DCGI Manual

This document is copyrighted © 1994-2011 by Daylight Chemical Information Systems, Inc. Daylight explicitly grants permission to reproduce this document under the condition that it is reproduced in its entirety, including this notice. All other rights are reserved.

Table of Contents

3.1 Depict
3.2 CLOGP
3.3 CMR
3.4 MedChem
3.5 WDI
3.6 ACD
3.7 Savant

4.1 Hyperthor
4.2 Wizard

5.1 smi2gif
5.2 depict, revisited
5.3 clogp, revisited

1. Introduction

2. Common features

The DCGI philosophy is to provide tools with interfaces which are as simple as possible. Given general familiarity with a web browser, a DCGI user should be able to click-and-play immediately without the need for special training. The DCGI system is a set of special-purpose programs which are designed to be run on an intranet. To this end, DCGI configuration is done centrally by an administrator, which frees the user from having to know things such as the names of current servers, databases and datatypes. Whenever possible, DCGI program interfaces are oriented to a "What do you want to know? Here it is." design, e.g., WDI. A small of general purpose DCGI programs are also provided for use by more advanced users (currently just two: Hyperthor and Wizard).

DCGI pages contain a standard header which identifies the program and provides links to instructions (Help), frequently asked questions (FAQ), database documentation (as appropriate) and other relevant HTML pages.

The DCGI programs all use a common mechanism for structure editing. If configured (see section 7), structure entry form elements will have one or two associated buttons. By selecting these buttons one can edit a structure using a preconfigured graphical editor. The structure can then be submitted back to the form element.

3. Special-purpose DCGI programs

3.1 Depict

3.2 CLOGP

3.3 CMR

3.4 MedChem

3.5 WDI (World Drug Index)

3.6 ACD (Available Chemicals Directory)

3.7 Savant

4 General-purpose DCGI programs

4.1 Hyperthor

4.2 Wizard

5. DCGI tools

5.1 smi2gif, smi2gif-bop, smi2gif-small

Function:	convert a SMILES to a structural diagram in GIF format
URL:	/daycgi/smi2gif /daycgi/smi2gif-bop /daycgi/smi2gif-small
Examples:	<A HREF="/daycgi/smi2gif?43434f"> <A HREF="/daycgi/smi2gif-bop?43434f"> <A HREF="/daycgi/smi2gif-small?43434f">
Notes:	smi2gif accepts one a hex-encoded SMILES argument and produces a depiction as a 400x200-pixel, color-on-black GIF file suitable for display on a web page. smi2gif-bop is identical to smi2gif, except that produces a black-on-paper GIF file (i.e., with transparent background) which is more suitable for printing than color-on-black. smi2gif-small is also identical to smi2gif, except that it produces a very small 96x64-pixel GIF image, suitable for use as a thumbnail, e.g.: <A HREF="/daycgi/smi2gif?43434f"> <IMG SRC="/daycgi/smi2gif-small?43434f"> </A> Produces this thumbnail (click on it for larger image): A more flexible utility is planned for the future (JavaDepict). However, these three smi2gif URLs will continue to be part of the supported DCGI package.

5.2 depict revisited

5.3 CLOGP revisited

6. DCGI Administration

6.1. Edit the DCGI initialization file dcgi_env.sh

CGI programs run as a special user (typically "nobody" or "http") in a very limited environment. Anything "special" needs to be defined by each CGI program. All DCGI programs execute the script /daycgi/dcgi_env.sh to set up a standard DCGI environment. As part of installation, you must edit this script (as distributed, the initial state is to fail with a warning).

(a) Make a copy of /daycgi/dcgi_env.sh (e.g., dcgi_env.sh.orig)

(b) Open /daycgi/dcgi_env.sh using your favorite text editor.

(c) If this is a fresh installation, remove or comment out the initial warning section.

(d) Edit symbols as per comments in the file. You can use the predefined settings for most things, but the following symbols typically need to be redefined:

DY_ROOT

The default value is /usr/local/daylight/version, but if it's installed somewhere else on your system, be sure to set DY_ROOT appropriately.

DY_LICENSEDATA

Should point to license file. Recommended: /usr/local/daylight/dy_license.dat.

LD_LIBRARY_PATH

The default value is usually correct, but this path must include $DY_ROOT/lib for all Daylight Software Releases 4.61 and later.

CX_ROOT

CEX is needed for RasMol 3D viewer.

DCGI_ACDSPEC

If you have the acd database running on a thorserver, change the default (demo) database spec to the appropriate value.

DCGI_MEDCHEMSPEC

If you have the medchem database running on a thorserver, change the default (demo) database spec to the appropriate value.

DCGI_WDISPEC

If you have the wdi database running on a thorserver, change the default (demo) database spec to the appropriate value.

DCGI_SAVANT_MERLINSPEC

If you have a spresi database running on a merlinserver, change the default database spec (spresi95demo) to the appropriate value. This is typically spresi95preps unless you are serving the whole spresi95 database in merlin.

DCGI_SAVANT_THORSPEC

If you are serving spresi95preps from merlinserver, change the change the default (spresi95demo) to the appropriate value (typically spresi95, not spresi95preps).

6.2. Check the Daylight passwords file dy_passwords.dat

Check that the daylight passwords file (typically /usr/local/daylight/dy_passwords.dat allows user "anonymous" access to database servers, e.g., if no server access password is required, it should include the line:

      user:anonymous:

6.3. Check the system services file /etc/services

Check that the file /etc/services defines thor and merlin services as:

      thor     5555/tcp   # Daylight server
      merlin   5556/tcp   # Daylight server

6.4. Check the httpd configuration file httpd.conf

Check that the httpd configuration file (typically httpd.conf, i.e., for Apache 1.3.9) defines the following three aliases, where /usr/local/daylight is replaced by the appropriate value for your system:

   Alias              /dayhtml/        /usr/local/daylight/v471/dayhtml/
   ScriptAlias        /daycgi/         /usr/local/daylight/v471/daycgi/

You will need to restart the httpd server for these to take effect.

7. Editor Configuration

Daycgi uses two sets of environment variables to control graphical input of structures.

DCGI_EDITOR1_URL

When set, this is the URL of an editor subwindow.

DCGI_EDITOR1_WLABEL

This is the name of the subwindow object. Note that this must be a valid javascript object name.

DCGI_EDITOR1_OPTIONS

This is the option string for the creation of the new subwindow.

DCGI_EDITOR1_BLABEL

This is the label for the editor button in the Daycgi application windows.

DCGI_EDITOR2_URL

When set, this is the URL of an editor subwindow.

DCGI_EDITOR2_WLABEL

This is the name of the subwindow object. Note that this must be a valid javascript object name.

DCGI_EDITOR2_OPTIONS

This is the option string for the creation of the new subwindow.

DCGI_EDITOR2_BLABEL

This is the label for the editor button in the Daycgi application windows.

One (or two) editor buttons will appear on the daycgi application pages if either (or both) of the DCGI_EDITOR1_URL and DCGI_EDITOR2_URL environment variables are set. The editor buttons case a subwindow to be loaded with the appropriate URL. The subwindow should provide Javascript functions to communicate with it's parent window. It refers to the parent windows structure entry form element with the functions "opener.GetRootSmiles()" and "opener.PutRootSmiles(val)".

The default configuration provides the CGI-based grins application as EDITOR1. Example subwindow HTML pages for JME and Chemdraw Plugin are provided in the /dayhtml/edit/ directory. These will need to be configured to work with the appropriate editor on the local server. The application /daycgi/testgrins can be used to test editor and inter-window communication.