diff --git a/dev/.documenter-siteinfo.json b/dev/.documenter-siteinfo.json index 66e51be..2578470 100644 --- a/dev/.documenter-siteinfo.json +++ b/dev/.documenter-siteinfo.json @@ -1 +1 @@ -{"documenter":{"julia_version":"1.9.4","generation_timestamp":"2023-12-04T04:15:19","documenter_version":"1.2.1"}} \ No newline at end of file +{"documenter":{"julia_version":"1.9.4","generation_timestamp":"2023-12-11T04:15:54","documenter_version":"1.2.1"}} \ No newline at end of file diff --git a/dev/api/index.html b/dev/api/index.html index ed3a795..0c8e289 100644 --- a/dev/api/index.html +++ b/dev/api/index.html @@ -83,4 +83,4 @@ waterselector(at)

Determines if an AbstractResidue or AbstractAtom represents a water molecule, i.e. whether the residue name is in waterresnames.

source
BioStructures.writemmcif — Method
writemmcif(output, element, atom_selectors...; gzip=false)
 writemmcif(output, mmcif_dict; gzip=false)

Write a StructuralElementOrList or a MMCIFDict to a mmCIF format file or output stream.

Atom selector functions can be given as additional arguments - only atoms that return true from all the functions are retained. The keyword argument expand_disordered (default true) determines whether to return all copies of disordered residues and atoms. The keyword argument gzip (default false) determines if the output is gzipped.

source
BioStructures.writemultimmcif — Method
writemultimmcif(filepath, cifs; gzip=false)
 writemultimmcif(io, cifs; gzip=false)

Write multiple MMCIFDicts as a Dict{String, MMCIFDict} to a filepath or stream. The keyword argument gzip (default false) determines if the output is gzipped.

source
BioStructures.writepdb — Method
writepdb(output, element, atom_selectors...)

Write a StructuralElementOrList to a Protein Data Bank (PDB) format file or output stream.

Only ATOM, HETATM, MODEL and ENDMDL records are written - there is no header and there are no TER records. Atom selector functions can be given as additional arguments - only atoms that return true from all the functions are retained. The keyword argument expand_disordered (default true) determines whether to return all copies of disordered residues and atoms.

source
BioStructures.x! — Method
x!(at, val)

Set the x coordinate of an AbstractAtom to val.

For DisorderedAtoms only the default atom is updated.

source
BioStructures.x — Method
x(at)

Get the x coordinate of an AbstractAtom as a Float64.

source
BioStructures.y! — Method
y!(at, val)

Set the y coordinate of an AbstractAtom to val.

For DisorderedAtoms only the default atom is updated.

source
BioStructures.y — Method
y(at)

Get the y coordinate of an AbstractAtom as a Float64.

source
BioStructures.z! — Method
z!(at, val)

Set the z coordinate of an AbstractAtom to val.

For DisorderedAtoms only the default atom is updated.

source
BioStructures.z — Method
z(at)

Get the z coordinate of an AbstractAtom as a Float64.

source
MMTF.writemmtf — Method
writemmtf(output, element, atom_selectors...; gzip=false)
-writemmtf(output, mmtf_dict; gzip=false)

Write a StructuralElementOrList or a MMTFDict to a MMTF file or output stream.

Atom selector functions can be given as additional arguments - only atoms that return true from all the functions are retained. The keyword argument expand_disordered (default true) determines whether to return all copies of disordered residues and atoms. The keyword argument gzip (default false) determines if the file should be gzipped.

source
+writemmtf(output, mmtf_dict; gzip=false)

Write a StructuralElementOrList or a MMTFDict to a MMTF file or output stream.

Atom selector functions can be given as additional arguments - only atoms that return true from all the functions are retained. The keyword argument expand_disordered (default true) determines whether to return all copies of disordered residues and atoms. The keyword argument gzip (default false) determines if the file should be gzipped.

source diff --git a/dev/documentation/index.html b/dev/documentation/index.html index be5d928..44d3665 100644 --- a/dev/documentation/index.html +++ b/dev/documentation/index.html @@ -3422,4 +3422,4 @@ var viewer = $3Dmol.viewers['3dmol_viewer_2']; viewer.render(); }); -

See the Bio3DView.jl tutorial for more information. BioMakie.jl can also be used to visualise BioStructures objects.

Other packages in the Julia ecosystem that deal with structural bioinformatics or related fields include:

+

See the Bio3DView.jl tutorial for more information. BioMakie.jl can also be used to visualise BioStructures objects.

Other packages in the Julia ecosystem that deal with structural bioinformatics or related fields include:

diff --git a/dev/examples/index.html b/dev/examples/index.html index c2a3aa6..5727003 100644 --- a/dev/examples/index.html +++ b/dev/examples/index.html @@ -72,4 +72,4 @@ describe(df) # Show summary mean(df.tempfactor) # Column-wise operations sort(df, :x) # Sorting -CSV.write("1ALW.csv", df) # CSV file writing +CSV.write("1ALW.csv", df) # CSV file writing diff --git a/dev/index.html b/dev/index.html index 2e5659e..8554f22 100644 --- a/dev/index.html +++ b/dev/index.html @@ -1,2 +1,2 @@ -Home · BioStructures.jl
GitHub

BioStructures.jl

Latest Release:

Latest release License Documentation stable BioJulia maintainer: jgreener64

Development status:

Build status codecov.io Documentation dev

Description

BioStructures provides functionality to read, write and manipulate macromolecular structures, in particular proteins. Protein Data Bank (PDB), mmCIF and MMTF format files can be read in to a hierarchical data structure. Spatial calculations and functions to access the PDB are also provided. It compares favourably in terms of performance to other PDB parsers - see some benchmarks online.

Installation

Install BioStructures from the Julia package REPL, which can be accessed by pressing ] from the Julia REPL:

add BioStructures

See the documentation for information on how to use BioStructures.

Citation

If you use BioStructures, please cite the paper:

Greener JG, Selvaraj J and Ward BJ. BioStructures.jl: read, write and manipulate macromolecular structures in Julia, Bioinformatics 36(14):4206-4207 (2020) - link - PDF

Contributing and questions

We appreciate contributions from users including reporting bugs, fixing issues, improving performance and adding new features.

If you have a question about contributing or using this package, you are encouraged to use the #biology channel of the Julia Slack or the Bio category of the Julia discourse site.

+Home · BioStructures.jl
GitHub

BioStructures.jl

Latest Release:

Latest release License Documentation stable BioJulia maintainer: jgreener64

Development status:

Build status codecov.io Documentation dev

Description

BioStructures provides functionality to read, write and manipulate macromolecular structures, in particular proteins. Protein Data Bank (PDB), mmCIF and MMTF format files can be read in to a hierarchical data structure. Spatial calculations and functions to access the PDB are also provided. It compares favourably in terms of performance to other PDB parsers - see some benchmarks online.

Installation

Install BioStructures from the Julia package REPL, which can be accessed by pressing ] from the Julia REPL:

add BioStructures

See the documentation for information on how to use BioStructures.

Citation

If you use BioStructures, please cite the paper:

Greener JG, Selvaraj J and Ward BJ. BioStructures.jl: read, write and manipulate macromolecular structures in Julia, Bioinformatics 36(14):4206-4207 (2020) - link - PDF

Contributing and questions

We appreciate contributions from users including reporting bugs, fixing issues, improving performance and adding new features.

If you have a question about contributing or using this package, you are encouraged to use the #biology channel of the Julia Slack or the Bio category of the Julia discourse site.