SUBSTRUCTURE SEARCHES

Typical Uses of Substructure Searching

Layout of the Draw Window

Modes in the Draw Window

Fundamentals of Drawing

Drawing a Bond

Drawing an Isolated Atom

Drawing a Bond from an Existing Atom

Drawing a Bond to an Existing Atom

Drawing a Bond between Two Existing Atoms

Undoing Mistakes when Drawing Substructures

Selecting Atoms and Bonds

Deleting Atoms and Bonds

Drawing and Fusing Rings

Adding a Ring to a Blank Drawing Area

Adding a Ring to an Atom in an Existing Substructure

Fusing a New Ring to an Existing Ring

Creating a Spiro-Fusion

Fusing Rings by Moving One Ring onto Another

Atom Properties

Changing the Current Element Type

Setting Variable Element Types

Changing the Element Types of Existing Atoms

Automatic Addition of Hydrogen Atoms

Adding Hydrogen Atoms Manually

Setting Atomic Charges

Setting Atom Coordination Numbers

Defining Cyclic or Acyclic Atoms

Bond Properties

Changing the Current Bond Type

Setting Variable Bond Types

Changing the Types of Existing Bonds

Defining Cyclic or Acyclic Bonds

Avoiding Unwanted Bonds and Rings

Avoiding Unwanted Bonds between Atoms in a Substructure

Avoiding Unwanted Cyclic Bonds to Atoms outside the Substructure

Ensuring that a Ring System has no Additional Bridging or Fusion

Specifying Variable Points of Attachment

Finding Molecules Containing Two or More Substructures

Using Chemical Groups and Substructure Templates

Adding a Chemical Group to an Existing Atom

Changing an Atom to a Chemical Group

Expanding a Chemical Group

Accessing Standard Substructure Templates

Saving and Using Customised Templates

Substructure Display Conventions

Advanced Drawing Options

Moving Atoms

Rotating Substructures

Resizing Substructures

Duplicating Substructures (Copy, Cut and Paste)

Changing Default Drawing Options

Pasting in Substructures from Isis/Draw

Reading MDL MOL Files

Starting Searches and Closing the Draw Window

Hints for Substructure Searching