Volume 1 Chapter 6 No Cyclic Routes Instruction

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6.2.17 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:

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:

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Volume 1 Chapter 6 Implicit and Explicit Hydrogen Atoms.