A molecule has an atomCount describing the number of atoms in the molecule
and an InChI key [16] that is meant to be a unique identifier for each molecule in
the system. The InChI string and InChI key are defined by IUPAC and may or may
not exist for each molecule. The value “nil” or “” indicates that no InChI key was
returned from IUPAC software. Each molecule is made up of atoms.
Atom
All atoms in a molecule must have an id attribute of the form “a1”, “a2”, “a3”, etc.
These identifiers are used to describe the resulting bonds.
An atom has a number of children including the elementSymbol, elementName,
etc.
• elementSymbol—this is just normal symbol such as C, Cl, etc.
• elementName—this is the full name for the element such as Carbon, Chlorine,
etc.
• atomName—for macromolecules an atom may have a pertinent name such as
CA, CB for the alpha, beta carbons in a chain. For normal molecules, the default
names are:
– H
– MainGroup
– Metal
– Row1TM
– Row2TM
– Row3TM
– Lanthanide
– Actinide
– NobleGas
• atomMass—the mass in amu
• formalAtomCharge—integer charge such as +1 for the N in NH 4
• calculatedAtomCharge—as used in molecular mechanics coulomb interactions
• x/y/zCoord3D—the three Cartesian coordinates of an atom
• basisSet—the basis set is a property of each atom and may be different for
different atoms
• coordination—describes the other atoms to which this atom is connected.
Bond
Bonds in CSX are a property of atoms. The XML coordination element describes
these, as children of coordination. The bondCount attribute of coordination is the
number of bonds that this atom participates in. Each bond is a child of the atom’s
coordination with attributes id1 and id2 that describe the two connected atoms. This
means that each bond is described twice—as a grandchild of the atom with attribute
A Portal for Quantum Chemistry Data …
13
and an InChI key [16] that is meant to be a unique identifier for each molecule in
the system. The InChI string and InChI key are defined by IUPAC and may or may
not exist for each molecule. The value “nil” or “” indicates that no InChI key was
returned from IUPAC software. Each molecule is made up of atoms.
Atom
All atoms in a molecule must have an id attribute of the form “a1”, “a2”, “a3”, etc.
These identifiers are used to describe the resulting bonds.
An atom has a number of children including the elementSymbol, elementName,
etc.
• elementSymbol—this is just normal symbol such as C, Cl, etc.
• elementName—this is the full name for the element such as Carbon, Chlorine,
etc.
• atomName—for macromolecules an atom may have a pertinent name such as
CA, CB for the alpha, beta carbons in a chain. For normal molecules, the default
names are:
– H
– MainGroup
– Metal
– Row1TM
– Row2TM
– Row3TM
– Lanthanide
– Actinide
– NobleGas
• atomMass—the mass in amu
• formalAtomCharge—integer charge such as +1 for the N in NH 4
• calculatedAtomCharge—as used in molecular mechanics coulomb interactions
• x/y/zCoord3D—the three Cartesian coordinates of an atom
• basisSet—the basis set is a property of each atom and may be different for
different atoms
• coordination—describes the other atoms to which this atom is connected.
Bond
Bonds in CSX are a property of atoms. The XML coordination element describes
these, as children of coordination. The bondCount attribute of coordination is the
number of bonds that this atom participates in. Each bond is a child of the atom’s
coordination with attributes id1 and id2 that describe the two connected atoms. This
means that each bond is described twice—as a grandchild of the atom with attribute
A Portal for Quantum Chemistry Data …
13