Commit ⋅ MobleyLab/chemper

Showing 3 of 7 files from the diff.

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chemper/smirksify.py changed.

69.66% 63.27% -16.05%

chemper/mol_toolkits/mol_toolkit.py changed.

62.07% 100.00% ø

chemper/chemper_utils.py changed.

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chemper/tests/test_basic_graphs.py has changed.

chemper/tests/test_smirksify.py has changed.

chemper/tests/test_graphs_output.py has changed.

README.md has changed.

@@ -283,11 +283,11 @@


    Attributes
    ----------
    current_smirks: list of tuples
    current_smirks : list of tuples
                    current SMIRKS patterns in the form (label, smirks)
    mols: list of chemper molecules
    mols : list of chemper molecules
          molecules being used to reduce the input SMIRKS
    cluster_dict: dictionary
    cluster_dict : dictionary
                  Dictionary specifying typing using current SMIRKS in the form:
                  {mol_idx:
                        { (tuple of atom indices): label } }

@@ -18,12 +18,13 @@

import os
from chemper.chemper_utils import get_data_path
from chemper.mol_toolkits.adapters import MolAdapter, BondAdapter, AtomAdapter
# define default_toolkit:

# identify which toolkits are available
HAS_OE = False
HAS_RDK = False
try:
    from openeye.oechem import OEChemIsLicensed
    if not OEChemIsLicensed():
        HAS_OE = False
    else:
    from openeye import oechem
    if oechem.OEChemIsLicensed():
        from chemper.mol_toolkits import cp_openeye
        HAS_OE = True
except ImportError:

@@ -36,105 +37,95 @@

except ImportError:
    HAS_RDK = False

if not HAS_OE and not HAS_RDK:
    raise ImportWarning("No Cheminformatics toolkit was found."\
                        " currently ChemPer supports OpenEye and RDKit")


def Mol(mol):
    """

    Parameters
    ----------
    mol : Mol
          Molecule from any supported toolkit (ChemPer, OpenEye, RDKit)

    Returns
    -------
    mol : ChemPer Mol

    """
    # if it is already a chemper molecule return as is
    if isinstance(mol, MolAdapter):
        return mol

    # check if this is an Openeye molecule
    if HAS_OE and isinstance(mol, oechem.OEMolBase):
        return cp_openeye.Mol(mol)

    # check if it is an RDK molecule
    if HAS_RDK and isinstance(mol, Chem.rdchem.Mol):
        return cp_rdk.Mol(mol)

    err_msg = """
    Your molecule has the type %s.
    Currently ChemPer only supports OpenEye and RDKit.
    To add support to a new toolkit submit an issue on GitHub at
    github.com/MobleyLab/chemper
    """
    raise TypeError(err_msg % type(mol))


def Atom(atom):
    """

    Parameters
    ----------
    atom : Atom
           Atom from any supported toolkit (ChemPer, OpenEye, RDKit)

    Returns
    -------
    atom : ChemPer Atom

    """
    if isinstance(atom, AtomAdapter):
        return atom

    if HAS_OE and isinstance(atom, oechem.OEAtomBase):
        return cp_openeye.Atom(atom)

    if HAS_RDK and isinstance(atom, Chem.rdchem.Atom):
        return cp_rdk.Atom(atom)

    err_msg = """
    Your atom has the type %s.
    Currently ChemPer only supports OpenEye and RDKit.
    To add support to a new toolkit submit an issue on GitHub at
    github.com/MobleyLab/chemper
    """
    raise TypeError(err_msg % type(atom))
# ======================================================================
# Find super Mol/Atom/Bond classes
# ======================================================================

if not HAS_OE and not HAS_RDK:
    raise ImportWarning("No Cheminformatics toolkit was found." \
                        " currently ChemPer supports OpenEye and RDKit")

def Bond(bond):
    """

    Parameters
    ----------
    bond : Bond
           Bond from any supported toolkit (ChemPer, OpenEye, RDKit)

    Returns
    -------
    bond : ChemPer Bond

    """
    if isinstance(bond, BondAdapter):
        return bond

    if HAS_OE and isinstance(bond, oechem.OEBondBase):
        return cp_openeye.Bond(bond)

    if HAS_RDK and isinstance(bond, Chem.rdchem.Bond):
        return cp_rdk.Bond(bond)

    err_msg = """
    Your bond has the type %s.
    Currently ChemPer only supports OpenEye and RDKit.
    To add support to a new toolkit submit an issue on GitHub at
    github.com/MobleyLab/chemper
    """
    raise TypeError(err_msg % type(bond))
class Mol:
    def __init__(self, mol):
        # if it is already a chemper molecule return as is
        if isinstance(mol, MolAdapter):
            self.mol = mol.mol
            self.__class__ = mol.__class__

