BioMakie API

UniProtData::DataType

A struct containing all the information from a UniProt entry.

General information

accession id protinfo gene gene_synonyms secondary_accession sequence organism datainfo

Features

molecule_processing domains_and_sites structural ptm sequence_information mutagenesis variants topology other_features

Comments

func catalytic_activity subunit subcellular_location interaction tissue_specificity polymorphism allergen web_resource similarity miscellaneous other_comments

Database references (EMBL, PDB, etc.)

dbrefs

atomcolors( atoms )

Get a Vector of colors for the atoms. To see all default element and amino acid colorschemes, use getbiocolors(). Keyword argument colors takes a Dict which maps element to color. ("C" => :red)

This function uses 'MIToS.PDB.bestoccupancy' or 'defaultatom' to ensure only one position per atom.

Keyword Arguments:

• colors –- elecolors | Options - elecolors, aquacolors

atomradii( atoms )

Collect atom radii based on element for plotting.

Keyword Arguments:

• radiustype –- :ballandstick | Options - :cov, :covalent, :vdw, :vanderwaals, :bas, :ballandstick, :spacefilling

atomradius( atom )

Collect atom radius based on element for plotting.

Keyword Arguments:

• radiustype –- :ballandstick | Options - :cov, :covalent, :vdw, :vanderwaals, :bas, :ballandstick, :spacefilling

atomsizes( atms )

Get a Vector of sizes for the atoms from a BioStructures.StructuralElementOrList.

This function uses 'MIToS.PDB.bestoccupancy' or 'defaultatom' to ensure only one position per atom.

Keyword Arguments:

• radiustype –- :ballandstick | Options - :cov, :covalent, :vdw, :vanderwaals, :bas, :ballandstick, :spacefilling

backbonebonds( chn::BioStructures.Chain ) -> BitMatrix

Returns a matrix of backbone bonds in chn, where Mat[i,j] = 1 if atoms i and j are bonded.

Keyword Arguments:

• cutoff –––––- 1.6 # distance cutoff for bonds

bestoccupants( residues::Vector{MIToS.PDB.PDBResidue} )

Get an OrderedDict of the best occupancy atoms for each residue.

bondshape( twoatoms )
bondshape( twopoints )

Returns a (mesh) cylinder between two atoms or atomic coordinates.

Keyword Arguments:

• bondwidth ––––––- 0.2

bondshapes( structure )
bondshapes( residues )
bondshapes( coordinates )
bondshapes( structure, bondmatrix )
bondshapes( residues, bondmatrix )
bondshapes( coordinates, bondmatrix )

Returns a (mesh) cylinder between two atoms or points.

Keyword Arguments:

• algo ––––––––– :knowledgebased | :distance, :covalent # unless bondmatrix is given
• distance ––––––– 1.9 # unless bondmatrix is given
• bondwidth ––––––- 0.2

covalentbonds( atms ) -> BitMatrix

Returns a matrix of all bonds in atms, where Mat[i,j] = 1 if atoms i and j are bonded.

This function uses 'bestoccupancy' or 'defaultatom' to ensure only one position per atom.

Keyword Arguments:

• extradistance –– 0.14 # fudge factor for better inclusion
• H –––––––– true # include bonds with hydrogen atoms
• disulfides –––- false # include disulfide bonds

distancebonds( atms ) -> BitMatrix

Returns a matrix of all bonds in atms, where Mat[i,j] = 1 if atoms i and j are bonded.

This function uses 'bestoccupancy' or 'defaultatom' to ensure only one position per atom.

Keyword Arguments:

• cutoff –––––- 1.9 # distance cutoff for bonds between heavy atoms
• hydrogencutoff –- 1.14 # distance cutoff for bonds with hydrogen atoms
• H –––––––– true # include bonds with hydrogen atoms
• disulfides –––- false # include disulfide bonds

firstlabel( inspectorfunc::Function )

Show an example of the inspector label function looks like. The position p will not be available to this function, so it will be set to nothing.

getbonds( chn::BioStructures.Chain, selectors... ) -> BitMatrix
getbonds( modl::BioStructures.Model, selectors... ) -> BitMatrix
getbonds( struc::BioStructures.MolecularStructure, selectors... ) -> BitMatrix

Returns a matrix of all bonds in chn, where Mat[i,j] = 1 if atoms i and j are bonded.

This function uses 'bestoccupancy' or 'defaultatom' to ensure only one position per atom.

Keyword Arguments:

• algo ––––––- :knowledgebased # (:distance, :covalent) algorithm to find bonds
• H –––––––– true # include bonds with hydrogen atoms
• cutoff –––––- 1.9 # distance cutoff for bonds between heavy atoms
• extradistance –– 0.14 # fudge factor for better inclusion
• disulfides –––- false # include disulfide bonds

getbonds( residues ) -> BitMatrix

Returns a matrix of all bonds in residues::Vector{MIToS.PDB.PDBResidue}, where Mat[i,j] = 1 if atoms i and j are bonded.

