acelleralivemoleculekit.smallmol.tools.tautomers.Fragment(name, ftype)¶Bases: object
The Fragment class store information about the molecule fragment
name (int - The id of the fragment) –
ftype (str - The fragment type (choices: single, aromatic, double)) –
name¶int - The id of the fragment
ftype¶str - The fragment type (choices: single, aromatic, double)
atoms¶list - List of the atom indeces
graphs¶list - List of the Fragment.name of the the Fragment object connected with this Fragment
connection¶this Fragment (Only double and aromatic.)
list - List of the Fragment.name of the the Fragment object connected with
get_connection()¶The function returns the connections :returns: connections – (Only double and aromatic.) :rtype: list - List of the Fragment.name of the the Fragment object connected with this Fragment
moleculekit.smallmol.tools.tautomers.MolFragmenter(mol)¶Bases: object
mol (rdkit.Chem.rdchem.Mol - the rdkit molecule object) –
mol¶rdkit.Chem.rdchem.Mol - the rdkit molecule object
fragments¶list - list of Fragment objects
paths¶list - list of list containing fragment objects part of the path
SCORE_dict = {'aromatic': 3, 'double': 1}¶compute_paths()¶The function inpect and detect all the possible conjugate paths
fragment()¶The method creates and stores Fragment objects for each bond in the molecule and based on the atom type
get_conjugate_length(path)¶The function returns the length of the conjugate path
path (list - List of Fragment objects that are part of the same conjugate path) –
length
int - The lenght of the conjugate path
get_depiction_atoms(path)¶The function returns all the atom indeces that are part of a conjugate path
path (list - List of Fragment objects that are part of the same conjugate path) –
atoms
list - List of atoms indeces part of a cpnjugate path
get_fragment(attr, value)¶The function returns the Fragment objects based on the attribute and value provided
attr (Fragment.attributename - the Fragment object attribute (selector)) –
value (Fragment.attributevalue - the Fragment object attribute value to match) –
fragments
list - The list of Fragment objects matching the parameters provided
get_graphs()¶The function inspect for each conjugate Fragment (double aromatic) all the possible pattern that will set as connections
get_longest_path()¶The function return the longest path
highest_path
list - The list of fragmaent that represents the longest path
get_num_fragments()¶Total number of fragments.
search_fragment_by_atom(atom_idx, fragmenttype=None)¶The function returns the Fragment objects based on the atomIdx and fragmenttype provided (default: all type)
atom_idx (int - The atom idx) –
fragmenttype (Fragment.ftype value - The fragment type to match) –
fragment
list - The list of Fragment objects matching the parameters provided
moleculekit.smallmol.tools.tautomers.TautomerCanonicalizer(transforms=TautomerTransform('1,3 (thio)keto/enol f', '[CX4!H0]-[C]=[O,S,Se,Te;X1]', [], []), TautomerTransform('1,3 (thio)keto/enol r', '[O,S,Se,Te;X2!H0]-[C]=[C]', [], []), TautomerTransform('1,5 (thio)keto/enol f', '[CX4,NX3;!H0]-[C]=[C][CH0]=[O,S,Se,Te;X1]', [], []), TautomerTransform('1,5 (thio)keto/enol r', '[O,S,Se,Te;X2!H0]-[CH0]=[C]-[C]=[C,N]', [], []), TautomerTransform('aliphatic imine f', '[CX4!H0]-[C]=[NX2]', [], []), TautomerTransform('aliphatic imine r', '[NX3!H0]-[C]=[CX3]', [], []), TautomerTransform('special imine f', '[N!H0]-[C]=[CX3R0]', [], []), TautomerTransform('special imine r', '[CX4!H0]-[c]=[n]', [], []), TautomerTransform('1,3 aromatic heteroatom H shift f', '[#7!H0]-[#6R1]=[O,#7X2]', [], []), TautomerTransform('1,3 aromatic heteroatom H shift r', '[O,#7;!H0]-[#6R1]=[#7X2]', [], []), TautomerTransform('1,3 heteroatom H shift', '[#7,S,O,Se,Te;!H0]-[#7X2,#6,#15]=[#7,#16,#8,Se,Te]', [], []), TautomerTransform('1,5 aromatic heteroatom H shift', '[#7,#16,#8;!H0]-[#6,#7]=[#6]-[#6,#7]=[#7,#16,#8;H0]', [], []), TautomerTransform('1,5 aromatic heteroatom H shift f', '[#7,#16,#8,Se,Te;!H0]-[#6,nX2]=[#6,nX2]-[#6,#7X2]=[#7X2,S,O,Se,Te]', [], []), TautomerTransform('1,5 aromatic heteroatom H shift r', '[#7,S,O,Se,Te;!H0]-[#6,#7X2]=[#6,nX2]-[#6,nX2]=[#7,#16,#8,Se,Te]', [], []), TautomerTransform('1,7 