Exemplo n.º 1
0
    def dock(self, engine, protein, *args, **kwargs):
        """Docking procedure.

        Parameters
        ----------
            engine: string
                Which docking engine to use.

        Note
        ----
            Additional parameters are passed directly to the engine.
        """
        if engine.lower() == 'autodock_vina':
            from oddt.docking import autodock_vina
            engine = autodock_vina(protein, *args, **kwargs)
        else:
            raise ValueError('Docking engine %s was not implemented in ODDT' % engine)
        if self.n_cpu != 1:
            _parallel_helper_partial = partial(_parallel_helper, engine, 'dock')
            docking_results = (Pool(self.n_cpu if self.n_cpu > 0 else None)
                               .imap(_parallel_helper_partial, ({'ligands': lig,
                                                                 'single': True}
                                                                for lig in self._pipe)))
        else:
            docking_results = (engine.dock(lig, single=True) for lig in self._pipe)
        self._pipe = chain.from_iterable(docking_results)
Exemplo n.º 2
0
    def dock(self, engine, protein, *args, **kwargs):
        """Docking procedure.

        Parameters
        ----------
            engine: string
                Which docking engine to use.

        Returns
        -------
            None

        Note
        ----
            Additional parameters are passed directly to the engine.
            Following docking engines are supported:

            1. Audodock Vina (``engine="autodock_vina"``), see
            `oddt.docking.autodock_vina`.
        """
        if engine.lower() == 'autodock_vina':
            from oddt.docking import autodock_vina
            engine = autodock_vina(protein, *args, **kwargs)
        else:
            raise ValueError('Docking engine %s was not implemented in ODDT'
                             % engine)
        self._pipe.append(partial(method_caller, engine, 'dock'))
Exemplo n.º 3
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    def dock(self, engine, protein, *args, **kwargs):
        """Docking procedure.

        Parameters
        ----------
            engine: string
                Which docking engine to use.

        Note
        ----
            Additional parameters are passed directly to the engine.
        """
        if engine.lower() == 'autodock_vina':
            from oddt.docking import autodock_vina
            engine = autodock_vina(protein, *args, **kwargs)
        else:
            raise ValueError('Docking engine %s was not implemented in ODDT' % engine)
        def _iter_conf(results):
            """ Generator to go through docking results, and put them to pipe """
            for confs in results:
                for conf in confs:
                    yield conf
        if self.n_cpu != 1:
            _parallel_helper_partial = partial(_parallel_helper, engine, 'dock')
            docking_results = self._pool.imap(_parallel_helper_partial, ({'ligands':lig, 'single': True} for lig in self._pipe))
        else:
            docking_results = (engine.dock(lig, single=True) for lig in self._pipe)
        self._pipe = _iter_conf(docking_results)
Exemplo n.º 4
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 def __init__(self, protein=None, vina_scores=None):
     self.protein = protein
     self.vina = autodock_vina(protein)
     self.vina_scores = vina_scores or [
         'vina_affinity', 'vina_gauss1', 'vina_gauss2', 'vina_repulsion',
         'vina_hydrophobic', 'vina_hydrogen'
     ]
     self.titles = self.vina_scores
Exemplo n.º 5
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    def score(self, function, protein = None, *args, **kwargs):
        """Scoring procedure.

        Parameters
        ----------
            function: string
                Which scoring function to use.

            protein: oddt.toolkit.Molecule
                Default protein to use as reference

