MetaAtoms

This command is used to input substructures having to do with thermodynamic corrections for substructures. The form of the command is:

MetaAtoms Filename Test

where:

• MetaAtoms: The command keyword
• Filename: The filename (relative to the current directory) of the thermodaynamic substructure information.
• Test: If true, just the file will be read in to check for errors (no database modifications). If false, the file will be read in and the database modified.

The Source is used to use to delete all thermodynamics having the same Source name. The purpose of this command is to initialize or update all thermodynamic entries with this Source name

Before running this command, it is suggested that you backup the database. A Sample input is:

     MetaAtoms MetaAtomsLinear.txt true

where:

MetaAtoms: The keyword

MetaAtomsLinear.txt: The filename in the current directory (this is to define linear meta atoms)

Test: true is to just read in the files without modifying the database.

Database Modifications

The databases that are modified are:

• MetaAtomInfo: Each line of the input file creates a meta atom
• CMLStructures: This is the structure created with each meta atom.

Sample Input

By convention, though not necessity, each file creates a single class of meta atoms. For example, the file for defining meta atoms for linear atoms would have several lines that look like this example:

R/C///C/R   LinearGeneralEthyne L-CtC LinearStructure

These four fields, the nancy format, the name of the meta-atom, the substitution string and the class of meta-atoms, define a new meta or replace an older meta-atom (with the same meta-atom name).

To find the expected input to the MetaAtoms command, just give:

java -jar JThermodynamicData-1.0-jar-with-dependencies.jar MetaAtoms

Structures Filename ReferenceName

Filename: 

Test: if true, will not enter data in database 

To test the input file, in this case MetaAtomsLinear.txt which is in the same directory as the terminal command, with test in the last field. The output shows for each for each line the input. Here show the output for the first line:

java -jar .JThermodynamicData-1.0-jar-with-dependencies.jar MetaAtoms MetaAtomsLinear.txt true

=========================================

Parsed Information=======================

NancyLinearFormToMolecule: R/C///C/R

NancyLinearFormToMolecule: R/C///C/R

org.openscience.cdk.libio.cml.Convertor WARN: Duplicate attempt to register a customizer

org.openscience.cdk.libio.cml.Convertor WARN: Duplicate attempt to register a customizer

org.openscience.cdk.libio.cml.Convertor WARN: Duplicate attempt to register a customizer

=========================================

MetaAtomInfo: Name: L-CtC  Type: LinearStructure Structure: LinearGeneralEthyne 

<?xml version="1.0" encoding="ISO-8859-1"?>

<molecule id="LinearGeneralEthyne" xmlns="http://www.xml-cml.org/schema">

  <atomArray>

    <atom id="a0" elementType="R" formalCharge="0"/>

    <atom id="a1" elementType="C" formalCharge="0"/>

    <atom id="a2" elementType="C" formalCharge="0"/>

    <atom id="a3" elementType="R" formalCharge="0"/>

  </atomArray>

  <bondArray>

    <bond id="b1" atomRefs2="a1 a0" order="S"/>

    <bond id="b2" atomRefs2="a2 a1" order="T"/>

    <bond id="b3" atomRefs2="a3 a2" order="S"/>

  </bondArray>

</molecule>

=========================================

If there were no errors in the test, then the command can be given to actually change the database. This is done with false as the last argument:

java -jar .JThermodynamicData-1.0-jar-with-dependencies.jar MetaAtoms MetaAtomsLinear.txt false

Read file and upload to database