added ketcher option
Navan Chauhan
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<!DOCTYPE html><p><strong>Ketcher</strong> is a tool to draw molecular structures and chemical
|
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reactions.</p>
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<h1>Ketcher Overview</h1>
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<p><strong>Ketcher</strong> is a tool to draw molecular structures and chemical
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reactions. Ketcher operates in two modes, the Server mode with most
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functions available and the client mode with limited functions
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available.</p>
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<p><strong>Ketcher</strong> consists of the following elements:</p>
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<p><img src="main.png" alt="" title="Main window"></p>
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<p><strong>Note</strong> : Depending on the screen size, some tools on the <em>Tool
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palette</em> can be displayed in expanded or collapsed forms.</p>
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<p>Using the <em>Tool palette</em>, you can</p>
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<ul>
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<li>
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<p>draw and edit a molecule or reaction by clicking on and dragging
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atoms, bonds, and other elements provided with the buttons on the
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<em>Atoms</em> toolbar and <em>Tool palette</em>;</p>
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</li>
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<li>
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<p>delete any element of the drawing (atom or bond) by clicking on it
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with the Erase tool;</p>
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</li>
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<li>
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<p>delete the entire molecule or its fragment by a lasso,
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rectangular, or fragment selection with the Erase tool;</p>
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</li>
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<li>
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<p>draw special structures (see the following sections);</p>
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</li>
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<li>
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<p>select the entire molecule or its fragment in one of the following
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ways (click on the button to see the list of available options):</p>
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<ul>
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<li>
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<p>in the expanded form</p>
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<p><img src="expanded.png" alt="" title="Expanded tool"></p>
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</li>
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<li>
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<p>in the collapsed form</p>
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<p><img src="collapsed.png" alt="" title="Collapsed tool"></p>
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</li>
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</ul>
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</li>
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</ul>
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<p>To select one atom or bond, click Lasso or Rectangle Selection tool,
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and then click the atom or bond.</p>
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<p>To select the entire structure:</p>
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<ul>
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<li>
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<p>Select the Fragment Selection tool and then click the object.</p>
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</li>
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<li>
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<p>Select the Lasso or Rectangle Selection tool, and then drag the
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mouse to select the object.</p>
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</li>
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<li>
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<p><code>Ctrl-click</code> with the Lasso or Rectangle Selection tool.</p>
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</li>
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</ul>
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<p>To select multiple atoms, bonds, structures, or other objects, do one
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of the following:</p>
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<ul>
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<li>
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<p><code>Shift-click</code> with the Lasso or Rectangle Selection tool selects
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some (connected or not) atoms/bonds.</p>
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</li>
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<li>
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<p>With the Lasso or Rectangle Selection tool click and drag the
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mouse around the atoms, bonds, or structures that you want to
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select.</p>
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</li>
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</ul>
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<p><strong>Note</strong> : <code>Ctrl+Shift-click</code> with the Lasso or Rectangle Selection tool
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selects several structures.</p>
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<p>You can use the buttons of the <em>Main</em> toolbar:</p>
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<p><img src="toolbar.png" alt="" title="Tolbar"></p>
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<ul>
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<li>
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<p><strong>Clear Canvas</strong> (1) button to start drawing a new molecule; this
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command clears the drawing area;</p>
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</li>
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<li>