aromatic heteroatom H shift f', '[#7,#8,#16,Se,Te;!H0]-[#6,#7X2]=[#6,#7X2]-[#6,#7X2]=[#6]-[#6,#7X2]=[#7X2,S,O,Se,Te,CX3]', [], []), TautomerTransform('1,7 aromatic heteroatom H shift r', '[#7,S,O,Se,Te,CX4;!H0]-[#6,#7X2]=[#6]-[#6,#7X2]=[#6,#7X2]-[#6,#7X2]=[NX2,S,O,Se,Te]', [], []), TautomerTransform('1,9 aromatic heteroatom H shift f', '[#7,O;!H0]-[#6,#7X2]=[#6,#7X2]-[#6,#7X2]=[#6,#7X2]-[#6,#7X2]=[#6,#7X2]-[#6,#7X2]=[#7,O]', [], []), TautomerTransform('1,11 aromatic heteroatom H shift f', '[#7,O;!H0]-[#6,nX2]=[#6,nX2]-[#6,nX2]=[#6,nX2]-[#6,nX2]=[#6,nX2]-[#6,nX2]=[#6,nX2]-[#6,nX2]=[#7X2,O]', [], []), TautomerTransform('furanone f', '[O,S,N;!H0]-[#6r5]=[#6X3r5;$([#6]([#6r5])=[#6r5])]', [], []), TautomerTransform('furanone r', '[#6r5!H0;$([#6]([#6r5])[#6r5])]-[#6r5]=[O,S,N]', [], []), TautomerTransform('keten/ynol f', '[C!H0]=[C]=[O,S,Se,Te;X1]', [rdkit.Chem.rdchem.BondType.TRIPLE, rdkit.Chem.rdchem.BondType.SINGLE], []), TautomerTransform('keten/ynol r', '[O,S,Se,Te;!H0X2]-[C]#[C]', [rdkit.Chem.rdchem.BondType.DOUBLE, rdkit.Chem.rdchem.BondType.DOUBLE], []), TautomerTransform('ionic nitro/aci-nitro f', '[C!H0]-[N+;$([N][O-])]=[O]', [], []), TautomerTransform('ionic nitro/aci-nitro r', '[O!H0]-[N+;$([N][O-])]=[C]', [], []), TautomerTransform('oxim/nitroso f', '[O!H0]-[N]=[C]', [], []), TautomerTransform('oxim/nitroso r', '[C!H0]-[N]=[O]', [], []), TautomerTransform('oxim/nitroso via phenol f', '[O!H0]-[N]=[C]-[C]=[C]-[C]=[OH0]', [], []), TautomerTransform('oxim/nitroso via phenol r', '[O!H0]-[c]=[c]-[c]=[c]-[N]=[OH0]', [], []), TautomerTransform('cyano/iso-cyanic acid f', '[O!H0]-[C]#[N]', [rdkit.Chem.rdchem.BondType.DOUBLE, rdkit.Chem.rdchem.BondType.DOUBLE], []), TautomerTransform('cyano/iso-cyanic acid r', '[N!H0]=[C]=[O]', [rdkit.Chem.rdchem.BondType.TRIPLE, rdkit.Chem.rdchem.BondType.SINGLE], []), TautomerTransform('isocyanide f', '[C-0!H0]#[N+0]', [rdkit.Chem.rdchem.BondType.TRIPLE], [- 1, 1]), TautomerTransform('isocyanide r', '[N+!H0]#[C-]', [rdkit.Chem.rdchem.BondType.TRIPLE], [- 1, 1]), TautomerTransform('phosphonic acid f', '[OH]-[PH0]', [rdkit.Chem.rdchem.BondType.DOUBLE], []), TautomerTransform('phosphonic acid r', '[PH]=[O]', [rdkit.Chem.rdchem.BondType.SINGLE], []), scores=TautomerScore('benzoquinone', '[#6]1([#6]=[#6][#6]([#6]=[#6]1)=,:[N,S,O])=,:[N,S,O]', 25), TautomerScore('oxim', '[#6]=[N][OH]', 4), TautomerScore('C=O', '[#6]=,:[#8]', 2), TautomerScore('N=O', '[#7]=,:[#8]', 2), TautomerScore('P=O', '[#15]=,:[#8]', 2), TautomerScore('C=hetero', '[#6]=[!#1;!#6]', 1), TautomerScore('methyl', '[CX4H3]', 1), TautomerScore('guanidine terminal=N', '[#7][#6](=[NR0])[#7H0]', 1), TautomerScore('guanidine endocyclic=N', '[#7;R][#6;R]([N])=[#7;R]', 2), TautomerScore('aci-nitro', '[#6]=[N+]([O-])[OH]', - 4), max_tautomers=1000)¶Bases: object
The molvs class refactores
__call__(mol)¶Calling a TautomerCanonicalizer instance like a function is the same as calling its canonicalize(mol) method.
canonicalize(mol)¶Return a canonical tautomer by enumerating and scoring all possible tautomers.
mol (Mol) – The input molecule
tau – The canonical tautomer.
Mol
compute_score(mol, returndetails=False, log=False)¶Return a canonical tautomer by enumerating and scoring all possible tautomers.
mol (Mol) – The input molecule
tau (list Mol) – The canonical tautomers
t_score (list) – The tautomer scores
depict_tautomers(tautomers, scores, atoms, details=None)¶filter_tautomers(tautomers, scores, threshold=2)¶The function returns the tautomers as rdkit molecule objects based on the scores and the threshold
tautomers (list - List of rdkit.Chem.Molecule of the tautomers identified) –
scores (list - List of the scores for each tatutomer) –
threshold (int - The threshold value to be used as difference from the highest one) –
t_filtered
list - List of rdkit.Chem.Molecule of the tautomers filtered
get_conjugate(tautomer)¶The functions called the MolFragmeter and returns the conjugate length and the atoms member of the path
tautomer (rdkit.Chem.Molecule - A tautomer object) –
n_conj (int - the lenght of the conjugate path)
atoms (list - The list of the atoms part of the path)