Volume 1 Chapter 6 Number of Fragments Instruction

The NFRAG instruction is used to ensure that a hit contains a minimum number of occurrences of the search fragment.

Consider the peptide fragment :

T1  *CONN
NFRAG  6
AT1  C  2
AT2  N  1  1
AT3  O  1
BO  1  2
BO  1  3  2
END
QUES  T1

NFRAG 6 requires that all hits must have at least 6 occurrences of the peptide search fragment and these occurrences must not overlap.

NFRAG -6 would allow overlap, thereby hitting urea-type structures.

If you wished to find structures having exactly 6 occurrences then you would proceed as follows:

Construct T1 using NFRAG 6, as above
Construct T2 using NFRAG 7
The question line would then be QUES T1 .NOT. T2

6.2.18 Same Residue Instruction

The SAMERES instruction is used to ensure that, if the search fragment consists of two or more disconnected sub-fragments, then these must all occur in the same residue for a hit to be registered.

Consider the search fragment :

Here we have two disconnected sub-fragments, the pyridinium cation and the sulfite anion.

If we include the instruction SAMERES in the connectivity test instruction packet a hit will be registered for (i) but not for (ii):

6.2.19 Comment Instruction

The Comment instruction is used to introduce any one-line remark which the user wishes to record.

It takes the form: C text

There is no limit on the number of comment instructions and they can occur at any position in the connectivity search test instruction packet between the *CONN instruction and the END instruction.

Ex.

C  This test specifies the enol-form of the barbiturate.

6.2.20 Noscreens Instruction

This instruction will switch off the connectivity screens which have been automatically set.

It takes the form: NOSC

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

6.2.21 Computational Limits

In normal practice it is unlikely that you would exceed program limits but a few constraints are listed here:

The total number of atom property records, summed over all *CONN tests, must not exceed 250.
Atom numbers p in ATp must be in the range 1-250. These numbers do not have to be sequential or continuous.
No atom may be involved in more than 15 connections to non-H atoms.
A single search question can involve a maximum of 29 ELDEF instructions, summed over all *CONN tests. Note that if, for example, you use MM as a new element symbol in test T1, you can use it again, unchanged or re-defined, in another test T2.
The total number of bond property records, summed over all *CONN tests, must not exceed 300.

Back to Table of Contents

Volume 1 Chapter 6 Implicit and Explicit Hydrogen Atoms .

6.2.17 Number of Fragments Instruction

6.2.18 Same Residue Instruction

6.2.19 Comment Instruction

6.2.20 Noscreens Instruction

6.2.21 Computational Limits