Volume 1 Chapter 7 Bit Screens for 3D Searching

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Overview

QUESTand QUEST3D offer a number of control instructions which can be used either in the course of preparation of the instruction document or which are used to determine the mode of operation of the search process.

The corresponding instruction keywords and an indication of their function are listed below:

BEGIN-AT-REFCODE
defines the reference code at which the search will begin
COMMENT
allows the user to introduce comments in the instruction document
CONCATENATE
changes the concatenation character for very long text strings (QUEST only)
EXIT
terminates the QUEST session immediately
HITALL
declares that all database entries are to be classed as hits
INFORMATION
provides information about the control parameters which have been set
JOURNAL
allows information to be written to the Journal file
LOCASE
switches off automatic conversion of text to upper-case in text searches
NOJOURNAL
switches off the writing of information to the Journal file
NOSCREENS
switches off bit screens
PRINT
defines the content and format of information displayed for hits
PURGE
purges the contents of the Journal file
RETRIEVE
retrieves and saves an ASER sub-file specified by reference codes
SAVE
saves specified file types for kept hits
SCREEN
assigns bit screens required for the search process
STATISTICS
generates bit screen statistics for the hit entries
STOP-LIMIT
specifies the maximum number of accepted hits
TYPE
displays the contents of the instruction document

8.1 Graphics QUEST3D

8.1.1 BEGIN-AT-REFCODE

BEGIN-AT-REFCODE, located in the SEARCH menu, is used to specify the reference code of the entry at which searching is to begin.

The specified refcode need not actually be present in the CSD. If this is the case then searching will begin at the next entry in the alphabetic sequence.

The instruction can also be used, in combination with COMMAND in the SEARCH menu, to specify a range of reference codes for searching.

Ex.1 Suppose we wish to begin the search at reference code PQRSTU.

Ex.2 Suppose we wish to begin the search at refcode AAAAAA and end it at KLMNOP.

8.1.2 COMMENT

COMMENT is used to introduce a general comment into an instruction document. However, in QUEST3D, you can use COMMAND in the SEARCH menu to achieve this.

Note that, in QUEST3D, there is a COMMENT command in the 2D-CONSTRAIN sub-menu. However this allows you to insert a comment line only into a 2D connectivity test packet.

8.1.3 EXIT

EXIT, located in all menus and sub-menus, is used to terminate the current session immediately.

Ex.1

This response results in no exit from QUEST.

Ex.2

This response results in an exit from QUEST.

If you have already defined any test or specified any other instructions then after EXIT these will be saved in the Journal file and can be re-used in a future session.

8.1.4 HITALL

HITALL, located in the SEARCH menu, is used to declare that all database entries are to be classed as hits.

It can be useful if you wish to browse through a section of the database, either starting at the first entry or from a later point defined by BEGIN-AT-REFCODE.

It is also used in similarity searching where all database entries are to be compared against the target fragment.

Ex.

8.1.5 INFORMATION

The command INFO, located in the SEARCH menu, is used to provide general information about the control parameters which have been set.

Ex.

8.1.6 JOURNAL

JOURNAL is used to ensure that appropriate information is written to the Journal file.

In fact, in QUEST 3D, this is the default and there is no JOURNAL command in any of the menus.

Suppose you have selected NOJOURNAL in the SEARCH menu and then change your mind.

If you re-select NOJOURNAL then this action will switch off NOJOURNAL, which is equivalent to specifying JOURNAL in QUEST.

8.1.7 LOCASE

LOCASE is used to switch off the automatic conversion of all text to upper-case during text searches.

In QUEST3D there is no LOCASE command in any of the menus.

To achieve this function you can use COMMAND in the SEARCH menu.

Ex.

8.1.8 NOJOURNAL

NOJOURNAL, located in the SEARCH menu, is used to suppress the writing to the Journal file of reference information for hits which are kept.

Although reference information for kept hits is not written to the Journal file the QUEST instructions are written to the Journal file.

