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Ketcher operates in two modes, the Server mode with most +functions available and the client mode with limited functions +available.</p> +<p><strong>Ketcher</strong> consists of the following elements:</p> +<p><img src="main.png" alt="" title="Main window"></p> +<p><strong>Note</strong> : Depending on the screen size, some tools on the <em>Tool +palette</em> can be displayed in expanded or collapsed forms.</p> +<p>Using the <em>Tool palette</em>, you can</p> +<ul> +<li> +<p>draw and edit a molecule or reaction by clicking on and dragging +atoms, bonds, and other elements provided with the buttons on the +<em>Atoms</em> toolbar and <em>Tool palette</em>;</p> +</li> +<li> +<p>delete any element of the drawing (atom or bond) by clicking on it +with the Erase tool;</p> +</li> +<li> +<p>delete the entire molecule or its fragment by a lasso, +rectangular, or fragment selection with the Erase tool;</p> +</li> +<li> +<p>draw special structures (see the following sections);</p> +</li> +<li> +<p>select the entire molecule or its fragment in one of the following +ways (click on the button to see the list of available options):</p> +<ul> +<li> +<p>in the expanded form</p> +<p><img src="expanded.png" alt="" title="Expanded tool"></p> +</li> +<li> +<p>in the collapsed form</p> +<p><img src="collapsed.png" alt="" title="Collapsed tool"></p> +</li> +</ul> +</li> +</ul> +<p>To select one atom or bond, click Lasso or Rectangle Selection tool, +and then click the atom or bond.</p> +<p>To select the entire structure:</p> +<ul> +<li> +<p>Select the Fragment Selection tool and then click the object.</p> +</li> +<li> +<p>Select the Lasso or Rectangle Selection tool, and then drag the +mouse to select the object.</p> +</li> +<li> +<p><code>Ctrl-click</code> with the Lasso or Rectangle Selection tool.</p> +</li> +</ul> +<p>To select multiple atoms, bonds, structures, or other objects, do one +of the following:</p> +<ul> +<li> +<p><code>Shift-click</code> with the Lasso or Rectangle Selection tool selects +some (connected or not) atoms/bonds.</p> +</li> +<li> +<p>With the Lasso or Rectangle Selection tool click and drag the +mouse around the atoms, bonds, or structures that you want to +select.</p> +</li> +</ul> +<p><strong>Note</strong> : <code>Ctrl+Shift-click</code> with the Lasso or Rectangle Selection tool +selects several structures.</p> +<p>You can use the buttons of the <em>Main</em> toolbar:</p> +<p><img src="toolbar.png" alt="" title="Tolbar"></p> +<ul> +<li> +<p><strong>Clear Canvas</strong> (1) button to start drawing a new molecule; this +command clears the drawing area;</p> +</li> +<li> +<p><strong>Open…</strong> (2) and <strong>Save As…</strong> (3) buttons to import a molecule +from a molecular file or save it to a supported molecular file +format;</p> +</li> +<li> +<p><strong>Undo</strong> / <strong>Redo</strong> (4), <strong>Cut</strong> (5), <strong>Copy</strong> (6), <strong>Paste</strong> (7), +<strong>Zoom In</strong> / <strong>Out</strong> (8), and <strong>Scaling</strong> (9) buttons to perform +the corresponding actions;</p> +</li> +<li> +<p><strong>Layout</strong> button (10) to change the position of the structure to +work with it with the most convenience;</p> +</li> +<li> +<p><strong>Clean Up</strong> button (11) to improve the appearance of the +structure by assigning them uniform bond lengths and angles.</p> +</li> +<li> +<p><strong>Aromatize</strong> / <strong>Dearomatize</strong> buttons (12) to mark aromatic +structures (to convert a structure to the Aromatic or Kekule +presentation);</p> +</li> +<li> +<p><strong>Calculate CIP</strong> button (13) to determine R/S and E/Z +configurations;</p> +</li> +<li> +<p><strong>Check Structure</strong> button (14) to check the following properties +of the structure:</p> +<p><img src="check.png" alt="" title="Structure Ckeck"></p> +</li> +<li> +<p><strong>Calculated Values</strong> button (15) to display some properties of +the structure:</p> +<p><img src="analyse.png" alt="" title="Calculated Values"></p> +</li> +<li> +<p><strong>Recognize Molecule</strong> button (16) to recognize a structure in the +image file and load it to the canvas;</p> +</li> +<li> +<p><strong>3D Viewer</strong> button (17) to open the structure in the +three-dimensional Viewer;</p> +</li> +<li> +<p><strong>Settings</strong> button (18) to make some settings for molecular +files:</p> +<p><img src="settings.png" alt="" title="Settings"></p> +</li> +<li> +<p><strong>Help</strong> button (19) to view Help;</p> +</li> +<li> +<p><strong>About</strong> button (20) to display version and copyright information +of the program.