Keyword Arguments:

• algo ––––––- :knowledgebased # (:distance, :covalent) algorithm to find bonds
• H –––––––– true # include bonds with hydrogen atoms
• cutoff –––––- 1.9 # distance cutoff for bonds between heavy atoms
• extradistance –– 0.14 # fudge factor for better inclusion
• disulfides –––- false # include disulfide bonds

getbonds( coords ) -> BitMatrix

Returns a matrix of all bonds using a N x 3 coordinates matrix. Uses a plain cutoff distance with algo option :distance. This is not recommended as it can lead to incorrect results since different atoms have different bond lengths and radii.

Keyword Arguments:

• algo ––––––- :distance # algorithm to find bonds
• H –––––––– true # include bonds with hydrogen atoms
• cutoff –––––- 1.9 # distance cutoff for bonds between heavy atoms
• extradistance –– 0.14 # fudge factor for better inclusion
• disulfides –––- false # include disulfide bonds

getinspectorlabel( structure )
getinspectorlabel( residues )
getinspectorlabel( atom )

Get the inspector label function for plotting a 'StructuralElementOrList'.

This function uses 'MIToS.PDB.bestoccupancy' or 'defaultatom' to ensure only one position per atom.

getuniprotdata(accession, filename=nothing; include_refs = false)

Downloads and reads a UniProt JSON file and returns a UniProtData struct.

Keyword Arguments:

• include_refs::Bool = false Whether to include all the database references (EMBL, PDB, etc.) in the struct. can be very large, so it is false by default.

msavalues( msa::AbstractMatrix, resdict::AbstractDict )::Matrix{Real}

Returns a matrix of numbers according to the given dictionary, where keys are residue letters and values are numbers. This matrix is used as input for plotmsa for the heatmap colors of the residue positions.

Default values for residue letters are from Kidera Factor values. From: Kenta Nakai, Akinori Kidera, Minoru Kanehisa, Cluster analysis of amino acid indices for prediction of protein structure and function, Protein Engineering, Design and Selection, Volume 2, Issue 2, July 1988, Pages 93–100, https://doi.org/10.1093/protein/2.2.93

kf 2 is Kidera Factor 2 (size/volume-related). The KF dictionary is in utils.jl, or you can look at the kideradict variable.

Keyword Arguments:

• resdict –––- kideradict by default, alternatively give a Dict{String,Vector{Float}}
• kf –––––– 2 by default, alternatively give an integer from 1:10

notwater( residues::Vector{MIToS.PDB.PDBResidue} )

Filter out water molecules from a Vector of residues.

plotmsa!( fig, msa )

Plot a multiple sequence alignment (MSA) into a Figure.

Example

fig = Figure(resolution = (1100, 400))

plotmsa!( fig::Figure, msa::T; kwargs... ) where {T<:Union{MSA.AbstractMultipleSequenceAlignment,
											   Vector{Tuple{String,String}},
											   Vector{FASTX.FASTA.Record}}}

Keyword Arguments:

• sheetsize ––- [40,20]
• gridposition – (1,1)
• markersize –– 12
• colorscheme –- :buda
• markercolor –- :black
• xticklabelsize - 11
• yticklabelsize - 11
• resolution ––- (700,300)
• kwargs... # forwarded to scatter plot

plotmsa( msa )
plotmsa( plotdata )

Plot a multiple sequence alignment (MSA). Returns a Figure, or a Figure and Observables for interaction.

Examples

MIToS.Pfam.downloadpfam("PF00062")	# download PF00062 MSA
msa = MIToS.MSA.read_file("PF00062.stockholm.gz", Stockholm, 
	generatemapping =true, useidcoordinates=true)

plotmsa( msa; kwargs... )

Keyword Arguments:

• figresolution ––- (1000,350) # because resolution applies to the MSA plot
• sheetsize ––––- [40,20]
• gridposition ––– (1,1:3)
• colorscheme –––- :buda
• markersize –––– 12
• markercolor –––- :black
• xticklabelsize –– 11
• yticklabelsize –– 11
• kwargs... # forwarded to scatter plot

plotstruc!( fig, structure )
plotstruc!( gridposition, structure )
plotstruc!( fig, plotdata )
plotstruc!( gridposition, plotdata )

Plot a protein structure(/chain/residues/atoms) into a Figure.