Ex.

8.1.9 NOSCREENS

NOSCREENS, located in the SEARCH menu and in the SCREEN sub-menu, is used to switch off any screens which have been set automatically or explicitly.

The screens which are switched off are:

The command can also be used within a connectivity test instruction packet to switch off the connectivity screens.

Normally this command would be used only by CCDC staff to test the efficiency of a screen.

NOSCREENS does not affect any tests set up with *BTEST.

Ex.

8.1.10 PRINT

In QUEST3D four commands are available in the SEARCH menu to specify the content and format of text information displayed for a hit.

These are:

These commands are fully discussed and illustrated in chapter 10 of Vol.2.

8.1.11 PURGE

PURGE is used to purge (delete) the contents of the Journal file.

In QUEST3D there is no PURGE command in any of the menus.

To achieve this function you can use COMMAND in the SEARCH menu.

Ex.

8.1.12 RETRIEVE

RETRIEVE, located in the SEARCH menu, is used to retrieve and save, in ASER format, a file of entries specified by their reference codes.

Ex.

8.1.13 SAVE

In QUEST3D seven commands are available in the SEARCH menu to specify which output files are to be saved for kept hits.

These are:

These commands are fully discussed and illustrated in chapter 10 of Vol.2.

8.1.14 SCREEN

SCREEN, located in the SCREEN sub-menu, is used to assign bit screens, either for a search based on screens alone or to be `combined' with defined tests to constitute the search question.

The bit screens set by the user are automatically linked by the .AND. logical operator, ie. all must be satisfied for a hit to be registered.

Normally you will only assign bit screen numbers in the range 1-155 (see Appendix 1 of the printed documentation). Assignment of connectivity bit screens can be dangerous and should be done only by experienced users.

At any time before you initiate the search process you can cancel an earlier specification:

Note also that you can cancel all bit screen assignments by specifying bit screen 0.

Ex. Suppose we wish to find all entries corresponding to error-free neutron studies.

Bit screen 49 corresponds to neutron studies.

Bit screen 34 corresponds to entries with one or more uncorrected errors.

In this example the bit screen 48 was typed accidentally but it was cancelled by typing -48 before pressing the RETURN key.

8.1.15 STATISTICS

STATISTICS, located in the SEARCH menu, is used to generate bit screen statistics for the hit entries.

At the end of the search, for each bit set, two numbers are displayed.

The first number is the number of hit entries having that bit set.

The second number is the first expressed as a percentage of the total number of entries in the database.

Ex.

8.1.16 STOP-LIMIT

STOP-LIMIT, located in the SEARCH menu, is used to specify the maximum number of accepted hits.

The default value is 1000 and this is normally an adequate setting.

By typing a stop-limit which is greater than the number of entries in the database you ensure that the search process is not terminated before the end of the database is reached.

Ex.

8.1.17 TYPE

TYPE, located in the BUILD and SEARCH menus, is used to display the contents of the instruction document.

Ex.

8.2 Basic QUEST

8.2.1 BEGIN-AT-REFCODE

Syntax BEGIN refcode

BEGIN-AT-REFCODE is used to specify the reference code of the entry at which searching is to begin.

The specified refcode need not actually be present in the CSD. If this is the case then searching will begin at the next entry in the alphabetic sequence.

The instruction can also be used to specify a range of reference codes for searching.

This facility can be used to good effect if a search was interrupted and has to be re-run at a later time.

Ex.1 If you wish QUEST to begin searching at refcode PQRSTU then the appropriate instruction would be:

     BEGI PQRSTU

Ex.2 If you wish QUEST to begin searching at refcode AAAAAA and finish searching after refcode KLMNOP then the appropriate instruction would be :

     BEGI  AAAAAA KLMNOP
  or BEGI  AAAAAA-KLMNOP

8.2.2 COMMENT

Syntax COMMENT text

COMMENT is used to insert one-line comments into the instruction document.

