Linear Atom Test

This set of tests examines the Linear Atoms. There are several ways to examine the LinearAtom database:

• List: List the set of LinearAtom elements available (by name).
• Examine: Examine a particular Linear Atom.
• Single: Test a single LinearAtom from the database on a molecule.
• Full: Test all the available LinearAtom on a molecule

List

The following command lists all the Linear Atom in the system:

LinearAtom List

where:

• LinearAtom: The keyword for examining the Linear Atom database
• List: The keyword to list all the names of the Linear Atom

For example, the following command:

LinearAtom List

gives the output:

Note that the Linear atom name is the substitution meta atom with a prefix "LinearStructure." and the CMLStructure is the CMLStructure the group definition found in CMLStructures.

Element

The following command lists all the Linear Atom in the system:

Linear Atom Element name

where:

• LinearAtom: The keyword for examining the Linear Atom database
• List: The keyword to retrieve the Linear atom
• name: the name of the symmetry element to retrieve

For example, the following command:

LinearAtom Element "LinearStructure.L-CN"

gives the output:

Single

The command:

LinearAtomTest Single molecule element

where:

• LinearAtomTest: the keyword for Linear Atom tests
• Single: The keyword signalling the testing of a single Linear Atom element
• molecule: The molecule in Nancy linear form
• element: The database name of the Linear Atom

The output is in three parts:

• The structure of the molecule
• The molecule after the linear atom is substituted

For example, to test one of the peroxyl group Linear Atom on dimethy peroxide (quotes are used around the molecule and element because of the special characters:

LinearAtomTest Single "ch3/o/o/ch3" LinearAtom.oo

The output is:

Here, the linear CN group atoms:

were replaced by a single LinearAtom

The bonding also changed from:

to:

Full

The command:

LinearAtomTest Full molecule

where:

• LinearAtomTestTest: the keyword for Linear Atom tests
• Full: The keyword signalling the testing of Linear Atom on the molecule
• molecule: The molecule in Nancy linear form

The output is in two parts:

• The structure of the molecule
• The molecule after the linear atom is substituted

For example, to test Linear Atom recognition of JThermodynamics on a completely linear dicyanide molecule (quotes are used around the molecule and element because of the special characters):

LinearAtomTest Full "n///c/c/c///n"

The output is:

Multiple substitutions

The following is to Illustrate that consecutive linear atoms get reduced down to single linear atom:

The case is NCCCH where there are two triple bonds in a row, CC and CN:

Basically the whole molecule is linear and is reduced to a single linear atom: