Grid generation, methods

Liseikiii, V.D., 1999. Grid Generation Methods, Springer-Verlag, Berlin. 

Once the vector fields are constructed, they can be used to extrapolate the internal boundaries to the external boimdary. This divides the volume inside the external boundary into large pieces whose boundaries can be used as the external boundary of a standard structured grid generation method such as the area-orthogonality method. See [57] for the details and some illustrations. 

Figure 6.16. Manual pharmacophore mapping by measuring distances between pharmacophore points in every compound and conformation considered. Pharmacophore elements are highlighted with circles. All structures were built and minimized using QUANTA. Conformers of 4-hydroxy piperidinol were generated using the Grid Scan method from QUANTA, followed by clustering, to identify unique conformers.

Within the quantum chemical description of molecular electron density clouds, a natural criterion, the Density Domain criterion, provides a quantum chemical definition for functional groups [14-18]. Furthermore, techniques that generate fuzzy electron density contributions for local molecular moieties that are analogous to the fuzzy electron density clouds of complete molecules, determined by the analytic Additive Fuzzy Density Fragmentation (AFDF) method [19-21], or the earlier numerical-grid MEDLA method [22,23], are also... 

The first generation methods that were proposed involved interface reconstruction and approximation of the singular interfacial term from the 2D interface properties. These models thus rely on a proper numerical procedure to locate the interface within the mesh based on the volume fraction field. The local curvature may then be calculated in each surface grid cell. 

The most common method of field-based descriptor generation draws a 3D grid around a molecule and then determines the value of the property of interest (steric, electrostatic, or hydrophobic) at each lattice intersection of the grid. This method originally came from work by Carbo et al. [72] to calculate electron density descriptors, and has been extended by others (e.g., Refs. 73 74 75) to include electrostatic potentials and steric fields. 

Molecular interaction fields can also be generated using GRIN/GRID. This method is especially reliable because it is based on a very careful parametrization of the interaction terms. The parameters are founded from experimental crystallographic data that is, the direction, type and typical strength of a particular interaction are classified according to actual crystals. 

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