This command would normally be used to store comments which act either as a "title" for the search or to remind you of some particular aspects of the search.

Ex.

 COMM This search for steroid entries added to the database since 1 January 1992 was run
 COMM on 13 October 1992.

8.2.3 CONCATENATE

Syntax CONCATENATE character

CONCATENATE is used to change the concatenation character.

No single line in the instruction document may be more than 80 characters long.

To enable the construction of very long instructions, lines may be joined together using the special concatenation character !

Any line containing this character will be joined to the next line of the instruction document.

Characters following the concatenation character and on the same line as that character are ignored.

A maximum of three concatenation lines are allowed and so no single instruction may be more than 320 characters long.

The last line of the instruction document must not contain the concatenation character.

As indicated above, the CONCATENATE command is used to change the default concatenation character from ! to another character.

This can be useful if, for example, the text to be searched already contains the ! character, as is the case in the nomenclature of bridged-ring systems (see *COMPOUND, *SYNONYM, *NAME, *XNAME).

Ex.

 CONC  %
 T1  *NAME  9-(p-Nitrophenoxycarbonyl)-tetracyclo(6.2.1.1$3,6!.0$2,7!)%
 dodec-2(7)-ene

8.2.4 EXIT

Syntax EXIT

EXIT is used to terminate the current session immediately.

Ex.

T1 *CONN
AT1  GE  1
AT2  N  1
BO  1  2  1
END
EXIT
 

Note that in the QUEST there is no safeguard against accidental use of EXIT.

Typing EXIT <R> causes an immediate exit from QUEST.

However, in the above example if you typed EXIT anywhere after the T1 line and before the END line you would be prompted:

XXXXX  ERROR  578  -  Test abandoned.
Now continue (or type "EXIT" to finish)

If you have already defined any test or specified any other instructions then after EXIT these will be saved in the Journal file and can be re-used in a future session.

8.2.5 HITALL

Syntax HITALL

HITALL is used to declare that all database entries are to be classed as hits.

It can be useful if you wish to browse through a section of the database, either starting at the first entry or from a later point defined by BEGIN-AT-REFCODE.

It is also used in similarity searching where all database entries are to be compared against the target fragment.

Ex.

BEGI  DAAAAA
STOP  100
HITA
STAR

The above instructions allow you to inspect the 100 entries beginning at refcode DAAAAA.

8.2.6 INFORMATION

Syntax INFORMATION

INFORMATION is used to provide general information about the control parameters which have been set.

Ex.

T1 *BCLA  .EQ.  51
INFO

At this point the following type of information is listed:

8.2.7 JOURNAL

Syntax JOURNAL

JOURNAL is used to ensure that appropriate information is written to the Journal file.

The writing of information to the Journal file is the default setting.

Therefore JOURNAL would normally be used only in the situation where NOJOURNAL has been specified and then you wish to reverse this decision.

Ex.

T1 *BCLA  .EQ.  51
NOJOURNAL
T2  *YEAR  .GT.  1989
JOUR
QUES  T1 .AND. T2

8.2.8 LOCASE

Syntax LOCASE

LOCASE is used to switch off the automatic conversion of all text to upper-case during text searches.

If LOCASE is specified the difference between upper- and lower-case is preserved. Correct use of this instruction requires a good working knowledge of upper- and lower-case syntax within the database.

Normally this instruction would be used only by CCDC staff and it is not recommended for general use.

Ex. Suppose that the database is known to contain a particular author's name spelt in two different ways, usually as A.B.de Boer, but in a few cases as A.B.De Boer.

Suppose that we wish to locate the latter and edit the entries to conform to the "normal" spelling.

LOCA
T1  *AUTH  A.B.De Boer
QUES  T1

8.2.9 NOJOURNAL

Syntax NOJOURNAL

NOJOURNAL is used to suppress the writing to the Journal file of reference information for kept hits.

Although reference information for kept hits is not written to the Journal file the QUEST instructions are written

to the Journal file.

