HeatMapWrapper (version 0.16)

Please see README.txt for details. This program was adapted from version 0.13: https://doi.org/10.5281/zenodo.161170

N.B. Please note the following points.

1. All atom and bond score values reported by this program are estimates of the original values, derived from the color vector of the HeatmapViewer.jar dependency. They may differ slightly from the true values, due to integer rounding of the color vector values by the HeatmapViewer.jar program, with color vector elements (0 - 255) recalculated from the estimated normalized scores differing by up to 1.0 (out of 255).

2. The magnitudes, but not the signs, of the raw atom score estimates are underestimated by a constant factor of 2.0. This bug has been fixed in version 0.17: https://doi.org/10.5281/zenodo.824214. Moreover, values generated via version 0.16 can be readily fixed using a script to multiply them by a constant value of 2.0, e.g. http://doi.org/10.5281/zenodo.557101

3. If the molecule of interest, for which a Heat Map image is being derived, contains Au or Ag atoms, the implementation of Symmetrized Single Molecule Normalization and Constant Symmetrized Normalization may fail. This is because these symmetrized normalization schemes are implemented via running Full Set Normalization using HeatmapViewer.jar, with the original molecule supplemented by Au and Ag diatomic dummy molecules.