This should get an integer value given a column and row. The binary search function only searches columns containing integers for a value. @param row

The neighbours (connected atoms) of any atom are sorted by their relevance:<br> 1. non-hydrogen atoms (bond order 1 and above) and unusual hydrogen at

@return the number of all atoms, which includes hydrogen atoms.

@param no 0 or 1 @param bond @return atom index

A validated molecule (after helper array creation) contains a sorted list of all atoms with the plain (neglegible) hydrogen atoms at the end of the li

In addition to the natural atomic numbers, we support additional pseudo atomic numbers. Most of these are for compatibility with the MDL atom table, e

The neighbours (connected atoms) of any atom are sorted by their relevance:<br> 1. non-hydrogen atoms (bond order 1 and above) and unusual hydrogen at

This function should return the total number of rows in a searchable table. This is normally just the length of the array. @return The number of elem

Returns the encoded reaction coordinates. @param row @return coords of this row or null, if no reaction is associated to this row

ensureHelperArrays() is the essential method when working with molecules. The Molecule class contains all primary information about a molecule, i.e. t

@param atom @return the formal atom charge

Returns an atom's pi electron count for the purpose of classifying a connected bond to determine its length. The returned value may differ from the fo

The neighbours (connected atoms) of any atom are sorted by their relevance:<br> 1. non-hydrogen atoms (bond order 1 and above) and unusual hydrogen at

The bond list is preprocessed such that all bonds leading to a plain hydrogen atom (natural abundance, no custom labels) are at the end of the list. O

Returns the formal bond order. Delocalized rings have alternating single and double bonds, which are returned as such. Bonds that are explicitly marke

The neighbours (connected atoms) of any atom are sorted by their relevance:<br> 1. non-hydrogen atoms (bond order 1 and above) and unusual hydrogen at

Returns an atom mapping number within the context of a reaction. Atoms that that share the same mapping number on the reactant and product side are co

@return the number of all bonds, which includes those connecting hydrogen atoms.

Returns bond type combining bond order and stereo orientation. @param bond @return one of cBondTypeSingle,cBondTypeDouble,cBondTypeUp,cBondTypeCross,.

Sets the bond type based on bond order without stereo orientation. @param bond @param order 1,2, or 3

@return a RingCollection object, which contains a total set of small rings

Returns all set query features for this atom. In order to get all features related to a certain subject use something like this: <i>getAtomQueryFeatur

High level function for constructing a molecule. @param x @param y @return

@return the nBondsMolecule

High level function for constructing a molecule. Adds a single or metal bond between the two atoms depending on whether one of them is a metal atom. @

The sum of bond orders of explicitly connected neighbour atoms. @param atom @return explicitly used valence

The atom parity is a calculated property available above/equal helper level cHelperParities. It describes the stereo configuration of a chiral atom an

Introduce or remove an atom query feature and make sure, the molecule is flagged to be a sub-structure fragment (see setFragment()). A query feature i

Defines a bond type combining bod order and stereo orientation. @param bond @param type one of cBondTypeSingle,cBondTypeDouble,cBondTypeUp,cBondTypeCr

The neighbours (connected atoms) of any atom are sorted by their relevance:<br> 1. non-hydrogen atoms (bond order 1 and above) and unusual hydrogen at

Returns the total number of atoms connected to an atom, including implicit and explicit hydrogens. @param mol The molecule that the atom is in. @par

Get the MMFF atom type of an atom. This returns the cached value. @param a The atom index in the molecule. @return The MMFF atom type.