        Note
        ----
            Additional parameters are passed directly to the scoring function.
        """
        if type(protein) is str:
            extension = protein.split('.')[-1]
            protein = six.next(toolkit.readfile(extension, protein))
            protein.protein = True
        # trigger cache
        protein.atom_dict

        if type(function) is str:
            if function.lower().startswith('rfscore'):
                from oddt.scoring.functions.RFScore import rfscore
                new_kwargs = {}
                for bit in function.lower().split('_'):
                    if bit.startswith('pdbbind'):
                        new_kwargs['pdbbind_version'] = int(bit.replace('pdbbind', ''))
                    elif bit.startswith('v'):
                        new_kwargs['version'] = int(bit.replace('v', ''))
                sf = rfscore.load(**new_kwargs)
                sf.set_protein(protein)
            elif function.lower().startswith('nnscore'):
                from oddt.scoring.functions.NNScore import nnscore
                new_kwargs = {}
                for bit in function.lower().split('_'):
                    if bit.startswith('pdbbind'):
                        new_kwargs['pdbbind_version'] = int(bit.replace('pdbbind', ''))
                sf = nnscore.load(**new_kwargs)
                sf.set_protein(protein)
            elif function.lower() == 'autodock_vina':
                from oddt.docking import autodock_vina
                sf = autodock_vina(protein, *args, **kwargs)
                sf.set_protein(protein)
            else:
                raise ValueError('Scoring Function %s was not implemented in ODDT' % function)
        else:
            if hasattr(function, 'set_protein') and hasattr(function, 'predict_ligands') and hasattr(function, 'predict_ligand'):
                sf = function
                sf.set_protein(protein)
            else:
                raise ValueError('Supplied object "%s" is not an ODDT scoring funtion' % function.__name__)
        if self.n_cpu != 1:
            _parallel_helper_partial = partial(_parallel_helper, sf, 'predict_ligand')
            self._pipe = Pool(self.n_cpu if self.n_cpu > 0 else None).imap(_parallel_helper_partial, ({'ligand': lig} for lig in self._pipe), chunksize=100)
        else:
            self._pipe = sf.predict_ligands(self._pipe)
Exemplo n.º 6
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    def score(self, function, protein = None, *args, **kwargs):
        """Scoring procedure.

        Parameters
        ----------
            function: string
                Which scoring function to use.

            protein: oddt.toolkit.Molecule
                Default protein to use as reference

        Note
        ----
            Additional parameters are passed directly to the scoring function.
        """
        if type(protein) is str:
            extension = protein.split('.')[-1]
            protein = toolkit.readfile(extension, protein).next()
            protein.protein = True
        # trigger cache
        protein.atom_dict

        if type(function) is str:
            if function.lower().startswith('rfscore'):
                from oddt.scoring.functions.RFScore import rfscore
                tmp = function.lower().split('_')
                v = int(tmp[-1][1:]) if len(tmp) > 1 else 1
                sf = rfscore.load(version=v)
                sf.set_protein(protein)
            elif function.lower() == 'nnscore':
                from oddt.scoring.functions.NNScore import nnscore
                sf = nnscore.load()
                sf.set_protein(protein)
            elif function.lower() == 'autodock_vina':
                from oddt.docking import autodock_vina
                sf = autodock_vina(protein, *args, **kwargs)
                sf.set_protein(protein)
            else:
                raise ValueError('Scoring Function %s was not implemented in ODDT' % function)
        else:
            if hasattr(function, 'set_protein') and hasattr(function, 'predict_ligands') and hasattr(function, 'predict_ligand'):
                sf = function
                sf.set_protein(protein)
            else:
                raise ValueError('Supplied object "%s" is not an ODDT scoring funtion' % function.__name__)
        if self.n_cpu != 1:
            _parallel_helper_partial = partial(_parallel_helper, sf, 'predict_ligand')
            self._pipe = self._pool.imap(_parallel_helper_partial, ({'ligand': lig} for lig in self._pipe), chunksize=100)
        else:
            self._pipe = sf.predict_ligands(self._pipe)
Exemplo n.º 7
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 def __init__(
     self,
     protein=None,
     vina_scores=[
         "vina_affinity",
         "vina_gauss1",
         "vina_gauss2",
         "vina_repulsion",
         "vina_hydrophobic",
         "vina_hydrogen",
     ],
 ):
     self.protein = protein
     self.vina = autodock_vina(protein)
     self.vina_scores = vina_scores
Exemplo n.º 8
0
Arquivo: binana.py Projeto: hainm/oddt
    def __init__(self, protein = None):
        """ Descriptor build from binana script (as used in NNScore 2.0

