From 0c2554a5a2c3aebf3e99d70fee2075a9b99f9abe Mon Sep 17 00:00:00 2001 From: gebele Date: Mon, 4 Mar 2013 10:28:02 +0100 Subject: first commit --- views/jme_help.html | 197 ++++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 197 insertions(+) create mode 100644 views/jme_help.html (limited to 'views/jme_help.html') 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 @@ + + + + + + + + JME Help + + + + + + +

JME Molecular Editor

+ +

Written by Peter Ertl, Novartis Pharma + AG

+ +

Basic Instructions

+ +

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.

+ +

Menu Buttons

+ + + +

Keyboard Shortcuts

+ +

Most of the commands may be accessed also by keyboard + shortcuts. It is possible to:

+ + + +

common functional groups may also be added by + keyboard shortcuts. Use t for t-butyl, ft for + trifluoromethyl, lt for trichloromethyl, a + for COOH, z for SO2Me and y for nitro, and + then click the atom where the group should be + connected.

+ +

Moving and Rotation

+ +

You can move molecule by "dragging free space" with the + left mouse button and rotate it by using the left mouse + button and Shift key (or left and right mouse + buttons together).

+ +

Adding rings

+ +

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 + Shift key must be pressed when clicking on the atom. + Spiro ring may be added only to atom with 2 single + bonds.

+ +

Multivalent nitrogen groups

+ +

Multivalent nitrogen groups, such as nitro, azide, + N-oxide, nitrile etc, should be drawn with a pentavalent + nitrogen as shown below.

+ +

+

+ +

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.

+ +

Stereochemistry

+ +

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.

+ +

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.

+ +

Stereochemistry may be completely disabled by the + "nostereo" option in the param tag.

+ +

Input of Multipart Structures

+ +

By default only non-disconnected structures are allowed. + This may be changed by a "multipart" option in the applet + param tag. A button NEW appears in the JME menu. + Creation of a new molecule may be started only after + clicking the NEW button, selecting a proper template + (atom, ring, bond) and clicking free space in the drawing + area. Without NEW 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 CLR button deletes the last touched + molecule.

+ +

Atom Numbering

+ +

Atom numbering (marking) is enabled with the option + "number" in the applet param tag (for reaction input this + is default). Button 123 appears in the JME menu. To + mark an atom press the 123 button and then the atom. + You can mark more atoms with the same number when pressing + Shift while clicking the 2nd and further atoms. + Second click on the marked atom deletes the number.

+ +

Reaction Input

+ +

Reaction input is enabled with the option "reaction" in + the applet param tag. Button with an arrow, NEW + button and 123 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 Shift is pressed during + this action all atoms will be automatically numbered.

+ +

Query Features

+ +

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.

+ + + + -- cgit v1.2.3