fragmentor distribution added.

CIMtools/preprocessing/fragmentor.py

@@ -18,6 +18,7 @@
 #
 from CGRtools.containers import MoleculeContainer, CGRContainer
 from CGRtools.files import SDFWrite
+from distutils.util import get_platform
 from logging import info
 from os import close
 from os.path import devnull
@@ -35,21 +36,28 @@
 
 class Fragmentor(BaseEstimator, TransformerMixin):
     def __init__(self, fragment_type=3, min_length=2, max_length=10, cgr_dynbonds=0, doallways=False,
-                 useformalcharge=False, header=None, workpath='.', version=None, verbose=False, remove_rare_ratio=0,
-                 return_domain=False):
+                 useformalcharge=False, header=None, workpath='.', version='2017',
+                 verbose=False, remove_rare_ratio=0, return_domain=False):
         """
         ISIDA Fragmentor wrapper
 
-        :param workpath: path for temp files.
-        :param version: fragmentor version. need for selecting Fragmentor executables named as fragmentor-{version}
+        :param fragment_type: fragmentation type. see Fragmentor manual (-t)
+        :param min_length: minimal length of fragments. see Fragmentor manual (-l)
+        :param max_length: maximal length of fragments. see Fragmentor manual (-u)
+        :param cgr_dynbonds: see Fragmentor manual (-d)
+        :param doallways: see Fragmentor manual (--DoAllWays)
+        :param useformalcharge: see Fragmentor manual (--UseFormalCharge)
         :param header: if None descriptors will be generated on train set
                        if False Fragmentor will work in headless mode. in this mod fit unusable and Fragmentor return
                            all found descriptors
                        else path string to existing header file acceptable
+        :param workpath: path for temp files
+        :param version: fragmentor version
+        :param verbose: silent Fragmentor output
         :param remove_rare_ratio: if descriptors found on train less then given ratio it will be removed from header.
                                   if partial fit used, be sure to use finalize method.
                                   unusable if headless mode set
-        :param return_domain: add AD bool column. if False molecule has new features
+        :param return_domain: add AD bool column. False in column is: molecule/CGR has new features
         """
         self.fragment_type = fragment_type
         self.min_length = min_length
@@ -73,6 +81,9 @@ def __getstate__(self):
                 k not in ('header', 'workpath') and not k.startswith('_Fragmentor__')}
 
     def __setstate__(self, state):
+        if state['version'] is None:
+            state['version'] = '2017'  # backward compatibility with <4.0
+
         super().__setstate__({k: v for k, v in state.items() if k != '_Fragmentor__head_dump'})
         # backward compatibility with 1.4.0 - 1.4.6
         if '_Fragmentor__head_less' not in state:
@@ -303,7 +314,7 @@ def __parse_svm(svm_file, head_dict):
         return DataFrame(vector, columns=list(head_dict.values())).fillna(0), Series(ad)
 
     def __exec_params(self, inp, out):
-        tmp = [f'fragmentor-{self.version}' if self.version else 'fragmentor', '-i', str(inp), '-o', str(out)]
+        tmp = [fragmentor % self.version, '-i', str(inp), '-o', str(out)]
 
         if self.__head_exec:
             tmp.extend(('-h', str(self.__head_exec)))
@@ -369,3 +380,14 @@ def __init_header(self):
 
 
 __all__ = ['Fragmentor']
+
+platform = get_platform()
+if platform == 'win-amd64':
+    fragmentor = 'fragmentor_win_%s.exe'
+elif platform == 'linux-x86_64':
+    fragmentor = 'fragmentor_lin_%s'
+# elif platform.startswith('macosx') and platform.endswith('x86_64'):
+#     fragmentor = 'fragmentor_mac_%s'
+else:
+    del Fragmentor
+    __all__ = []

