Could this atom have been a tetrahedral center? If yes, template atom is considered achiral and will not match a chiral rct If no, the te

This function takes an RDKit atom and turns it into a wildcard using heuristic generalization rules. This function should be used when candid

Checks for consistency in chirality between a template atom and a molecule atom. Also checks to see if chirality needs to be inverted in cop

rxn = rdchiralReaction (rdkit reaction + auxilliary information) reactants = rdchiralReactants (rdkit mol + auxilliary information) note

This function takes an RDKit bond and creates a label describing the most important attributes

This function takes an RDKit bond and creates a label describing the most important attributes

Given a list of RDKit mols and a list of changed atom tags, this function computes the SMILES string of molecular fragments using MolFragmentToSmi

For an RDkit atom object, generate a SMARTS pattern that matches the atom as strictly as possible

Takes a list of RDKit molecules and returns total list of atoms and their tags

Given a list of smiles strings, this function creates rdkit molecules

Thanks to http://www.dalkescientific.com/writings/diary/archive/2016/08/15/fragment_parity_calculation.html

Copy over single-bond directions (ENDUPRIGHT, ENDDOWNRIGHT) to the single bonds attached to some double-bonded atom, a a - atom with a doubl

Compares two RDKit atoms based on basic properties

This function takes one-half of a template SMARTS string (i.e., reactants or products) and re-orders them based on an equivalent string witho

This function takes an atom-mapped SMARTS transform and converts it to a canonical form by, if nececssary, rearranging the order of reactant a

Checks to see if tetrahedral centers are equivalent in chirality, ignoring the ChiralTag. Owning molecules of the input atoms must have been I

If two products are identical except for an inverted CW/CCW or an opposite cis/trans, then just strip that from the product. Return the a

This function is meant to take a reactant template and fully enumerate all the ways in which different double-bonds can have their cis/trans

Given an RDKit molecule and a list of AtomIdX which should be included in the reaction, this function expands the list of AtomIdXs to include one

Given an RDKit molecule and a list of AtomIdx which should be included in the reaction, this function extends the list of atoms_to_use by consider

Given a list of changed atom tags (numbers as strings) and a string consisting of the reactant_fragments to include in the reaction transform, thi

This function takes a molecule and returns a list of cis/trans specifications according to the following: (mapnums, dirs) where ato

Looks at mapped atoms in a reaction and determines which ones changed

Builds a MolFragment using neighbors of a tetrahedral atom, where the molecule has already been updated to include isotopes

Given an RDKit molecule, this function returns a list of tuples, where each tuple contains the AtomIdx's for a special group of atoms which should

Takes an RDKit molecule and returns list of tagged atoms and their corresponding numbers