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<p><strong>Open…</strong> (2) and <strong>Save As…</strong> (3) buttons to import a molecule
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from a molecular file or save it to a supported molecular file
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format;</p>
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</li>
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<li>
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<p><strong>Undo</strong> / <strong>Redo</strong> (4), <strong>Cut</strong> (5), <strong>Copy</strong> (6), <strong>Paste</strong> (7),
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<strong>Zoom In</strong> / <strong>Out</strong> (8), and <strong>Scaling</strong> (9) buttons to perform
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the corresponding actions;</p>
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</li>
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<li>
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<p><strong>Layout</strong> button (10) to change the position of the structure to
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work with it with the most convenience;</p>
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</li>
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<li>
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<p><strong>Clean Up</strong> button (11) to improve the appearance of the
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structure by assigning them uniform bond lengths and angles.</p>
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</li>
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<li>
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<p><strong>Aromatize</strong> / <strong>Dearomatize</strong> buttons (12) to mark aromatic
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structures (to convert a structure to the Aromatic or Kekule
|
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presentation);</p>
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</li>
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<li>
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<p><strong>Calculate CIP</strong> button (13) to determine R/S and E/Z
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configurations;</p>
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</li>
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<li>
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<p><strong>Check Structure</strong> button (14) to check the following properties
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of the structure:</p>
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<p><img src="check.png" alt="" title="Structure Ckeck"></p>
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</li>
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<li>
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<p><strong>Calculated Values</strong> button (15) to display some properties of
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the structure:</p>
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<p><img src="analyse.png" alt="" title="Calculated Values"></p>
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</li>
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<li>
|
||||||
|
<p><strong>Recognize Molecule</strong> button (16) to recognize a structure in the
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image file and load it to the canvas;</p>
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|
</li>
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<li>
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<p><strong>3D Viewer</strong> button (17) to open the structure in the
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three-dimensional Viewer;</p>
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|
</li>
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<li>
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<p><strong>Settings</strong> button (18) to make some settings for molecular
|
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files:</p>
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<p><img src="settings.png" alt="" title="Settings"></p>
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</li>
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<li>
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|
<p><strong>Help</strong> button (19) to view Help;</p>
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|
</li>
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|
<li>
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|
<p><strong>About</strong> button (20) to display version and copyright information
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|
of the program.</p>
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|
</li>
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|
</ul>
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<p><strong>Note</strong> : <strong>Layout,</strong> <strong>Clean Up,</strong> <strong>Aromatize</strong> / <strong>Dearomatize,</strong>
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||||||
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<strong>Calculate CIP,</strong> <strong>Check Structure,</strong> <strong>Calculated Values,</strong>
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<strong>Recognize Molecule</strong> and <strong>3D View</strong> buttons are active only in the
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Server mode.</p>
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<h1>3D Viewer</h1>
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<p>The structure appears in a modal window after clicking on the <strong>3D
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Viewer</strong> button:</p>
|
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<p><img src="miew.png" alt="" title="3D Viewer"></p>
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<p>You can perform the following actions:</p>
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<ul>
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<li>
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<p>Rotate the structure holding the left mouse button;</p>
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|
</li>
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||||||
|
<li>
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|
<p>Zoom In/Out the structure;</p>
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|
</li>
|
||||||
|
</ul>
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<p>Ketcher Settings allow to change the appearance of the structure and background coloring.</p>
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<p>“Lines” drawing method, “Bright” atom name coloring
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method and “Light” background coloring are default.</p>
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<h1>Drawing Atoms</h1>
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<p>To draw/edit atoms you can:</p>
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<ul>
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<li>