        Parameters
        ----------
            protein: oddt.toolkit.Molecule object (default=None)
                Protein object to be used while generating descriptors.
        """
        self.protein = protein
        self.vina = autodock_vina(protein)
        # Close contacts descriptor generators
        cc_4_types = (('A', 'A'), ('A', 'C'), ('A', 'CL'), ('A', 'F'), ('A', 'FE'), ('A', 'HD'), ('A', 'MG'), ('A', 'MN'), ('A', 'N'), ('A', 'NA'), ('A', 'OA'), ('A', 'SA'), ('A', 'ZN'), ('BR', 'C'), ('BR', 'HD'), ('BR', 'OA'), ('C', 'C'), ('C', 'CL'), ('C', 'F'), ('C', 'HD'), ('C', 'MG'), ('C', 'MN'), ('C', 'N'), ('C', 'NA'), ('C', 'OA'), ('C', 'SA'), ('C', 'ZN'), ('CL', 'FE'), ('CL', 'HD'), ('CL', 'MG'), ('CL', 'N'), ('CL', 'OA'), ('CL', 'ZN'), ('F', 'HD'), ('F', 'N'), ('F', 'OA'), ('F', 'SA'), ('FE', 'HD'), ('FE', 'N'), ('FE', 'OA'), ('HD', 'HD'), ('HD', 'I'), ('HD', 'MG'), ('HD', 'MN'), ('HD', 'N'), ('HD', 'NA'), ('HD', 'OA'), ('HD', 'P'), ('HD', 'S'), ('HD', 'SA'), ('HD', 'ZN'), ('MG', 'NA'), ('MG', 'OA'), ('MN', 'N'), ('MN', 'OA'), ('N', 'N'), ('N', 'NA'), ('N', 'OA'), ('N', 'SA'), ('N', 'ZN'), ('NA', 'OA'), ('NA', 'SA'), ('NA', 'ZN'), ('OA', 'OA'), ('OA', 'SA'), ('OA', 'ZN'), ('S', 'ZN'), ('SA', 'ZN'), ('A', 'BR'), ('A', 'I'), ('A', 'P'), ('A', 'S'), ('BR', 'N'), ('BR', 'SA'), ('C', 'FE'), ('C', 'I'), ('C', 'P'), ('C', 'S'), ('CL', 'MN'), ('CL', 'NA'), ('CL', 'P'), ('CL', 'S'), ('CL', 'SA'), ('CU', 'HD'), ('CU', 'N'), ('FE', 'NA'), ('FE', 'SA'), ('I', 'N'), ('I', 'OA'), ('MG', 'N'), ('MG', 'P'), ('MG', 'S'), ('MG', 'SA'), ('MN', 'NA'), ('MN', 'P'), ('MN', 'S'), ('MN', 'SA'), ('N', 'P'), ('N', 'S'), ('NA', 'P'), ('NA', 'S'), ('OA', 'P'), ('OA', 'S'), ('P', 'S'), ('P', 'SA'), ('P', 'ZN'), ('S', 'SA'), ('SA', 'SA'), ('A', 'CU'), ('C', 'CD') )
        cc_4_rec_types, cc_4_lig_types = zip(*cc_4_types)
        self.cc_4 = cc_4_nn = close_contacts(protein, cutoff=4, protein_types=cc_4_rec_types, ligand_types=cc_4_lig_types, mode='atom_types_ad4', aligned_pairs=True)
        cc_25_types = [('A', 'A'), ('A', 'C'), ('A', 'CL'), ('A', 'F'), ('A', 'FE'), ('A', 'HD'), ('A', 'MG'), ('A', 'MN'), ('A', 'N'), ('A', 'NA'), ('A', 'OA'), ('A', 'SA'), ('A', 'ZN'), ('BR', 'C'), ('BR', 'HD'), ('BR', 'OA'), ('C', 'C'), ('C', 'CL'), ('C', 'F'), ('C', 'HD'), ('C', 'MG'), ('C', 'MN'), ('C', 'N'), ('C', 'NA'), ('C', 'OA'), ('C', 'SA'), ('C', 'ZN'), ('CD', 'OA'), ('CL', 'FE'), ('CL', 'HD'), ('CL', 'MG'), ('CL', 'N'), ('CL', 'OA'), ('CL', 'ZN'), ('F', 'HD'), ('F', 'N'), ('F', 'OA'), ('F', 'SA'), ('F', 'ZN'), ('FE', 'HD'), ('FE', 'N'), ('FE', 'OA'), ('HD', 'HD'), ('HD', 'I'), ('HD', 'MG'), ('HD', 'MN'), ('HD', 'N'), ('HD', 'NA'), ('HD', 'OA'), ('HD', 'P'), ('HD', 'S'), ('HD', 'SA'), ('HD', 'ZN'), ('MG', 'NA'), ('MG', 'OA'), ('MN', 'N'), ('MN', 'OA'), ('N', 'N'), ('N', 'NA'), ('N', 'OA'), ('N', 'SA'), ('N', 'ZN'), ('NA', 'OA'), ('NA', 'SA'), ('NA', 'ZN'), ('OA', 'OA'), ('OA', 'SA'), ('OA', 'ZN'), ('S', 'ZN'), ('SA', 'ZN')]
        cc_25_rec_types, cc_25_lig_types = zip(*cc_25_types)
        self.cc_25 = close_contacts(protein, cutoff=2.5, protein_types=cc_25_rec_types, ligand_types=cc_25_lig_types, mode='atom_types_ad4', aligned_pairs=True)
Exemplo n.º 9
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    def dock(self, engine, protein, *args, **kwargs):
        """Docking procedure.

