files parsers docs updated

CGRtools/files/INCHIrw.py

@@ -29,8 +29,9 @@
 
 class INCHIread(CGRread, WithMixin):
     """
-    accept file wich consist INCHI per lines
-
+    INCHI separated per lines files reader. works similar to opened file object. support `with` context manager.
+    on initialization accept opened in text mode file, string path to file,
+    pathlib.Path object or another buffered reader object.
     line should be start with INCHI string and
     optionally continues with space/tab separated list of key:value [or key=value] data.
     AuxInfo also can be stored in data.
@@ -45,6 +46,11 @@ def __init__(self, file, *args, **kwargs):
         self.__data = self.__reader()
 
     def read(self):
+        """
+        parse whole file
+
+        :return: list of parsed molecules
+        """
         return list(self.__data)
 
     def __iter__(self):

CGRtools/files/MRVrw.py

@@ -67,12 +67,22 @@ def xml_dict(parent_element, stop_list=None):
 
 
 class MRVread(CGRread, WithMixin):
+    """
+    ChemAxon MRV files reader. works similar to opened file object. support `with` context manager.
+    on initialization accept opened in binary mode file, string path to file,
+    pathlib.Path object or another binary buffered reader object
+    """
     def __init__(self, file, *args, **kwargs):
         super().__init__(*args, **kwargs)
         super(CGRread, self).__init__(file, 'rb')
         self.__data = self.__reader()
 
     def read(self):
+        """
+        parse whole file
+
+        :return: list of parsed molecules or reactions
+        """
         return list(self.__data)
 
     def __iter__(self):
@@ -260,17 +270,30 @@ def __parse_molecule(self, data):
 
 
 class MRVwrite(CGRwrite, WithMixin):
+    """
+    ChemAxon MRV files writer. works similar to opened for writing file object. support `with` context manager.
+    on initialization accept opened for writing in text mode file, string path to file,
+    pathlib.Path object or another buffered writer object
+    """
     def __init__(self, file, *args, **kwargs):
         super().__init__(*args, **kwargs)
         super(CGRwrite, self).__init__(file, 'w')
 
     def close(self, *args, **kwargs):
+        """
+        write close tag of MRV file and close opened file
+
+        :param force: force closing of externally opened file or buffer
+        """
         if not self.__finalized:
             self._file.write('</cml>')
             self.__finalized = True
         super().close(*args, **kwargs)
 
     def write(self, data):
+        """
+        write single molecule or reaction into file
+        """
         self._file.write('<cml>')
         self.__write(data)
         self.write = self.__write

CGRtools/files/RDFrw.py

@@ -27,12 +27,22 @@
 
 
 class RDFread(CGRread, WithMixin):
+    """
+    MDL RDF files reader. works similar to opened file object. support `with` context manager.
+    on initialization accept opened in text mode file, string path to file,
+    pathlib.Path object or another buffered reader object
+    """
     def __init__(self, file, *args, **kwargs):
         super().__init__(*args, **kwargs)
         super(CGRread, self).__init__(file)
         self.__data = self.__reader()
 
     def read(self):
+        """
+        parse whole file
+
+        :return: list of parsed molecules or reactions
+        """
         return list(self.__data)
 
     def __iter__(self):
@@ -127,11 +137,19 @@ def __reader(self):
 
 
 class RDFwrite(MOLwrite, WithMixin):
+    """
+    MDL RDF files writer. works similar to opened for writing file object. support `with` context manager.
+    on initialization accept opened for writing in text mode file, string path to file,
+    pathlib.Path object or another buffered writer object
+    """
     def __init__(self, file, *args, **kwargs):
         super().__init__(*args, **kwargs)
         super(CGRwrite, self).__init__(file, 'w')
 
     def write(self, data):
+        """
+        write single molecule or reaction into file
+        """
         self._file.write(strftime('$RDFILE 1\n$DATM    %m/%d/%y %H:%M\n'))
         self.__write(data)
         self.write = self.__write

CGRtools/files/SDFrw.py

@@ -24,12 +24,22 @@
 
 
 class SDFread(CGRread, WithMixin):
+    """
+    MDL SDF files reader. works similar to opened file object. support `with` context manager.
+    on initialization accept opened in text mode file, string path to file,
+    pathlib.Path object or another buffered reader object
+    """
     def __init__(self, file, *args, **kwargs):
         super().__init__(*args, **kwargs)
         super(CGRread, self).__init__(file)
         self.__data = self.__reader()
 
     def read(self):
+        """
+        parse whole file
+
+        :return: list of parsed molecules
+        """
         return list(self.__data)
 
     def __iter__(self):
@@ -101,11 +111,19 @@ def __reader(self):
 
 
 class SDFwrite(MOLwrite, WithMixin):
+    """
+    MDL SDF files writer. works similar to opened for writing file object. support `with` context manager.
+    on initialization accept opened for writing in text mode file, string path to file,
+    pathlib.Path object or another buffered writer object
+    """
     def __init__(self, file, *args, **kwargs):
         super().__init__(*args, **kwargs)
         super(CGRwrite, self).__init__(file, 'w')
 
     def write(self, data):
+        """
+        write single molecule into file
+        """
         m = self._convert_structure(data)
         self._file.write(self._format_mol(*m))
         self._file.write('M  END\n')

CGRtools/files/SMILESrw.py

@@ -26,9 +26,10 @@
 
 class SMILESread(CGRread, WithMixin):
     """
-    accept file wich consist smiles/smirks per lines
-
-    line should be start with smiles/smirks string and
+    SMILES separated per lines files reader. works similar to opened file object. support `with` context manager.
+    on initialization accept opened in text mode file, string path to file,
+    pathlib.Path object or another buffered reader object.
+    line should be start with SMILES string and
     optionally continues with space/tab separated list of key:value [or key=value] data.
     for reactions . [dot] in bonds should be used only for molecules separation.
 
@@ -42,6 +43,11 @@ def __init__(self, file, *args, **kwargs):
         self.__data = self.__reader()
 
     def read(self):
+        """
+        parse whole file
+
+        :return: list of parsed molecules or reactions
+        """
         return list(self.__data)
 
     def __iter__(self):

CGRtools/files/_CGRrw.py

@@ -55,6 +55,11 @@ def __init__(self, file, mode='r'):
         self.__write = mode == 'w'
 
     def close(self, force=False):
+        """
+        close opened file
+
+        :param force: force closing of externally opened file or buffer
+        """
         if self.__write:
             self.write = self.__write_adhoc
             self.__write = False