Volume 1 Chapter 6 2D Similarity Searching in Graphics QUEST3D

Ex.1 As for Basic QUEST, we will again use the example of p-aminophenol.

Select STOP-LIMIT from the SEARCH menu

What is the maximum number of hits allowed ?
Enter a NEGATIVE number for QUEST's default : 1000

Type 16 <R>
16 appears against the STOP-LIMIT command
Select TO-BUILD
The SEARCH menu is replaced by the BUILD menu.
Select AROM
The red box around SING vanishes and a red box appears around AROM.
Select RING

How many atoms in RING ? (Type 0 if you don't want a ring after all)

Type 6 <R>

Please use cursor to select the CENTRE of the RING or select CANCEL.

Select a position in the centre of the drawing area.
A six-membered aromatic ring of carbon atoms is now displayed.
Select N from the elements section of the menu.
Select SING from the bond types section of the menu.
Select a position for the N atom.
Select the ring atom to which the N is to be bonded.
A single bond now joins N to a ring C atom.
Select O from the elements section of the menu.
Select a position for the O atom.
Select the para-ring atom to which the O is to be bonded.
A single bond now joins O to the para-ring C atom.
Select 2D-CONSTRAIN
The BUILD menu is replaced by the 2D-CONSTRAIN sub-menu.
Select HYDROGENS

Type EXACT number of terminal HYDROGENS.
You may use multiple values, separated by SPACE or COMMA
(Press <RETURN> to mean "Unspecified")

Type 2 <R>

Move the cursor over the required ATOM and click a BUTTON.
(Select another command to end HYDROGENS)

Select the N atom.
Select HYDROGENS

Type EXACT number of terminal HYDROGENS.
You may use multiple values, separated by SPACE or COMMA
(Press <RETURN> to mean "Unspecified")

Type 1 <R>

Move the cursor over the required ATOM and click a BUTTON.
(Select another command to end HYDROGENS)

Select the O atom.
At this point the query fragment is as shown below.
Select GENERATE-HYDS
Select CYCLICITY

C appears in the CYCLICITY box.

Select ATOM or BOND for cyclicity specification.
Re-select CYCLICITY to toggle A and C.
(Select another command to end CYCLICITY)

Select CYCLICITY
A appears in the CYCLICITY box.
Select in turn each of the 2 single bonds.
Select ALL-EXACT

(To switch off ALL-EXACT, simply re-select it)
Select a MENU command, or select an ATOM or BOND to display its properties.

Select SIMIL
```
maximum of 16 entries will be returned by similarity search
- SIMILarity search : Record Ignored
```
The connectivity bit screens are displayed and are terminated by:
```
Total Number of Screens Set  =  43
```
At this stage the 2D-CONSTRAIN sub-menu is replaced by the BUILD menu.
The query fragment is as shown in (a) below.
(a)
Select TYPE

The instruction document is displayed as shown in (b) below.

(b) STOP-LIMIT 16
    SIMILAR TANI
    NFRAG   1
    AT1 C 3 0 E                                        :XY   500   301
    AT2 C 2 1 E                                        :XY   327   401
    AT3 C 2 1 E                                        :XY   327   601
    AT4 C 3 0 E                                        :XY   500   700
    AT5 C 2 1 E                                        :XY   673   600
    AT6 C 2 1 E                                        :XY   673   400
    AT7 N 1 2 E                                        :XY   499   100
    AT8 O 1 1 E                                        :XY   499   900
    BO 1 2 5
    BO 2 3 5
    BO 3 4 5
    BO 4 5 5
    BO 5 6 5
    BO 1 6 5
    BO 1 7 1 A
    BO 4 8 1 A
    END

Note that TANI has been assigned as the default similarity coefficient.
If you wished to use DICE then you would select it before selecting SIMIL.

Select TO-SEARCH
The BUILD menu is replaced by the SEARCH menu.
Select HITALL

All entries will be classed as hits. Select START to begin searching database.