        # check if this is an Openeye molecule
        elif HAS_OE and isinstance(mol, oechem.OEMolBase):
            self.__class__ = cp_openeye.Mol
            self.__class__.__init__(self,mol)

        # check if it is an RDK molecule
        elif HAS_RDK and isinstance(mol, Chem.rdchem.Mol):
            self.__class__ = cp_rdk.Mol
            self.__class__.__init__(self, mol)

        else:
            err_msg = """
            Your molecule has the type %s.
            Currently ChemPer only supports OpenEye and RDKit.
            To add support to a new toolkit submit an issue on GitHub at
            github.com/MobleyLab/chemper
            """
            raise TypeError(err_msg % type(mol))

    @staticmethod
    def from_smiles(smiles):
        if HAS_OE:
            return cp_openeye.Mol.from_smiles(smiles)
        return cp_rdk.Mol.from_smiles(smiles)

class Atom:
    def __init__(self, atom):

        if isinstance(atom, AtomAdapter):
            self.atom = atom.atom
            self.__class__ = atom.__class__

        elif HAS_OE and isinstance(atom, oechem.OEAtomBase):
            self.__class__ = cp_openeye.Atom
            self.__class__.__init__(self, atom)

        elif HAS_RDK and isinstance(atom, Chem.rdchem.Atom):
            self.__class__ = cp_rdk.Atom
            self.__class__.__init__(self, atom)

        else:
            err_msg = """
            Your atom has the type %s.
            Currently ChemPer only supports OpenEye and RDKit.
            To add support to a new toolkit submit an issue on GitHub at
            github.com/MobleyLab/chemper
            """
            raise TypeError(err_msg % type(atom))


class Bond:
    def __init__(self, bond):
        if isinstance(bond, BondAdapter):
            self.bond = bond.bond
            self.__class__ = bond.__class__

        elif HAS_OE and isinstance(bond, oechem.OEBondBase):
            self.__class__ = cp_openeye.Bond
            self.__class__.__init__(self,bond)

        elif HAS_RDK and isinstance(bond, Chem.rdchem.Bond):
            self.__class__ = cp_rdk.Bond
            self.__class__.__init__(self,bond)

        else:
            err_msg = """
            Your bond has the type %s.
            Currently ChemPer only supports OpenEye and RDKit.
            To add support to a new toolkit submit an issue on GitHub at
            github.com/MobleyLab/chemper
            """
            raise TypeError(err_msg % type(bond))

# =======================================
# check user specifications

@@ -202,32 +193,6 @@


    return path


# ================================================================
# get molecule from SMILES
# ================================================================

def mol_from_smiles(smiles, toolkit=None):
    """

    Parameters
    ----------
    smiles : str
             SMILES string
    toolkit : str or None
              'openeye' or 'rdkit'
              if None ChemPer will use whichever is available

    Returns
    -------
    mol : ChemPer Mol
    """
    toolkit = check_toolkit(toolkit)
    if toolkit.lower() == 'openeye':
        return cp_openeye.Mol.from_smiles(smiles)

    return cp_rdk.Mol.from_smiles(smiles)

# =======================================
# get molecules from files
# =======================================

@@ -81,8 +81,8 @@

    -------
    is_valid : boolean
    """
    from chemper.mol_toolkits.mol_toolkit import mol_from_smiles
    mol = mol_from_smiles('C')
    from chemper.mol_toolkits.mol_toolkit import Mol
    mol = Mol.from_smiles('C')
    try:
        mol.smirks_search(smirks)
        return True

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    - test_helper.py
    - setup.py
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283	283
284	284		Attributes
285	285		----------
286		-	current_smirks: list of tuples
	286	+	current_smirks : list of tuples
287	287		current SMIRKS patterns in the form (label, smirks)
288		-	mols: list of chemper molecules
	288	+	mols : list of chemper molecules
289	289		molecules being used to reduce the input SMIRKS
290		-	cluster_dict: dictionary
	290	+	cluster_dict : dictionary
291	291		Dictionary specifying typing using current SMIRKS in the form:
292	292		{mol_idx:
293	293		{ (tuple of atom indices): label } }