        Parameters
        ----------
        engine: string
            Which docking engine to use.

        Notes
        -----
        Additional parameters are passed directly to the engine.
        Following docking engines are supported:

        1. Audodock Vina (```engine="autodock_vina"```), see
        :class:`oddt.docking.autodock_vina`.
        """
        if engine.lower() == 'autodock_vina':
            from oddt.docking import autodock_vina
            engine = autodock_vina(protein, *args, **kwargs)
        else:
            raise ValueError('Docking engine %s was not implemented in ODDT'
                             % engine)
        self._pipe.append(partial(method_caller, engine, 'dock'))
Exemplo n.º 10
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    def dock(self, engine, protein, *args, **kwargs):
        """Docking procedure.

        Parameters
        ----------
            engine: string
                Which docking engine to use.

        Note
        ----
            Additional parameters are passed directly to the engine.
        """
        if engine.lower() == 'autodock_vina':
            from oddt.docking import autodock_vina
            engine = autodock_vina(protein, *args, **kwargs)
        else:
            raise ValueError('Docking engine %s was not implemented in ODDT' %
                             engine)

        def _iter_conf(results):
            """ Generator to go through docking results, and put them to pipe """
            for confs in results:
                for conf in confs:
                    yield conf

        if self.n_cpu != 1:
            _parallel_helper_partial = partial(_parallel_helper, engine,
                                               'dock')
            docking_results = self._pool.imap(_parallel_helper_partial,
                                              ({
                                                  'ligands': lig,
                                                  'single': True
                                              } for lig in self._pipe))
        else:
            docking_results = (engine.dock(lig, single=True)
                               for lig in self._pipe)
        self._pipe = _iter_conf(docking_results)
Exemplo n.º 11
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    def score(self, function, protein=None, *args, **kwargs):
        """Scoring procedure compatible with any scoring function implemented
        in ODDT and other pickled SFs which are subclasses of
        `oddt.scoring.scorer`.

