What's new in PaDEL-Descriptor 2.21
Jul 21, 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.
New in PaDEL-Descriptor 2.20 (Jul 17, 2014)
- Fixed bug involving descriptors based on Barysz matrix and Burden modified eigenvalues that prevent program from stopping when molecule contained invalid atoms.
New in PaDEL-Descriptor 2.19 (Jul 17, 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.
New in PaDEL-Descriptor 2.18 (Jul 2, 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.
New in PaDEL-Descriptor 2.17 (Apr 4, 2013)
- Fixed bug in Fragment complexity descriptor where it includes the number of bonds to hydrogen atoms in its calculation.
New in PaDEL-Descriptor 2.15 (Mar 5, 2013)
- Fixed bug introduced in v2.14 preventing SubstructureFingerprintCount and KlekotaRothFingerprintCount from working
New in PaDEL-Descriptor 2.14 (Dec 7, 2012)
- Bug fixes for mol2 files.
- Added option to restrict maximum descriptor calculation time for a molecule as suggested by Dr Filip Stefaniak.
- Developed KNIME nodes for PaDEL-Descriptor.
- Updated CDK library to 1.4.15.
New in PaDEL-Descriptor 2.13 (Sep 27, 2012)
- Update "Standardize nitro groups" to standarize nitro groups to N+(=O)O-, following a feedback by Prof Paola Gramatica and Dr Stefano Cassani.
- Updated "Detect aromaticity" code to handle dearomatization and re-aromatization of rings better and to dearomatize conjugation compounds. Due to these changes, some descriptors (e.g. nH, nBondsM, nHBDon_Lipinski, MAXDN2, MAXDP2 and DELS2) may have different values from v2.12, especially for compounds containing nitro groups, multiple fused aromatic rings and conjugation.
- Updated CDK library to 1.4.13.
New in PaDEL-Descriptor 2.12 (May 23, 2012)
- Added the following descriptors (nX, nBondsM, CrippenLogP, CrippenMR, MAXDN2, MAXDP2 and DELS2) as suggested by Prof Paola Gramatica and Dr Stefano Cassani. Fixed a bug in atom type electrotopological state which prevented some aromatic atoms from being recognized as hydrogen bond donors or acceptors.
- Updated "Detect aromaticity" code and added "Standardize tautomers" and "Standardize nitro groups" to help standardize molecules prior to 2D descriptors calculations.
- Updated CDK library to a customized version of 1.4.9, which fixed some concurrency problems.
- Uses AMBIT2 library to standardize tautomers and handling of SMIRKS.
- Replaced "Remove salt" and "Detect aromaticity" operators for RapidMiner with "Standardize" operator.
- Added "Get SMILES" operator for RapidMiner.
New in PaDEL-Descriptor 2.11 (Jan 5, 2012)
- Fixed a bug in extended topochemical atom (ETA) descriptors which did not take into account conjugation with an aromatic system. Thanks to A/Prof Kunal Roy for pointing it out.
New in PaDEL-Descriptor 2.10 (Dec 23, 2011)
- Added 43 extended topochemical atom (ETA) descriptors as suggested by the developer, A/Prof Kunal Roy. A/Prof Kunal provided invaluable help by describing the ETA algorithm detailedly, providing correct ETA descriptor values for some compounds, and taking part in the testing of the beta version.
New in PaDEL-Descriptor 2.9 (Dec 7, 2011)
- Updated CDK library to 1.4.6. This new version of CDK library has a bug fix which affects the value of chi valence descriptors (i.e. VCH-3, VCH-4, VCH-5, VCH-6, VCH-7, VC-3, VC-4, VC-5, VC-6, VPC-4, VPC-5, VPC-6, VP-0, VP-1, VP-2, VP-3, VP-4, VP-5, VP-6, VP-7) for all molecules containing SO2. In earlier versions of CDK library, the delta valence value for S in SO2 was calculated as 1.33 instead of 2.67. This was fixed in CDK 1.4.6.
New in PaDEL-Descriptor 2.7 (Sep 21, 2011)
- Added feature to allow PaDEL-Descriptor to retain order of molecules in the descriptor file as suggested by Dr Tobias Kind.
- Added variants of hydrogen bond acceptor and donor counts descriptors (nHBAcc2, nHBAcc3, nHBAcc_Lipinski, nHBDon_Lipinski) as suggested by Prof Paola Gramatica and Dr Stefano Cassani.
- Added feature to allow PaDEL-Descriptor to calculate descriptors from a single structural file as suggested by Prof Alexander Tropsha and Dr Andy Fant.
- Added VABC descriptors.
- Added feature to allow PaDEL-Descriptor to get molecule name from filename instead of from within the file.
- Fixed bug with reading Hyperchem (HIN) files. Revert CDK library to 1.4.2.
New in PaDEL-Descriptor 2.6 (Aug 9, 2011)
- Change PubChem fingerprints (PubChemFP) to start numbering from 0 instead of 1 so as to be consistent with naming convention in PubChem fingerprints documentation.
New in PaDEL-Descriptor 2.4 (Sep 23, 2010)
- Fixed bug which prevents PaDEL-Descriptor from working properly.
- Added ability to write multiple molecules into a SDF file when used as a RapidMiner extension.
New in PaDEL-Descriptor 2.3 (Aug 30, 2010)
- Fixed bug which prevents PaDEL-Descriptor from working properly when used as a RapidMiner extension.
New in PaDEL-Descriptor 2.1 (May 25, 2010)
- Change descriptor names from nB, nBs, nBd, nBt, nBq to bBonds, nBondsS, nBondsD, nBondsT, nBondsQ to prevent conflict in names between nB (number of bonds excluding bonds with hydrogen atoms) and nB (number of Boron atoms).
New in PaDEL-Descriptor 1.10 (May 12, 2010)
- Fixed bug which causes Java Exception errors if file to save descriptors to does not have a file extension.