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<p>select an atom in the Atoms toolbar and click inside the drawing
|
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area;</p>
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|
</li>
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<li>
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<p>if the desired atom is absent in the toolbar, click on
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the <img src="periodic-table.png" alt=""> button to invoke the Periodic Table and
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click on the desired atom (available options: <em>Single</em> – selection
|
||||||
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of a single atom, <em>List</em> – choose an atom from the list of selected
|
||||||
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options (To allow one atom from a list of atoms of your choice at
|
||||||
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that position), <em>Not List</em> - exclude any atom on your list at that
|
||||||
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position).</p>
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||||||
|
<p><img src="periodic-dialog.png" alt="" title="Periodic Table"></p>
|
||||||
|
</li>
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||||||
|
<li>
|
||||||
|
<p>add an atom to the existing molecule by selecting an atom in the
|
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<em>Atoms</em> toolbar, clicking on an atom in the molecule, and dragging
|
||||||
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the cursor; the atom will be added with a single bond; vacant
|
||||||
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valences will be filled with the corresponding number of hydrogen
|
||||||
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atoms;</p>
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|
</li>
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||||||
|
<li>
|
||||||
|
<p>change an atom by selecting an atom in the <em>Atoms</em> toolbar and
|
||||||
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clicking on the atom to be changed; in the case a wrong valence thus
|
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appears the atom will be underlined in red;</p>
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||||||
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</li>
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||||||
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<li>
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<p>change an atom by clicking on an existing atom with the
|
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<em>Selection</em> tool and waiting for a couple of seconds for the text
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||||||
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box to appear; type another atom symbol in the text box:</p>
|
||||||
|
<p><img src="inline-edit.png" alt="" title="Change Atom"></p>
|
||||||
|
</li>
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||||||
|
<li>
|
||||||
|
<p>change the charge of an atom by selecting the Charge Plus or
|
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|
Charge Minus tool and clicking consecutively on an atom to
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increase/decrease its charge</p>
|
||||||
|
<p><img src="charge.png" alt="" title="Ions"></p>
|
||||||
|
</li>
|
||||||
|
<li>
|
||||||
|
<p>change an atom or its properties by double-clicking on the atom to
|
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|
invoke the Atom Properties dialog (the dialog also provides atom
|
||||||
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query features):</p>
|
||||||
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<p><img src="atom-dialog.png" alt="" title="Atom Properties"></p>
|
||||||
|
</li>
|
||||||
|
<li>
|
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<p>click on the Periodic Table button, open the Extended table and
|
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select a corresponding Generic group or Special Node:</p>
|
||||||
|
<p><img src="periodic-dialog-ext.png" alt="" title="Generic Groups"></p>
|
||||||
|
</li>
|
||||||
|
</ul>
|
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<h1>Drawing Bonds</h1>
|
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<p>To draw/edit bonds you can:</p>
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||||||
|
<ul>
|
||||||
|
<li>
|
||||||
|
<p>Click an arrow on the Bond tool <img src="bond.png" alt=""> in the Tools palette
|
||||||
|
to open the drop-down list with the following bond types:</p>
|
||||||
|
<p><img src="bonds.png" alt=""></p>
|
||||||
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<p>For the full screen format, the Bond tool from the Tools palette
|
||||||
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splits into three: _Single Bond,_<em>Single Up Bond,</em> and <em>Any
|
||||||
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Bond</em>,which include the corresponding bond types:</p>
|
||||||
|
<p><img src="bond-types.png" alt=""></p>
|
||||||
|
</li>
|
||||||
|
<li>
|
||||||
|
<p>select a bond type from the drop down list and click inside the
|
||||||
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drawing area; a bond of the selected type will be drawn;</p>
|
||||||
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</li>
|
||||||
|
<li>
|
||||||
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<p>click on an atom in the molecule; a bond of the selected type will
|
||||||
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be added to the atom at the angle of 120 degrees;</p>
|
||||||
|
</li>
|
||||||
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<li>
|
||||||
|
<p>add a bond to the existing molecule by clicking on an atom in the
|
||||||
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molecule and dragging the cursor; in this case you can set the angle
|
||||||
|
manually;</p>
|
||||||
|
</li>
|
||||||
|
<li>
|
||||||
|
<p>change the bond type by clicking on it;</p>
|
||||||
|
</li>
|
||||||
|
<li>
|
||||||
|
<p>use the Chain Tool <img src="chain.png" alt=""> to draw consecutive single
|
||||||
|
bonds;</p>
|
||||||
|
</li>
|
||||||
|
<li>
|
||||||
|
<p>change a bond or its properties by double-clicking on the bond to
|
||||||
|
invoke the Bond Properties dialog:</p>
|
||||||
|
<p><img src="bond-dialog.png" alt="" title="Bond Properties"></p>
|
||||||
|
</li>
|
||||||
|
<li>
|
||||||
|
<p>clicking on a drawn stereo bond changes its direction.</p>
|
||||||
|
</li>
|
||||||
|
<li>
|
||||||
|
<p>clicking with the Single Bond tool or Chain tool switches the bond type
|
||||||
|
cyclically: Single-Double-Triple-Single.</p>
|
||||||
|
</li>
|
||||||
|
</ul>
|
||||||
|
<h1>Drawing R-Groups</h1>
|
||||||
|
<p>Use the <em>R-Group</em> toolbox <img src="rgroup.png" alt=""> to draw R-groups in Markush
|
||||||
|
structures:</p>
|
||||||
|
<p><img src="rgroup-types.png" alt=""></p>
|
||||||
|
<p>Selecting the <em>R-Group</em> <em>Label</em> Tool and clicking on an atom in the
|
||||||
|
