Software | Details |
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CDK | Theoretically, the roto-translation of a molecule should not change any molecular property. However, TPSA and LengthOverBreadth descriptors resulted in different values of molecules before and after roto-translation transformation |
The value of ChiPathCluster is invalid because the patterns are not adequate (fixed in the latest version of CDK) | |
PaDEL | Several molecules (e.g., Cyanidin) resulted in invalid values in many descriptors (e.g., nH (hydrogen count) returned 12) when using the default configuration owing to a bug in the aromaticity detecting procedure and/or 3D conformer generator of PaDEL-Descriptor. This caused breakage of an aromatic ring and attachment to an invalid hydrogen |
Some descriptors use the log sum exponential (LSE) function (\({\text{LSE}}_{1}\) below), which is prone to arithmetic overflow or underflow. The LSE trick (\({\text{LSE}}_{2}\) below) should be used to avoid this issue \({\text{LSE}}_{1} \left( {x_{1} ,x_{2} , \ldots , x_{n} } \right) = { \log }\left( {\mathop \sum \limits_{i = 1}^{n} { \exp }\left( {x_{i} } \right)} \right)\) \(\begin{array}{*{20}c} {{\text{LSE}}_{2} \left( {x_{1} ,x_{2} , \ldots , x_{n} } \right) = x^{ *} + \log \left( {\mathop \sum \limits_{i = 1}^{n} \exp \left( {x_{i} - x^{*} } \right)} \right)} \\ {x^{ *} = \hbox{max} \left( {x_{1} ,x_{2} , \ldots ,x_{n} } \right)} \\ \end{array}\) | |
In the constitutional descriptor, discrepancies might be induced in the algorithm implementation owing to incorrect code reuse | |
ChemoPy | Cannot calculate exact values of modified Zagreb index 2 |