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CONTENTS

Function

The 2D-CONSTRAIN sub-menu, shown on below, is accessed from the BUILD menu.

It is used to apply 2D constraints to a search fragment; also to set up a similarity search.

Remarks

The commands available via the menu buttons are fully described in this chapter, ordered alphabetically by command name. The functions of the commands can be summarised as follows:

• NUMBER-OF-FRAGS to specify the required minimum number of occurrences of the search fragment for a hit to be registered
• SAME-RESIDUE to specify that search sub-fragments must be in the same residue for a hit to be registered
• NOSCREENS to switch off any screens which have been set automatically or explicitly

• HYDROGENS to specify the number of terminal hydrogen atoms attached to an atom
• CHARGE to specify the charge on an atom
• MIN-CONNECTIONS to specify that an atom must have a minimum number of connected atoms, excuding terminal hydrogen atoms
• EXACT to specify that an atom must have an exact number of connected atoms, excuding terminal hydrogen atoms
• TOTAL-COORD-NO to specify that an atom has a required total coordination number
• CYCLICITY to specify that an atom or bond must be part of a ring or part of a chain
• NUMBERS to number the atoms of the fragment and display these numbers

• ALLBOND to specify that all bonds in the fragment must be cyclic or acyclic
• NO-CYCLIC-ROUTES to constrain the fragment in terms of allowed cyclic substitution
• NO-LINKS to constrain the fragment in terms of extra direct links between the atoms of the fragment

• COMMENT to introduce a comment line into a connectivity test instruction packet
• DEFINE-STRUCTURE to declare that the formulation of the search test is complete

• TANI to use the Tanimoto Coefficient for similarity searching
• DICE to use the Dice Coefficient for similarity searching
• GENERATE-HYDS to assign terminal H atoms to all carbon atoms in the fragment which do not already carry terminal H atoms
• ALL-EXACT to specify the EXACT constraint for all atoms of the fragment
• SIMIL to declare that the formulation of the query structure for a similarity search is complete

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