Examples

fig = Figure()

using MIToS.PDB

pdbfile = MIToS.PDB.downloadpdb("2vb1", format=PDBFile)
struc = MIToS.PDB.read_file(pdbfile, PDBFile) |> Observable
strucplot = plotstruc!(fig, struc)

chain_A = select_residues(struc, model="1", chain="A", group="ATOM")
strucplot = plotstruc!(fig, chain_A)

chnatms = select_atoms(struc, model="1", chain="A", group="ATOM")
strucplot = plotstruc!(fig, chnatms)
-------------------------
using BioStructures

struc = retrievepdb("2vb1", dir = "data/") |> Observable
strucplot = plotstruc!(fig, struc)

struc = read("data/2vb1_mutant1.pdb", BioStructures.PDBFormat) |> Observable
strucplot = plotstruc!(fig, struc)

chain_A = retrievepdb("2vb1", dir = "data/")["A"] |> Observable
strucplot = plotstruc!(fig, chain_A)

Keyword Arguments:

• resolution ––- (600,600)
• gridposition –- (1,1) # if an MSA is already plotted, (2,1:3) works well
• plottype –––- :ballandstick, :covalent, or :spacefilling
• atomcolors ––- elecolors, others in getbiocolors(), or provide a Dict like: "N" => :blue
• markersize ––- 0.0
• markerscale –– 1.0
• bondtype –––- :knowledgebased, :covalent, or :distance
• distance –––- 1.9 # distance cutoff for covalent bonds
• inspectorlabel - :default, or define your own function like: (self, i, p) -> "atom: ... coords: ..."
• water ––––– false # show water molecules
• kwargs... ––– keyword arguments passed to the atom meshscatter

plotstruc( structure )
plotstruc( residues )
plotstruc( plotdata )

Create and return a Makie Figure for a protein structural element.

Examples

using MIToS.PDB

pdbfile = MIToS.PDB.downloadpdb("2vb1", format=PDBFile)
struc = MIToS.PDB.read_file(pdbfile, PDBFile) |> Observable
strucplot = plotstruc(struc)

chain_A = select_residues(struc, model="1", chain="A", group="ATOM")
strucplot = plotstruc(chain_A)

chnatms = select_atoms(struc, model="1", chain="A", group="ATOM")
strucplot = plotstruc(chnatms)
-------------------------
using BioStructures

struc = retrievepdb("2vb1", dir = "data/") |> Observable
strucplot = plotstruc(struc)

struc = read("data/2vb1_mutant1.pdb", BioStructures.PDBFormat) |> Observable
strucplot = plotstruc(struc)

chain_A = retrievepdb("2hhb", dir = "data/")["A"] |> Observable
strucplot = plotstruc(chain_A)

Keyword Arguments:

• figresolution – (600,600) # because resolution applies to the plot
• resolution ––- (600,600)
• gridposition –- (1,1) # if an MSA is already plotted, (2,1:3) works well
• plottype –––- :ballandstick, :covalent, or :spacefilling
• atomcolors ––- elecolors, others in getbiocolors(), or provide a Dict like: "N" => :blue
• markersize ––- 0.0
• markerscale –– 1.0
• bondtype –––- :knowledgebased, :covalent, or :distance
• distance –––- 1.9 # distance cutoff for covalent bonds
• inspectorlabel - :default, or define your own function like: (self, i, p) -> "atom: ... coords: ..."
• water ––––– false # show water molecules
• kwargs... ––– keyword arguments passed to the atom meshscatter

plottingdata( structure )
plottingdata( residues )
plottingdata( atoms )

This function returns an OrderedDict of the main data used for plotting. This function uses 'MIToS.PDB.bestoccupancy' or 'defaultatom' to ensure only one position per atom. By default the kwarg 'water' is set to false, so water molecules are not included.

Returns:

OrderedDict(:atoms => ..., 
            :coords => ..., 
            :colors => ...,
            :sizes => ...,
            :bonds => ...)

Keyword Arguments:

• colors –––- elecolors | Options - elecolors, aquacolors, shapelycolors, maecolors
• radiustype –- :ballandstick | Options - :cov, :covalent, :vdw, :vanderwaals, :bas, :ballandstick, :spacefilling
• water –––– false | Options - true, false

plottingdata( msa )

Collects data for plotting (residue string matrix, matrix heatmap values, x labels, and y labels) from a multiple sequence alignment (MSA) object.

The MSA object can be a:

• AbstractMultipleSequenceAlignment from MIToS.MSA,
• vector of tuples 'Vector{Tuple{String,String}}' from FastaIO,
• vector of FASTA records 'Vector{FASTX.FASTA.Record}' from FASTX.

readuniprotdata(jsonfile; include_refs = false)

Reads a UniProt JSON file and returns a UniProtData struct.

Keyword Arguments:

• include_refs::Bool = false Whether to include all the database references (EMBL, PDB, etc.) in the struct. can be very large, so it is false by default.

rescolors( residues )

Get a Vector of colors for the atoms. To see all default element and amino acid colorschemes, use getbiocolors(). Keyword argument colors takes a Dict which maps residue to color. ("C" => :red)

This function uses 'MIToS.PDB.bestoccupancy' or 'defaultatom' to ensure only one position per atom.

