Chapter 2

3    Creating, Modifying and Deleting Atoms and Molecules

3.1 Creating Molecules

Although molecules are normally read into THINK from an external file (see section 2.1), there are occasions when it may be more convenient to create a simple molecule by typing the appropriate SMILES string instead of creating a file and then reading the file into THINK. Molecules may be entered by typing the SMILES string into the Edit > Create dialog and then picking the Create button. Alternatively they may be entered in command mode using the OPEN command and supplying "TTY" as the name of the input file. Note that the filename is case-sensitive (to support the LINUX operating system) and "TTY" must be supplied in uppercase.

THINK v1.25 does not support the creation of individual atoms.

Commands		Dialogs
OPEN FILE=TTY MOLECULE=c1cncc1		Edit > Create

3.2 Graphical 2D editor

The 2D molecule display includes functionality to edit a molecule using the mouse, the drawing tools and the right mouse button popup menu. The drawing tools provide a subset of the functionality found on the menu and are described in the following table.

Tool	Menu item	Action
	Element ..	Selects the element for new or existing picked atoms (includes a periodic table)
	Insert atom	Insert atom at picked coordinates
	Insert bond	Insert bond between picked atoms
	Bond order ..	Changes the order of the picked bond
	Sprout atom	Insert atom connected to picked atom
	Delete atom	Delete picked atom
	Delete bond	Delete bond between picked atoms or bond
	Rings > 6 atoms	Insert 6-membered saturated ring at picked coordinates, atom or bond
	Rings > 5 atoms	Insert 5-membered saturated ring at picked coordinates, atom or bond
	Rings > 4 atoms	Insert 4-membered saturated ring at picked coordinates, atom or bond
	Rings > 3 atoms	Insert 3-membered saturated ring at picked coordinates, atom or bond
	Rings > Aromatic 6	Insert 6-membered aromatic ring at picked coordinates, atom or bond
	Rings > Aromatic 5	Insert 5-membered aromatic ring at picked coordinates, atom or bond
	Undo	Undo previous action (maximum 10)
	Tidy	Regenerates 2D coordinates

Notes

• When a bond is picked with the Insert Bond tool the bond order cycles through the series single > double > triple.
• When an atom is picked with a ring insertion tool, the atom is included in the ring.
• When a bond is picked with a ring insertion tool, the bond is included in the ring. This can be used to build fused rings. The order of the existing bond will be changed to aromatic when an aromatic ring is being inserted.
• Hydrogens are not normally displayed and need not be drawn - they are added automatically when using other functionality in the program.

THINK v1.25 does not contain functionality to select sets of atoms for deletion or supporting splitting a molecule into multiple molecules.

3.3 Modifying Molecules

Bonds may be made or broken within the MODIFY command using the MAKE-BOND and BREAK-BOND keywords respectively. The bond is defined by the two atoms and the bond order:

The MAKE-BOND keyword may be used to change the bond order of an existing bond.

The atom type, name, serial number or group number of any atom or collection of atoms may be changed using the MODIFY command. The atom(s) to be altered are identified with the CHANGE keyword, and the new data is supplied with the TYPE, NAME, SERIAL and GROUP keywords. If a set of atoms is to be changed, it may be specified as a range of serial numbers, such as (3:7), or via a symbol (see sections 1.4 and 1.6.1). All the atoms in the set will be given the new name, etc, which may lead to multiple atoms sharing the same identification, so this option must be used with caution.

If the keyword construct "SERIAL=#" is used, the serial number of each atom in the set will be altered to reflect the position of the atom within the molecule. Thus, the first atom will be given serial number 1, the second 2, etc. When applied to all the atoms in a molecule, this is a quick method of assigning unique serial numbers.

After deleting atoms (see below) or changing the bonds or atom types within a molecule, it is recommended that the molecule is rebuilt to update the coordinates and connectivity. THINK will regenerate the 2D or 3D coordinates or just the connectivity depending upon the REBUILD option used (2D, 3D or CONNECTIONS respectively). The molecule to be rebuilt is identified with the MOLECULE keyword.

The molecule name may be altered. The molecule is identified with the MOLECULE keyword and the new name is supplied with the TO keyword. If desired, the conformation number may be set or altered as part of the same command.

3.4 Deleting Molecules

The Edit > Delete dialog is used to delete molecules. An individual molecule may be deleted by selecting its name from the list, or all the molecules in the list may be cleared in a single operation. Selective lists of molecules may be deleted by changing the filter at the top of the dialog (the default filter is "*", which lists all molecules) and then deleting all the molecules in the resulting list.

Alternatively, molecules may be deleted using the DELETE command. The molecule(s) are specified with the MOLECULE keyword, and may include wildcards. The keyword construct "MOLECULE=*" may be used to delete all molecules.

Individual atoms or sets of atoms may be deleted using the DELETE keyword within the MODIFY command.

Commands		Dialogs
DELETE MOLECULE=CAPSINV5		Edit > Delete
DELETE MOLECULE=GLY*		Edit > Delete
MODIFY DELETE=H(*)		Not available from dialog

Chapter 4