PaDEL-Descriptor KNIME plugin


  1. Version 2.21.0 [21 Jul 2014]: Fixed bug involving descriptors based calculation of intrinsic states (e.g. electrotopological state, extended topochemical atom) that sometimes prevents the calculation of these descriptors. Modified the chi path descriptors such that average simple path and average valence path will output zero instead of blank if there are no paths of a particular order. Modified Barysz matrix, detour matrix and topological distance descriptors so that they will not given invalid values for EE and VE3 or very large values for VR1 and VR2.
  2. Version 2.20.0 [16 Jul 2014]: Fixed bug involving descriptors based on Barysz matrix and Burden modified eigenvalues that prevent program from stopping when molecule contained invalid atoms.
  3. Version 2.19.0 [26 Jun 2014]: Added Average molecular weight, 346 2D autocorrelation descriptors (these replaced the previous 15 autocorrelation descriptors and the values of ATSc1-c5, ATSm1-m5 and ATSp1-p5 will have different values from previous version), 91 descriptors based on Barysz matrix, 96 Burden modified eigenvalues, 16 chi path descriptors (average simple path and average valence path), 12 constitutional descriptors, 11 descriptors based on detour matrix, 42 information content descriptors, 22 path counts descriptors, 20 topological charge descriptors (globalTopoChargeIndex was shifted from topological descriptor to this and renamed as JGT), 11 descriptors based on topological distance matrix, 20 walk counts descriptors, 80 3D autocorrelation descriptors, 210 RDF descriptors and 91 WHIM descriptors (the previous 85 WHIM descriptors were removed as the weightings were not consistent with the new set of descriptors such as autocorrelation, Barysz, Burden modified, etc. G1 to G3 descriptors could not be calculated due to error in algorithm which could not be fixed). Add two fingerprints based on 2D atom pairs. Improve calculation speed for WeightedPathDescriptor, ElectrotopologicalStateAtomTypeDescriptor, ExtendedTopochemicalAtomDescriptor.
  4. Version 2.18.0 [01 Jul 2013]: Added 3 rotatable bond descriptors (RotBFrac, nRotBt, RotBtFrac), 34 ring count descriptors for rings containing heteroatoms, 3 topological descriptors (topoRadius, topoDiameter, globalTopoChargeIndex), 2 geometrical descriptors (geomRadius, geomDiameter). Shifted topoShape descriptor from PetitjeanShapeIndexDescriptor (3D descriptor) to TopologicalDescriptor (2D descriptor) since it is a 2D descriptor so as to prevent repeated calculations of distance matrix. Fixed bug in dearomatization of some compounds. Thanks to Dr Carol Marchant for reporting the bug.
  5. Version 2.17.0 [27 Mar 2013]: Fixed bug in Fragment complexity descriptor where it includes the number of bonds to hydrogen atoms in its calculation. Thanks to Dr Tom Dickson for reporting the bug.
  6. Version 2.16.0 [15 Mar 2013]: Fixed bug in Carbon types descriptors where it may calculate the number of carbons types wrong for aromatic compounds. Thanks to Prof Paola Gramatica and Dr Stefano Cassani for reporting the bug.
  7. Version 2.15.0 [04 Feb 2013]: Fixed bug introduced in v2.14 preventing SubstructureFingerprintCount and KlekotaRothFingerprintCount from working. Thanks to Daichi Yukihira from Kyushu University for reporting the bug.
  8. Version 2.14.1 [05 Dec 2012]: Added CDK "Molecule to CDK" node as a temporary workaround to the current incompatibility with CDK nodes. Note that the output from this "Molecule to CDK" node is to serve as input for the "PaDEL-Descriptor" node only.
  9. Version 2.14.0 [04 Dec 2012]: First release.

Last modified on 17 July, 2014 by Yap Chun Wei