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| author | gebele <gebele@in-silico.ch> | 2013-03-04 10:28:02 +0100 |
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| committer | gebele <gebele@in-silico.ch> | 2013-03-04 10:28:02 +0100 |
| commit | 0c2554a5a2c3aebf3e99d70fee2075a9b99f9abe (patch) | |
| tree | 5b4085247b2a9edebdb027a75f85c4ae584f3017 /views/jme_help.html | |
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diff --git a/views/jme_help.html b/views/jme_help.html new file mode 100644 index 0000000..adf3e1f --- /dev/null +++ b/views/jme_help.html @@ -0,0 +1,197 @@ +<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"> + +<html> +<head> + <meta name="generator" content= + "HTML Tidy for Linux/x86 (vers 12 April 2005), see www.w3.org"> + <meta http-equiv="content-type" content= + "text/html; charset=us-ascii"> + + <title>JME Help</title> + <meta name="author" content="Peter Ertl, Novartis Pharma AG"> + <link rel="stylesheet" href="../style.css" type="text/css"> +<style type="text/css"> + body { + background-color: white; + } + h2.c3 {text-align: center} + p.c2 {font-style: italic; text-align: right} + p.c1 {text-align: center} +</style> +</head> + +<body> +<h1>JME Molecular Editor</h1> + + <p class="c2">Written by Peter Ertl, Novartis Pharma + AG</p> + + <h2 class="c3">Basic Instructions</h2> + + <p>This editor is intended to be used without any special + documentation or training, but there are some tricks which + can help you to work with it more efficiently.</p> + + <h3>Menu Buttons</h3> + + <ul> + <li><b>D-R</b> deletes functional groups - choose this + option and then click on the bond connecting the group + with the main skeleton</li> + + <li><b>UDO</b> undo last editing step</li> + + <li><b>QRY</b> (if enabled in the param tag) allows easy + specification of atomic queries for substructure + searches</li> + + <li><b>Stereo bonds</b> - the type of stereo bond (up, + down) may be changed by clicking on the already created + stereo bond; this cycles through two / four possible + stereo bond types</li> + + <li><b>Atomic charges</b> may be changed by the + <b>+/-</b> button. Editor enables modification of charges + only in "reasonable" cases. If you are not satisfied with + the editor's inteligence (concerning charges and the + explicit number of hydrogens) you can force your will by + using the <b>X</b> button</li> + + <li><b>"Non-organic" atoms</b> or atoms with nonstandard + valence may be entered with help of <b>X</b> button by + specifying atomic SMILES (without [ ] brackets, i.e. Si, + Fe++, NH3+).</li> + </ul> + + <h3>Keyboard Shortcuts</h3> + + <p>Most of the commands may be accessed also by keyboard + shortcuts. It is possible to:</p> + + <ul> + <li>change <b>atom type</b> by pressing <b>C</b>, + <b>N</b>, <b>O</b>, <b>S</b>, <b>F</b>, <b>L</b> (for Cl) + <b>B</b> (for Br) <b>I</b>, <b>P</b>, <b>H</b>, <b>X</b>, + <b>R</b> and clicking the respective atom</li> + + <li>choose <b>bond order</b>: <b>-</b> for single bond, + <b>=</b> for double bond, <b>#</b> for triple bond</li> + + <li>choose <b>ring type</b> by pressing <b>3</b>, + <b>4</b>, <b>5</b>, <b>6</b>, <b>7</b>, <b>8</b>, + <b>9</b> or <b>1</b> for phenyl, <b>0</b> for furyl</li> + + <li>start <b>delete mode</b> by pressing <b>D</b> or + <b>Del</b> and</li> + + <li>return to the <b>standard state</b> (carbon, single + bond) with <b>Esc</b></li> + </ul> + + <p><b>common functional groups</b> may also be added by + keyboard shortcuts. Use <b>t</b> for t-butyl, <b>ft</b> for + trifluoromethyl, <b>lt</b> for trichloromethyl, <b>a</b> + for COOH, <b>z</b> for SO2Me and <b>y</b> for nitro, and + then click the atom where the group should be + connected.</p> + + <h3>Moving and Rotation</h3> + + <p>You can move molecule by "dragging free space" with the + left mouse button and rotate it by using the left mouse + button and <b>Shift</b> key (or left and right mouse + buttons together).