structure invokes the dialog to select the R-Group label for a current
|
||||||
|
atom position in the structure:</p>
|
||||||
|
<p><img src="rgroup-dialog.png" alt=""></p>
|
||||||
|
<p>Selecting the R-Group label and clicking <strong>OK</strong> converts the structure
|
||||||
|
into a Markush structure with the selected R-Group label:</p>
|
||||||
|
<p><img src="rgroup-example1.png" alt=""></p>
|
||||||
|
<p><strong>Note</strong> : You can choose several R-Group labels simultaneously:</p>
|
||||||
|
<p><img src="rgroup-example2.png" alt=""></p>
|
||||||
|
<p>Particular chemical fragments that may be substituted for a given
|
||||||
|
R-Group form a set of R-Group members. R-Group members can be any
|
||||||
|
structural fragment, including functional groups and single atoms or
|
||||||
|
atom lists.</p>
|
||||||
|
<p>To create a set of R-Group members:</p>
|
||||||
|
<ol>
|
||||||
|
<li>
|
||||||
|
<p>Draw a structure to become an R-Group member.</p>
|
||||||
|
</li>
|
||||||
|
<li>
|
||||||
|
<p>Select the structure using the <em>R-Group Fragment Tool</em> to invoke
|
||||||
|
the R-Group dialog; in this dialog select the label of the
|
||||||
|
R-Group to assign the fragment to.</p>
|
||||||
|
</li>
|
||||||
|
<li>
|
||||||
|
<p>Click on <strong>OK</strong> to convert the structure into an R-Group member.</p>
|
||||||
|
</li>
|
||||||
|
</ol>
|
||||||
|
<p>An R-Group attachment point is the atom in an R-Group member fragment
|
||||||
|
that attaches the fragment to the initial Markush structure.</p>
|
||||||
|
<p>Selecting the <em>Attachment Point Tool</em> and clicking on an atom in the
|
||||||
|
R-Group fragment converts this atom into an attachment point. If the
|
||||||
|
R-Group contains more than one attachment point, you can specify one
|
||||||
|
of them as primary and the other as secondary. You can select between
|
||||||
|
either the primary or secondary attachment point using the dialog that
|
||||||
|
appears after clicking on the atom:</p>
|
||||||
|
<p><img src="attpoints-dialog.png" alt=""></p>
|
||||||
|
<p>If there are two attachment points on an R-Group member, there must be
|
||||||
|
two corresponding attachments (bonds) to the R-Group atom that has the
|
||||||
|
same R-Group label. Clicking on <strong>OK</strong> in the above dialog creates the
|
||||||
|
attachment point.</p>
|
||||||
|
<p>Schematically, the entire process of the R-Group member creation can
|
||||||
|
be presented as:</p>
|
||||||
|
<p><img src="rgroup-example3.png" alt=""></p>
|
||||||
|
<p><img src="rgroup-example4.png" alt=""></p>
|
||||||
|
<h1>R-Group Logic</h1>
|
||||||
|
<p><strong>Ketcher</strong> enables one to add logic when using R-Groups. To access
|
||||||
|
the R-Group logic:</p>
|
||||||
|
<ol>
|
||||||
|
<li>
|
||||||
|
<p>Create an R-Group member fragment as described above.</p>
|
||||||
|
</li>
|
||||||
|
<li>
|
||||||
|
<p>Move the cursor over the entire fragment for the green frame to
|
||||||
|
appear, then click inside the fragment. The following dialog
|
||||||
|
appears:</p>
|
||||||
|
<p><img src="rlogic-dialog.png" alt=""></p>
|
||||||
|
</li>
|
||||||
|
<li>
|
||||||
|
<p>Specify <strong>Occurrence</strong> to define how many of an R-Group
|
||||||
|
occurs. If an R-Group atom appears several times in the initial
|
||||||
|
structure, you will specify <strong>Occurrence</strong>">n", n
|
||||||
|
being the number of occurrences; if it appears once, you see
|
||||||
|
"R1 > 0".</p>
|
||||||
|
</li>
|
||||||
|
<li>
|
||||||
|
<p>Specify H at <strong>unoccupied</strong> R-Group sites ( <strong>RestH</strong> ): check or
|
||||||
|
clear the checkbox.</p>
|
||||||
|
</li>
|
||||||
|
<li>
|
||||||
|
<p>Specify the logical <strong>Condition</strong>. Use the R-Group condition <strong>If
|
||||||
|
R(i) Then</strong> to specify whether the presence of an R-Group is
|
||||||
|
dependent on the presence of another R-Group.</p>
|
||||||
|
</li>
|
||||||
|
</ol>
|
||||||
|
<h1>Marking S-Groups</h1>
|
||||||
|
<p>To mark S-Groups, use the <em>S-Group tool</em> <img src="sgroup.png" alt=""> and the
|
||||||
|
following dialog that appears after selecting a fragment with this
|
||||||
|
tool:</p>
|
||||||
|
<p><img src="sgroup-dialog.png" alt="" title="S-Group Dialog"></p>
|
||||||
|
<p>Available S-Group types:</p>
|
||||||
|
<p><em>Generic</em></p>
|
||||||
|
<p>Generic is a pair of brackets without any labels.</p>
|
||||||
|
<p><em>Multiple group</em></p>
|
||||||
|
<p>A Multiple group indicates a number of replications of a fragment or a part of a
|
||||||
|
structure in contracted form.</p>
|
||||||
|
<p><em>SRU Polymer</em></p>
|
||||||
|
<p>The Structural Repeating Unit (SRU) brackets enclose the structural
|
||||||
|
repeating of a polymer. You have three available patterns:
|
||||||
|
head-to-tail (the default), head-to-head, and either/unknown.</p>
|
||||||
|
<p><em>Superatom</em></p>
|
||||||
|
<p>An abbreviated structure (abbreviation) is all or part of a structure
|
||||||
|
(molecule or reaction component) that has been abbreviated to a text
|
||||||
|
label. Structures that you abbreviate keep their chemical
|
||||||
|
significance, but their underlying structure is hidden. The current
|
||||||
|
version can't display contracted structures but correctly
|
||||||
|
saves/reads them into/from files.</p>
|
||||||
|
<h1>Data S-Groups</h1>
|
||||||
|
<p>The <em>Data S-Groups Tool</em> <img src="sdata.png" alt=""> is a separate tool for
|
||||||
|
comfortable use with the accustomed set of descriptors (like Attached
|
||||||
|
Data in <strong>Marvin</strong> Editor).</p>
|
||||||
|
<p>You can attach data to an atom, a fragment, a single bond, or a
|
||||||
|
group. The defined set of <em>Names</em> and <em>Values</em> is introduced for each
|
||||||
|
type of selected elements:</p>
|
||||||
|
<p><img src="sdata-dialog.png" alt=""></p>
|
||||||
|
<ul>
|
||||||
|
<li>
|
||||||
|
<p>Select the appropriate S-Group Field Name.</p>
|
||||||
|
</li>
|
||||||
|
<li>
|
||||||
|
<p>Select or type the appropriate Field Value.</p>
|
||||||
|
</li>
|
||||||
|
<li>
|
||||||
|
<p>Labels can be specified as Absolute, Relative or Attached.</p>
|
||||||
|
</li>
|
||||||
|
</ul>
|
||||||
|
<h1>Changing Structure Display</h1>
|
||||||
|
<p>Use the <em>Flip/Rotate</em> tool <img src="transform.png" alt=""> to change the structure
|
||||||
|
display:</p>
|
||||||
|
<p><img src="transform-types.png" alt=""></p>
|
||||||
|
<p>For the full screen format, the <em>Flip/Rotate</em> tool is split into
|
||||||
|
separate buttons:</p>
|
||||||
|
<p><img src="rotate.png" alt=""></p>
|
||||||
|
<p><em>Rotate Tool</em></p>
|
||||||
|
<p>This tool allows rotating objects.</p>
|
||||||
|
<ul>
|
||||||
|
<li>If some objects are selected, the tool rotates the selected objects.</li>
|
||||||
|
<li>If no objects are selected, or all objects are selected, the tool rotates the whole canvas</li>
|
||||||
|
<li>The default rotation step is 15 degrees.</li>
|
||||||
|
<li>Press and hold the Ctrl key for more gradual continuous rotation with 1 degree rotation step</li>
|
||||||
|
</ul>
|
||||||
|
<p>Select any bond on the structure and click Alt+H to rotate the structure so that the selected bond is placed horizontally.
