Clean all data about read atoms.
429316
protected void newAtomData() {
        atomCounter = 0;
        elsym = new ArrayList<String>();
        elid = new ArrayList<String>();
        eltitles = new ArrayList<String>();
        formalCharges = new ArrayList<String>();
        partialCharges = new ArrayList<String>();
        isotope = new ArrayList<String>();
        atomicNumbers = new ArrayList<String>();
        exactMasses = new ArrayList<String>();
        x3 = new ArrayList<String>();
        y3 = new ArrayList<String>();
        z3 = new ArrayList<String>();
        x2 = new ArrayList<String>();
        y2 = new ArrayList<String>();
        xfract = new ArrayList<String>();
        yfract = new ArrayList<String>();
        zfract = new ArrayList<String>();
        hCounts = new ArrayList<String>();
        atomParities = new ArrayList<String>();
        parityARef1 = new ArrayList<String>();
        parityARef2 = new ArrayList<String>();
        parityARef3 = new ArrayList<String>();
        parityARef4 = new ArrayList<String>();
        atomAromaticities = new ArrayList<String>();
        atomDictRefs = new ArrayList<String>();
        spinMultiplicities = new ArrayList<String>();
        occupancies = new ArrayList<String>();
        atomCustomProperty = new HashMap<Integer, List<String>>();
    }
853998
def clear_data(self):
        """"""
        self.tab = None
        self.cols = []
        self._idx = []
        self.x_col = ''
        self.y_col = ''
        self.w.xcombo.clear()
        self.w.ycombo.clear()
        self.w.x_lo.set_text('')
        self.w.x_hi.set_text('')
        self.w.y_lo.set_text('')
        self.w.y_hi.set_text('')
1074169
private void cleanData(List<GalenTestInfo> testInfos) {
        for (GalenTestInfo testInfo : testInfos) {
            if (testInfo.getReport() != null) {
                try {
                    FileTempStorage storage = testInfo.getReport().getFileStorage();
                    if (storage != null) {
                        storage.cleanup();
                    }
                } catch (Exception e) {
                    LOG.error("Unkown error during report cleaning", e);
                }
            }
        }
    }
1219791
def cleanup(self):
        

        all([delete_file_or_tree(f) for f in self.to_delete])
        self.to_delete = []
492485
def clean(ctx, state, dry_run=False, bare=False, user=False):
    """"""
    from ..core import do_clean
    do_clean(ctx=ctx, three=state.three, python=state.python, dry_run=dry_run,
             system=state.system)
604044
def cleanup(self):
        """"""
        self.num_puts = 0
        cached = []
        for i, url_data in enumerate(self.queue):
            key = url_data.cache_url
            cache = url_data.aggregate.result_cache
            if cache.has_result(key):
                cached.append(i)
        for pos in cached:
            self._move_to_top(pos)
1227059
def cleanup():
    
    script_dir = os.path.dirname(__file__) if not os.path.islink(__file__) else os.path.dirname(os.readlink(__file__))
    script_dir = os.path.realpath(os.path.join(script_dir, ".."))
    shutil.rmtree(os.path.join(script_dir, "dist"), ignore_errors=True)
    shutil.rmtree(os.path.join(script_dir, "tmp"), ignore_errors=True)
    shutil.rmtree(os.path.join(script_dir, "urh.egg-info"), ignore_errors=True)
    shutil.rmtree(os.path.join(script_dir, "src", "urh.egg-info"), ignore_errors=True)
    shutil.rmtree(os.path.join(script_dir, "src", "urh", "tmp"), ignore_errors=True)
252655
def _cleanup(self):
        """"""
        self._expkg = None
        self._extmp = None
        self._flag_e = True
        self._ifile.close()
1215146
def clean(self):
        """"""

        # Deleting seems to be really weird and unrelable.
        self._session \
            .query(Process) \
            .filter(Process.d_vid == self._d_vid) \
            .delete(synchronize_session='fetch')

        for r in self.records:
            self._session.delete(r)

        self._session.commit()
712014
def clean(self):
        """"""
        connection = self._backend._get_connection()
        self._backend.clean(connection)
1026084
def cleanup(self):
        """"""

        if not len(self.water_ids) == 0:
            # Hide all non-interacting water molecules
            water_selection = []
            for wid in self.water_ids:
                water_selection.append('serialNumber=%i' % wid)
            self.rc("~display :HOH")
            self.rc("display :@/%s" % " or ".join(water_selection))

        # Show all interacting binding site residues
        self.rc("~display #%i & ~:/isHet" % self.model_dict[self.plipname])
        self.rc("display :%s" % ",".join([str(self.atoms[bsid].residue.id) for bsid in self.bs_res_ids]))
        self.rc("color lightblue :HOH")
296301
def cleanup(self):
        """"""
        for file in glob.glob(self.basename + '*'):
            os.unlink(file)
1221333
def clean_all(self, args):
        """"""
        self.clean_dists(args)
        self.clean_builds(args)
        self.clean_download_cache(args)
1355412
def _cleanup(self, ref):
        ''
        self.transitor_states[self._weakref_holder[ref]] -= 1
        del self._weakref_holder[ref]
1290111
def clean(ctx, docs=False, bytecode=False, extra=''):
    ''''''
    patterns = ['build', 'dist', 'cover', 'docs/_build', '**/*.pyc', '*.egg-info', '.tox']
    for pattern in patterns:
        print('Removing {0}'.format(pattern))
        with ctx.cd(ROOT):
            ctx.run('rm -rf {0}'.format(pattern))
1107247
def cleanup(self):
        """"""
        keys = self.client.smembers(self.keys_container)
        for key in keys:
            entry = self.client.get(key)
            if entry:
                entry = pickle.loads(entry)
                if self._is_expired(entry, self.timeout):
                    self.delete_entry(key)
669177
def clean():
        """"""
        screenshot_dir = settings.SELENIUM_SCREENSHOT_DIR
        if screenshot_dir and os.path.isdir(screenshot_dir):
            rmtree(screenshot_dir, ignore_errors=True)