Volume 1 Chapter 6 2D Searching in Graphics QUEST3D
Back to Table of Contents
The menus and sub-menus relevant to the construction of a 2D connectivity
search question in QUEST3D are listed below:
- BUILD menu
- Used to build the skeleton of the fragment
- PERIODIC-TABLE
- sub-menu Used to assign "uncommon" element types
- 2D-CONSTRAIN
- sub-menu Used to apply constraints to the fragment or its environment
- EDIT menu
- Used to edit the fragment, chemically or graphically
- FILES menu
- Used to store fragments for later use and to fetch them
- SEARCH menu
- Used to set control commands
- QUEST sub-menu
- Used to combine tests to form the search question.
In practice the EDIT menu is not used very often nor is the FILES menu,
although the latter is very useful for searches which are to be repeated after
each update of the database.
The functions of the relevant commands in the BUILD menu (see below) are
summarised below:
- DRAW
- builds the fragment atom-by-atom bond-by-bond in the DRAW mode
- MOVE
- builds the fragment atom-by-atom bond-by-bond in the MOVE mode
- ELEMENT TYPES
- assigns element types; OTHER accesses the PERIODIC-TABLE sub-menu
- BOND TYPES
- assigns bond types; V.B.T for variable bond type; V.P.A. for variable point of attachment
- TEMPLATES
- accesses the TEMPLATES sub-menu, yielding 168 pre-defined fragments
- GROUPS
- accesses the GROUPS sub-menu, yielding 26 commonly occurring groups
- CHAIN
- builds a chain of a specified number of atoms
- RING
- builds a ring of a specified number of atoms
- LIGAND
- builds a ligand of specified multiplicity
- FUSE
- fuses two fragments by a common face
- SPIRO
- fuses two fragments by a common atom
- REPEAT
- builds a repeat unit of specified multiplicity
- DELATM
- deletes one or more atoms
- DELBND
- deletes one or more bonds
- CLEAR
- deletes the complete fragment from the drawing area
- 2D-CONSTRAIN
- accesses the 2D-CONSTRAIN sub-menu
- DEFINE-STRUCTURE
- declares that the search formulation is complete
- GRID
- toggles a hexagonal grid of points to assist the building of "tidy"
diagrams
This sub-menu (see below), accessed by the OTHER command in the BUILD
menu, allows you to assign element types other than C, N, O, S, P, Cl, Br, F;
it is also used to generate an ELDEF instruction.
6.3.2.3 2D-CONSTRAIN Sub-Menu
The functions of the relevant commands in the 2D-CONSTRAIN sub-menu are summarised below:
- NUMBER-OF-FRAGS
- specifies the required minimum number of occurrences of the search fragment for a
hit to be registered
- SAME-RESIDUE
- specifies that search sub-fragments must be in the same residue for a hit to be
registered
- NOSCREENS
- switches off any screens which have been set automatically or explicitly
- HYDROGENS
- specifies the number of terminal hydrogen atoms attached to an atom
- CHARGE
- specifies the charge on an atom
- MIN-CONNECTIONS
- specifies that an atom must have a minimum number of connected atoms, excuding
terminal hydrogen atoms
- EXACT
- specifies that an atom must have an exact number of connected atoms, excuding
terminal hydrogen atoms
- TOTAL-COORD-NO
- specifies that an atom has a required total coordination number
- CYCLICITY
- specifies that an atom or bond must be part of a ring or part of a chain
- NUMBERS
- numbers the atoms of the fragment and display these numbers
- ALLBOND
- specifies that all bonds in the fragment must be cyclic or acyclic
- NO-CYCLIC-ROUTES
- constrains the fragment in terms of allowed cyclic substitution
- NO-LINKS
- constrains the fragment in terms of extra direct links between the atoms of the
fragment
- COMMENT
- introduces a comment line into a connectivity test instruction packet
- DEFINE-STRUCTURE
- declares that the formulation of the search test is complete
- TANI
- uses the Tanimoto Coefficient for similarity searching
- DICE
- uses the Dice Coefficient for similarity searching
- GENERATE-HYDS
- assigns terminal H atoms to all carbon atoms in the fragment which do not
already carry terminal H atoms
- ALL-EXACT
- specifies the EXACT constraint for all atoms of the fragment
- SIMIL
- declares that the formulation of the query structure for a similarity search
is complete
Back to Table of Contents
Volume 1 Chapter 6 2D Similarity Searching Overview.