|
||||||
|
Select any bond on the structure and click Alt+V to rotate the structure so that the selected bond is placed vertically.</p>
|
||||||
|
<p><em>Flip Tool</em></p>
|
||||||
|
<p>This tool flips the objects horizontally or vertically.</p>
|
||||||
|
<ul>
|
||||||
|
<li>If some objects are selected, the Horizontal Flip tool (or Alt+H) flips the selected objects horizontally</li>
|
||||||
|
<li>If no objects are selected, or all objects are selected, the Horizontal Flip tool (or Alt+H) flips each structure horizontally</li>
|
||||||
|
<li>If some objects are selected, the Vertical Flip tool (or Alt+V) flips the selected objects vertically</li>
|
||||||
|
<li>If no objects are selected, or all objects are selected, the Vertical Flip tool (or Alt+V) flips each structure vertically</li>
|
||||||
|
</ul>
|
||||||
|
<h1>Drawing Reactions</h1>
|
||||||
|
<p>To draw/edit reactions you can</p>
|
||||||
|
<ul>
|
||||||
|
<li>
|
||||||
|
<p>draw reagents and products as described above;</p>
|
||||||
|
</li>
|
||||||
|
<li>
|
||||||
|
<p>use options of the <em>Reaction Arrow Tool</em> <img src="reaction.png" alt=""> to draw an
|
||||||
|
arrow and pluses in the reaction equation and map same atoms in
|
||||||
|
reagents and products.</p>
|
||||||
|
<p><img src="reaction-types.png" alt=""></p>
|
||||||
|
</li>
|
||||||
|
</ul>
|
||||||
|
<p><strong>Note</strong> : Reaction Auto-Mapping Tool is available only in the Server
|
||||||
|
mode.</p>
|
||||||
|
<h1>Templates toolbar</h1>
|
||||||
|
<p>You can add templates (rings or other predefined structures) to the
|
||||||
|
structure using the <em>Templates</em> toolbar together with the <em>Custom
|
||||||
|
Templates</em> button located at the bottom:</p>
|
||||||
|
<p><img src="template.png" alt=""></p>
|
||||||
|
<p>To add a ring to the molecule, select a ring from the toolbar and
|
||||||
|
click inside the drawing area, or click on an atom or a bond in the
|
||||||
|
molecule.</p>
|
||||||
|
<p>Rules of using templates:</p>
|
||||||
|
<ul>
|
||||||
|
<li>
|
||||||
|
<p>Selecting a template and clicking on an atom in the existing
|
||||||
|
structure adds the template to the structure connected with a single
|
||||||
|
bond:</p>
|
||||||
|
<p><img src="template-example1.png" alt=""></p>
|
||||||
|
</li>
|
||||||
|
<li>
|
||||||
|
<p>Selecting a template and dragging the cursor from an atom in the
|
||||||
|
existing structure adds the template directly to this atom resulting
|
||||||
|
in the fused structure:</p>
|
||||||
|
<p><img src="template-example2.png" alt=""></p>
|
||||||
|
</li>
|
||||||
|
<li>
|
||||||
|
<p>Dragging the cursor from an atom in the existing structure results
|
||||||
|
in the single bond attachment if the cursor is dragged to more than
|
||||||
|
the bond length; otherwise the fused structure is drawn.</p>
|
||||||
|
</li>
|
||||||
|
<li>
|
||||||
|
<p>Selecting a template and clicking on a bond in the existing
|
||||||
|
structure created a bond-to-bond fused structure:</p>
|
||||||
|
<p><img src="template-example3.png" alt=""></p>
|
||||||
|
</li>
|
||||||
|
<li>
|
||||||
|
<p>The bond in the initial structure is replaced with the bond in the
|
||||||
|
template.</p>
|
||||||
|
</li>
|
||||||
|
<li>
|
||||||
|
<p>This procedure doesn't change the length of the bond in the
|
||||||
|
initial structure.</p>
|
||||||
|
</li>
|
||||||
|
<li>
|
||||||
|
<p>Dragging the cursor relative to the initial bond applies the