Keyword Arguments:

• colors –- elecolors | Options - elecolors, aquacolors, shapelycolors, maecolors

showsummary(pdata)

Prints some of the most important information from a UniProtData object.

sidechainbonds( res::BioStructures.AbstractResidue, selectors... ) -> BitMatrix

Returns a matrix of sidechain bonds in res, where Mat[i,j] = 1 if atoms i and j are bonded.

This function uses 'bestoccupancy' or 'defaultatom' to ensure only one position per atom.

Keyword Arguments:

• algo ––––––- :knowledgebased # (:distance, :covalent) algorithm to find bonds
• H –––––––– true # include bonds with hydrogen atoms
• cutoff –––––- 1.9 # distance cutoff for bonds between heavy atoms
• extradistance –– 0.14 # fudge factor for better inclusion

heatmap!( fig, dmap; kwargs... )

Plot a MIToS distance or contact map.

Example

fig = Figure()

using MIToS.PDB

pdbfile = MIToS.PDB.downloadpdb("1IVO", format=PDBFile)
residues_1ivo = read_file(pdbfile, PDBFile)
pdb = select_residues(residues_1ivo, model="1", chain="A", group="ATOM")
dmap = MIToS.PDB.distance(pdb, criteria="All") # distance map 
cmap = contact(pdb, 8.0, criteria="CB") # contact map

heatmap!(fig, dmap)

Keyword Arguments:

• xlabel ––––––––- "Item 2"
• ylabel ––––––––- "Item 1"
• colormap –––––––- :viridis
• kwargs... ––––––– additional keyword arguments to pass to heatmap

heatmap!( fig, cmap; kwargs... )

Plot a BioStructures contact map.

Example

fig = Figure()

using BioStructures

struc = retrievepdb("1IVO")[1]
cbetas_A = collectatoms(struc["A"], cbetaselector)
cbetas_B = collectatoms(struc["B"], cbetaselector)
cmap = ContactMap(cbetas_A, cbetas_B)
heatmap!(fig, cmap)

Keyword Arguments:

• xlabel ––––––––- "Item 2"
• ylabel ––––––––- "Item 1"
• colormap –––––––- :ice
• kwargs... ––––––– Keyword arguments to pass to heatmap

heatmap( dmap; kwargs... )

Plot a BioStructures distance map.

Example

using BioStructures

struc = retrievepdb("1IVO")[1]
cbetas_A = collectatoms(struc["A"], cbetaselector)
cbetas_B = collectatoms(struc["B"], cbetaselector)
dmap = DistanceMap(cbetas_A, cbetas_B)
heatmap(dmap)

Keyword Arguments:

• xlabel ––––––––- "Item 2"
• ylabel ––––––––- "Item 1"
• colormap –––––––- :viridis
• kwargs... ––––––– additional keyword arguments to pass to heatmap

heatmap( dmap; kwargs... )

Plot a MIToS distance or contact map.

Example

using MIToS.PDB

pdbfile = MIToS.PDB.downloadpdb("1IVO", format=PDBFile)
residues_1ivo = read_file(pdbfile, PDBFile)
pdb = select_residues(residues_1ivo, model="1", chain="A", group="ATOM")
dmap = MIToS.PDB.distance(pdb, criteria="All") # distance map
cmap = contact(pdb, 8.0, criteria="CB") # contact map

heatmap(dmap)

Keyword Arguments:

• xlabel ––––––––- "Item 2"
• ylabel ––––––––- "Item 1"
• colormap –––––––- :viridis
• kwargs... ––––––– additional keyword arguments to pass to heatmap

heatmap( cmap; kwargs... )

Plot a BioStructures contact map.

Example

using BioStructures

struc = retrievepdb("1IVO")[1]
cbetas_A = collectatoms(struc["A"], cbetaselector)
cbetas_B = collectatoms(struc["B"], cbetaselector)
cmap = ContactMap(cbetas_A, cbetas_B)
heatmap(cmap)

Keyword Arguments:

• xlabel ––––––––- "Item 2"
• ylabel ––––––––- "Item 1"
• colormap –––––––- :ice
• kwargs... ––––––– additional keyword arguments to pass to heatmap

heatmap( dmap; kwargs... )

Plot a BioStructures distance map.

Example

using BioStructures

struc = retrievepdb("1IVO")[1]
cbetas_A = collectatoms(struc["A"], cbetaselector)
cbetas_B = collectatoms(struc["B"], cbetaselector)
dmap = DistanceMap(cbetas_A, cbetas_B)
heatmap(dmap)

Keyword Arguments:

• xlabel ––––––––- "Item 2"
• ylabel ––––––––- "Item 1"
• colormap –––––––- :viridis
• kwargs... ––––––– additional keyword arguments to pass to heatmap