Description Usage Arguments Details Value Note Author(s) References Examples
View source: R/411extractDrugBCUT.R
BCUT – Eigenvalue Based Descriptor
1  extrDrugBCUT(molecules, silent = TRUE)

molecules 
Parsed molucule object. 
silent 
Logical. Whether the calculating process
should be shown or not, default is 
Eigenvalue based descriptor noted for its utility in chemical diversity. Described by Pearlman et al. The descriptor is based on a weighted version of the Burden matrix which takes into account both the connectivity as well as atomic properties of a molecule. The weights are a variety of atom properties placed along the diagonal of the Burden matrix. Currently three weighting schemes are employed:
Atomic Weight
Partial Charge (Gasteiger Marsilli)
Polarizability (Kang et al.)
A data frame, each row represents one of the molecules, each column represents one feature. This function returns 6 columns:
BCUTw1l, BCUTw2l ...
 n high lowest atom weighted BCUTS
BCUTw1h, BCUTw2h ...
 n low highest atom weighted BCUTS
BCUTc1l, BCUTc2l ...
 n high lowest partial charge weighted BCUTS
BCUTc1h, BCUTc2h ...
 n low highest partial charge weighted BCUTS
BCUTp1l, BCUTp2l ...
 n high lowest polarizability weighted BCUTS
BCUTp1h, BCUTp2h ...
 n low highest polarizability weighted BCUTS
By default, the descriptor will return the highest and lowest eigenvalues for the three classes of descriptor in a single ArrayList (in the order shown above). However it is also possible to supply a parameter list indicating how many of the highest and lowest eigenvalues (for each class of descriptor) are required. The descriptor works with the hydrogen depleted molecule.
A side effect of specifying the number of highest and lowest eigenvalues is that it is possible to get two copies of all the eigenvalues. That is, if a molecule has 5 heavy atoms, then specifying the 5 highest eigenvalues returns all of them, and specifying the 5 lowest eigenvalues returns all of them, resulting in two copies of all the eigenvalues.
Note that it is possible to specify an arbitrarily large number of
eigenvalues to be returned. However if the number (i.e., nhigh or nlow)
is larger than the number of heavy atoms, the remaining eignevalues
will be NaN
.
Given the above description, if the aim is to gt all the eigenvalues for a molecule, you should set nlow to 0 and specify the number of heavy atoms (or some large number) for nhigh (or vice versa).
Minfeng Zhu <wind2zhu@163.com>, Nan Xiao <http://r2s.name>
Pearlman, R.S. and Smith, K.M., Metric Validation and the ReceptorRelevant Subspace Concept, J. Chem. Inf. Comput. Sci., 1999, 39:2835.
Burden, F.R., Molecular identification number for substructure searches, J. Chem. Inf. Comput. Sci., 1989, 29:225227.
Burden, F.R., Chemically Intuitive Molecular Index, Quant. Struct. Act. Relat., 1997, 16:309314
Kang, Y.K. and Jhon, M.S., Additivity of Atomic Static Polarizabilities and Dispersion Coefficients, Theoretica Chimica Acta, 1982, 61:4148
1 2 3 4  smi = system.file('vignettedata/test.smi', package = 'BioMedR')
mol = readMolFromSmi(smi, type = 'mol')
dat = extrDrugBCUT(mol)
head(dat)

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