Saturate and Bondify

The one action I use the most is "saturate-atoms". You select a number of atoms and then activate it: It will add hydrogen atoms including bonds to each selected atom depending on the remaining valence of the atom.

In the following images I have added an oxygen atom and used saturate-atoms: once with "outer shell" option activate, the second time without.

You see that using "outer shell", two hydrogens are added in approximately the typical bond angle for a water molecule. Without the option, it's also two hydrogens but they are no longer added in the typical angle. In the first case, molecuilder is aware that there are 4 orbitals in the outer shell, two of which are unoccupied. Hence, it finds two empty spots in the corners of a tetrahedron, resulting in the typical angle. In the latter case, there are two orbitals to fill and without any knowledge about the outer shell, molecuilder simply adds the hydrogens with greatest spatial separation to each other. Therefore, they lie on a line with the oxygen atom in the middle.

Note that in v1.7.0 the internal polyhedra have been improved and the saturate action should be even more useful. For example, it is used at the core of walking-organic-chemical-space's algorithm.

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Additionally, there is now also an action for the opposite effect: bondify-atoms.

This action will look for atoms in the vicinity of tabulated bonding distances (see data/bondtables/bondtable.dat​) given some slack ([-0.4, 0.4] angstroem) and replaces up to as many hydrogens as stated in the action's option and replaces it with a bond to the atom that bonded to the hydrogen.

In the following image we have a carbon atom, fully saturated with four hydrogen atoms bonded to it and one lone carbon atom without bonds: If we then call "bondify-atoms" on the lone carbon requesting to remove up to one, two or three hydrogens, then we see that as many hydrogens are removed from the neighboring saturated carbon atoms and they are replaced by a single, double or triple bond to the lone carbon atom.