Volume 1 Chapter 6 2D Searching in Basic QUEST

Before describing the details of connectivity searching in Basic QUEST it will be instructive to consider a few simple examples.

Ex.1

Find all entries which contain the thiourea substructure:

The search question could be formulated as follows:

T1  *CONN
AT1  N  1
AT2  C  3  0
AT3  N  1
AT4  S  1  0
BO  1  2  1
BO  2  3  1
BO  2  4  2
END
QUES  T1

The first step in preparing a connectivity test is to sketch the structural fragment and arbitrarily number all atoms except for terminal H atoms.
The connectivity test is composed of a set of instructions, known as the connectivity instruction packet.
The instruction packet begins with Tn *CONN and is terminated by END.
Between these two records atom property records ATp and bond property records BO define the topology of the fragment.
Other types of records can be present to place special restrictions on the fragment and its environment. These will be introduced later in the chapter.
The first atom property record specifies that atom 1 is a nitrogen atom with mca=1.
mca is the minimum number of connected atoms excluding terminal H atoms.
We use the minimum value rather than the actual value to allow for different levels of substitution at an atom.
Atom 2 is carbon with mca=3 and nh=0.
nh is the number of attached terminal H atoms.
The bond property records indicate that: atom 1 is bonded to atom2 by a bond of type 1 (single);
atom 2 is bonded to atom 3 by a single bond;
atom 2 is bonded to atom 4 by a double bond.
You should note that the above coding contains some redundant information.
The 2 single bonds and 1 double bond at C result in a valency of 4 and therefore there is really no need to specify nh=0 in the atom property record of atom 2.
The above connectivity search question would register hits for:

Ex.2 Find all entries in which the carboxylate group is bonded through both oxygen atoms to Cd or Zn:

The search question could be formulated as follows:

T1  *CONN
ELDEF  MM = Cd, ZN
AT1  MM  2
AT2  O  2
AT3  C  2
AT4  O  2
BO  1  2
BO  1  4
BO  2  3  1,2,7
BO  3  4  1,2,7
END
QUES  T1

This example introduces the ELDEF instruction which allows you to define an atom to be other than an individual element.
A new element symbol must be declared, in this case MM, which is then set equal to Cd or ZN.
No distinction is made between upper- and lower-case.
If you use an ELDEF instruction then it must appear ahead of the atom property record in which the new element symbol is used
In this example no bond type is specified for the bonds 1-2 and 1-4.
These are single bonds and the default bond type in a bond property record is 1, ie. single.
Hence there is no need to specify it explicitly.
The carbon-oxygen bonds are specified to be of type 1 single
or 2 double
or 7 delocalised double.
This illustrates the use of a variable bond type which is important if you suspect that the database may not be consistent in the connectivity representation of a particular bonded fragment.
The above connectivity search question would register hits for:

Ex.3 Find acyclic ethers represented by the substructure:

In this case three different connectivity search tests will be used to illustrate various features:

T1  *CONN         T2  *CONN         T3  *CONN
AT1  C  1         AT1  C  1  E      AT1  C  1  3
AT2  O  2         AT2  O  2         AT2  O  2
AT3  C  1         AT3  C  1         AT3  C  T3
BO  1  2  A       BO  1  2  A       BO  1  2  A
BO  2  3  A       BO  2  3  A       BO  2  3  A
END               END               END
QUES  T1          QUES  T2          QUES  T3

In test T1 the bond property records each contain the sub-keyword A.
This requires that the two bonds be acyclic.
The sub-keyword C can be used if you wish to specify that a bond must be cyclic.
The only constraints placed on the atoms are the mca values of the diagram.
Accordingly a search with test T1 would register hits for all acyclic ethers.
In test T2 the atom property record for atom 1 contains the sub-keyword E.
When E (for EXACT) is present the mca value is interpreted as the exact number of connected atoms, excluding terminal H atoms.
A search with test T2 would register hits for all acyclic methyl ethers:
In test T3 atom 1 has nh=3 and mca=1, implying that atom 1 is a methyl carbon.
Thus the coding here has the same effect as the use of E in test T2.
This illustrates the fact that it is often possible to code a connectivity test in several different ways, each producing the same result.
In test T3 the atom property record for atom 3 contains the sub-keyword T3.
T3 specifies that atom 3 has a total coordination number of 3, ie. the total number of atoms connected to atom 3, including terminal H atoms, is 3.
In other words, atom 3 has sp2 hybridisation.
A search using test T3 would register hits for acyclic methyl ethers of the type:

Ex.4 Find entries containing the substructure:

Three different connectivity search tests will be used to illustrate new features:

T1  *CONN         T2  *CONN           T3  *CONN
AT1  S  2         AT1  S  2           AT1  S  2
AT2  C  2         AT2  C  2           AT2  C  2
AT3  N  2         AT3  N  2           AT3  N  2
AT4  C  2         AT4  C  2           AT4  C  2
AT5  C  1         AT5  C  1           AT5  C  1
BO   1  2         BO   1  2           BO   1  2
BO   2  3         BO   2  3           BO   2  3
BO   3  4         BO   3  4           BO   3  4
BO   4  1         BO   4  1           BO   4  1
BO   3  5         BO   3  5           BO   3  5
END               NOCR                NOLN
QUES  T1          END                 END
                  QUES  T2            QUES  T3

In test T1 the only constraints placed on the atoms are the mca values of the diagram.
A search with test T1 would register hits for all of the structures (i)-(iv) shown below.
In test T2 there is an instruction NOCR.
NOCR requires that, for a hit to be registered, the atoms of the fragment cannot be connected to atoms outside the fragment by cyclic routes (bonds).
A search with test T2 would register a hit only for (i).
In test T3 there is an instruction NOLN.
NOLN requires that, for a hit to be registered, the atoms of the fragment cannot be directly linked to any other atoms of the search fragment except by the bonds specified in the bond property records, ie. the bonds in the diagram.
A search with test T3 would register hits for (i)-(iii).

Back to Table of Contents

Volume 1 Chapter 6 Summary of Connectivity Search Test Instructions .

6.2 Basic QUEST

6.2.1 Simple Examples