topology: Topological Descriptor Characterizing the Carbon Connectivity...

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

Description

Topological Descriptor Characterizing the Carbon Connectivity in Terms of Hybridization

Calculates the Eccentric Connectivity Index Descriptor

Calculates the FMF Descriptor

Calculate Complexity of a System

Calculate Molecular Distance Edge (MDE) Descriptors for C, N and O

Descriptor that Calculates the Petitjean Number of a Molecule

Descriptor that Calculates the Petitjean Shape Indices

Descriptor that Calculates the Volume of A Molecule

Descriptor that Calculates the Vertex Adjacency Information of A Molecule

Descriptor that Calculates the Weighted Path (Molecular ID)

Descriptor that Calculates Wiener Path Number and Wiener Polarity Number

Descriptor that Calculates the Sum of the Squared Atom Degrees of All Heavy Atoms

Usage

extrDrugCarbonTypes(molecules, silent = TRUE)

extrDrugECI(molecules, silent = TRUE)

extrDrugFMF(molecules, silent = TRUE)

extrDrugFragmentComplexity(molecules, silent = TRUE)

extrDrugMDE(molecules, silent = TRUE)

extrDrugPetitjeanNumber(molecules, silent = TRUE)

extrDrugPetitjeanShapeIndex(molecules, silent = TRUE)

extrDrugVABC(molecules, silent = TRUE)

extrDrugVAdjMa(molecules, silent = TRUE)

extrDrugWeightedPath(molecules, silent = TRUE)

extrDrugWienerNumbers(molecules, silent = TRUE)

extrDrugZagrebIndex(molecules, silent = TRUE)

Arguments

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

Details

Calculates the carbon connectivity in terms of hybridization. The function calculates 9 descriptors in the following order:

• C1SP1 - triply hound carbon bound to one other carbon

• C2SP1 - triply bound carbon bound to two other carbons

• C1SP2 - doubly hound carbon bound to one other carbon

• C2SP2 - doubly bound carbon bound to two other carbons

• C3SP2 - doubly bound carbon bound to three other carbons

• C1SP3 - singly bound carbon bound to one other carbon

• C2SP3 - singly bound carbon bound to two other carbons

• C3SP3 - singly bound carbon bound to three other carbons

• C4SP3 - singly bound carbon bound to four other carbons

Eccentric Connectivity Index (ECI) is a topological descriptor combining distance and adjacency information. This descriptor is described by Sharma et al. and has been shown to correlate well with a number of physical properties. The descriptor is also reported to have good discriminatory ability. The eccentric connectivity index for a hydrogen supressed molecular graph is given by

x_i^c = ∑_{i = 1}^{n} E(i) V(i)

where E(i) is the eccentricity of the i-th atom (path length from the i-th atom to the atom farthest from it) and V(i) is the vertex degree of the i-th atom.

Calculates the FMF descriptor characterizing molecular complexity in terms of its Murcko framework. This descriptor is the ratio of heavy atoms in the framework to the total number of heavy atoms in the molecule. By definition, acyclic molecules which have no frameworks, will have a value of 0. Note that the authors consider an isolated ring system to be a framework (even though there is no linker).

This descriptor calculates the complexity of a system. The complexity is defined in Nilakantan, R. et al. as:

C = abs(B^2 - A^2 + A) + \frac{H}{100}

where C is complexity, A is the number of non-hydrogen atoms, B is the number of bonds and H is the number of heteroatoms.

This descriptor calculates the 10 molecular distance edge (MDE) descriptor described in Liu, S., Cao, C., & Li, Z, and in addition it calculates variants where O and N are considered.

This descriptor calculates the Petitjean number of a molecule. According to the Petitjean definition, the eccentricity of a vertex corresponds to the distance from that vertex to the most remote vertex in the graph.

The distance is obtained from the distance matrix as the count of edges between the two vertices. If r(i) is the largest matrix entry in row i of the distance matrix D, then the radius is defined as the smallest of the r(i). The graph diameter D is defined as the largest vertex eccentricity in the graph. (http://www.edusoft-lc.com/molconn/manuals/400/chaptwo.html)

The topological and geometric shape indices described Petitjean and Bath et al. respectively. Both measure the anisotropy in a molecule.

This descriptor calculates the volume of a molecule.

Vertex adjacency information (magnitude): 1 + \log_2^m where m is the number of heavy-heavy bonds. If m is zero, then 0 is returned.

This descriptor calculates the weighted path (molecular ID) described by Randic, characterizing molecular branching. Five descriptors are calculated, based on the implementation in the ADAPT software package. Note that the descriptor is based on identifying all paths between pairs of atoms and so is NP-hard. This means that it can take some time for large, complex molecules.

This descriptor calculates the Wiener numbers, including the Wiener Path number and the Wiener Polarity Number. Wiener path number: half the sum of all the distance matrix entries; Wiener polarity number: half the sum of all the distance matrix entries with a value of 3.

Zagreb index: the sum of the squares of atom degree over all heavy atoms i.

Value

A data frame, each row represents one of the molecules, each column represents one feature. This function returns 9 columns named C1SP1, C2SP1, C1SP2, C2SP2, C3SP2, C1SP3, C2SP3, C3SP3 and C4SP3.

