(0).split()[0])
restrobj = re.search(r'[0-9]+\s+restraints', list_file[find_line(list_file, r" GooF = S =.*")])
restraints = float(restrobj.group(0).split()[0])
except AttributeError:
return False
try:
data_to_parameter_ratio = data / parameters
restr_ratio = ((data + restraints) / parameters)
except ZeroDivisionError:
return False
lattline = find_line(list_file, r'^ LATT.*')
centro = None
if lattline:
try:
latt = int(list_file[lattline].split()[1])
except ValueError:
latt = False
if latt > 0:
centro = True
else:
centro = False
if centro and data_to_parameter_ratio < 10:
print('*** Warning! The data/parameter ratio is getting low (ratio = {:.1f})! ***'
'\n*** but consider (data+restraints)/parameter = {:.1f} ***'
.format(data_to_parameter_ratio, restr_ratio))
if not centro and data_to_parameter_ratio < 7.5:
print('*** Warning! The data/parameter ratio is getting low (ratio = {:.1f})! ***'
'\n*** but consider (data+restraints)/parameter = {:.1f} ***'
.format(data_to_parameter_ratio, restr_ratio))
try:
misc.remove_file(self.backup_file)
except IOError:
print('Unable to delete backup file {}.'.format(self.backup_file))
def get_lyrics_thread(self, search_artist, search_title, filename_artist, filename_title, song_dir):
filename_artist = misc.strip_all_slashes(filename_artist)
filename_title = misc.strip_all_slashes(filename_title)
filename = self.info_check_for_local_lyrics(filename_artist, filename_title, song_dir)
search_str = misc.link_markup(_("search"), True, True, self.linkcolor)
edit_str = misc.link_markup(_("edit"), True, True, self.linkcolor)
if filename:
# If the lyrics only contain "not found", delete the file and try to
# fetch new lyrics. If there is a bug in Sonata/SZI/LyricWiki that
# prevents lyrics from being found, storing the "not found" will
# prevent a future release from correctly fetching the lyrics.
f = open(filename, 'r')
lyrics = f.read()
f.close()
if lyrics == _("Lyrics not found"):
misc.remove_file(filename)
filename = self.info_check_for_local_lyrics(filename_artist, filename_title, song_dir)
if filename:
# Re-use lyrics from file:
f = open(filename, 'r')
lyrics = f.read()
f.close()
# Strip artist - title line from file if it exists, since we
# now have that information visible elsewhere.
header = filename_artist + " - " + filename_title + "\n\n"
if lyrics[:len(header)] == header:
lyrics = lyrics[len(header):]
gobject.idle_add(self.info_show_lyrics, lyrics, filename_artist, filename_title)
gobject.idle_add(self.info_searchlabel.set_markup, search_str)
gobject.idle_add(self.info_editlyricslabel.set_markup, edit_str)
else:
# Use default filename:
filename = self.target_lyrics_filename(filename_artist, filename_title, song_dir)
# Fetch lyrics from lyricwiki.org
gobject.idle_add(self.info_show_lyrics, _("Fetching lyrics..."), filename_artist, filename_title)
if self.lyricServer is None:
wsdlFile = "http://lyricwiki.org/server.php?wsdl"
try:
self.lyricServer = True
timeout = socketgettimeout()
socketsettimeout(consts.LYRIC_TIMEOUT)
self.lyricServer = ServiceProxy.ServiceProxy(wsdlFile, cachedir=os.path.expanduser("~/.service_proxy_dir"))
except:
socketsettimeout(timeout)
lyrics = _("Couldn't connect to LyricWiki")
gobject.idle_add(self.info_show_lyrics, lyrics, filename_artist, filename_title)
self.lyricServer = None
gobject.idle_add(self.info_searchlabel.set_markup, search_str)
gobject.idle_add(self.info_editlyricslabel.set_markup, edit_str)
return
try:
timeout = socketgettimeout()
socketsettimeout(consts.LYRIC_TIMEOUT)
lyrics = self.lyricServer.getSong(artist=self.lyricwiki_format(search_artist), song=self.lyricwiki_format(search_title))['return']["lyrics"]
if lyrics.lower() != "not found":
lyrics = misc.unescape_html(lyrics)
lyrics = misc.wiki_to_html(lyrics)
lyrics = lyrics.encode("ISO-8859-1")
gobject.idle_add(self.info_show_lyrics, lyrics, filename_artist, filename_title)
# Save lyrics to file:
misc.create_dir('~/.lyrics/')
f = open(filename, 'w')
lyrics = misc.unescape_html(lyrics)
try:
f.write(lyrics.decode(self.enc).encode('utf8'))
except:
f.write(lyrics)
f.close()
else:
lyrics = _("Lyrics not found")
gobject.idle_add(self.info_show_lyrics, lyrics, filename_artist, filename_title)
except:
lyrics = _("Fetching lyrics failed")
gobject.idle_add(self.info_show_lyrics, lyrics, filename_artist, filename_title)
gobject.idle_add(self.info_searchlabel.set_markup, search_str)
gobject.idle_add(self.info_editlyricslabel.set_markup, edit_str)
socketsettimeout(timeout)
"""
This file is used to export the DSR database to sqlite for Olex2.
Every fragemnt needs a picture with the same name as the fragment tag in ./pictures
"""
import os
import sqlite3 as lite
import sys
import misc
from constants import SHX_CARDS
from dbfile import ParseDB
misc.remove_file('./fragment-database.sqlite')
gl = ParseDB()
db = gl.parse(dbpath="./olex_dsr_db.txt", dbname='olex_db')
dbfilename = 'fragment-database.sqlite'
con = lite.connect(dbfilename)
con.text_factory = str
cur = con.cursor()
def get_fragment_atoms_cartesian(fragment):
"""
returns the coordinates of the fragment as cartesian coords
as list of lists [['-2.7538', '15.9724', '22.6810'], ['0.7939', '16.3333', '21.3135'], ...
:param fragment:
:type fragment:
"""
from export import Export
ex = Export(gl, invert=False)
