Input formats

Currently supported input file formats with different models:

File type	Surface model	Volume model	Charges included
HMO	✓		✓
Mcsf		✓
MSMS	✓
OFF	✓
PQR			✓ (charges only)
STL	✓

HMO

NESSie.Format.readhmo — Function

readhmo(
    stream::IOStream,
          ::Type{T}=Float64
)

Reads a complete surface model from the given HMO file.

Return type

Model{T, Triangle{T}}

Alias

readhmo(fname::AbstractString, ::Type{T}=Float64)

Reads the model using a file name rather than a IOStream object.

source

Mcsf

NESSie.Format.readmcsf — Function

readmcsf(
    stream::IOStream,
          ::Type{T}=Float64;
    # kwargs
    domain::Symbol=:none
)

Reads a volume model from the given GAMer-generated mcsf file.

Note

This file type does not support charge models! Hence, the charge list of the returning Model object is empty and has to be set separately.

Arguments

domain Element domain (solute :Ω, solvent :Σ, or :none)

Return type

Model{T, Tetrahedron{T}}

Aliases

readmcsf(
    fname ::AbstractString,
          ::Type{T}=Float64;
    # kwargs
    domain::Symbol=:none
)

Reads the model using a file name rather than a IOStream object.

readmcsf(
    fnameΩ::AbstractString,
    fnameΣ::AbstractString,
          ::Type{T}=Float64
)

Reads the contents of two separate files (given by name), sets the element domains to :Ω or :Σ, respectively, and returns a single (merged) Model object.

source

MSMS

NESSie.Format.readmsms — Function

readmsms(
    vertstream::IOStream,
    facestream::IOStream,
              ::Type{T}=Float64
)

Reads a surface model from the given MSMS-generated .face and .vert files.

Note

This file type does not support charge models! Hence, the charge list of the returning Model object is empty and has to be set separately.

Return type

Model{T, Triangle{T}}

Alias

readmsms(fname::AbstractString, ::Type{T}=Float64)

Reads the model using a common file name prefix (fname.{vert,face}) for both files rather than IOStream objects.

source

OFF

NESSie.Format.readoff — Function

readoff(
    stream::IOStream,
          ::Type{T}=Float64
)

Reads a surface model from the given OFF file.

Note

This file type does not support charge models! Hence, the charge list of the returning Model object is empty and has to be set separately.

Specification

http://www.geomview.org/docs/html/OFF.html

Return type

Model{T}

Alias

readoff(fname::AbstractString, ::Type{T}=Float64)

Reads the model using a file name rather than a IOStream object.

source

PQR

NESSie.Format.readpqr — Function

readpqr(
    stream::IOStream,
          ::Type{T}=Float64
)

Reads a charge model from the given PQR file.

Specification

https://pdb2pqr.readthedocs.io/en/latest/formats/pqr.html

Return type

Vector{Charge{T}}

Alias

readpqr(fname::AbstractString, ::Type{T}=Float64)

Reads the charge model using a file name rather than a IOStream object.

source

STL

NESSie.Format.readstl — Function

readstl(
    stream::IOStream,
          ::Type{T}=Float64
)

Reads a surface model from the given STL file.

Note

This file type does not support charge models! Hence, the charge list of the returning Model object is empty and has to be set separately.

Specification

https://fabbers.com/tech/STL_Format

Return type

Model{T, Triangle{T}}

Alias

readstl(
    fname::AbstractString,
         ::Type{T}=Float64
)

Reads the model using a file name rather than an IOStream object.

source