</p> +</li> +</ul> +<p><strong>Note</strong> : <strong>Layout,</strong> <strong>Clean Up,</strong> <strong>Aromatize</strong> / <strong>Dearomatize,</strong> +<strong>Calculate CIP,</strong> <strong>Check Structure,</strong> <strong>Calculated Values,</strong> +<strong>Recognize Molecule</strong> and <strong>3D View</strong> buttons are active only in the +Server mode.</p> +<h1>3D Viewer</h1> +<p>The structure appears in a modal window after clicking on the <strong>3D +Viewer</strong> button:</p> +<p><img src="miew.png" alt="" title="3D Viewer"></p> +<p>You can perform the following actions:</p> +<ul> +<li> +<p>Rotate the structure holding the left mouse button;</p> +</li> +<li> +<p>Zoom In/Out the structure;</p> +</li> +</ul> +<p>Ketcher Settings allow to change the appearance of the structure and background coloring.</p> +<p>“Lines” drawing method, “Bright” atom name coloring +method and “Light” background coloring are default.</p> +<h1>Drawing Atoms</h1> +<p>To draw/edit atoms you can:</p> +<ul> +<li> +<p>select an atom in the Atoms toolbar and click inside the drawing +area;</p> +</li> +<li> +<p>if the desired atom is absent in the toolbar, click on +the <img src="periodic-table.png" alt=""> button to invoke the Periodic Table and +click on the desired atom (available options: <em>Single</em> – selection +of a single atom, <em>List</em> – choose an atom from the list of selected +options (To allow one atom from a list of atoms of your choice at +that position), <em>Not List</em> - exclude any atom on your list at that +position).</p> +<p><img src="periodic-dialog.png" alt="" title="Periodic Table"></p> +</li> +<li> +<p>add an atom to the existing molecule by selecting an atom in the +<em>Atoms</em> toolbar, clicking on an atom in the molecule, and dragging +the cursor; the atom will be added with a single bond; vacant +valences will be filled with the corresponding number of hydrogen +atoms;</p> +</li> +<li> +<p>change an atom by selecting an atom in the <em>Atoms</em> toolbar and +clicking on the atom to be changed; in the case a wrong valence thus +appears the atom will be underlined in red;</p> +</li> +<li> +<p>change an atom by clicking on an existing atom with the +<em>Selection</em> tool and waiting for a couple of seconds for the text +box to appear; type another atom symbol in the text box:</p> +<p><img src="inline-edit.png" alt="" title="Change Atom"></p> +</li> +<li> +<p>change the charge of an atom by selecting the Charge Plus or +Charge Minus tool and clicking consecutively on an atom to +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 +invoke the Atom Properties dialog (the dialog also provides atom +query features):</p> +<p><img src="atom-dialog.png" alt="" title="Atom Properties"></p> +</li> +<li> +<p>click on the Periodic Table button, open the Extended table and +select a corresponding Generic group or Special Node:</p> +<p><img src="periodic-dialog-ext.png" alt="" title="Generic Groups"></p> +</li> +</ul> +<h1>Drawing Bonds</h1> +<p>To draw/edit bonds you can:</p> +<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> +<p>For the full screen format, the Bond tool from the Tools palette +splits into three: _Single Bond,_<em>Single Up Bond,</em> and <em>Any +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 +drawing area; a bond of the selected type will be drawn;</p> +</li> +<li> +<p>click on an atom in the molecule; a bond of the selected type will +be added to the atom at the angle of 120 degrees;</p> +</li> +<li> +<p>add a bond to the existing molecule by clicking on an atom in the +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 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