Molecule Diagrams ================= Atoms ----- The molecule diagrams are rendered with a custom molecule renderer that emphasizes its purpose of representing the data in the database and not illustration of the chemical properties. Therefore it does not show radicals or lone pairs but rather represents an atom with only 3 possible properties: * element type * hydrogen count * charge If a node in the molecule diagram has an implicit hydrogen atom associated with it, it will always be shown except for saturated carbon atoms in a chain. The silicon atom in this structure has no hydrogen connected to it and only two bonds therefore it is two valued: .. figure:: a3a93b7af7.* :width: 170px In the next structure Silicon has an implicit hydrogen: .. figure:: 852db75646.* :width: 400px Carbon monoxide is complicated to represent. Usually one would make the diagram like: .. figure:: cc36e2daa7.* :width: 70px But the viewer and editor can collapse this structure to a simple "CO". Bonds ----- Also the way to represent bonds is limited. There are only 4 types of bonds: * single bonds * double bonds * triple bonds * coordinative bonds So aromatic bonds have to be represented as conjugated bonds. .. _moledit: Molecule Editor =============== .. figure:: mol1.png The ACNMR app comes with its own molecule editor. It is based on the same SVG code as we use for the display. It is however, a data entry tool not an illustration tool. You can only create objects on the canvas that are also represented in the database. Special features for this database include the ability to color atom labels with color codes as used for the NMR shifts data and to make "*" pseudo atoms to represent polymers. .. figure:: 52ef61d581.* :width: 200px The Hand Tool ------------- .. figure:: hand35.* :width: 50px The default mode of the molecule editor is to use the hand tool. The hand tool is able to manipulate all properties of the molecule. The features include: Pan Dragging the background allows moving the canvas Drag node Hovering over a node will allow to grab it with the mouse and drag it around Drag bond Bonds can also be grabbed and dragged Change color Clicking a label or node will open a color select menu to choose a color code Keyboard shortcuts allow to extent the hand. So far as you can do almost anything. Shift click Add single bond with C atom to selected atom Hover over node + letter Toggle through elements starting with the typed letter Hover over node + "+" or "-" Change charge Hover over node + "." Change hydrogen count Hover over bond + number Change bond type. Repeat to change direction. Hover and press Del Delete node or bond The Erase Tool -------------- .. figure:: double31.* :width: 50px With the erase tool active you can delete single nodes or bonds For deleting more than one use the lasso tool The Lasso Tool -------------- .. figure:: lasso.* :width: 50px The lasso tool is for manipulating a group of nodes. In this mode you have two ways to select nodes. You can circle the nodes with lasso or shift click on nodes to add them to the selection. On selected atoms you can do the following operations. Drag Drag the crossed arrows to drag the selected atoms or grab one selected node and drag all the nodes. Rotate Drag the rotating arrow symbol to rotate selected structure. Delete Press Del to delete selected atoms. The Bond Tools -------------- .. figure:: bonds.png There are buttons to add C atoms with bonds of an specific order or change the order of bonds in the drawing. The modes it has are the following. Hover over node click Add C with bond into the direction where there is the most space. Hover over node drag Add C with bond and drag around Hover bond click Change bond order. Repeat to change direction. The add Fragment Tools ---------------------- .. figure:: frag.png There are a collection of rings and other fragments that can be added via a special tool. The fragments may be added in one of these ways. Click on canvas Insert fragment here and drag. Click on node. Attach fragment here and rotate in order to use the direction with the most space. After inserting you may rotate it around the attachment point by dragging. Click on bond Insert fragment by aligning it with the bond. After inserting you may flip the alignment side by dragging the mouse around. The Hydrogen Count Tool ------------------------ .. figure:: Hcount.* :width: 50px Hover over atom and click to change hydrogen count. Same as hover and press "." The Charge Tools ---------------- .. figure:: minus20.* :width: 50px .. figure:: plus26.* :width: 50px Hover over atom and click to change charge.Same as hover and press "+" or "-" Undo, Redo buttons ------------------ .. figure:: reply8.* :width: 50px Buttons to undo and redo edits. Ctrl-Z for undo and Ctrl-Y for redo work too. Cut and Paste ------------- Ctrl-C and Ctrl-V work within one editor as expected on selected groups of atoms. Mark All Atoms In Editor ------------------------ Ctrl-A will mark all atoms in the editor. Snap Mode --------- .. figure:: snapmode.* :width: 50px When moving fragments around the editor offeres guides to simplify matching angles and lengths. The three modes available are: Hexagon Mode: Angles snap to 90/6° angles. Pentagon Mode: Angles snap to 90/5° angles. Circle Mode: Snap disabled.