Volume 1 Chapter 6 2D Searching in Basic QUEST

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6.2.2 Summary of Connectivity Search Test Instructions

The different instructions which can occur in a connectivity search test instruction packet are listed below with respect to their keywords and summary definitions are given:

  1. Tn *CONN this must be the first line of the test instruction packet
  2. C comment instructions can be included anywhere in the packet
  3. NOSC switches off automatic connectivity screens
  4. ELDEF defines special element groups
  5. DEFB changes the default bond type
  6. ATp atom property records (see below)
  7. BO bond property records (see below)
  8. ALLBOND requires that all bonds in the fragment are acyclic or cyclic
  9. NOCR prevents cyclic substitution
  10. NOLN prevents extra direct links
  11. NFRAG specifies the minimum number of occurrences of the fragment
  12. SAMERES requires that sub-fragments be in the same residue
  13. END this must be the last line of the test instruction packet
Atom Property Record

An atom property record takes the general form:

ATp el mca nh nch E Tn A/C

where

Bond Property Record

A bond property record takes the general form:

BO i j bt A/C

where

Most of the rest of this chapter is devoted to a detailed description of the various instructions listed above.

6.2.3 Bond Property Record

A bond property record takes the general form:

BO i j bt A/C

6.2.4 DEFB Instruction

The default bond type is 1, ie. single bond.

This means that in typing the bond property record for a single bond you need not specify bt.

Thus BO 4 5 1 and BO 4 5 are equivalent bond property records.

Suppose that your search fragment is composed almost entirely of aromatic bonds (bond type 5) then you can change the default bond type to 5 before typing the individual bond property records.

Thus DEFB 5

BO 8 9 QUEST will interpret the bond type of 8-9 as 5.

6.2.5 Atom Property Record - Element Symbol

Atom property record ATp el mca nh nch E Tn A/C

Consider the search fragment below, with its associated search question.

T1  *CONN
ELDEF  RR= S, SE, TE
AT1  7A  1
AT2  C  3
AT3  C  2
AT4  C  2
AT5  C  3
AT6  C  2
AT7  C  2
AT8  RR  1
DEFB  5
BO  1  2  1
BO  2  3
BO  3  4
BO  4  5
BO  5  6
BO  6  7
BO  7  2
BO  5  8  1
END
QUES  T1

This example illustrates that the element symbol el in an atom property record must be :

either
a conventional 1- or 2-letter symbol eg. C for atoms 2-7
or
an element group symbol eg. 7A for atom 1
or
a symbol defined by an ELDEF instruction eg. RR for atom 8 (see below).

Valid element group symbols are listed in Appendix 1 (bits 1-29).

Note that, in addition to the symbols in Appendix 1, the symbol AA can be used to indicate any element other than hydrogen.

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Volume 1 Chapter 6 ELDEL in Basic QUEST.