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A Variety of Descriptors Combining Surface Area and Partial Charge Information

Source: R/315-extractDrugCPSA.R
extractDrugCPSA.Rd

A Variety of Descriptors Combining Surface Area and Partial Charge Information

Usage

extractDrugCPSA(molecules, silent = TRUE)

Arguments

molecules

Parsed molucule object.

silent

Logical. Whether the calculating process should be shown or not, default is TRUE.

Value

A data frame, each row represents one of the molecules, each column represents one feature. This function returns 29 columns:

  • PPSA.1 - partial positive surface area – sum of surface area on positive parts of molecule

  • PPSA.2 - partial positive surface area * total positive charge on the molecule

  • PPSA.3 - charge weighted partial positive surface area

  • PNSA.1 - partial negative surface area – sum of surface area on negative parts of molecule

  • PNSA.2 - partial negative surface area * total negative charge on the molecule

  • PNSA.3 - charge weighted partial negative surface area

  • DPSA.1 - difference of PPSA.1 and PNSA.1

  • DPSA.2 - difference of FPSA.2 and PNSA.2

  • DPSA.3 - difference of PPSA.3 and PNSA.3

  • FPSA.1 - PPSA.1 / total molecular surface area

  • FFSA.2 - PPSA.2 / total molecular surface area

  • FPSA.3 - PPSA.3 / total molecular surface area

  • FNSA.1 - PNSA.1 / total molecular surface area

  • FNSA.2 - PNSA.2 / total molecular surface area

  • FNSA.3 - PNSA.3 / total molecular surface area

  • WPSA.1 - PPSA.1 * total molecular surface area / 1000

  • WPSA.2 - PPSA.2 * total molecular surface area /1000

  • WPSA.3 - PPSA.3 * total molecular surface area / 1000

  • WNSA.1 - PNSA.1 * total molecular surface area /1000

  • WNSA.2 - PNSA.2 * total molecular surface area / 1000

  • WNSA.3 - PNSA.3 * total molecular surface area / 1000

  • RPCG - relative positive charge – most positive charge / total positive charge

  • RNCG - relative negative charge – most negative charge / total negative charge

  • RPCS - relative positive charge surface area – most positive surface area * RPCG

  • RNCS - relative negative charge surface area – most negative surface area * RNCG

  • THSA - sum of solvent accessible surface areas of atoms with absolute value of partial charges less than 0.2

  • TPSA - sum of solvent accessible surface areas of atoms with absolute value of partial charges greater than or equal 0.2

  • RHSA - THSA / total molecular surface area

  • RPSA - TPSA / total molecular surface area

Details

Calculates 29 Charged Partial Surface Area (CPSA) descriptors. The CPSA's were developed by Stanton et al.

References

Stanton, D.T. and Jurs, P.C. , Development and Use of Charged Partial Surface Area Structural Descriptors in Computer Assissted Quantitative Structure Property Relationship Studies, Analytical Chemistry, 1990, 62:2323.2329.

Examples

sdf = system.file('sysdata/OptAA3d.sdf', package = 'Rcpi')
# \donttest{
mol = readMolFromSDF(sdf)
#> Error in loadMolecules(normalizePath(sdffile)): The package "rcdk" is required to load molecular structures
dat = extractDrugCPSA(mol)
#> Error in evaluateDescriptor(molecules, type = "CPSADescriptor", silent = silent): The package "rcdk" is required to compute molecular descriptors
head(dat)# }
#> Error: object 'dat' not found