Atomic coordinates canonical order

In a molecular structure file, an atom record typically contains all of the information about that atom the atomic number or symbol, the charge, coordinates, etc. When such a file is parsed into a SMILES string and an array of coordinates, it is important to be able to associate the proper coordinate with the proper atom. The use of canonical SMILES ensures this. Because canonical SMILES defines a unique order of the atoms in a molecule, that order is used to store the coordinates. Later sections of this chapter will discuss ways in which atomic coordinates might be stored in columns of a table. 

The column structure.id is a unique integer relating the structure, sdf and property tables. The sdf.molfile column contains the molfile for each structure as defined by the vendor. The structure.name and structure.cansmiles columns contain the name and canonical smiles parsed and computed from the molfile. The structure.coord column will contain an array of atomic coordinates. The structure, atom column will contain an array of atom numbers from the file in canonical order to correspond to the atom order in the canonical SMILES. The OpenBabel/plpythonu extension functions molfile mol and molfile properties will be used to parse the vendor SDF molfiles and populate these tables. The molfile column of the sdf table is first populated from the SDF file, using the following perl script. 

With an accurate expression for the configurational energy, i.e., the energy as a function of the coordinates of all atoms in the system, it is, in principle, possible to compute with confidence any property of the system. For example, we can formally apply the FEP, TI, or LRA methods to compute the free energy of solvation. In order to obtain these thermodynamic quantities it is necessary to generate the canonical ensemble. 

Here Xk is the coordinate for the fcth vibrational mode, Pk is the canonical momentum, and 1 is the 2 x 2 unit matrix. Mass- and frequency-weighted coordinates are used here, as well as atomic units (n = l. Each individual Hamiltonian Hk consists of three different parts The first one is a harmonic Oth-order Hamiltonian with frequency cOk, the second term represents the linear elements which couple the two electronic states, while the third contribution contains the quadratic and bilinear terms. The quantities and i Y j) are the intrastate and interstate... 

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