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Showing 2 of 2 files from the diff.

96.05% 91.30% -0.50%

chemper/mol_toolkits/cp_rdk.py changed.

96.50% 88.24% -1.29%

chemper/mol_toolkits/cp_openeye.py changed.

@@ -30,8 +30,8 @@

Loading

        mol: openeye RDKMol object
            openeye molecule to convert to chemper Mol object
        """
        if type(mol) != Chem.rdchem.Mol:
            raise Exception("Expecting an rdchem.Mol instead of %s" % type(mol))
        if not isinstance(mol, Chem.rdchem.Mol):
            raise TypeError("Expecting an rdchem.Mol instead of %s" % type(mol))
        self.mol = mol

    def __str__(self): return self.get_smiles()

@@ -186,9 +186,12 @@

Loading

        atom: RDKAtom
            Atom object from an RDK molecule
        """
        if type(atom) != Chem.rdchem.Atom:
            raise Exception("Expecting an rdchem.Atom instead of %s" % type(atom))
        if not isinstance(atom, Chem.rdchem.Atom):
            raise TypeError("Expecting a rdchem.Atom instead of %s" % type(atom))
        self.atom = atom
        self._idx = self.atom.GetIdx()

    def __str__(self): return '%i%s' % (self._idx, self.atom.GetSymbol())

    def atomic_number(self):
        """

@@ -284,7 +287,7 @@

Loading

        index: int
            atom index in its molecule
        """
        return self.atom.GetIdx()
        return self._idx

    def is_connected_to(self, atom2):
        """

@@ -298,8 +301,7 @@

Loading

        connected: boolean
            True if atom2 is a direct neighbor or atom1
        """
        if not type(atom2.atom) is Chem.rdchem.Atom:
            # TODO: raise exception/return something else?
        if not isinstance(atom2.atom, Chem.rdchem.Atom):
            return False
        neighbors = [a.GetIdx() for a in self.atom.GetNeighbors()]
        return atom2.get_index() in neighbors

@@ -350,21 +352,34 @@

Loading

        bond: RDKBond
            Bond object from an RDK molecule
        """
        if type(bond) != Chem.rdchem.Bond:
            raise Exception("Expecting an rdchem.Bond instead of %s" % type(bond))
        if not isinstance(bond, Chem.rdchem.Bond):
            raise TypeError("Expecting an rdchem.Bond instead of %s" % type(bond))
        self.bond = bond
        self.order = self.bond.GetBondTypeAsDouble()

        # save index
        self._idx = self.bond.GetIdx()

        # save order information
        self._order = self.bond.GetBondTypeAsDouble()
        orders = {1:'-', 2:'=', 3:'#', 1.5:':'}
        self._order_symbol = orders.get(self._order, '~')

        # save atoms in bond
        self.beginning = Atom(self.bond.GetBeginAtom())
        self.end = Atom(self.bond.GetEndAtom())

    def __str__(self):
        return "%i %s%s%s" % (self.get_index(), self.beginning,
                              self._order_symbol, self.end)

    def get_order(self):
        """
        Returns
        -------
        order: int or float
            This is the absolute order, returns 1.5 if bond is aromatic
        """
        return self.order
        return self._order

    def get_atoms(self):
        """

@@ -400,7 +415,7 @@

Loading

        is_single: boolean
            True if it is a single bond
        """
        return self.order == 1
        return self._order == 1

    def is_double(self):
        """

@@ -409,7 +424,7 @@

Loading

        is_double: boolean
            True if it is a double bond
        """
        return self.order == 2
        return self._order == 2

    def is_triple(self):
        """

@@ -418,7 +433,7 @@

Loading

        is_triple: boolean
            True if it is a triple bond
        """
        return self.order == 3
        return self._order == 3

    def get_molecule(self):
        """

@@ -439,7 +454,11 @@

Loading

439	454		index: int
440	455		index of this bond in its parent molecule
441	456		"""
442		-	return self.bond.GetIdx()
	457	+	return self._idx
	458	+
	459	+	# =====================================================================
	460	+	# functions for importing molecules from files
	461	+	# =====================================================================
443	462
444	463		def mols_from_mol2(mol2_file):
445	464		"""

