© Modgraph Consultants 2006 The information contained herein is the property of Modgraph Consultants Limited and may not be copied, used or disclosed in whole or in part except with the prior written permission of Modgraph Consultants Limited.

MODGRAPH Consultants Ltd Cedar House, 1 Oakland View, Oaklands, Welwyn, Herts, AL6 ORJ. Tel: 01438 717 217

MODGRAPH CONSULTANTS LIMITED

DOCSCAN USER GUIDE

Version 0.3

© Modgraph Consultants 2006 The information contained herein is the property of Modgraph Consultants Limited and may not be copied, used or disclosed in whole or in part except with the prior written permission of Modgraph Consultants Limited.

Contents Contents .........................................................................................................................2 1. Introduction........................................................................................................3 2. Getting started....................................................................................................3 3. Creating a search query......................................................................................4 4. Selecting which folders will be searched...........................................................6 5. Initiating the search............................................................................................7 6. Whilst the search is taking place........................................................................8 7. Examining the results.......................................................................................11 8. Saving / retrieving search queries and starting new searches ..........................13

© Modgraph Consultants 2006 The information contained herein is the property of Modgraph Consultants Limited and may not be copied, used or disclosed in whole or in part except with the prior written permission of Modgraph Consultants Limited.

1. Introduction DocScan is an application from Modgraph Consultants that allows you to search for chemical structures that are stored as MOL files, RXN files, SDF files or are embedded as MOL files within Word documents, Excel spreadsheets or Powerpoint presentations. It allows sub-structure and exact match searching as well as the selection of exactly which folders and sub-folders are to be searched. It will not find chemical structures that are stored as images (e.g. BMP files) or those in ISIS-BASE databases. N.B. To access the internet based help system, click on the “Help” button on the top menu-bar:

2. Getting started Double clicking the DocScan icon will open the application to give:

© Modgraph Consultants 2006 The information contained herein is the property of Modgraph Consultants Limited and may not be copied, used or disclosed in whole or in part except with the prior written permission of Modgraph Consultants Limited.

Creating a search query Double clicking in the top-left window will either open ISIS Draw or Chem Draw, depending on which of the editors you have selected from the “Options” menu button.

E.G. If the “Edit with ISIS” option was checked, you will get the following:

Here you have all the standard functionality to draw your search query. Once drawn, click on the top-left button:

and this will return your search query to the DocScan application:

© Modgraph Consultants 2006 The information contained herein is the property of Modgraph Consultants Limited and may not be copied, used or disclosed in whole or in part except with the prior written permission of Modgraph Consultants Limited.

The “Search Type” radio-buttons allow you to specify just how your chemical structure search will function:

N.B. Both “Sub-Structure” and “Exact” searches ignore hash and wedge bonds drawn either in the search query or the structures that are being searched.

© Modgraph Consultants 2006 The information contained herein is the property of Modgraph Consultants Limited and may not be copied, used or disclosed in whole or in part except with the prior written permission of Modgraph Consultants Limited.

3. Selecting which folders will be searched When using DocScan, you can search all the files on a particular drive or restrict the search to just certain folders. The more files you search, the longer it will take but the search will be more exhaustive – the choice is yours. The name of the top-most drive / folder to be searched is displayed in the “Address” window (and is highlighted in blue):

To change this you can either click in the “Address” window and edit it directly or click on the button to the right of that line [ ] to give the “Select Folder” window:

Where you can double-click on the folder names and then on the “OK” button to select the appropriate folder to be searched. Another way to move back up a folder hierarchy is to click on the “UP” button on the top menu-bar:

© Modgraph Consultants 2006 The information contained herein is the property of Modgraph Consultants Limited and may not be copied, used or disclosed in whole or in part except with the prior written permission of Modgraph Consultants Limited.

Once a search has been performed, you can go back and forth between the last two selected directories by clicking on the “Back” and “Forward” buttons on the top menu-bar:

The “Search Depth” radio-buttons allow you to specify if you only want to search the selected folder or to also search all its sub-folders as well:

If you wish to only search through certain file formats, check those file types in the bottom left-hand side of the DocScan window:

4. Initiating the search Click on the “Search” button that is found either on the top menu-bar or at the bottom of the DocScan window:

© Modgraph Consultants 2006 The information contained herein is the property of Modgraph Consultants Limited and may not be copied, used or disclosed in whole or in part except with the prior written permission of Modgraph Consultants Limited.

5. Whilst the search is taking place DocScan will dynamically show the progress of the search including:

• The structures that are currently being searched • Their filenames • The number of structures that have been searched • The number of hits that have been found • The number of files that have not been searched for some reason

(“skipped”) Also, the “Search” button that is normally found at the bottom of the DocScan window is replaced by the “Stop” button which can be used to halt a search:

The following are some “snapshots” of a search in progress:

© Modgraph Consultants 2006 The information contained herein is the property of Modgraph Consultants Limited and may not be copied, used or disclosed in whole or in part except with the prior written permission of Modgraph Consultants Limited.

© Modgraph Consultants 2006 The information contained herein is the property of Modgraph Consultants Limited and may not be copied, used or disclosed in whole or in part except with the prior written permission of Modgraph Consultants Limited.

© Modgraph Consultants 2006 The information contained herein is the property of Modgraph Consultants Limited and may not be copied, used or disclosed in whole or in part except with the prior written permission of Modgraph Consultants Limited.

6. Examining the results When the search is over, the name of all the files containing the required structure and their pathnames are given in the right-hand of the DocScan window.

To open files (so you can view the data) double-click on the filename.

© Modgraph Consultants 2006 The information contained herein is the property of Modgraph Consultants Limited and may not be copied, used or disclosed in whole or in part except with the prior written permission of Modgraph Consultants Limited.

In the above case, the Word document (Test_11.doc) was opened to give:

And the molfile (test6.mol) was opened to give:

© Modgraph Consultants 2006 The information contained herein is the property of Modgraph Consultants Limited and may not be copied, used or disclosed in whole or in part except with the prior written permission of Modgraph Consultants Limited.

7. Saving / retrieving search queries and starting new searches

To save the search query structure that is currently in your DocScan window, click on the “Save” button on the top menu-bar:

to give the “Save Structure” dialog box:

From where, you can navigate to the required folder and save your query structure as required. N.B. You can currently only save search query structures as MOL files.

© Modgraph Consultants 2006 The information contained herein is the property of Modgraph Consultants Limited and may not be copied, used or disclosed in whole or in part except with the prior written permission of Modgraph Consultants Limited.

To retrieve a structure for use as a search query, click on the “Load” button on the top menu-bar:

To give the “Open Structure file” dialog box:

From where you can navigate to the required file and then click on “Open” to bring that structure back to the DocScan window. N.B. You can currently only retrieve query structures that have been saved as MOL and SDF files. To prepare for a brand new search, click on the “New” button on the top menu-bar:

And this will clear out your existing search query structure as well as all previously found hits.