The Atom Context Menu
Select
Makes this atom the current selection.
Select Molecule
Makes the molecule the atom is in the current selection.
Cut
Removes the atom and all of its bonds from the molecule and puts it into the
clipboard for later paste actions.
Cut Selected
Removes the selected part from the model.
Change Element...
Changes the element symbol of the atom to the selected symbol.
Change Isotope...
Changes the isotope of the atom to the selected option.
Convert to radical...
TODO when does this work?.
Hydrogens
Add Implicit Hydrogens
JCP can run in two different modes with respect to implicit hydrogens. You can
switch between them here. The two modes are:
- Tracking of Implicit Hydrogens on: JCP will update atoms on which anything (e. g. charge, symbol)
gets changed, for their
implicit H count, so that atoms will always be fully saturated.
- Tracking of Implicit Hydrogens off: No implicit hydrogens will get added.
You need to take care of hydrogens yourself, if you want any.
Note that:
- Switching between modes will not change hydrogen count, i. e. if switching off
implicit hydrogens will stay and future changes will lead to wrong counts, whereas
switching on will not add hydrogens on existing atoms, only new/changed atoms
will get the correct count.
- The implicit hydrogens will be only visible when the option "Show
implicit hydrogens when the atom symbol is shown" is selected in View ->
Options (default: on). For which atoms the symbols are visible is controlled by
other settings here.
- You can set hydrogen count of individual atoms via the context menu of the
atom (item Properties). This can be used on difficult configurations.
- Whether or not the hydrogens will be contained in an exported file.
Depends on the file format.(e.g. CML has got implicit Hs, mol has not).
The following menu options allow manipulations of the implicit Hs.
Make Hydrogens Explicit
This will transform implicit hydrogens to
separate atoms connected by a single bond. This will only have an effect if you
are in implicit mode (see "Add Implicit Hydrogens")
Make Hydrogens Implicit
This will delete bonds to hydrogens and add hydrogens directly to their
parent atoms as implicit hydrogens.
Update Implicit Hydrogen Count
This will set the implicit hydrogens on all atoms to satisfy valency. This can be
called in both modes. If tracking of implicit Hs is off, this will only have a one-off
effect.
Reaction
Here you can make the molecule in which the atom is part of either a new reaction
or an existing one as either reactant or product.
Reset Bond Orders
Sets the order of all bonds to single.
Run validate
Runs a validation on this atom. See Report menu help for details.
Properties
Here you can directly set symbol, charge and hydrogen count.
Molecule Properties
Here you can directly set properties (title) of the molecule the atom is in.