@@ -469,7 +488,7 @@

Loading

        mol_path = get_data_path(os.path.join('molecules', mol2_file))

        if not os.path.exists(mol_path):
            raise IOError("File '%s' not found locally or in chemper/data/molecules." % mol_file)
            raise IOError("File '%s' not found locally or in chemper/data/molecules." % mol2_file)
        else:
            mol2_file = mol_path


@@ -484,7 +503,7 @@

Loading

    molecules = list()
    mol2_block = list()

    file_open = open(mol2_file, 'r')
    file_open = open(mol2_file)

    for line in file_open:
        if line.startswith(delimiter) and mol2_block:

@@ -31,7 +31,7 @@

Loading

            openeye molecule to convert to chemper Mol object
        """
        if not isinstance(mol, oechem.OEMolBase):
            raise Exception("Expecting an OEMol object instead of %s" % type(mol))
            raise TypeError("Expecting an OEMol object instead of %s" % type(mol))
        self.mol = mol

    def __str__(self): return self.get_smiles()

@@ -188,9 +188,12 @@

Loading

            Atom object from an OpenEye molecule
        """
        if not isinstance(atom, oechem.OEAtomBase):
            raise Exception("Expecting an OEAtomBase object instead of %s" % type(atom))
            raise TypeError("Expecting an OEAtomBase object instead of %s" % type(atom))
        self.atom = atom
        self._index = self.atom.GetIdx()
        self._idx = self.atom.GetIdx()

    def __str__(self): return "%i%s" % (self._idx,
                                        oechem.OEGetAtomicSymbol(self.atomic_number()))

    def atomic_number(self):
        """

@@ -280,7 +283,7 @@

Loading

        index: int
            atom index in its molecule
        """
        return self._index
        return self._idx

    def is_connected_to(self, atom2):
        """

@@ -294,6 +297,8 @@

Loading

        connected: boolean
            True if atom2 is a direct neighbor or atom1
        """
        if not isinstance(atom2.atom, oechem.OEAtomBase):
            return False
        return self.atom.IsConnected(atom2.atom)

    def get_neighbors(self):

@@ -324,7 +329,7 @@

Loading

            molecule this atom is stored in
        """
        mol = oechem.OEMol(self.atom.GetParent())
        self.atom = mol.GetAtom(oechem.OEHasAtomIdx(self._index))
        self.atom = mol.GetAtom(oechem.OEHasAtomIdx(self._idx))
        return Mol(mol)

# =======================================

@@ -344,13 +349,27 @@

Loading

            Bond object from an OpenEye molecule
        """
        if not isinstance(bond, oechem.OEBondBase):
            raise Exception("Expecting an OEBondBase object instead of %s" % type(bond))
            raise TypeError("Expecting an OEBondBase object instead of %s" % type(bond))
        self.bond = bond

        # save index
        self._idx = self.bond.GetIdx()

        # store order information
        self._order = self.bond.GetOrder()
        if self.is_aromatic():
            self._order = 1.5

        self._idx = self.bond.GetIdx()
        orders = {1:'-', 2:'=', 3:'#', 1.5:':'}
        self._order_symbol = orders.get(self._order, '~')

        # save atoms in bond
        self.beginning = Atom(self.bond.GetBgn())
        self.end = Atom(self.bond.GetEnd())

    def __str__(self):
        return "%i %s%s%s" % (self.get_index(), self.beginning,
                              self._order_symbol, self.end)

    def get_order(self):
        """

@@ -368,9 +387,7 @@

Loading

        atoms: list of chemper Atoms
            the two atoms connected by this bond
        """
        beginning = Atom(self.bond.GetBgn())
        end = Atom(self.bond.GetEnd())
        return [beginning, end]
        return [self.beginning, self.end]

    def is_ring(self):
        """

Everything is accounted for!

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Lines, not adjusted in diff, that have changed coverage data.

Files that introduced coverage data that had none before.

Files that have missing coverage data that once were tracked.