202	193
203	194		return path
204	195
205		-
206		-	# ================================================================
207		-	# get molecule from SMILES
208		-	# ================================================================
209		-
210		-	def mol_from_smiles(smiles, toolkit=None):
211		-	"""
212		-
213		-	Parameters
214		-	----------
215		-	smiles : str
216		-	SMILES string
217		-	toolkit : str or None
218		-	'openeye' or 'rdkit'
219		-	if None ChemPer will use whichever is available
220		-
221		-	Returns
222		-	-------
223		-	mol : ChemPer Mol
224		-	"""
225		-	toolkit = check_toolkit(toolkit)
226		-	if toolkit.lower() == 'openeye':
227		-	return cp_openeye.Mol.from_smiles(smiles)
228		-
229		-	return cp_rdk.Mol.from_smiles(smiles)
230		-
231	196		# =======================================
232	197		# get molecules from files
233	198		# =======================================

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18	18		import os
19	19		from chemper.chemper_utils import get_data_path
20	20		from chemper.mol_toolkits.adapters import MolAdapter, BondAdapter, AtomAdapter
21		-	# define default_toolkit:
	21	+
	22	+	# identify which toolkits are available
	23	+	HAS_OE = False
	24	+	HAS_RDK = False
22	25		try:
23		-	from openeye.oechem import OEChemIsLicensed
24		-	if not OEChemIsLicensed():
25		-	HAS_OE = False
26		-	else:
	26	+	from openeye import oechem
	27	+	if oechem.OEChemIsLicensed():
27	28		from chemper.mol_toolkits import cp_openeye
28	29		HAS_OE = True
29	30		except ImportError:

36	37		except ImportError:
37	38		HAS_RDK = False
38	39
39		-	if not HAS_OE and not HAS_RDK:
40		-	raise ImportWarning("No Cheminformatics toolkit was found."\
41		-	" currently ChemPer supports OpenEye and RDKit")
42		-
43		-
44		-	def Mol(mol):
45		-	"""
46		-
47		-	Parameters
48		-	----------
49		-	mol : Mol
50		-	Molecule from any supported toolkit (ChemPer, OpenEye, RDKit)
51		-
52		-	Returns
53		-	-------
54		-	mol : ChemPer Mol
55		-
56		-	"""
57		-	# if it is already a chemper molecule return as is
58		-	if isinstance(mol, MolAdapter):
59		-	return mol
60		-
61		-	# check if this is an Openeye molecule
62		-	if HAS_OE and isinstance(mol, oechem.OEMolBase):
63		-	return cp_openeye.Mol(mol)
64		-
65		-	# check if it is an RDK molecule
66		-	if HAS_RDK and isinstance(mol, Chem.rdchem.Mol):
67		-	return cp_rdk.Mol(mol)
68		-
69		-	err_msg = """
70		-	Your molecule has the type %s.
71		-	Currently ChemPer only supports OpenEye and RDKit.
72		-	To add support to a new toolkit submit an issue on GitHub at
73		-	github.com/MobleyLab/chemper
74		-	"""
75		-	raise TypeError(err_msg % type(mol))
76		-
77		-
78		-	def Atom(atom):
79		-	"""
80		-
81		-	Parameters
82		-	----------
83		-	atom : Atom
84		-	Atom from any supported toolkit (ChemPer, OpenEye, RDKit)
85	40
86		-	Returns
87		-	-------
88		-	atom : ChemPer Atom
89		-
90		-	"""
91		-	if isinstance(atom, AtomAdapter):
92		-	return atom
93		-
94		-	if HAS_OE and isinstance(atom, oechem.OEAtomBase):
95		-	return cp_openeye.Atom(atom)
96		-
97		-	if HAS_RDK and isinstance(atom, Chem.rdchem.Atom):
98		-	return cp_rdk.Atom(atom)
99		-
100		-	err_msg = """
101		-	Your atom has the type %s.
102		-	Currently ChemPer only supports OpenEye and RDKit.
103		-	To add support to a new toolkit submit an issue on GitHub at
104		-	github.com/MobleyLab/chemper
105		-	"""
106		-	raise TypeError(err_msg % type(atom))
	41	+	# ======================================================================
	42	+	# Find super Mol/Atom/Bond classes
	43	+	# ======================================================================
107	44
	45	+	if not HAS_OE and not HAS_RDK:
	46	+	raise ImportWarning("No Cheminformatics toolkit was found." \
	47	+	" currently ChemPer supports OpenEye and RDKit")
108	48
109		-	def Bond(bond):
110		-	"""
111		-
112		-	Parameters
113		-	----------
114		-	bond : Bond
115		-	Bond from any supported toolkit (ChemPer, OpenEye, RDKit)
116		-
117		-	Returns
118		-	-------
119		-	bond : ChemPer Bond
120		-
121		-	"""
122		-	if isinstance(bond, BondAdapter):
123		-	return bond
124		-
125		-	if HAS_OE and isinstance(bond, oechem.OEBondBase):
126		-	return cp_openeye.Bond(bond)
127		-
128		-	if HAS_RDK and isinstance(bond, Chem.rdchem.Bond):
129		-	return cp_rdk.Bond(bond)
130	49
131		-	err_msg = """
132		-	Your bond has the type %s.
133		-	Currently ChemPer only supports OpenEye and RDKit.
134		-	To add support to a new toolkit submit an issue on GitHub at
135		-	github.com/MobleyLab/chemper
136		-	"""
137		-	raise TypeError(err_msg % type(bond))
	50	+	class Mol:
	51	+	def __init__(self, mol):
	52	+	# if it is already a chemper molecule return as is
	53	+	if isinstance(mol, MolAdapter):
	54	+	self.mol = mol.mol
	55	+	self.__class__ = mol.__class__
	56	+
	57	+	# check if this is an Openeye molecule
	58	+	elif HAS_OE and isinstance(mol, oechem.OEMolBase):
	59	+	self.__class__ = cp_openeye.Mol
	60	+	self.__class__.__init__(self,mol)
	61	+
	62	+	# check if it is an RDK molecule
	63	+	elif HAS_RDK and isinstance(mol, Chem.rdchem.Mol):
	64	+	self.__class__ = cp_rdk.Mol
	65	+	self.__class__.__init__(self, mol)
	66	+
	67	+	else:
	68	+	err_msg = """
	69	+	Your molecule has the type %s.
	70	+	Currently ChemPer only supports OpenEye and RDKit.
	71	+	To add support to a new toolkit submit an issue on GitHub at
	72	+	github.com/MobleyLab/chemper
	73	+	"""
	74	+	raise TypeError(err_msg % type(mol))
	75	+
	76	+	@staticmethod
	77	+	def from_smiles(smiles):
	78	+	if HAS_OE:
	79	+	return cp_openeye.Mol.from_smiles(smiles)
	80	+	return cp_rdk.Mol.from_smiles(smiles)
	81	+
	82	+	class Atom:
	83	+	def __init__(self, atom):
	84	+
	85	+	if isinstance(atom, AtomAdapter):
	86	+	self.atom = atom.atom
	87	+	self.__class__ = atom.__class__
	88	+
	89	+	elif HAS_OE and isinstance(atom, oechem.OEAtomBase):
	90	+	self.__class__ = cp_openeye.Atom
	91	+	self.__class__.__init__(self, atom)
	92	+
	93	+	elif HAS_RDK and isinstance(atom, Chem.rdchem.Atom):
	94	+	self.__class__ = cp_rdk.Atom
	95	+	self.__class__.__init__(self, atom)
	96	+
	97	+	else:
	98	+	err_msg = """
	99	+	Your atom has the type %s.
	100	+	Currently ChemPer only supports OpenEye and RDKit.
	101	+	To add support to a new toolkit submit an issue on GitHub at
	102	+	github.com/MobleyLab/chemper
	103	+	"""
	104	+	raise TypeError(err_msg % type(atom))
	105	+
	106	+
	107	+	class Bond:
	108	+	def __init__(self, bond):
	109	+	if isinstance(bond, BondAdapter):
	110	+	self.bond = bond.bond
	111	+	self.__class__ = bond.__class__
	112	+
	113	+	elif HAS_OE and isinstance(bond, oechem.OEBondBase):
	114	+	self.__class__ = cp_openeye.Bond
	115	+	self.__class__.__init__(self,bond)
	116	+
	117	+	elif HAS_RDK and isinstance(bond, Chem.rdchem.Bond):
	118	+	self.__class__ = cp_rdk.Bond
	119	+	self.__class__.__init__(self,bond)
	120	+
	121	+	else:
	122	+	err_msg = """
	123	+	Your bond has the type %s.
	124	+	Currently ChemPer only supports OpenEye and RDKit.
	125	+	To add support to a new toolkit submit an issue on GitHub at
	126	+	github.com/MobleyLab/chemper
	127	+	"""
	128	+	raise TypeError(err_msg % type(bond))
138	129
139	130		# =======================================
140	131		# check user specifications

81	81		-------
82	82		is_valid : boolean
83	83		"""
84		-	from chemper.mol_toolkits.mol_toolkit import mol_from_smiles
85		-	mol = mol_from_smiles('C')
	84	+	from chemper.mol_toolkits.mol_toolkit import Mol
	85	+	mol = Mol.from_smiles('C')
86	86		try:
87	87		mol.smirks_search(smirks)
88	88		return True

1	coverage:
2	ignore:
3	- test/.*
4	- compare/.*
5	- test_helper.py
6	- setup.py
7	status:
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12	comment:
13	layout: "header"
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