</p> + + <h3>Adding rings</h3> + + <p>When a ring template is selected and multivalent atom is + clicked, a new ring will be created connected by single + bond to this atom. When spiro ring is required, the + <b>Shift</b> key must be pressed when clicking on the atom. + Spiro ring may be added only to atom with 2 single + bonds.</p> + + <h3>Multivalent nitrogen groups</h3> + + <p>Multivalent nitrogen groups, such as nitro, azide, + N-oxide, nitrile etc, should be drawn with a pentavalent + nitrogen as shown below.</p> + + <p class="c1"><img src="images/nitro.gif" alt= + "nitro stuff"></p> + + <p>The program automatically converts polar form of these + groups into non-polar one with pentavalent nitrogen. If you + prefer polar nitro (and similar) groups, use keyword + "polarnitro" in the applet param tag.</p> + + <h3>Stereochemistry</h3> + + <p>Stereochemistry at C4 centers, double bonds and allenes + is supported. Use the up/down wedge bonds to indicate + stereochemistry at the C4 centers. Remember, that only + bonds with a "sharp point" towards the atom are considered. + When creating SMILES the editor tries to guess missing + stereo features, in unresolvable cases an error message is + issued and the SMILES without stereo information is + created.</p> + + <p>When the autoez keyword is set, SMILES with E,Z + stereochemistry on all non-ring double bonds is generated + automatically. Without this keyword (or for ring double + bonds) you have to mark a double bond as stereo by clicking + on it with the stereo bond button selected. The bond color + will change to violet.</p> + + <p>Stereochemistry may be completely disabled by the + "nostereo" option in the param tag.</p> + + <h3>Input of Multipart Structures</h3> + + <p>By default only non-disconnected structures are allowed. + This may be changed by a "multipart" option in the applet + param tag. A button <b>NEW</b> appears in the JME menu. + Creation of a new molecule may be started only after + clicking the <b>NEW</b> button, selecting a proper template + (atom, ring, bond) and clicking free space in the drawing + area. Without <b>NEW</b> button the click on the free space + has the same effect as in the standard mode (i.e moving or + rotation of the last touched molecule). In the multipart + mode <b>CLR</b> button deletes the last touched + molecule.</p> + + <h3>Atom Numbering</h3> + + <p>Atom numbering (marking) is enabled with the option + "number" in the applet param tag (for reaction input this + is default). Button <b>123</b> appears in the JME menu. To + mark an atom press the <b>123</b> button and then the atom. + You can mark more atoms with the same number when pressing + <b>Shift</b> while clicking the 2nd and further atoms. + Second click on the marked atom deletes the number.</p> + + <h3>Reaction Input</h3> + + <p>Reaction input is enabled with the option "reaction" in + the applet param tag. Button with an arrow, <b>NEW</b> + button and <b>123</b> button appear in the JME menu and + arrow appears also in the drawing area. Now simply draw + reactant(s), product(s) and modulator(s) (modulators have + to be above the arrow) as explained in the description of + input of multipart structures. The arrow button enables + simplified input of reactions. After clicking it, the + reactant will be copied to the product (including atom + numbering, if any). When the <b>Shift</b> is pressed during + this action all atoms will be automatically numbered.</p> + + <h3>Query Features</h3> + + <p>Query button (when enabled in the option tag) launches a + query window which allows creation of SMARTS atom queries + by combining various atom attributes. Create a SMARTS query + and then click the respective atom in the + molecule.</p> +</body> +</html> + + |