Fragmentor/LICENCE

@@ -0,0 +1,5 @@
+This program (ISIDA Fragmentor2017) is distributed as is
+in the hope that it will be useful, but WITHOUT ANY WARRANTY.
+
+(c) G. Marcou, D. Horvath, A. Varnek F. Ruggiu, V. Solov'ev, E. Moyemont
+Universite de Strasbourg Faculte de Chimie Laboratoire d'infochimie

Fragmentor/readme.txt

@@ -0,0 +1,16 @@
+*********************************************
+
+                ISIDA Fragmentor2017
+       This is a terminal interface for
+       generating molecular fragments
+
+       G. Marcou, D. Horvath, A. Varnek
+     F. Ruggiu, V. Solov'ev, E. Moyemont
+
+                      2017
+
+ Universite de Strasbourg
+ Faculte de Chimie
+ Laboratoire d'infochimie
+
+*********************************************

README.md

@@ -20,5 +20,3 @@ or latest repository version
 * add CHEMAXON_REST (optional)
 
         export CHEMAXON_REST="url/to/webservices"
-
-* edit PATH for Fragmentor using. Add path to fragmentor bin files

setup.py

@@ -16,34 +16,58 @@
 #  You should have received a copy of the GNU General Public License
 #  along with this program; if not, see <https://www.gnu.org/licenses/>.
 #
+from distutils.util import get_platform
 from pathlib import Path
 from setuptools import setup, find_packages
+from wheel.bdist_wheel import bdist_wheel
 
 
 version = '4.0.0'
 
+platform = get_platform()
+if platform == 'win-amd64':
+    fragmentor = ['Fragmentor/fragmentor_win_2017.exe']
+elif platform == 'linux-x86_64':
+    fragmentor = ['Fragmentor/fragmentor_lin_2017']
+# elif platform.startswith('macosx') and platform.endswith('x86_64'):
+#    fragmentor = ['Fragmentor/fragmentor_mac_2017']
+else:
+    fragmentor = []
+
+
+class _bdist_wheel(bdist_wheel):
+    def finalize_options(self):
+        super().finalize_options()
+        self.root_is_pure = False
+
 
 setup(
     name='CIMtools',
     version=version,
     packages=find_packages(),
-    zip_safe=True,
     url='https://github.com/stsouko/CIMtools',
     license='GPLv3',
     author='Dr. Ramil Nugmanov',
     author_email='stsouko@live.ru',
     python_requires='>=3.6.1',
-    install_requires=['CGRtools>=4.0,<4.1', 'pandas>=0.22.0,<0.26', 'scikit-learn>=0.20.1,<0.22',
+    cmdclass={'bdist_wheel': _bdist_wheel},
+    install_requires=['CGRtools[mrv]>=4.0,<4.1', 'pandas>=0.22.0,<0.26', 'scikit-learn>=0.20.1,<0.22',
                       'requests>=2.21,<2.23', 'pyparsing>=2.2.0,<2.5', 'numpy>=1.15.0,<1.18'],
+    data_files=[('bin', fragmentor)],
+    zip_safe=False,
     long_description=(Path(__file__).parent / 'README.md').open().read(),
     classifiers=['Environment :: Plugins',
                  'Intended Audience :: Science/Research',
-                 'Intended Audience :: Developers',
-                 'Topic :: Scientific/Engineering :: Chemistry',
-                 'Topic :: Software Development :: Libraries :: Python Modules',
                  'License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)',
                  'Operating System :: OS Independent',
                  'Programming Language :: Python',
-                 'Programming Language :: Python :: 3',
-                 'Programming Language :: Python :: 3.7']
+                 'Programming Language :: Python :: 3 :: Only',
+                 'Programming Language :: Python :: 3.6',
+                 'Programming Language :: Python :: 3.7',
+                 'Topic :: Scientific/Engineering',
+                 'Topic :: Scientific/Engineering :: Chemistry',
+                 'Topic :: Scientific/Engineering :: Information Analysis',
+                 'Topic :: Software Development',
+                 'Topic :: Software Development :: Libraries',
+                 'Topic :: Software Development :: Libraries :: Python Modules']
 )