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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
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<title>JME Help</title>
<meta name="author" content="Peter Ertl, Novartis Pharma AG">
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<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>
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