Volume 1 Chapter 6 Implicit and Explicit Hydrogen Atoms
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QUEST3D allows you to construct a connectivity search test instruction packet
through the use of menus and sub-menus. Full details of the functionality of
the commands in these menus are set out in Vol.2.
The BUILD menu (see below) is used to construct the fragment skeleton
- atom-by-atom and bond-by-bond
- and/or by the use of short-cut commands
The 2D-CONSTRAIN sub-menu (see below) is used to specify the parameters of atom
property records and other fragment environment parameters.
It is instructive to show here two simple examples - numerous others are given
in chapters 1 and 2 of Vol.2.
Ex.1 This illustrates the atom-by-atom and bond-by-bond construction of a
Please press <RETURN> to continue. Thank you.
- On entering the BUILD menu the current settings are C, SING, MOVE.
Suppose we wish to construct the skeleton fragment (i) - see below.
- A possible sequence of actions is tabulated in (ii).
You are recommended to carry out this exercise in the same order of steps and
check the results of each action against this table.
- Step 1 indicates that when a new atom is created it becomes the active atom.
An active atom is indicated by a red + beside the atom.
The program state switches to DRAW.
- When the program state is DRAW then successive selection of new positions
creates bonds from old atom to new atom, with new atom becoming the active
This is illustrated by steps 2 - 6.
- In step 7 we return to an existing atom (atom 1).
The program state switches from DRAW to MOVE and now no atom is active.
This allows us to branch to a different part of the diagram, as we do in step
- It is evident from the tabulation that:
when an atom is active the program state is DRAW
when no atom is active the program state is MOVE.
- When an atom is active we can switch from DRAW to MOVE
either by selecting the menu command MOVE
or by re-selecting the active atom (see steps 11 and 16).
- Steps 14 - 16 and 17 - 18 illustrate that we can use the BUILD menu to edit
element types and bond types - there is no need to select the EDIT menu for
such simple editing.
Ex.2 Suppose we wish to search for the azetidine fragment shown in (a)
We will impose the constraint that the the N atom must carry one terminal
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- Select RING in the BUILD menu.
How many atoms in RING ? (Type 0 if you don't want a ring after all)
- Type 4 <R>
Please use cursor to select the CENTRE of the ring or select CANCEL.
- Select the centre of the drawing area.
- The drawing area now contains (b).
- Select N from the elements in the upper-right of the menu.
- The current element box (outlined in red) now contains N.
- Select the top-left atom of the ring.
- This atom is now N and the red + indicates that it is active.
- Select the N atom again.
- The red + vanishes (the fragment now has no active atom) and the
drawing area contains (c).
- Select 2D-CONSTRAIN
- The BUILD menu is replaced by the 2D-CONSTRAIN sub-menu.
Select a MENU command, or select an ATOM or BOND to display its properties.
- Select HYDROGENS
Type EXACT number of terminal HYDROGENS.
You may use multiple values, separated by SPACE or COMMA
(Press <RETURN> to mean "Unspecified")
- Type 1 <R>
- 1 appears in the HYDROGENS box.
Move the cursor over the required ATOM and click a BUTTON.
(Select another command to end HYDROGENS)
- Select the N atom.
- The fragment is now as shown in (d).
At this stage we have completed the formulation of the fragment.
- Select DEFINE-STRUCTURE
- The 2D-CONSTRAIN sub-menu is replaced by the BUILD menu.
The connectivity bit screens for the fragment are displayed.
- Select TYPE
- The screen is cleared and the instruction document displayed - see (e)
(e) T1 *CONN
AT1 N 2 1 :XY 350 650
AT2 C 2 :XY 650 650
AT3 C 2 :XY 650 350
AT4 C 2 :XY 350 350
BO 1 2 1
BO 2 3 1
BO 3 4 1
BO 1 4 1
- Press <R>
- The SEARCH menu is restored.
- Select FASTQUEST
- The screen clears and the search process is initiated.
Volume 1 Chapter 6 Menu and Sub-menu Summary.