WTPT WTPT.1, WTPT.2, WTPT.3, WTPT.4, WTPT.5:

• WTPT.1 - molecular ID

• WTPT.2 - molecular ID / number of atoms

• WTPT.3 - sum of path lengths starting from heteroatoms

• WTPT.4 - sum of path lengths starting from oxygens

• WTPT.5 - sum of path lengths starting from nitrogens

Author(s)

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

References

Sharma, V. and Goswami, R. and Madan, A.K. (1997), Eccentric Connectivity Index: A Novel Highly Discriminating Topological Descriptor for Structure-Property and Structure-Activity Studies, Journal of Chemical Information and Computer Sciences, 37:273-282

Yang, Y., Chen, H., Nilsson, I., Muresan, S., & Engkvist, O. (2010). Investigation of the relationship between topology and selectivity for druglike molecules. Journal of medicinal chemistry, 53(21), 7709-7714.

Nilakantan, R. and Nunn, D.S. and Greenblatt, L. and Walker, G. and Haraki, K. and Mobilio, D., A family of ring system-based structural fragments for use in structure-activity studies: database mining and recursive partitioning., Journal of chemical information and modeling, 2006, 46:1069-1077

Liu, S., Cao, C., & Li, Z. (1998). Approach to estimation and prediction for normal boiling point (NBP) of alkanes based on a novel molecular distance-edge (MDE) vector, lambda. Journal of chemical information and computer sciences, 38(3), 387-394.

Petitjean, M., Applications of the radius-diameter diagram to the classification of topological and geometrical shapes of chemical compounds, Journal of Chemical Information and Computer Science, 1992, 32:331-337

Bath, P.A. and Poirette, A.R. and Willet, P. and Allen, F.H. , The Extent of the Relationship between the Graph-Theoretical and the Geometrical Shape Coefficients of Chemical Compounds, Journal of Chemical Information and Computer Science, 1995, 35:714-716.

Randic, M., On molecular identification numbers (1984). Journal of Chemical Information and Computer Science, 24:164-175.

Wiener, H. (1947). Structural determination of paraffin boiling points. Journal of the American Chemical Society, 69(1), 17-20.

Examples

# Topological Descriptor Characterizing the Carbon Connectivity 
# in Terms of Hybridization
smi = system.file('vignettedata/test.smi', package = 'BioMedR')
mol = readMolFromSmi(smi, type = 'mol')
dat = extrDrugCarbonTypes(mol)
head(dat)

# Calculates the Eccentric Connectivity Index Descriptor
smi = system.file('vignettedata/test.smi', package = 'BioMedR')
mol = readMolFromSmi(smi, type = 'mol')
dat = extrDrugECI(mol)
head(dat)

# Calculates the FMF Descriptor
smi = system.file('vignettedata/test.smi', package = 'BioMedR')
mol = readMolFromSmi(smi, type = 'mol')
dat = extrDrugFMF(mol)
head(dat)

# Calculate Complexity of a System
smi = system.file('vignettedata/test.smi', package = 'BioMedR')
mol = readMolFromSmi(smi, type = 'mol')
dat = extrDrugFragmentComplexity(mol)
head(dat)

# Calculate Molecular Distance Edge (MDE) Descriptors for C, N and O
smi = system.file('vignettedata/test.smi', package = 'BioMedR')
mol = readMolFromSmi(smi, type = 'mol')
dat = extrDrugMDE(mol)
head(dat)

# Calculates the Petitjean Number of a Molecule
smi = system.file('vignettedata/test.smi', package = 'BioMedR')
mol = readMolFromSmi(smi, type = 'mol')
dat = extrDrugPetitjeanNumber(mol)
head(dat)

# Calculates the Petitjean Shape Indices
sdf = system.file('sysdata/test.sdf', package = 'BioMedR')
mol = readMolFromSDF(sdf)
dat = extrDrugPetitjeanShapeIndex(mol)
head(dat)

# Calculates the Volume of A Molecule
smi = system.file('vignettedata/test.smi', package = 'BioMedR')
mol = readMolFromSmi(smi, type = 'mol')
dat = extrDrugVABC(mol)
head(dat)

# Calculates the Vertex Adjacency Information of A Molecule
smi = system.file('vignettedata/test.smi', package = 'BioMedR')
mol = readMolFromSmi(smi, type = 'mol')
dat = extrDrugVAdjMa(mol)
head(dat)

# Calculates the Weighted Path (Molecular ID)
smi = system.file('vignettedata/test.smi', package = 'BioMedR')
mol = readMolFromSmi(smi, type = 'mol')
dat = extrDrugWeightedPath(mol)
head(dat)

# Calculates Wiener Path Number and Wiener Polarity Number
smi = system.file('vignettedata/test.smi', package = 'BioMedR')
mol = readMolFromSmi(smi, type = 'mol')
dat = extrDrugWienerNumbers(mol)
head(dat)

# Calculates the Sum of the Squared Atom Degrees 
# of All Heavy Atoms
smi = system.file('vignettedata/test.smi', package = 'BioMedR')
mol = readMolFromSmi(smi, type = 'mol')
dat = extrDrugZagrebIndex(mol)
head(dat)

BioMedR documentation built on July 5, 2019, 9:03 a.m.