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)) –
int - The id of the fragment
str - The fragment type (choices: single, aromatic, double)
list - List of the atom indeces
list - List of the Fragment.name of the the Fragment object connected with this Fragment
this Fragment (Only double and aromatic.)
list - List of the Fragment.name of the the Fragment object connected with
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
Bases: object
mol (rdkit.Chem.rdchem.Mol - the rdkit molecule object) –
rdkit.Chem.rdchem.Mol - the rdkit molecule object
list - list of Fragment objects
list - list of list containing fragment objects part of the path
The function inpect and detect all the possible conjugate paths
The method creates and stores Fragment objects for each bond in the molecule and based on the atom type
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
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
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
The function inspect for each conjugate Fragment (double aromatic) all the possible pattern that will set as connections
The function return the longest path
highest_path
list - The list of fragmaent that represents the longest path
Total number of fragments.
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
Bases: object
The molvs class refactores
Calling a TautomerCanonicalizer instance like a function is the same as calling its canonicalize(mol) method.
Return a canonical tautomer by enumerating and scoring all possible tautomers.
mol (Mol
) – The input molecule
tau – The canonical tautomer.
Mol
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
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
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)