Ex. T1 *BCLA .EQ. 12 NOJO QUES T1

8.2.10 NOSCREENS

Syntax NOSCREENS

NOSCREENS is used to switch off any screens which have been set automatically or explicitly.

The screens which are switched off are:

The command can also be used within a connectivity test instruction packet to switch off the connectivity screens.

Normally this command would be used only by CCDC staff to test the efficiency of a screen.

NOSCREENS does not affect any tests set up with *BTEST.

Ex.

NOSC
T1  *COMP PROGESTERONE
QUES  T1

If the above search question were run you would notice that the search is much slower than if the automatic compound name screens were allowed to operate.

8.2.11 PRINT

Syntax PRINT n abcd efgh .....

n is the print option number, abcd, efgh etc. are optional search keywords

PRINT is used to specify the content and format of text information displayed for a hit.

The information which can be displayed for a hit is of 3 types:

The value of n in PRINT n controls both the content and format of the hit display.

Allowed values of n are: 1-5 and 7-10.

For n=7-10 there are two possible formats - standard and compact.

In standard format each standard reference item starts on a new line whereas in compact format all items are concatenated and separated from each other by //

The standard format is undoubtedly much easier to read.

The various print options are now summarised with an indication of the examples which illustrate their use:

Option Number 1  Hit statistics only
Option Number 2  Reference codes for hits and statistics
Option Number 3  Debug display of SCREEN record for each hit
Option Number 4  Debug display of TEXT record for each hit
Option Number 5  Debug display of all records for each hit
Option Number 7  Standard reference items and specified items for each hit
                 Compact format
Option Number 8  Standard reference items, search test items and specified items
                 for each hit Compact format
Option Number 9  Standard reference items and specified items for each hit
                 Standard format
Option Number 10 Standard reference items, search test items and specified
                 items for each hit Standard format

In practice, option number 10 is the most widely used and is recommended by the CCDC.

In the above list option number 6 is missing - this value could be used for a special user-defined display.

N.B.

Numerous examples of the PRINT options are to be found in chapter 10 of Vol.2.

Here it is sufficient to show one example:

Ex.

PRIN 10
T1 *SURN JACOBSON
QUES T1

The hit display, in standard format, is as follows:

---------+---------+---------+---------+---------+---------+---------+---------+
ALDCAR
2-Methyl-2-methylthio-propionaldehyde O-(methylcarbamoyl) oxime
Aldicarb
orthorhombic form, insecticidal activity
C7 H14 N2 O2 S1
F.Takusagawa,R.A.Jacobson
J.Agric.Food Chem., 25, 333,1977
---------+---------+---------+---------+---------+---------+---------+---------+
Type "K"(Keep), "R"(Reject) or "O"(for list of options)

8.2.12 PURGE

Syntax PURGE

PURGE is used to purge (delete) the contents of the Journal file.

If PURGE is used prior to the initiation of the search then the instruction document is purged.

Ex.

SCRE  153
T1  *BCLA  .EQ.  51
TYPE

At this stage TYPE would display the contents of the instruction document as:

SCRE  153
T1  *BCLA  .EQ.  51

If we now type:

PURG

QUEST displays the following prompt:

Now continue (or type "EXIT" to finish)

SCRE  22
TYPE

At this stage TYPE would display the contents of the instruction document as:

SCRE  22

8.2.13 RETRIEVE

Syntax RETR n

list of refcodes terminated by END

RETRIEVE is used to retrieve and save, in ASER format, a file of entries specified by their reference codes.

n=1
retrieves refcode families of entries

Instead of n=1 the keyword FAMILY (or FAMI) can be used.

n=2
retrieves individual entries

Instead of n=2 the keyword EXACT (or EXAC) can be used.