89.40% 100.00% -0.08%

fix broken cp_openeye

bannanc

7a118ce

CI Passed

Hiding 3 contexual commits

+14

+11

+3

89.47% ø -0.04%

add unnecessary print statements

bannanc

373a2f1

CI Passed

Files		•	•	•	Coverage
chemper	+14	+11	ø	+3	^-0.08% 89.40%
Project Totals (11 files)	1,952	1,745	0	207	89.40%

186	186		atom: RDKAtom
187	187		Atom object from an RDK molecule
188	188		"""
189		-	if type(atom) != Chem.rdchem.Atom:
190		-	raise Exception("Expecting an rdchem.Atom instead of %s" % type(atom))
	189	+	if not isinstance(atom, Chem.rdchem.Atom):
	190	+	raise TypeError("Expecting a rdchem.Atom instead of %s" % type(atom))
191	191		self.atom = atom
	192	+	self._idx = self.atom.GetIdx()
	193	+
	194	+	def __str__(self): return '%i%s' % (self._idx, self.atom.GetSymbol())
192	195
193	196		def atomic_number(self):
194	197		"""

284	287		index: int
285	288		atom index in its molecule
286	289		"""
287		-	return self.atom.GetIdx()
	290	+	return self._idx
288	291
289	292		def is_connected_to(self, atom2):
290	293		"""

350	352		bond: RDKBond
351	353		Bond object from an RDK molecule
352	354		"""
353		-	if type(bond) != Chem.rdchem.Bond:
354		-	raise Exception("Expecting an rdchem.Bond instead of %s" % type(bond))
	355	+	if not isinstance(bond, Chem.rdchem.Bond):
	356	+	raise TypeError("Expecting an rdchem.Bond instead of %s" % type(bond))
355	357		self.bond = bond
356		-	self.order = self.bond.GetBondTypeAsDouble()
	358	+
	359	+	# save index
	360	+	self._idx = self.bond.GetIdx()
	361	+
	362	+	# save order information
	363	+	self._order = self.bond.GetBondTypeAsDouble()
	364	+	orders = {1:'-', 2:'=', 3:'#', 1.5:':'}
	365	+	self._order_symbol = orders.get(self._order, '~')
	366	+
	367	+	# save atoms in bond
357	368		self.beginning = Atom(self.bond.GetBeginAtom())
358	369		self.end = Atom(self.bond.GetEndAtom())
359	370
	371	+	def __str__(self):
	372	+	return "%i %s%s%s" % (self.get_index(), self.beginning,
	373	+	self._order_symbol, self.end)
	374	+
360	375		def get_order(self):
361	376		"""
362	377		Returns
363	378		-------
364	379		order: int or float
365	380		This is the absolute order, returns 1.5 if bond is aromatic
366	381		"""
367		-	return self.order
	382	+	return self._order
368	383
369	384		def get_atoms(self):
370	385		"""

400	415		is_single: boolean
401	416		True if it is a single bond
402	417		"""
403		-	return self.order == 1
	418	+	return self._order == 1
404	419
405	420		def is_double(self):
406	421		"""

409	424		is_double: boolean
410	425		True if it is a double bond
411	426		"""
412		-	return self.order == 2
	427	+	return self._order == 2
413	428
414	429		def is_triple(self):
415	430		"""

Compare `373a2f1 ... +3 ... 7a118ce`

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Everything is accounted for!

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Show failed CI and contexual commits `c`

5 Commits

30	30		mol: openeye RDKMol object
31	31		openeye molecule to convert to chemper Mol object
32	32		"""
33		-	if type(mol) != Chem.rdchem.Mol:
34		-	raise Exception("Expecting an rdchem.Mol instead of %s" % type(mol))
	33	+	if not isinstance(mol, Chem.rdchem.Mol):
	34	+	raise TypeError("Expecting an rdchem.Mol instead of %s" % type(mol))
35	35		self.mol = mol
36	36
37	37		def __str__(self): return self.get_smiles()

298	301		connected: boolean
299	302		True if atom2 is a direct neighbor or atom1
300	303		"""
301		-	if not type(atom2.atom) is Chem.rdchem.Atom:
302		-	# TODO: raise exception/return something else?
	304	+	if not isinstance(atom2.atom, Chem.rdchem.Atom):
303	305		return False
304	306		neighbors = [a.GetIdx() for a in self.atom.GetNeighbors()]
305	307		return atom2.get_index() in neighbors

418	433		is_triple: boolean
419	434		True if it is a triple bond
420	435		"""
421		-	return self.order == 3
	436	+	return self._order == 3
422	437
423	438		def get_molecule(self):
424	439		"""