|
||||||
|
template at the corresponding side of the bond.</p>
|
||||||
|
</li>
|
||||||
|
</ul>
|
||||||
|
<p><strong>Note</strong> : The added template will be fused by the default attachment
|
||||||
|
atom or bond preset in the program.</p>
|
||||||
|
<p><strong>Note</strong> : User is able to define the attachment atom and bond by clicking
|
||||||
|
the Edit button for template structure.</p>
|
||||||
|
<p>The <em>Custom Templates</em> button <img src="template-lib.png" alt="">invokes the scrolling
|
||||||
|
list of templates available in the program; both built-in and created
|
||||||
|
by user:</p>
|
||||||
|
<p><img src="template-dialog.png" alt=""></p>
|
||||||
|
<p>To create a user template:</p>
|
||||||
|
<ul>
|
||||||
|
<li>draw a structure.</li>
|
||||||
|
<li>click the Save as button.</li>
|
||||||
|
<li>click the Save to Templates button.</li>
|
||||||
|
<li>enter a name and define the attachment atom and bond.</li>
|
||||||
|
</ul>
|
||||||
|
<h1>Working with Files</h1>
|
||||||
|
<p>Ketcher supports the following molecular formats that can be entered
|
||||||
|
either manually or from files:</p>
|
||||||
|
<ul>
|
||||||
|
<li>
|
||||||
|
<p>MDL Molfile or RXN file;</p>
|
||||||
|
</li>
|
||||||
|
<li>
|
||||||
|
<p>Daylight SMILES (Server mode only);</p>
|
||||||
|
</li>
|
||||||
|
<li>
|
||||||
|
<p>Daylight SMARTS (Server mode only);</p>
|
||||||
|
</li>
|
||||||
|
<li>
|
||||||
|
<p>InChi string (Server mode only);</p>
|
||||||
|
</li>
|
||||||
|
<li>
|
||||||
|
<p>CML file (Server mode only).</p>
|
||||||
|
</li>
|
||||||
|
</ul>
|
||||||
|
<p>You can use the <strong>Open…</strong> and <strong>Save As…</strong> buttons of the <em>Main</em>
|
||||||
|
toolbar to import a molecule from a molecular file or save it to a
|
||||||
|
supported molecular file format. The <em>Open Structure</em> dialog enables
|
||||||
|
one to either browse for a file (Server mode) or manually input, e.g.,
|
||||||
|
the Molfile ctable for the molecule to be imported:</p>
|
||||||
|
<p><img src="open.png" alt=""></p>
|
||||||
|
<p>The <em>Save Structure</em> dialog enables one to save the molecular file:</p>
|
||||||
|
<p><img src="save.png" alt=""></p>
|
||||||
|
<p><strong>Note</strong> : In the standalone version only mol/rxn are supported for
|
||||||
|
Open and mol/rxn/SMILES for Save.</p>
|
||||||
|
<h1>Hotkeys</h1>
|
||||||
|
<p>You can use keyboard hotkeys (including Numeric keypad) for some
|
||||||
|
features/commands of the Editor. To display the hotkeys just place the
|
||||||
|
cursor over a toolbar button. If a hotkey is available for the button,
|
||||||
|
it will appear in brackets after the description of the button.</p>
|
||||||
|
<table>
|
||||||
|
<thead>
|
||||||
|
<tr>
|
||||||
|
<th>Key</th>
|
||||||
|
<th>Action</th>
|
||||||
|
</tr>
|
||||||
|
</thead>
|
||||||
|
<tbody>
|
||||||
|
<tr>
|
||||||
|
<td><code>Esc</code></td>
|
||||||
|
<td>Switching between the Lasso/Rectangle/Fragment Selection tools</td>
|
||||||
|
</tr>
|
||||||
|
<tr>
|
||||||
|
<td><code>Del</code></td>
|
||||||
|
<td>Delete the selected objects</td>
|
||||||
|
</tr>
|
||||||
|
<tr>
|
||||||
|
<td><code>0</code></td>
|
||||||
|
<td>Draw Any bond.</td>
|
||||||
|
</tr>
|
||||||
|
<tr>
|
||||||
|
<td><code>1</code></td>
|
||||||
|
<td>Single / Single Up / Single Down / Single Up/Down bond. Consecutive pressing switches between these types.</td>
|
||||||
|
</tr>
|
||||||
