From e64830992db27939840bc68364de3f47441c154f Mon Sep 17 00:00:00 2001 From: Navan Chauhan Date: Sun, 30 Aug 2020 12:50:38 +0530 Subject: added ketcher option --- app/static/ketcher/doc/help.html | 686 +++++++++++++++++++++++++++++++++++++++ 1 file changed, 686 insertions(+) create mode 100644 app/static/ketcher/doc/help.html (limited to 'app/static/ketcher/doc/help.html') diff --git a/app/static/ketcher/doc/help.html b/app/static/ketcher/doc/help.html new file mode 100644 index 0000000..9f800fa --- /dev/null +++ b/app/static/ketcher/doc/help.html @@ -0,0 +1,686 @@ +

Ketcher is a tool to draw molecular structures and chemical +reactions.

+

Ketcher Overview

+

Ketcher is a tool to draw molecular structures and chemical +reactions. Ketcher operates in two modes, the Server mode with most +functions available and the client mode with limited functions +available.

+

Ketcher consists of the following elements:

+

+

Note : Depending on the screen size, some tools on the Tool +palette can be displayed in expanded or collapsed forms.

+

Using the Tool palette, you can

+ +

To select one atom or bond, click Lasso or Rectangle Selection tool, +and then click the atom or bond.

+

To select the entire structure:

+ +

To select multiple atoms, bonds, structures, or other objects, do one +of the following:

+ +

Note : Ctrl+Shift-click with the Lasso or Rectangle Selection tool +selects several structures.

+

You can use the buttons of the Main toolbar:

+

+ +

Note : Layout, Clean Up, Aromatize / Dearomatize, +Calculate CIP, Check Structure, Calculated Values, +Recognize Molecule and 3D View buttons are active only in the +Server mode.

+

3D Viewer

+

The structure appears in a modal window after clicking on the 3D +Viewer button:

+

+

You can perform the following actions:

+ +

Ketcher Settings allow to change the appearance of the structure and background coloring.

+

“Lines” drawing method, “Bright” atom name coloring +method and “Light” background coloring are default.

+

Drawing Atoms

+

To draw/edit atoms you can:

+ +

Drawing Bonds

+

To draw/edit bonds you can:

+ +

Drawing R-Groups

+

Use the R-Group toolbox to draw R-groups in Markush +structures:

+

+

Selecting the R-Group Label 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:

+

+

Selecting the R-Group label and clicking OK converts the structure +into a Markush structure with the selected R-Group label:

+

+

Note : You can choose several R-Group labels simultaneously:

+

+

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.

+

To create a set of R-Group members:

+
    +
  1. +

    Draw a structure to become an R-Group member.

    +
    2. +
  2. +

    Select the structure using the R-Group Fragment Tool to invoke +the R-Group dialog; in this dialog select the label of the +R-Group to assign the fragment to.

    +
    3. +
  3. +

    Click on OK to convert the structure into an R-Group member.

    +
    4. +
+

An R-Group attachment point is the atom in an R-Group member fragment +that attaches the fragment to the initial Markush structure.

+

Selecting the Attachment Point Tool 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:

+

+

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 OK in the above dialog creates the +attachment point.

+

Schematically, the entire process of the R-Group member creation can +be presented as:

+

+

+

R-Group Logic

+

Ketcher enables one to add logic when using R-Groups. To access +the R-Group logic:

+
    +
  1. +

    Create an R-Group member fragment as described above.

    +
    2. +
  2. +

    Move the cursor over the entire fragment for the green frame to +appear, then click inside the fragment. The following dialog +appears:

    +

    +
    3. +
  3. +

    Specify Occurrence to define how many of an R-Group +occurs. If an R-Group atom appears several times in the initial +structure, you will specify Occurrence">n", n +being the number of occurrences; if it appears once, you see +"R1 > 0".

    +
    4. +
  4. +

    Specify H at unoccupied R-Group sites ( RestH ): check or +clear the checkbox.

