View Hypothesis Workbench

To Set Specifications for Bonds and Atoms

In a hypothesis you can specify that an atom can be any of several elements and that a bond can be any of several bond types. You can specify additional characteristics for each atom, such as its charge and valence.

For example, you might want to search a database for a compound that contains a halogen atom located between 10 and 12 angstroms from either a nitrogen, an oxygen, or a sulphur atom, which in turn is bonded to a carbon that is bonded to another carbon either by a double or an aromatic bond. You can describe these requirements in a hypothesis, and then use the hypothesis to search the database.

For more information, select the NEXT PAGE button below, or make a choice:

To Set Atom Specifications

To specify elements and attributes for atom specifications in a hypothesis in the View Hypothesis workbench, do the following:

Select the atom specification in the hypothesis that you want to change.
Notice that you cannot change the specifications on hydrogens; they are treated differently than other atoms, as is discussed later in this section.
Select the Atom Specification button in the Toolbox.

A window appears displaying the Atom Specification Editor as shown below.

This editor shows the choices you are most likely to want when specifying elements and attributes for an atom in a hypothesis. It is similar to the Periodic Table in the View Compound workbench in that you can expand it by selecting the Editor Expansion button at the bottom left corner of the editor.

When you select the Expansion button, a bigger Atom Specification Editor appears. The new editor shows all the elements in the Periodic Table. It also has fields for atom attributes such as Valence, Coordination, Mass Number, Lone Pair Count and Hydrogen Count, as shown below.

This expanded editor provides all the choices of the contracted editor, with several additional choices. However, the contracted editor contains the choices you are likely to want most of the time.

To return from the expanded editor to the contracted version, select the Editor Contraction button at the bottom left of the editor.

Each time you change from a contracted editor to an expanded editor, or vice versa, any changes you made to settings in the editor are lost. The changes are only implemented when you select the OK button.
Use either the contracted or expanded Atom Specification editor to select the range of elements for the selected atom. Whenever you select an element, that element is added to the range of possible elements for the selected atom. For example, to specify that the selected atom can be Al, Si or P, select each of Al, Si and P in the editor. After selecting an element, you can deselect it again by left clicking it.

You can also specify that the atom is
You can clear everything in the selection and then select carbon by pressing the Clear Elements button. This button is available only in the expanded editor.

You can return the specification to what it was when the editor first opened by selecting the Reset button. This button is available in both expanded and contracted editors.

Notice that you cannot select hydrogen as one of the elements of an atom. If you want to specify that an atom has a particular number of hydrogens bonded to it, then select that atom before opening the Atom Specification Editor and put a value in the Hydrogen Count field in the Atom Specification Editor. For example, if an oxygen is part of a hydroxyl group, it has a Hydrogen Count of 1.
In either the contracted or expanded editor, you can use the buttons on the left of the editor to specify the following:
Aromatic The atom is aromatic.
Aliphatic The atom is aliphatic.
Exocyclic The atom is not in a ring.
Endocyclic The atom is in a ring.
Bridgehead The atom is a bridgehead in a ring system. That is, the atom is a member of two or more rings.
Use Atom Stereochemistry The atom's present stereochemistry is specified.
In either the expanded or contracted editor you can specify a charge by selecting a Charge field as follows:
Positive To specify that the atom has a positive charge, select the Positive button.
Negative To specify that the atom has a negative charge, select the Negative button.
Specific To specify a particular charge, enter a value in the Specific field.
In the expanded Atom Specification Editor, you can additionally specify the following attributes:
Mass Number Enter an integer for the mass number. This is useful for selecting isotopes, such as 13 for 13C.
Valence To specify a valence, enter a positive integer value in the Valence field, for example, 4.
Coordination Enter the coordination number-the number of other atoms connected to the atom.
Lone Pair Count Enter the number of lone pairs the atom must have.
Hydrogen Count Enter the number of hydrogens to be connected to the atom.
Catalyst does not check for chemical consistency when you set these constraints. For example, Catalyst does not prevent you from specifying a positive charge of 10 or a hydrogen count of 14 for a carbon atom.
When you have finished specifying constraints, select the OK button to implement the changes and remove the Atom Specification Editor from the screen. The dialog box disappears. If you originally selected more than one atom in the hypothesis, an Atom Specification Editor appears for each one in turn.
If you specified more than one permissible element for the atom, its display color is mauve.

To Display the Atom Specifications

To see the atom specification, switch on atom labeling by switching on the 3D option of the Atom Labels command of the View menu.

The label shows the set of possible elements enclosed in braces, { }. Each atom in the hypothesis has a number for identification purposes that appears at the right of the braces.

For example, if Atom 4 can be carbon, nitrogen or oxygen, the label appears as

If the set of possible elements contains more than three values, the label shows the first three values followed by ellipses (...). For example, if Atom4 can be an nitrogen, oxygen, fluorine or chlorine, the label appears as

Opening the Atom Specification Editor

If the attributes you specified for a selected atom in a hypothesis can only be found in the expanded Atom Specification editor, then the next time you open the editor to change the attributes of that same atom, you see a dialog box. It warns you that the atom has specifications that can only be found in the expanded Atom Specification Editor. You must immediately select the Expand Editor button to expand the editor. If you do not do so, and then you select OK in the contracted editor, you will lose all attributes that can only be specified in the expanded editor.

This is because when you select OK in any Atom Specification Editor, Catalyst clears all existing attributes and implements the ones that are specified in the Editor that you are currently using.

To Set Bond Specifications

You can use the Bond Specification editor to specify the possible bond types for a bond in a hypothesis, as follows:

Select the bond or bonds in the hypothesis.
Select the Bond Specification button in the Toolbox.

A window appears displaying the Bond Specification Editor as shown.
Use the Bond Specification Editor to select the possible bond types and to specify whether the bond is in a ring or not.
You can specify as many bond types as you want. For example, to specify that the bond must be a single bond, select the Single Bond button, or to specify that it must be a triple bond, select the Triple Bond button. To specify that it can be a double or an aromatic bond, select both the Double Bond and Aromatic Bond buttons. To specify that it can be any type of bond, select all bond types.

After selecting a bond type, you can click on it again to deselect it.

To specify that the bond is in a ring, select the Endocyclic button.

To specify that the bond is not in a ring, select the Exocyclic button.

If it doesn't matter whether the bond is in a ring or not, select both the Endocyclic and Exocyclic button.

To specify that the atoms at each end of a cis or trans double bond have the stereochemistry displayed in the hypothesis fragment, select the Use Bond Stereochemistry button.

You can return the specification to what it was when the editor first opened by selecting the Reset button.
When you have finished specifying bond constraints, select the OK button.

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Last updated April 18, 1996 at 05:22pm PDT.