Select START
```
Now searching D/B ...
```

At the end of the search the results are displayed, as shown for the Basic QUEST example, terminating with:
CSD SIMILARITY SEARCH --------------------- Information for 16 Entries Now Follows Entries are ordered by decreasing similarity to the input fragment >More(Y/N)?

At this stage there are 3 possible responses:

Response 1

>More (Y/N)?

Type Y <R>

>Full printout (Y/N)?

Type Y <R>

The screen clears and the first entry, AMPHOL, in the retrieved sub-database is displayed, as shown in (a) below.

The other 15 entries can then be inspected by "stepping through" the sub-database, using CONTROL KEEP or CONTROL REJECT.

Response 2

>More (Y/N)?

Type Y <R>

>Full printout (Y/N)?

Type N <R>

The similarity coefficients and screen information, shown in (b) below, scroll through and the SEARCH menu displaying the query fragment is restored.
(b)

Refcode Rank No. Entry Screens Common to Fragment Similarity Coefficient AMPHOL 1 44 43 0.977 AMPHOM02 2 44 42 0.933 AMPHOM10 3 44 42 0.933 MAMPOL 4 44 42 0.933 AMCPHO 5 53 43 0.811 AMPHCL 6 48 40 0.784 GEBVAK 7 55 43 0.782 PANISD 8 49 40 0.769 PANISD01 9 49 40 0.769 ANCPOL 10 56 43 0.768 ANLPCP 11 56 43 0.768 HYQUIN 12 36 34 0.756 HYQUIN02 13 36 34 0.756 HYQUIN05 14 36 34 0.756 JAMKEN 15 36 34 0.756 PENDAM 16 36 34 0.756 Saving hits in database format now
At this stage you can inspect the 16 entries of the retrieved sub-database by selecting HITALL and then START in the SEARCH menu.

Response 3

>More (Y/N)?

Type N <R>

The SEARCH menu displaying the query fragment is restored.
At this stage you can inspect the 16 entries of the retrieved sub-database by selecting HITALL and then START in the SEARCH menu.

Ex.2 This illustrates a very useful facility whereby you can specify the query fragment simply by its refcode.
It obviates the need to construct a very large query fragment using the BUILD menu and 2D- CONSTRAIN sub-menu.
We will repeat the similarity search for p-aminophenol, using its refcode AMPHOL.
The dialogue will be as follows:

Select STOP-LIMIT from the SEARCH menu

What is the maximum number of hits allowed ? Enter a NEGATIVE number for QUEST's default : 1000

Type 16 <R>
16 appears against the STOP-LIMIT command

Select COMMAND

Please type a single-line instruction for QUEST (Press <RETURN> if you don't want to type a line)

Type SIMI TO REFCODE <R>

maximum of 16 entries will be returned by similarity search refcode or END >

Type AMPHOL <R>

refcode or END >

Type END <R>

refcode AMPHOL will provide definition of similarity search

Select TYPE
The contents of the instruction document are displayed as follows:

STOP-LIMIT 16 SIMI TO REFCODE AMPHOL END

Select HITALL

All entries will be classed as hits. Select START to begin searching database.

Select START

Now searching D/B ...

At the end of the search of the database the output is displayed as shown earlier in this chapter for Ex.2 using Basic QUEST.
In the above example the Tanimoto similarity coefficient (the default) is used.
If you wish to use the Dice coefficient then instead of typing SIMI TO REFCODE,

Type SIMI DICE TO REFCODE <R>

Similarity searches need not be conducted against all entries in the database.
As indicated earlier in Basic QUEST, you can conduct a similarity search using assigned bit screens and/or defined tests. If tests are utilised then the search should be initiated using the QUEST sub- menu.
Back to Table of Contents
Volume 1 Chapter 7 3D Searching The 3D CONSTRAIN Menu .

6.4.2 GRAPHICS QUEST3D