Surface Calculation

Description

The function executes the implemented methods. Using this function, it is possible to calculate occluded areas through the traditional methodology, 'Occluded Surface', or by applying the 'Fibonacci OS' methodology. At the end of the method execution, the 'prot.srf' file is generated, and returned for the function. The data in this file refers to all contacts between atoms of molecules present in a protein's PDB.

Usage

execute(pdb, method, density_dots)

Arguments

Value

A data frame containing the protein surface data read from the generated SRF file.

Author(s)

Carlos Henrique da Silveira (carlos.silveira@unifei.edu.br)

Herson Hebert Mendes Soares (hersonhebert@hotmail.com)

Joao Paulo Roquim Romanelli (joaoromanelli@unifei.edu.br)

Patrick Fleming (Pat.Fleming@jhu.edu)

Install the 'Python' 'fibos' Module

Description

This function creates a 'Python' virtual environment and installs the 'Python' module 'fibos' required for the full functionality of this package. It handles different system configurations and ensures that the correct compiler paths are set.

Usage

fibos_config()

Note

This function will install external software (a 'Python' package) on your system. Administrator/sudo privileges might be required on some systems.

See Also

occluded_surface()

osp()

Examples

# Set up the 'Python' environment and install the required module
fibos_config()

Load Radii Values

Description

The 'get_radii' function is responsible for loading the atomic radii values used for surface-occlusion calculations. The values it returns are those currently employed in those calculations.

Usage

get_radii()

Value

A data frame containing the radii values.

Author(s)

Carlos Henrique da Silveira (carlos.silveira@unifei.edu.br)

Herson Hebert Mendes Soares (hersonhebert@hotmail.com)

Joao Paulo Roquim Romanelli (joaoromanelli@unifei.edu.br)

Patrick Fleming (Pat.Fleming@jhu.edu)

See Also

set_radii()

reset_radii()

Examples

library(fibos)
fibos_config()
#Loads the radius values that have been configured for code execution.
radii = get_radii()
#Displays the first three lines.
radii |> utils::head(3) |> print()

Occluded Surface (OS)

Description

The 'Occluded Surface (OS)' algorithm is a widely used approach for analyzing atomic packing in biomolecules. Here, we introduce 'FIBOS', an 'R' and 'Python' package that extends the 'OS' methodology with enhancements. The homonymous function 'occluded_surface' calculates 'OS' per atom.

Usage

occluded_surface(pdb, method = "FIBOS", density_dots = 5)

Arguments

Details

'Occluded Surface (OS)' (Pattabiraman et al. 1995) method distributes dots (representing patches of area) across the atom surfaces. Each dot has a normal that extends until it reaches either a van der Waals surface of a neighboring atom (the dot is considered occluded) or covers a distance greater than the diameter of a water molecule (the dot is considered non-occluded and disregarded). Thus, with the summed areas of dots and the lengths of normals, it is possible to compose robust metrics capable of inferring the average packing density of atoms, residues, proteins, as well as any other group of biomolecules.

For more details, see (Fleming et al, 2000) and (Soares, et al, 2024)

Value

A table containing:

ATOM

the atomic contacts for each atom.

NUMBER OF POINTS

the number of dots (patches of area) on atomic surface.

AREA

the summed areas of dots.

RAYLENGTH

the average lengths of normals normalized by 2.8 \text{\AA} (water diameter). So, raylen is a value between 0 and 1. A raylen close to 1 indicates worse packaging.

DISTANCE

the average distances of contacts in (\text{\AA}).

Author(s)

Herson Soares, Joao Romanelli, Patrick Fleming, Carlos Silveira.

References

Fleming PJ, Richards FM (2000). "Protein packing: Dependence on protein size, secondary structure and amino acid composition." doi:10.1006/jmbi.2000.3750

Pattabiraman N, Ward KB, Fleming PJ (1995). "Occluded molecular surface: Analysis of protein packing." doi:10.1002/jmr.300080603

Soares HHM, Romanelli JPR, Fleming PJ, da Silveira CH (2024). "bioRxiv, 2024.11.01.621530." doi:10.1101/2024.11.01.621530

See Also

osp()

Examples

library(fibos)

#Configure the environment
fibos_config()

# Calculate FIBOS per atom and create .srf files in fibos_files folder
pdb_fibos <- occluded_surface("1ptx", method = "FIBOS", density_dots = 5.0)

# Calculate OSP metric per residue from .srf file in fibos_files folder
pdb_osp <- osp(fs::path("fibos_files","prot_1ptx.srf"))

Occluded Surface Packing (OSP)

Description

Implements the 'occluded surface' packing density metric (OSP) averaged by residue, as described in (Fleming and Richards 2000).

Usage

osp(file)

Arguments

Value

A table containing:

Resnum

residue id.

Resname

residue name.

OS

the summed areas of dots in residue.

