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6.2.2 Summary of Connectivity Search Test Instructions

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

An atom property record takes the general form:

ATp el mca nh nch E Tn A/C

where

• p is the node number of the atom in the fragment diagram
• el is the element symbol
• mca is the minimum number of connected atoms, excluding terminal H atoms
• nh is the number of attached terminal H atoms
• nch is the charge on the atom
• E indicates that the mca value is to be interpreted as the exact value
• Tn indicates that the total number of attached atoms, incl. terminal H atoms, is n
• A/C acyclic/cyclic:
  • A indicates that the atom is a member of a chain
  • C indicates that the atom is a member of a ring

Bond Property Record

A bond property record takes the general form:

BO i j bt A/C

where

• i is the node number of one atom of the bond
• j is the node number of the other atom of the bond
• bt is the bond type, eg. single, double., etc.
• A/C acyclic/cyclic:
  • A indicates that the bond is acyclic
  • C indicates that the bond is cyclic

6.2.3 Bond Property Record

BO i j bt A/C

• where
  • i is the node number of one atom of the bond
  • j is the node number of the other atom of the bond
  • bt is the bond type, eg. single, double., etc.
  • A/C acyclic/cyclic:
    • A indicates that the bond is acyclic
    • C indicates that the bond is cyclic

• The atom numbers i and j must have already been defined in atom property records ATp.

• j is normally the node number of a single atom but it can also take a set of alternative values.

  This facility is referred to as variable point of attachment.

  Consider Ex.1.

  Ex.1

  T1  *CONN
  AT1  C  3
  AT2  C  2
  AT3  C  2
  AT4  C  2
  AT5  C  2
  AT6  C  2
  AT7  O  1  1
  AT8  N  1  2
  BO  1  2  5
  BO  2  3  5
  BO  3  4  5
  BO  4  5  5
  BO  5  6  5
  BO  6  1  5
  BO  1  7  1
  BO  8  2, 3, 4  1
  END
  QUES  T1

  Suppose you wish to find o-aminophenol, m-aminophenol and p-aminophenol.

  There is no need to run 3 separate searches. Instead, the bonding of the NH2 group is coded as shown:

  BO 8 2,3,4 1

  QUEST interprets this as atom 8 bonded to 2 or 3 or 4 by a single bond.

• The following bond types are recognised by QUEST:
  1 single bond
  5 aromatic Bond
  2 double bond
  6 polymeric bond
  3 triple bond
  7 delocalised double bond
  4 quadruple bond
  9 pi-bond
  99 any bond

  Notes are provided later in this chapter on conventions for bond type assignment in the database.

  Normally the bond type in a search test is a single value but it can also take a set of alternative values. This facility is referred to as variable bond type.

  An example of its use is shown in Ex.2 below. Since the database is not completely consistent with respect to the assignment of bond type it is safer to code each carbon-oxygen bond of the carboxylate group as either bond type 1 or 2 or 7.

  Ex.2

  T2  *CONN
  AT1  CU  2
  AT2  O  2
  AT3  C  2
  AT4  O  2
  BO  1  2  1
  BO  2  3  1, 2, 7
  BO  3  4  1, 2, 7
  BO  4  1  1
  END
  QUES  T2

  An alternative would be to use bt 99, but this could substantially slow down the search process.

• Wherever possible, you should specify that a bond must be acyclic or cyclic by including A or C in the bond property record. This can often noticeably increase the search speed.

  There is no need to specify C if the bond is part of a ring in the search fragment.

6.2.4 DEFB Instruction

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

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).

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.