geometric: Descriptor Characterizing the Mass Distribution of the...

In wind22zhu/BioMedR: Generating Various Molecular Representations for Chemicals, Proteins, DNAs, RNAs and Their Interactions

Description

Descriptor Characterizing the Mass Distribution of the Molecule.

Calculates the Ratio of Length to Breadth Descriptor

Descriptor that Calculates the Principal Moments of Inertia and Ratios of the Principal Moments

Usage

extrDrugGravitationalIndex(molecules, silent = TRUE)

extrDrugLengthOverBreadth(molecules, silent = TRUE)

extrDrugMomentOfInertia(molecules, silent = TRUE)

Arguments

molecules	Parsed molucule object.
silent	Logical. Whether the calculating process should be shown or not, default is TRUE.

Details

Descriptor characterizing the mass distribution of the molecule described by Katritzky et al. For modelling purposes the value of the descriptor is calculated both with and without H atoms. Furthermore the square and cube roots of the descriptor are also generated as described by Wessel et al.

Calculates the Ratio of Length to Breadth, as a result ti does not perform any orientation and only considers the X & Y extents for a series of rotations about the Z axis (in 10 degree increments).

A descriptor that calculates the moment of inertia and radius of gyration. Moment of inertia (MI) values characterize the mass distribution of a molecule. Related to the MI values, ratios of the MI values along the three principal axes are also well know modeling variables. This descriptor calculates the MI values along the X, Y and Z axes as well as the ratio's X/Y, X/Z and Y/Z. Finally it also calculates the radius of gyration of the molecule.

Value

A data frame, each row represents one of the molecules, each column represents one feature. This function returns 9 columns:

• GRAV.1 - gravitational index of heavy atoms

• GRAV.2 - square root of gravitational index of heavy atoms

• GRAV.3 - cube root of gravitational index of heavy atoms

• GRAVH.1 - gravitational index - hydrogens included

• GRAVH.2 - square root of hydrogen-included gravitational index

• GRAVH.3 - cube root of hydrogen-included gravitational index

• GRAV.4 - grav1 for all pairs of atoms (not just bonded pairs)

• GRAV.5 - grav2 for all pairs of atoms (not just bonded pairs)

• GRAV.6 - grav3 for all pairs of atoms (not just bonded pairs)

extrDrugLengthOverBreadth: This function returns two columns named LOBMAX and LOBMIN:

• LOBMAX - The maximum L/B ratio;

• LOBMIN - The L/B ratio for the rotation that results in the minimum area (defined by the product of the X & Y extents for that orientation).

extrDrugMomentOfInertia: This function returns 7 columns named MOMI.X, MOMI.Y, MOMI.Z, MOMI.XY, MOMI.XZ, MOMI.YZ, MOMI.R:

• MOMI.X - MI along X axis

• MOMI.Y - MI along Y axis

• MOMI.Z - MI along Z axis

• MOMI.XY - X/Y

• MOMI.XZ - X/Z

• MOMI.YZ - Y/Z

• MOMI.R - Radius of gyration

One important aspect of the algorithm is that if the eigenvalues of the MI tensor are below 1e-3, then the ratio's are set to a default of 1000.

Note

extrDrugLengthOverBreadth : The descriptor assumes that the atoms have been configured.

Author(s)

Min-feng Zhu <[e-mail]>, Nan Xiao <http://r2s.name>

References

Katritzky, A.R. and Mu, L. and Lobanov, V.S. and Karelson, M., Correlation of Boiling Points With Molecular Structure. 1. A Training Set of 298 Diverse Organics and a Test Set of 9 Simple Inorganics, J. Phys. Chem., 1996, 100:10400-10407.

Wessel, M.D. and Jurs, P.C. and Tolan, J.W. and Muskal, S.M. , Prediction of Human Intestinal Absorption of Drug Compounds From Molecular Structure, Journal of Chemical Information and Computer Sciences, 1998, 38:726-735.

Examples

sdf = system.file('sysdata/test.sdf', package = 'BioMedR')
mol = readMolFromSDF(sdf)
# Descriptor Characterizing the Mass Distribution of the Molecule
dat = extrDrugGravitationalIndex(mol)
head(dat)

# Calculates the Ratio of Length to Breadth Descriptor
dat = extrDrugLengthOverBreadth(mol)
head(dat)

# Descriptor that Calculates the Principal Moments of 
# Inertia and Ratios of the Principal Moments
dat = extrDrugMomentOfInertia(mol)
head(dat)

wind22zhu/BioMedR documentation built on Oct. 21, 2019, 12:51 p.m.