        Parameters
        ----------
            function: string
                Which scoring function to use.

            protein: oddt.toolkit.Molecule
                Default protein to use as reference

        Note
        ----
            Additional parameters are passed directly to the scoring function.
        """
        if isinstance(protein, six.string_types):
            extension = protein.split('.')[-1]
            protein = next(oddt.toolkit.readfile(extension, protein))
            protein.protein = True
        elif protein is None:
            raise ValueError('Protein needs to be set for structure based '
                             'scoring')
        # trigger cache
        protein.atom_dict

        if isinstance(function, six.string_types):
            if isfile(function):
                sf = scorer.load(function)
                sf.set_protein(protein)
            elif function.lower().startswith('rfscore'):
                from oddt.scoring.functions.RFScore import rfscore
                new_kwargs = {}
                for bit in function.lower().split('_'):
                    if bit.startswith('pdbbind'):
                        new_kwargs['pdbbind_version'] = int(bit.replace('pdbbind', ''))
                    elif bit.startswith('v'):
                        new_kwargs['version'] = int(bit.replace('v', ''))
                sf = rfscore.load(**new_kwargs)
                sf.set_protein(protein)
            elif function.lower().startswith('nnscore'):
                from oddt.scoring.functions.NNScore import nnscore
                new_kwargs = {}
                for bit in function.lower().split('_'):
                    if bit.startswith('pdbbind'):
                        new_kwargs['pdbbind_version'] = int(bit.replace('pdbbind', ''))
                sf = nnscore.load(**new_kwargs)
                sf.set_protein(protein)
            elif function.lower() == 'autodock_vina':
                from oddt.docking import autodock_vina
                sf = autodock_vina(protein, *args, **kwargs)
                sf.set_protein(protein)
            else:
                raise ValueError('Scoring Function %s was not implemented in '
                                 'ODDT' % function)
        else:
            if isinstance(function, scorer):
                sf = function
                sf.set_protein(protein)
            else:
                raise ValueError('Supplied object "%s" is not an ODDT scoring '
                                 'funtion' % function.__name__)
        self._pipe.append(partial(method_caller, sf, 'predict_ligands'))
Exemplo n.º 12
0
    def score(self, function, protein=None, *args, **kwargs):
        """Scoring procedure compatible with any scoring function implemented
        in ODDT and other pickled SFs which are subclasses of
        `oddt.scoring.scorer`.

        Parameters
        ----------
        function: string
            Which scoring function to use.

        protein: oddt.toolkit.Molecule
            Default protein to use as reference

        Notes
        -----
        Additional parameters are passed directly to the scoring function.
        """
        if isinstance(protein, six.string_types):
            extension = protein.split('.')[-1]
            protein = next(oddt.toolkit.readfile(extension, protein))
            protein.protein = True
        elif protein is None:
            raise ValueError('Protein needs to be set for structure based '
                             'scoring')
        # trigger cache
        protein.atom_dict