469	488		mol_path = get_data_path(os.path.join('molecules', mol2_file))
470	489
471	490		if not os.path.exists(mol_path):
472		-	raise IOError("File '%s' not found locally or in chemper/data/molecules." % mol_file)
	491	+	raise IOError("File '%s' not found locally or in chemper/data/molecules." % mol2_file)
473	492		else:
474	493		mol2_file = mol_path
475	494

484	503		molecules = list()
485	504		mol2_block = list()
486	505
487		-	file_open = open(mol2_file, 'r')
	506	+	file_open = open(mol2_file)
488	507
489	508		for line in file_open:
490	509		if line.startswith(delimiter) and mol2_block:

31	31		openeye molecule to convert to chemper Mol object
32	32		"""
33	33		if not isinstance(mol, oechem.OEMolBase):
34		-	raise Exception("Expecting an OEMol object instead of %s" % type(mol))
	34	+	raise TypeError("Expecting an OEMol object instead of %s" % type(mol))
35	35		self.mol = mol
36	36
37	37		def __str__(self): return self.get_smiles()

188	188		Atom object from an OpenEye molecule
189	189		"""
190	190		if not isinstance(atom, oechem.OEAtomBase):
191		-	raise Exception("Expecting an OEAtomBase object instead of %s" % type(atom))
	191	+	raise TypeError("Expecting an OEAtomBase object instead of %s" % type(atom))
192	192		self.atom = atom
193		-	self._index = self.atom.GetIdx()
	193	+	self._idx = self.atom.GetIdx()
	194	+
	195	+	def __str__(self): return "%i%s" % (self._idx,
	196	+	oechem.OEGetAtomicSymbol(self.atomic_number()))
194	197
195	198		def atomic_number(self):
196	199		"""

280	283		index: int
281	284		atom index in its molecule
282	285		"""
283		-	return self._index
	286	+	return self._idx
284	287
285	288		def is_connected_to(self, atom2):
286	289		"""

294	297		connected: boolean
295	298		True if atom2 is a direct neighbor or atom1
296	299		"""
	300	+	if not isinstance(atom2.atom, oechem.OEAtomBase):
	301	+	return False
297	302		return self.atom.IsConnected(atom2.atom)
298	303
299	304		def get_neighbors(self):

324	329		molecule this atom is stored in
325	330		"""
326	331		mol = oechem.OEMol(self.atom.GetParent())
327		-	self.atom = mol.GetAtom(oechem.OEHasAtomIdx(self._index))
	332	+	self.atom = mol.GetAtom(oechem.OEHasAtomIdx(self._idx))
328	333		return Mol(mol)
329	334
330	335		# =======================================

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344	349		Bond object from an OpenEye molecule
345	350		"""
346	351		if not isinstance(bond, oechem.OEBondBase):
347		-	raise Exception("Expecting an OEBondBase object instead of %s" % type(bond))
	352	+	raise TypeError("Expecting an OEBondBase object instead of %s" % type(bond))
348	353		self.bond = bond
	354	+
	355	+	# save index
	356	+	self._idx = self.bond.GetIdx()
	357	+
	358	+	# store order information
349	359		self._order = self.bond.GetOrder()
350	360		if self.is_aromatic():
351	361		self._order = 1.5
352	362
353		-	self._idx = self.bond.GetIdx()
	363	+	orders = {1:'-', 2:'=', 3:'#', 1.5:':'}
	364	+	self._order_symbol = orders.get(self._order, '~')
	365	+
	366	+	# save atoms in bond
	367	+	self.beginning = Atom(self.bond.GetBgn())
	368	+	self.end = Atom(self.bond.GetEnd())
	369	+
	370	+	def __str__(self):
	371	+	return "%i %s%s%s" % (self.get_index(), self.beginning,
	372	+	self._order_symbol, self.end)
354	373
355	374		def get_order(self):
356	375		"""

368	387		atoms: list of chemper Atoms
369	388		the two atoms connected by this bond
370	389		"""
371		-	beginning = Atom(self.bond.GetBgn())
372		-	end = Atom(self.bond.GetEnd())
373		-	return [beginning, end]
	390	+	return [self.beginning, self.end]
374	391
375	392		def is_ring(self):
376	393		"""

Compare 373a2f1 ... +3 ... 7a118ce

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Compare `373a2f1 ... +3 ... 7a118ce`

Show failed CI and contexual commits `c`

5 Commits