Message-ID: <1049003118.51.1632427449657.JavaMail.bigchem@cpu> Subject: Exported From Confluence MIME-Version: 1.0 Content-Type: multipart/related; boundary="----=_Part_50_1206447212.1632427449657" ------=_Part_50_1206447212.1632427449657 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Content-Location: file:///C:/exported.html KrakenX

KrakenX

Types of descriptors

KrakenX mainly focuses on 3D and topographical descriptors (topological = descriptors with 3D features included). Using the software, the following s= et of descriptors can be either derived or directly extracted from the MOPA= C output files:

1. Quantum chemical: Quantities such as the heat of for= mation, area, volume, HOMO, LUMO, HOMO-LUMO gap, dipole moment, electronic = energy, total self polarizability, electron-nuclear attraction and repulsio= n energies, total electrophilic and nucleophilic delocalizabilities, princi= pal moments of inertia, polarizability and hyperpolarizability, the vibrati= onal, rotational and translational values for the enthalpy, enthalpy and he= at capacity.

2. Atomic charge-based: Minimum and maximum atomic part= ial charge, polarity parameters, partial charge-weighted topological electr= onic descriptor, local dipole index, total squared charge, total absolute c= harge, total positive and negative charge.

3. CPSA: Charge partial surface area descriptors that c= ombine partial charges and atomic solvent accessible surface areas (solvent= radius set to 1.4 Å).

4. EVA/EEVA: A density distribution-based (pseudo-= spectral descriptors) eigenvalue (EVA) and electronic eigenvalue (EEVA) des= criptors that are derived from the vibrational frequencies and molecular or= bital energies of a geometry-optimized structure.

5. Shape and geometry: This class of descriptors includ= es 3D Wiener index, inertial shape factor, radius of gyration, ovality, mol= ecular eccentricity, asphericity, globularity, radial distribution function= (RDF), 3D Molecule Representation of Structure based on Electron diffracti= on (MoRSE), Weighted Holistic Invariant Molecular (WHIM).

6. Topographical: 3D topological distance-based autocor= relation descriptors can be calculated by considering the average Euclidean= distance between all atoms located at a given topological distance $d$. 3D= BCUT values can be calculated by encoding 3D atomic properties (charge, se= lf-polarizability etc.) on the diagonals of the molecular connection table = with off-diagonals encoding interatomic distances.

7. Coulomb Matrix: A global descriptor which mimics the= electrostatic interaction between nuclei.

8. Graph energy: The ordinary energy of a graph is= defined as the sum of the absolute values of the eigenvalues of its adjace= ncy matrix. Here, ```KrakenX ``` calculates an atomic property weighted equ= ivalent.

 

For each atom, the charge, electrophilic and nucleophilic frontier elect= ron density, the electrophilic, nucleophilic and radical superdelocalizabil= ity, and the atom selfpolarizability are used as atom-level weights in the = calculation of descriptors such as the RDF, MoRSE, WHIM, and autocorrelatio= n vectors. The atom-centered charges can be set to either the default MOPAC= derived values, electrostatic potential (ESP), or user-defined charges (UD= F) such as those based on the electronegativity equalization method.

 

If you use the software in your study, kindly cite the following article= :

KRAKENX: software for the generation of alignment-independent 3D descrip= tors. Venkatraman, V. and Alsberg, B.K. J. Mol. Model., 22(4), 1-8, 2016.

 

The source code is available at https://gitlab.com/vishsof= t/krakenx

 

 

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