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Calculation of topological/topochemical descriptors.

































































































periodicTable = rdchem.GetPeriodicTable()


_log2val = 0.69314718056


__package__ =

Imports: Chem, Graphs, rdchem, rdMolDescriptors, PeriodicTable, numpy, math, entropy

*Internal Use Only* this is just a row sum of the matrix... simple, neh? 
calculate the HallKier alpha value for a molecule From equations (58) of Rev. Comp. Chem. vol 2, 367422, (1991) 
This returns the information content of the coefficients of the characteristic polynomial of the adjacency matrix of a hydrogensuppressed graph of a molecule. 'avg = 1' returns the information content divided by the total population. From D. Bonchev & N. Trinajstic, J. Chem. Phys. vol 67, 45174533 (1977) 
HallKier Kappa1 value From equations (58) and (59) of Rev. Comp. Chem. vol 2, 367422, (1991) 
HallKier Kappa2 value From equations (58) and (60) of Rev. Comp. Chem. vol 2, 367422, (1991) 
HallKier Kappa3 value From equations (58), (61) and (62) of Rev. Comp. Chem. vol 2, 367422, (1991) 
From equations (1),(9) and (10) of Rev. Comp. Chem. vol 2, 367422, (1991) 
From equations (1),(11) and (12) of Rev. Comp. Chem. vol 2, 367422, (1991) 
From equations (5),(9) and (10) of Rev. Comp. Chem. vol 2, 367422, (1991) 
From equations (5),(11) and (12) of Rev. Comp. Chem. vol 2, 367422, (1991) 
From equations (5),(15) and (16) of Rev. Comp. Chem. vol 2, 367422, (1991) **NOTE**: because the current path finding code does, by design, detect rings as paths (e.g. in C1CC1 there is *1* atom path of length 3), values of ChiNv with N >= 3 may give results that differ from those provided by the old code in molecules that have rings of size 3. 
From equations (5),(15) and (16) of Rev. Comp. Chem. vol 2, 367422, (1991) 
From equations (5),(15) and (16) of Rev. Comp. Chem. vol 2, 367422, (1991) 
From equations (5),(15) and (16) of Rev. Comp. Chem. vol 2, 367422, (1991) **NOTE**: because the current path finding code does, by design, detect rings as paths (e.g. in C1CC1 there is *1* atom path of length 3), values of Chi4v may give results that differ from those provided by the old code in molecules that have 3 rings. 
Similar to Hall Kier ChiNv, but uses nVal instead of valence This makes a big difference after we get out of the first row. **NOTE**: because the current path finding code does, by design, detect rings as paths (e.g. in C1CC1 there is *1* atom path of length 3), values of ChiNn with N >= 3 may give results that differ from those provided by the old code in molecules that have rings of size 3. 
Similar to Hall Kier Chi4v, but uses nVal instead of valence This makes a big difference after we get out of the first row. **NOTE**: because the current path finding code does, by design, detect rings as paths (e.g. in C1CC1 there is *1* atom path of length 3), values of Chi4n may give results that differ from those provided by the old code in molecules that have 3 rings. 
Calculate Balaban's J value for a molecule **Arguments**  mol: a molecule  dMat: (optional) a distance/adjacency matrix for the molecule, if this is not provide, one will be calculated  forceDMat: (optional) if this is set, the distance/adjacency matrix will be recalculated regardless of whether or not _dMat_ is provided or the molecule already has one **Returns**  a float containing the J value We follow the notation of Balaban's paper: Chem. Phys. Lett. vol 89, 399404, (1982) 
Used by BertzCT vdList: the number of neighbors each atom has bdMat: "balaban" distance matrix 
_Internal Use Only_ Used by BertzCT 
A topological index meant to quantify "complexity" of molecules. Consists of a sum of two terms, one representing the complexity of the bonding, the other representing the complexity of the distribution of heteroatoms. From S. H. Bertz, J. Am. Chem. Soc., vol 103, 35993601 (1981) "cutoff" is an integer value used to limit the computational expense. A cutoff value tells the program to consider vertices topologically identical if their distance vectors (sets of distances to all other vertices) are equal out to the "cutoff"th nearestneighbor. **NOTE** The original implementation had the following comment: > this implementation treats aromatic rings as the > corresponding Kekule structure with alternating bonds, > for purposes of counting "connections". Upon further thought, this is the WRONG thing to do. It results in the possibility of a molecule giving two different CT values depending on the kekulization. For example, in the old implementation, these two SMILES: CC2=CN=C1C3=C(C(C)=C(C=N3)C)C=CC1=C2C CC3=CN=C2C1=NC=C(C)C(C)=C1C=CC2=C3C which correspond to differentk kekule forms, yield different values. The new implementation uses consistent (aromatic) bond orders for aromatic bonds. THIS MEANS THAT THIS IMPLEMENTATION IS NOT BACKWARDS COMPATIBLE. Any molecule containing aromatic rings will yield different values with this implementation. The new behavior is the correct one, so we're going to live with the breakage. **NOTE** this barfs if the molecule contains a second (or nth) fragment that is one atom. 
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