Ex.1

RETR  1
ACALDA  AACFAZ  ACCLCU  END

As each entry is retrieved the information is displayed:

AACFAZ retrieved
AACFAZ10 retrieved
ACALDA retrieved
ACCLCU retrieved

You are then informed:

Searches will now act on ASER subset (4  entries)

and you are prompted:

Now continue (or type "EXIT" to finish)

Ex.2

RETR  2
acalda  aacfaz
acclcu end

As each entry is retrieved the information is displayed:

AACFAZ retrieved
ACALDA retrieved
ACCLCU retrieved
You are then informed:

Searches will now act on ASER subset (3  entries)

and you are prompted:

Now continue (or type "EXIT" to finish)

8.2.14 SAVE

Syntax SAVE file1 file2 file3 ....

where file1, file2, file3 etc. are the mnemonics of the files to be saved.

SAVE is used to specify which output files are to be saved for kept hits. A number of different output files can be saved from the search process :

These output files can then be used as input to programs supplied by the CCDC or written by users.

A separate SAVE command can be used for each output file to be saved or the various files can be specified in a single command. Examples of saved output files are shown in chapter 10 of Vol.2.

Ex.1

SAVE ASER
T1  *CLAS  .EQ.   58
QUES  T1

In this example we save a search file ASER of all entries corresponding to alkaloids (class 58).

This saved file can then be used in later detailed connectivity searches.

This procedure would result in faster connectivity searches and this would benefit the user who wishes to conduct many searches of this specialised subset of the total database.

Ex.2

SAVE NONE

This command cancels all previous SAVE commands.

8.2.15 SCREEN

Syntax SCREEN n1 n2 n3 ....

SCREEN is used to assign bit screens, either for a search based on screens alone or to be `combined' with defined tests to constitute the search question.

The bit screens n1, n2, n3 etc. are automatically linked by the .AND. logical operator, ie. all must be satisfied for a hit to be registered.

Normally you will only assign bit screen numbers in the range 1-155 (see Appendix 1). Assignment of connectivity bit screens can be dangerous and should be done only by experienced users.

At any time before you initiate the search process you can cancel an earlier specification:

Note also that you can cancel all bit screen specifications by specifying SCRE 0

Ex.

SCRE  48  49  -34  -48

Hits will be registered for: neutron studies (bit screen 49) .AND. error-free entries (bit screen -34)

In this example the bit screen 48 was typed accidentally but it was cancelled by typing -48 before pressing the RETURN key. If the RETURN key had been pressed before the mistake was noticed then you could proceed as follows:

SCRE  48  49  -34
SCRE  -48

8.2.16 STATISTICS

Syntax STATISTICS

STATISTICS is used to generate bit screen statistics for the hit entries.

At the end of the search, for each bit set, two numbers are displayed.

The first number is the is the number of hit entries having that bit set.

The second number is the first expressed as a percentage of the total number of entries in the database.

Ex.

STAT

At the end of the search the bit screen statistics for the hits are displayed as follows:

Statistics
Bit       N    %D/B
  1     721      0%
  2     117      0%
  4     921      0%
...................
345    4938      4%
...................
682    4705      3%

8.2.17 STOP-LIMIT

Syntax STOP n

STOP is used to specify the maximum number of accepted hits.

The default value is 1000 and this is normally an adequate setting.

If, on the other hand, you wish to raise the stop-limit substantially you must remember to ensure that there is adequate disk space available for any saved output files.

By typing a stop-limit which is greater than the number of entries in the database you ensure that the search process is not terminated before the end of the database is reached.

Ex. Suppose you wish QUEST to stop searching after 500 hits then the appropriate instruction would be :

STOP 500

If the stop limit is exceeded then QUEST displays:

8.2.18 TYPE

Syntax TYPE

TYPE is used to display the contents of the instruction document.

Ex.

T1  *BCLA  .EQ.  49
SCRE  153
TYPE

The contents of the instruction document at this point would be displayed:

T1  *BCLA  .EQ.  49
SCRE  153

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Volume 1 Chapter 9 Initiating the Search Process.