        if isinstance(function, six.string_types):
            if isfile(function):
                sf = scorer.load(function)
                sf.set_protein(protein)
            elif function.lower().startswith('rfscore'):
                from oddt.scoring.functions.RFScore import rfscore
                new_kwargs = {}
                for bit in function.lower().split('_'):
                    if bit.startswith('pdbbind'):
                        new_kwargs['pdbbind_version'] = int(bit.replace('pdbbind', ''))
                    elif bit.startswith('v'):
                        new_kwargs['version'] = int(bit.replace('v', ''))
                sf = rfscore.load(**new_kwargs)
                sf.set_protein(protein)
            elif function.lower().startswith('nnscore'):
                from oddt.scoring.functions.NNScore import nnscore
                new_kwargs = {}
                for bit in function.lower().split('_'):
                    if bit.startswith('pdbbind'):
                        new_kwargs['pdbbind_version'] = int(bit.replace('pdbbind', ''))
                sf = nnscore.load(**new_kwargs)
                sf.set_protein(protein)
            elif function.lower().startswith('plec'):
                from oddt.scoring.functions.PLECscore import PLECscore
                new_kwargs = {}
                for bit in function.lower().split('_'):
                    if bit.startswith('pdbbind'):
                        new_kwargs['pdbbind_version'] = int(bit.replace('pdbbind', ''))
                    elif bit.startswith('plec'):
                        new_kwargs['version'] = bit.replace('plec', '')
                    elif bit.startswith('p'):
                        new_kwargs['depth_protein'] = int(bit.replace('p', ''))
                    elif bit.startswith('l'):
                        new_kwargs['depth_ligand'] = int(bit.replace('l', ''))
                    elif bit.startswith('s'):
                        new_kwargs['size'] = int(bit.replace('s', ''))
                sf = PLECscore.load(**new_kwargs)
                sf.set_protein(protein)
            elif function.lower() == 'autodock_vina':
                from oddt.docking import autodock_vina
                sf = autodock_vina(protein, *args, **kwargs)
                sf.set_protein(protein)
            else:
                raise ValueError('Scoring Function %s was not implemented in '
                                 'ODDT' % function)
        else:
            if isinstance(function, scorer):
                sf = function
                sf.set_protein(protein)
            else:
                raise ValueError('Supplied object "%s" is not an ODDT scoring '
                                 'funtion' % function.__name__)
        self._pipe.append(partial(method_caller, sf, 'predict_ligands'))
Exemplo n.º 13
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 def __init__(self, protein = None, vina_scores = ['vina_affinity', 'vina_gauss1', 'vina_gauss2', 'vina_repulsion', 'vina_hydrophobic', 'vina_hydrogen']):
     self.protein = protein
     self.vina = autodock_vina(protein)
     self.vina_scores = vina_scores
Exemplo n.º 14
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    def __init__(self, protein=None):
        """ Descriptor build from binana script (as used in NNScore 2.0

