Volume 1 Chapter 6 Summary of Connectivity Search Test Instructions

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6.2.6 ELDEF Instruction

ELDEF is used to define a new element symbol for a set of elements which does not correspond to one of the standard element groups.

The new element symbol can be one or two alphabetic characters but cannot be a conventional element symbol, element group symbol or a symbol already defined by an ELDEF instruction.

In the example below the ELDEF instruction defines the new element symbol RR to be S or Se or Te.

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

Note that the ELDEF instruction for an element symbol must appear before the atom property record in which the symbol is used.

A few examples will illustrate the syntax of ELDEF instructions:

Ex.1

ELDEF  MM = V  Cr  mn

The new element symbol MM is defined tobe V or Cr or Mn.

The set of old element symbols can be separated by blanks or commas.

The = sign is mandatory and no distinction is made between upper- and lower-case.

Ex.2 The element group symbol 6A covers O, S, Se, Te, Po.

Thus an alternative but equivalent definition of RR (see above) would be:

ELDEF   RR = 6A - O,Po

When the negative sign is used in an ELDEF instruction the program checks to ensure that negated elements are contained within the positive set.

Thus, for example, ELDEF RR = 6A - F would be invalid.

Ex.3

ELDEF  NS = 1A  2A
ELDEF  NT = NS - BA

This illustrates that already defined new element symbols can be used to define further new element symbols.

An equivalent single instruction would be:

ELDEF  Nu = 1A, 2A - Ba

Ex.4

ELDEF  PP = - TR

The new element symbol PP is defined to be not a transition element.

6.2.7 Atom Property Record - mca Value

Atom property record ATp el mca nh nch E Tn A/C

The value of mca specifies the minimum number of atoms, excluding terminal H atoms, connected to atom p.

The specification of the minimum number rather than the exact number allows us flexibility in defining the degree of substitution at a particular atom.

Consider the search fragment below, with the associated search question and target structures (a)-(c).

T1  *CONN
AT1  TR  4
AT2  N  1
AT3  N  1
AT4  N  1
AT5  N  1
BO  1  2
BO  1  3
BO  1  4
BO  1  5
END
QUES  T1

Ex. A search using test T1 will register hits for (a), (b), (c), etc.

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Volume 1 Chapter 6 Atom Property Record Exacy Value of mca.