|
<tr>
|
||||||
|
<td><code>2</code></td>
|
||||||
|
<td>Double / Double Cis/Trans bond</td>
|
||||||
|
</tr>
|
||||||
|
<tr>
|
||||||
|
<td><code>3</code></td>
|
||||||
|
<td>Draw a triple bond.</td>
|
||||||
|
</tr>
|
||||||
|
<tr>
|
||||||
|
<td><code>4</code></td>
|
||||||
|
<td>Draw an aromatic bond.</td>
|
||||||
|
</tr>
|
||||||
|
<tr>
|
||||||
|
<td><code>5</code></td>
|
||||||
|
<td>Charge Plus/Charge Minus</td>
|
||||||
|
</tr>
|
||||||
|
<tr>
|
||||||
|
<td><code>A</code></td>
|
||||||
|
<td>Draw any atom</td>
|
||||||
|
</tr>
|
||||||
|
<tr>
|
||||||
|
<td><code>H</code></td>
|
||||||
|
<td>Draw a hydrogen</td>
|
||||||
|
</tr>
|
||||||
|
<tr>
|
||||||
|
<td><code>C</code></td>
|
||||||
|
<td>Draw a carbon</td>
|
||||||
|
</tr>
|
||||||
|
<tr>
|
||||||
|
<td><code>N</code></td>
|
||||||
|
<td>Draw a nitrogen</td>
|
||||||
|
</tr>
|
||||||
|
<tr>
|
||||||
|
<td><code>O</code></td>
|
||||||
|
<td>Draw an oxygen</td>
|
||||||
|
</tr>
|
||||||
|
<tr>
|
||||||
|
<td><code>S</code></td>
|
||||||
|
<td>Draw a sulfur</td>
|
||||||
|
</tr>
|
||||||
|
<tr>
|
||||||
|
<td><code>F</code></td>
|
||||||
|
<td>Draw a fluorine</td>
|
||||||
|
</tr>
|
||||||
|
<tr>
|
||||||
|
<td><code>P</code></td>
|
||||||
|
<td>Draw a phosphorus</td>
|
||||||
|
</tr>
|
||||||
|
<tr>
|
||||||
|
<td><code>I</code></td>
|
||||||
|
<td>Draw an iodine</td>
|
||||||
|
</tr>
|
||||||
|
<tr>
|
||||||
|
<td><code>T</code></td>
|
||||||
|
<td>Basic templates. Consecutive pressing switches between different templates</td>
|
||||||
|
</tr>
|
||||||
|
<tr>
|
||||||
|
<td><code>Shift+t</code></td>
|
||||||
|
<td>Open template library</td>
|
||||||
|
</tr>
|
||||||
|
<tr>
|
||||||
|
<td><code>Alt+r</code></td>
|
||||||
|
<td>Rotate tool</td>
|
||||||
|
</tr>
|
||||||
|
<tr>
|
||||||
|
<td><code>Alt+v</code></td>
|
||||||
|
<td>Flip vertically</td>
|
||||||
|
</tr>
|
||||||
|
<tr>
|
||||||
|
<td><code>Alt+h</code></td>
|
||||||
|
<td>Flip horizontally</td>
|
||||||
|
</tr>
|
||||||
|
<tr>
|
||||||
|
<td><code>Ctrl+g</code></td>
|
||||||
|
<td>S-Group tool / Data S-Group tool</td>
|
||||||
|
</tr>
|
||||||
|
<tr>
|
||||||
|
<td><code>Ctrl+d</code></td>
|
||||||
|
<td>Align and select all S-Group data</td>
|
||||||
|
</tr>
|
||||||
|
<tr>
|
||||||
|
<td><code>Ctrl+r</code></td>
|
||||||
|
<td>Switching between the R-Group Label Tool/R-Group Fragment Tool/Attachment Point Tool</td>
|
||||||
|
</tr>
|
||||||
|
<tr>
|
||||||
|
<td><code>Ctrl+Shift+r</code></td>
|
||||||
|
<td>R-Group Fragment Tool</td>
|
||||||
|
</tr>
|
||||||
|
<tr>
|
||||||
|
<td><code>Ctrl+Del</code></td>
|
||||||
|
<td>Clear canvas</td>
|
||||||
|
</tr>
|
||||||
|
<tr>
|
||||||
|
<td><code>Ctrl+o</code></td>
|
||||||
|
<td>Open</td>
|
||||||
|
</tr>
|
||||||
|
<tr>
|
||||||
|
<td><code>Ctrl+s</code></td>
|
||||||
|
<td>Save As</td>
|
||||||
|
</tr>
|
||||||
|
<tr>
|
||||||
|
<td><code>Ctrl+z</code></td>
|
||||||
|
<td>Undo</td>
|
||||||
|
</tr>
|
||||||
|
<tr>
|
||||||
|
<td><code>Ctrl+Shift+z</code></td>
|
||||||
|
<td>Redo</td>
|
||||||
|
</tr>
|
||||||
|
<tr>
|
||||||
|
<td><code>Ctrl+x</code></td>
|
||||||
|
<td>Cut selected objects</td>
|
||||||
|
</tr>
|
||||||
|
<tr>
|
||||||
|
<td><code>Ctrl+c</code></td>
|
||||||
|
<td>Copy selected objects</td>
|
||||||
|
</tr>
|
||||||
|
<tr>
|
||||||
|
<td><code>Ctrl+v</code></td>
|
||||||
|
<td>Paste selected objects</td>
|
||||||
|
</tr>
|
||||||
|
<tr>
|
||||||
|
<td><code>+</code></td>
|