        Parameters
        ----------
            protein: oddt.toolkit.Molecule object (default=None)
                Protein object to be used while generating descriptors.
        """
        self.protein = protein
        self.vina = autodock_vina(protein)
        # Close contacts descriptor generators
        cc_4_types = (('A', 'A'), ('A', 'C'), ('A', 'CL'), ('A', 'F'),
                      ('A', 'FE'), ('A', 'HD'), ('A', 'MG'), ('A', 'MN'),
                      ('A', 'N'), ('A', 'NA'), ('A', 'OA'), ('A', 'SA'),
                      ('A', 'ZN'), ('BR', 'C'), ('BR', 'HD'), ('BR', 'OA'),
                      ('C', 'C'), ('C', 'CL'), ('C', 'F'), ('C', 'HD'), ('C',
                                                                         'MG'),
                      ('C', 'MN'), ('C', 'N'), ('C', 'NA'), ('C', 'OA'),
                      ('C', 'SA'), ('C', 'ZN'), ('CL', 'FE'), ('CL', 'HD'),
                      ('CL', 'MG'), ('CL', 'N'), ('CL', 'OA'), ('CL', 'ZN'),
                      ('F', 'HD'), ('F', 'N'), ('F', 'OA'), ('F', 'SA'),
                      ('FE', 'HD'), ('FE', 'N'), ('FE', 'OA'), ('HD', 'HD'),
                      ('HD', 'I'), ('HD', 'MG'), ('HD', 'MN'), ('HD', 'N'),
                      ('HD', 'NA'), ('HD', 'OA'), ('HD', 'P'), ('HD', 'S'),
                      ('HD', 'SA'), ('HD', 'ZN'), ('MG', 'NA'), ('MG', 'OA'),
                      ('MN', 'N'), ('MN', 'OA'), ('N', 'N'), ('N', 'NA'),
                      ('N', 'OA'), ('N', 'SA'), ('N', 'ZN'), ('NA', 'OA'),
                      ('NA', 'SA'), ('NA', 'ZN'), ('OA', 'OA'), ('OA', 'SA'),
                      ('OA', 'ZN'), ('S', 'ZN'), ('SA', 'ZN'), ('A', 'BR'),
                      ('A', 'I'), ('A', 'P'), ('A', 'S'), ('BR', 'N'), ('BR',
                                                                        'SA'),
                      ('C', 'FE'), ('C', 'I'), ('C', 'P'), ('C', 'S'), ('CL',
                                                                        'MN'),
                      ('CL', 'NA'), ('CL', 'P'), ('CL', 'S'), ('CL', 'SA'),
                      ('CU', 'HD'), ('CU', 'N'), ('FE', 'NA'), ('FE', 'SA'),
                      ('I', 'N'), ('I', 'OA'), ('MG', 'N'), ('MG', 'P'), ('MG',
                                                                          'S'),
                      ('MG', 'SA'), ('MN', 'NA'), ('MN', 'P'), ('MN', 'S'),
                      ('MN', 'SA'), ('N', 'P'), ('N', 'S'), ('NA', 'P'), ('NA',
                                                                          'S'),
                      ('OA', 'P'), ('OA',
                                    'S'), ('P', 'S'), ('P', 'SA'), ('P', 'ZN'),
                      ('S', 'SA'), ('SA', 'SA'), ('A', 'CU'), ('C', 'CD'))
        cc_4_rec_types, cc_4_lig_types = zip(*cc_4_types)
        self.cc_4 = cc_4_nn = close_contacts(protein,
                                             cutoff=4,
                                             protein_types=cc_4_rec_types,
                                             ligand_types=cc_4_lig_types,
                                             mode='atom_types_ad4',
                                             aligned_pairs=True)
        cc_25_types = [('A', 'A'), ('A', 'C'), ('A', 'CL'), ('A', 'F'),
                       ('A', 'FE'), ('A', 'HD'), ('A', 'MG'), ('A', 'MN'),
                       ('A', 'N'), ('A', 'NA'), ('A', 'OA'), ('A', 'SA'),
                       ('A', 'ZN'), ('BR', 'C'), ('BR', 'HD'), ('BR', 'OA'),
                       ('C', 'C'), ('C', 'CL'), ('C', 'F'), ('C', 'HD'),
                       ('C', 'MG'), ('C', 'MN'), ('C', 'N'), ('C', 'NA'),
                       ('C', 'OA'), ('C', 'SA'), ('C', 'ZN'), ('CD', 'OA'),
                       ('CL', 'FE'), ('CL', 'HD'), ('CL', 'MG'), ('CL', 'N'),
                       ('CL', 'OA'), ('CL', 'ZN'), ('F', 'HD'), ('F', 'N'),
                       ('F', 'OA'), ('F', 'SA'), ('F', 'ZN'), ('FE', 'HD'),
                       ('FE', 'N'), ('FE', 'OA'), ('HD', 'HD'), ('HD', 'I'),
                       ('HD', 'MG'), ('HD', 'MN'), ('HD', 'N'), ('HD', 'NA'),
                       ('HD', 'OA'), ('HD', 'P'), ('HD', 'S'), ('HD', 'SA'),
                       ('HD', 'ZN'), ('MG', 'NA'), ('MG', 'OA'), ('MN', 'N'),
                       ('MN', 'OA'), ('N', 'N'), ('N', 'NA'), ('N', 'OA'),
                       ('N', 'SA'), ('N', 'ZN'), ('NA', 'OA'), ('NA', 'SA'),
                       ('NA', 'ZN'), ('OA', 'OA'), ('OA', 'SA'), ('OA', 'ZN'),
                       ('S', 'ZN'), ('SA', 'ZN')]
        cc_25_rec_types, cc_25_lig_types = zip(*cc_25_types)
        self.cc_25 = close_contacts(protein,
                                    cutoff=2.5,
                                    protein_types=cc_25_rec_types,
                                    ligand_types=cc_25_lig_types,
                                    mode='atom_types_ad4',
                                    aligned_pairs=True)