extractDrugCPSA {Rcpi} | R Documentation

## A Variety of Descriptors Combining Surface Area and Partial Charge Information

### Description

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`.

### Details

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

### 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

### Author(s)

Nan Xiao <https://nanx.me>

### 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')

    mol = readMolFromSDF(sdf)
    dat = extractDrugCPSA(mol)
    head(dat)

[Package Rcpi version 1.20.1 Index]