`os*[1-raylen]`

'OS' areas weighted by (1-raylen). Raylen is the average lengths of normals normalized by 2.8 \text{\AA} (water diameter). So, raylen is a value between 0 and 1. A raylen close to 1 indicates worse packaging, and the 'OS' will be reduced.

OSP

average occluded surface packing value (OSP) by residue.

Author(s)

Herson Soares

Joao Romanelli

Patrick Fleming

Carlos Silveira.

References

Fleming PJ, Richards FM (2000). "Protein packing: Dependence on protein size, secondary structure and amino acid composition." doi:10.1006/jmbi.2000.3750

Pattabiraman N, Ward KB, Fleming PJ (1995). "Occluded molecular surface: Analysis of protein packing." doi:10.1002/jmr.300080603

Soares HHM, Romanelli JPR, Fleming PJ, da Silveira CH (2024). "bioRxiv, 2024.11.01.621530." doi:10.1101/2024.11.01.621530

See Also

occluded_surface()

Examples

library(fibos)

#Configure the Environment
fibos_config() 

# Calculate FIBOS per atom and create .srf files in fibos_files folder
pdb_fibos <- occluded_surface("1ptx", method = "FIBOS", density_dots = 5.0)
# Calculate OSP metric per residue from .srf file in fibos_files folder
pdb_osp <- osp(fs::path("fibos_files","prot_1ptx.srf"))

Calculate OSP Metric

Description

Internal function to calculate the OSP metric from an SRF file. This function calls the 'Python' implementation of the OSP calculation.

Usage

osp_internal(file)

Arguments

Value

A data frame containing the OSP metric data read from the generated PAK file.

Author(s)

Carlos Henrique da Silveira (carlos.silveira@unifei.edu.br)

Herson Hebert Mendes Soares (hersonhebert@hotmail.com)

Joao Paulo Roquim Romanelli (joaoromanelli@unifei.edu.br)

Patrick Fleming (Pat.Fleming@jhu.edu)

Read OSP Values

Description

Internal function to read OSP values from a PAK file generated by the OSP calculation.

Usage

read_osp(prot_file)

Arguments

Value

A data frame containing the OSP data.

Read Protein Surface File

Description

Reads and processes data from protein surface files generated by the 'occluded_surface' function. The results enable important analyses of protein behavior at the atomic level.

Arguments

Details

The function reads a surface file containing data calculated using the 'OS' or 'FIBOS' methodology. The file should be in the format generated by the 'occluded_surface' function.

Value

A data frame with the following columns:

ATOM

atomic contact identifiers

NUMBER_POINTS

number of points (integer) on atomic surface

AREA

surface area (numeric)

RAYLENGTH

average ray length (numeric)

DISTANCE

average distance of contacts (numeric)

Author(s)

Carlos Henrique da Silveira (carlos.silveira@unifei.edu.br)

Herson Hebert Mendes Soares (hersonhebert@hotmail.com)

Joao Paulo Roquim Romanelli (joaoromanelli@unifei.edu.br)

Patrick Fleming (Pat.Fleming@jhu.edu)

Reset Radii Values

Description

This function reloads the 'OS' default atomic radii values.

Usage

reset_radii()

Author(s)

Carlos Henrique da Silveira (carlos.silveira@unifei.edu.br)

Herson Hebert Mendes Soares (hersonhebert@hotmail.com)

Joao Paulo Roquim Romanelli (joaoromanelli@unifei.edu.br)

Patrick Fleming (Pat.Fleming@jhu.edu)

See Also

get_radii()

set_radii()

Examples

library(fibos)
fibos_config()
#Loads the radius values that have been configured for code execution.
radii = get_radii()
#Displays the first three lines.
radii |> utils::head(3) |> print()
#Modifies the value of a specific radius.
radii$RAY[1] = 2.15
#Sets the radius value from a tibble.
set_radii(radii)
#Displays the first three lines.
get_radii() |> utils::head(3) |> print()
#Loads the default radius values.
reset_radii()
#Displays the first three lines.
get_radii() |> utils::head(3) |> print()

Change Radii Values

Description

This function enables modification of the radius values by passing a 'data.frame' as an argument.

Usage

set_radii(radii_values)

Arguments

Author(s)

Carlos Henrique da Silveira (carlos.silveira@unifei.edu.br)

Herson Hebert Mendes Soares (hersonhebert@hotmail.com)

Joao Paulo Roquim Romanelli (joaoromanelli@unifei.edu.br)

Patrick Fleming (Pat.Fleming@jhu.edu)

See Also

get_radii()

reset_radii()

Examples

library(fibos)
fibos_config()
#Loads the radius values that have been configured for code execution.
radii = get_radii()
#Displays the first three lines.
radii |> utils::head(3) |> print()
#Modifies the value of a specific radius.
radii$RAY[1] = 2.15
#Sets the radius value from a tibble.
set_radii(radii)
#Displays the first three lines.
get_radii() |> utils::head(3) |> print()