    +
    5. +
  5. +

    Specify the logical Condition. Use the R-Group condition If +R(i) Then to specify whether the presence of an R-Group is +dependent on the presence of another R-Group.

    +
    6. +
+

Marking S-Groups

+

To mark S-Groups, use the S-Group tool and the +following dialog that appears after selecting a fragment with this +tool:

+

+

Available S-Group types:

+

Generic

+

Generic is a pair of brackets without any labels.

+

Multiple group

+

A Multiple group indicates a number of replications of a fragment or a part of a +structure in contracted form.

+

SRU Polymer

+

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.

+

Superatom

+

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.

+

Data S-Groups

+

The Data S-Groups Tool is a separate tool for +comfortable use with the accustomed set of descriptors (like Attached +Data in Marvin Editor).

+

You can attach data to an atom, a fragment, a single bond, or a +group. The defined set of Names and Values is introduced for each +type of selected elements:

+

+ +

Changing Structure Display

+

Use the Flip/Rotate tool to change the structure +display:

+

+

For the full screen format, the Flip/Rotate tool is split into +separate buttons:

+

+

Rotate Tool

+

This tool allows rotating objects.

+ +

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.

+

Flip Tool

+

This tool flips the objects horizontally or vertically.

+ +

Drawing Reactions

+

To draw/edit reactions you can

+ +

Note : Reaction Auto-Mapping Tool is available only in the Server +mode.

+

Templates toolbar

+

You can add templates (rings or other predefined structures) to the +structure using the Templates toolbar together with the Custom +Templates button located at the bottom:

+

+

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.

+

Rules of using templates:

+ +

Note : The added template will be fused by the default attachment +atom or bond preset in the program.

+

Note : User is able to define the attachment atom and bond by clicking +the Edit button for template structure.

+

The Custom Templates button invokes the scrolling +list of templates available in the program; both built-in and created +by user:

+

+

To create a user template:

+ +

Working with Files

+

Ketcher supports the following molecular formats that can be entered +either manually or from files:

+ +

You can use the Open… and Save As… buttons of the Main +toolbar to import a molecule from a molecular file or save it to a +supported molecular file format. The Open Structure 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:

+

+

The Save Structure dialog enables one to save the molecular file:

+

+

Note : In the standalone version only mol/rxn are supported for +Open and mol/rxn/SMILES for Save.

+

Hotkeys

+

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.

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KeyAction
EscSwitching between the Lasso/Rectangle/Fragment Selection tools
DelDelete the selected objects
0Draw Any bond.
1Single / Single Up / Single Down / Single Up/Down bond. Consecutive pressing switches between these types.
2Double / Double Cis/Trans bond
3Draw a triple bond.
4Draw an aromatic bond.
5Charge Plus/Charge Minus
ADraw any atom
HDraw a hydrogen
CDraw a carbon
NDraw a nitrogen
ODraw an oxygen
SDraw a sulfur
FDraw a fluorine
PDraw a phosphorus
IDraw an iodine
TBasic templates. Consecutive pressing switches between different templates
Shift+tOpen template library
Alt+rRotate tool
Alt+vFlip vertically
Alt+hFlip horizontally
Ctrl+gS-Group tool / Data S-Group tool
Ctrl+dAlign and select all S-Group data
Ctrl+rSwitching between the R-Group Label Tool/R-Group Fragment Tool/Attachment Point Tool
Ctrl+Shift+rR-Group Fragment Tool
Ctrl+DelClear canvas
Ctrl+oOpen
Ctrl+sSave As
Ctrl+zUndo
Ctrl+Shift+zRedo
Ctrl+xCut selected objects
Ctrl+cCopy selected objects
Ctrl+vPaste selected objects
+Zoom In
-Zoom Out
Ctrl+lLayout
Ctrl+Shift+lClean Up
Ctrl+pCalculate CIP
?Help
+

Note : Please, use Ctrl+V to paste the selected object in +Google Chrome and Mozilla Firefox browsers.

+

Note 2 : 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: https://stackoverflow.com/a/20848924

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