Merge remote-tracking branch 'origin/master'

CGRtools/files/RDFrw.py

@@ -46,9 +46,12 @@ def __init__(self, file, *args, indexable=False, **kwargs):
         if indexable and platform != 'win32' and not self._is_buffer:
             self.__file = iter(self._file.readline, '')
             if next(self._data):
-                self._shifts = [int(x.split(b':', 1)[0]) for x in
-                                check_output(['grep', '-boE', r'^\$[RM]FMT', self._file.name]).split()]
-                self._shifts.append(getsize(self._file.name))
+                self._shifts = self._load_cache()
+                if self._shifts is None:
+                    self._shifts = [int(x.split(b':', 1)[0]) for x in
+                                    check_output(['grep', '-boE', r'^\$[RM]FMT', self._file.name]).split()]
+                    self._shifts.append(getsize(self._file.name))
+                    self._dump_cache(self._shifts)
         else:
             self.__file = self._file
             next(self._data)

CGRtools/files/SDFrw.py

@@ -40,10 +40,13 @@ def __init__(self, file, *args, indexable=False, **kwargs):
 
         if indexable and platform != 'win32' and not self._is_buffer:
             self.__file = iter(self._file.readline, '')
-            self._shifts = [0]
-            for x in BytesIO(check_output(['grep', '-bE', r'\$\$\$\$', self._file.name])):
-                _pos, _line = x.split(b':', 1)
-                self._shifts.append(int(_pos) + len(_line))
+            self._shifts = self._load_cache()
+            if self._shifts is None:
+                self._shifts = [0]
+                for x in BytesIO(check_output(['grep', '-bE', r'\$\$\$\$', self._file.name])):
+                    _pos, _line = x.split(b':', 1)
+                    self._shifts.append(int(_pos) + len(_line))
+                self._dump_cache(self._shifts)
         else:
             self.__file = self._file
 

CGRtools/files/_MDLrw.py

@@ -16,9 +16,13 @@
 #  You should have received a copy of the GNU Lesser General Public License
 #  along with this program; if not, see <https://www.gnu.org/licenses/>.
 #
+from base64 import urlsafe_b64encode
 from csv import reader
 from logging import warning
 from itertools import count, chain, islice
+from os.path import abspath, join
+from pickle import dump, load, UnpicklingError
+from tempfile import gettempdir
 from ._CGRrw import CGRwrite, cgr_keys
 from ..exceptions import EmptyMolecule
 from ..periodictable import common_isotopes
@@ -435,6 +439,25 @@ def getvalue(self):
 
 
 class MDLread:
+    def _load_cache(self):
+        try:
+            with open(self.__cache_path, 'rb') as f:
+                return load(f)
+        except FileNotFoundError:
+            return
+        except IsADirectoryError as e:
+            raise IsADirectoryError(f'Please delete {self.__cache_path} directory') from e
+        except (UnpicklingError, EOFError) as e:
+            raise UnpicklingError(f'Invalid cache file {self.__cache_path}. Please delete it') from e
+
+    @property
+    def __cache_path(self):
+        return abspath(join(gettempdir(), 'cgrtools_' + urlsafe_b64encode(abspath(self._file.name).encode()).decode()))
+
+    def _dump_cache(self, _shifts):
+        with open(self.__cache_path, 'wb') as f:
+            dump(_shifts, f)
+
     def read(self):
         """
         parse whole file