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NUMBER-OF-FRAGS

NUMBER-OF-FRAGS is used to specify that the search fragment must occur at least n times in the structure for a hit to be registered.

You can also specify that the multiple occurrences must not overlap or may overlap.

Examples

Ex. 1 Suppose we wish to search for compounds containing at least two carboxylic acid groups.

Suppose we have built the fragment (i) - see below.

• Select NUMBER-OF-FRAGS

• Enter number of occurrences required (Press <RETURN> to mean "Unspecified")
  (If these fragments must NOT OVERLAP, enter a POSITIVE number
  If these fragments MAY OVERLAP, enter a NEGATIVE number)

• Type 2 <R>

  2 appears in NUMBER-OF-FRAGS box.

• Select a MENU command, or select an ATOM or BOND to display its
  properties.

• Select DEFINE-STRUCTURE

A search would produce hits for (ii) - (v).

Note that the clathrate structure (iv) contains two carboxylic acid groups but they are split between two residues. This illustrates the fact that NUMBER-OF-FRAGS operates on the total structure.

You should note that if you change your mind and decide not to use this constraint re-select the NUMBER-OF-FRAGS command and press<RETURN> to mean unspecified.

Ex. 2 Suppose we wish to search for compounds containing at least 5 occurrences of the fragment:

Suppose we have built the fragment (i) - see below.

• Select NUMBER-OF-FRAGS

• Enter number of occurrences required (Press <RETURN> to mean "Unspecified")
  (If these fragments must NOT OVERLAP, enter a POSITIVE number
  If these fragments MAY OVERLAP, enter a NEGATIVE number)

• Type 5 <R>

  5 appears in NUMBER-OF-FRAGS box.

• Select a MENU command, or select an ATOM or BOND to display its
  properties.

• Select DEFINE-STRUCTURE

A search would now register hits for structures such as (ii).

In (ii) the 5 non-overlapping fragments are indicated by 1 2 3 4 5.

Ex. 3 As for Ex. 2, but now allow the 5 occurrences to overlap.

• Select NUMBER-OF-FRAGS

• Enter number of occurrences required (Press <RETURN> to mean "Unspecified")
  (If these fragments must NOT OVERLAP, enter a POSITIVE number
  If these fragments MAY OVERLAP, enter a NEGATIVE number)

• Type -5 <R>

  -5 appears in NUMBER-OF-FRAGS box.

• Select a MENU command, or select an ATOM or BOND to display its
  properties.

• Select DEFINE-STRUCTURE

A search would register hits for structures (ii) and (iii).

In (iii) there are, in fact, 7 overlapping fragments:

1-2-3 2-1-4 5-2-3 2-5-8 6-5-8 5-6-7 9-6-7

Note: NUMBER-OF-FRAGS locates entries with a minimum number of occurrences of the fragment. To locate entries with an exact number of occurrences of the fragment, e.g. 6, you would define

test T1 with NFRAG = 6

test T2 with NFRAG = 7

then use T1.NOT.T2 as the search question.

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Volume 2 Chapter 2 2D-Constrain Sub-menu NUMBERS.