This is related to the current moleculeWithH. The order is NOT canonized
Returns the distance matrix for the current moleculeWithH
Computes a canonical ID for each atom in moleculeWithH that encodes
absolute stereochemistry (no makeRacemic step). Unlike diaIDs,
these IDs differ between enantiomers and are used as cache keys for
pro-R / pro-S assignment so that each enantiomer gets an independent
computation.
Returns finalRanks for all the atoms including hydrogens. Those ranks deals with topicity and is related to the current moleculeWithH. All the atoms have a unique identifier.j In order to calculate the ranks we replace all the hydrogens with a X atom.
Returns symmetryRanks for all the atoms including hydrogens. Those ranks deals with topicity and is related to the current moleculeWithH. In order to calculate the ranks we replace all the hydrogens with a X atom.
This is related to the current moleculeWithH. The order is NOT canonized
Returns a molecule with all the hydrogens added. The order is NOT canonized
Returns an array, indexed by atom number in moleculeWithH, holding the
pro-R / pro-S descriptor ('r' or 's') for every hydrogen of a CH2
whose two hydrogens are diastereotopic. Atoms that are not labelled
prochiral hydrogens hold undefined. The underlying hash
(prochiralityByEnantioID) is keyed by enantioID, which encodes
absolute stereochemistry, so two enantiomers receive independent
assignments. Hydrogens are never R or S themselves (that is a
stereocenter descriptor), so the label is always lowercase regardless
of whether the prochiral carbon is a true or a pseudoasymmetric centre.
The assignment is determined by replacing one H with a higher-priority
pseudo-atom (via tagAtom) and reading getAtomCIPParity of the carbon.
array of 'r' / 's' / undefined indexed by atom number
This method ensures that all the atoms have a mapNo in the molecule (and not the moleculeWithH! )
Returns a new TopicMolecule but will copy precalculated information if possible (same idCode). This is very practical when expanding hydrogens for example.
This method returns a mapping between the diaIDs of the current molecule. It expects that the initial molfile and the final molfile contains atomMapNo in order to track which atom becomes which one.
We return the atomIDs corresponding to the specified diaID as well has the attached hydrogens or heavy atoms
Returns an array of objects containing the oclID and the corresponding hydrogens and atoms for the specified atomLabel (if any) This always applied to the molecule with expanded hydrogens and chirality
For each atom we will return an array of objects that contains the different possible path as well as the canonic hose codes
Return one fragment for a specific sphere size and specific root atoms
Remove a trailing pro-R / pro-S character (r or s) from the
customLabel of every hydrogen that carries one, in both molecule
and moleculeWithH. Idempotent. Hydrogens whose customLabel does
not end with r or s are left untouched.
The number of labels that were stripped from moleculeWithH
This method ensures that all the atoms have a mapNo corresponding to the atom number. It will enforce mapNo in molecule and moleculeWithH We start numbering the atoms at 1
Set a pro-R / pro-S customLabel on each diastereotopic CH2 hydrogen,
appended as lowercase r or s. Idempotent: calling it again replaces
any trailing pro-R / pro-S letter rather than stacking. The label is
appended to whatever customLabel the hydrogen already has, falling
back to the parent carbon's customLabel when the hydrogen has none.
Both molecule and moleculeWithH are labelled in place, sharing the
same cached prochiralityByEnantioID hash; on molecule only hydrogens
that are explicit (i.e. exist as atoms there) receive a label.
Repeated calls do no extra CIP work.
The number of hydrogens labelled in moleculeWithH
This class deals with topicity information and hose codes It is optimized to avoid recalculation of the same information