||||||
|
<td>Zoom In</td>
|
||||||
|
</tr>
|
||||||
|
<tr>
|
||||||
|
<td><code>-</code></td>
|
||||||
|
<td>Zoom Out</td>
|
||||||
|
</tr>
|
||||||
|
<tr>
|
||||||
|
<td><code>Ctrl+l</code></td>
|
||||||
|
<td>Layout</td>
|
||||||
|
</tr>
|
||||||
|
<tr>
|
||||||
|
<td><code>Ctrl+Shift+l</code></td>
|
||||||
|
<td>Clean Up</td>
|
||||||
|
</tr>
|
||||||
|
<tr>
|
||||||
|
<td><code>Ctrl+p</code></td>
|
||||||
|
<td>Calculate CIP</td>
|
||||||
|
</tr>
|
||||||
|
<tr>
|
||||||
|
<td><code>?</code></td>
|
||||||
|
<td>Help</td>
|
||||||
|
</tr>
|
||||||
|
</tbody>
|
||||||
|
</table>
|
||||||
|
<p><strong>Note</strong> : Please, use <code>Ctrl+V</code> to paste the selected object in
|
||||||
|
Google Chrome and Mozilla Firefox browsers.</p>
|
||||||
|
<p><strong>Note 2</strong> : Probably, you have forbidden access to the local storage.
|
||||||
|
If you are using IE10 or IE11 and didn’t forbid access to local storage
|
||||||
|
intentionally, you can pay attention here: <a href="https://stackoverflow.com/a/20848924">https://stackoverflow.com/a/20848924</a></p>
|
||||||
|
After Width: | Height: | Size: 12 KiB |
|
After Width: | Height: | Size: 39 KiB |
|
After Width: | Height: | Size: 24 KiB |
|
After Width: | Height: | Size: 16 KiB |
|
After Width: | Height: | Size: 18 KiB |
|
After Width: | Height: | Size: 65 KiB |
|
After Width: | Height: | Size: 49 KiB |
|
After Width: | Height: | Size: 903 B |
|
After Width: | Height: | Size: 5.6 KiB |
|
After Width: | Height: | Size: 887 B |
|
After Width: | Height: | Size: 23 KiB |
|
After Width: | Height: | Size: 4.8 KiB |
|
After Width: | Height: | Size: 2.8 KiB |
|
After Width: | Height: | Size: 10 KiB |
|
After Width: | Height: | Size: 7.4 KiB |
|
After Width: | Height: | Size: 4.6 KiB |
|
After Width: | Height: | Size: 757 B |
|
After Width: | Height: | Size: 19 KiB |
|
After Width: | Height: | Size: 1.0 KiB |
|
After Width: | Height: | Size: 22 KiB |
|
After Width: | Height: | Size: 37 KiB |
|
After Width: | Height: | Size: 995 B |
|
After Width: | Height: | Size: 17 KiB |
|
After Width: | Height: | Size: 25 KiB |
|
After Width: | Height: | Size: 29 KiB |
|
After Width: | Height: | Size: 460 B |
|
After Width: | Height: | Size: 45 KiB |
|
After Width: | Height: | Size: 5.1 KiB |
|
After Width: | Height: | Size: 4.5 KiB |
|
After Width: | Height: | Size: 4.1 KiB |
|
After Width: | Height: | Size: 817 B |
|
After Width: | Height: | Size: 2.6 KiB |
|
After Width: | Height: | Size: 18 KiB |
|
After Width: | Height: | Size: 4.5 KiB |
|
After Width: | Height: | Size: 604 B |
|
After Width: | Height: | Size: 60 KiB |
|
After Width: | Height: | Size: 2.4 MiB |
|
After Width: | Height: | Size: 12 KiB |
|
After Width: | Height: | Size: 600 B |
|
After Width: | Height: | Size: 1.2 KiB |
|
After Width: | Height: | Size: 15 KiB |
|
After Width: | Height: | Size: 5.1 KiB |
|
|
@ -6,6 +6,10 @@
|
||||||
|
|
||||||
<p>Powered by <a href="https://github.com/partridgejiang/Kekule.js">Kekule.js</a>
|
<p>Powered by <a href="https://github.com/partridgejiang/Kekule.js">Kekule.js</a>
|
||||||
|
|
||||||
|
|
||||||
|
<h4>Prefer Ketcher instead?</h4>
|
||||||
|
<p>Click <a href="{{ url_for('static', filename='ketcher/ketcher.html') }}">here.</a></p>
|
||||||
|
|
||||||
<br>
|
<br>
|
||||||
|
|
||||||
|
|
||||||
|
|
@ -48,4 +52,6 @@
|
||||||
|
|
||||||
<br>
|
<br>
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
{% endblock %}
|
{% endblock %}
|
||||||