BioStructures API

On Julia 1.9 and later the DataFrame and MetaGraph constructors are in package extensions in order to reduce the number of dependencies. Call using DataFrames and using Graphs, MetaGraphs respectively to access these functions.

BioSequences.LongAAMethod
LongAA(el)

Return the amino acid sequence of a structural element.

Additional arguments are residue selector functions - only residues that return true from all the functions are retained. The gaps keyword argument determines whether to add gaps to the sequence based on missing residue numbers (default true). See BioSequences.jl for more on how to use sequences. LongAA is an alias for LongSequence{AminoAcidAlphabet}.

BioStructures.ContactMapType
ContactMap(element, contact_distance)
ContactMap(element_one, element_two, contact_distance)
ContactMap(bit_array_2D)

Calculate the contact map for a StructuralElementOrList, or between two StructuralElementOrLists.

This returns a ContactMap type containing a BitArray{2} with true where the sub-elements are no further than the contact distance and false otherwise. When one element is given as input this returns a symmetric square matrix. To directly access the underlying data of ContactMap cm, use cm.data.

Examples

cbetas_A = collectatoms(struc["A"], cbetaselector)
cbetas_B = collectatoms(struc["B"], cbetaselector)

# Contact map of chain A using conventional Cβ and 8 Å definitions
cm = ContactMap(cbetas_A, 8.0)

# Returns true if a contact is present between the tenth and twentieth element
cm[10, 20]

# Rectangular contact map of chains A and B
cm = ContactMap(cbetas_A, cbetas_B, 8.0)

# Write the contact map to file
using DelimitedFiles
writedlm("contacts.out", Int64.(cm.data), " ")
BioStructures.DistanceMapType
DistanceMap(element)
DistanceMap(element_one, element_two)
DistanceMap(float_array_2D)

Calculate the distance map for a StructuralElementOrList, or between two StructuralElementOrLists.

This returns a DistanceMap type containing a Array{Float64, 2} with minimum distances between the sub-elements. When one element is given as input this returns a symmetric square matrix. To directly access the underlying data of DistanceMap dm, use dm.data.

Examples

cbetas_A = collectatoms(struc["A"], cbetaselector)
cbetas_B = collectatoms(struc["B"], cbetaselector)

# Distance map of chain A showing how far each Cβ atom is from the others
dm = DistanceMap(cbetas_A)

# Returns the distance between the tenth and twentieth element
dm[10, 20]

# Rectangular distance map of chains A and B
dm = DistanceMap(cbetas_A, cbetas_B)

# Write the distance map to file
using DelimitedFiles
writedlm("distances.out", dm.data, " ")
BioStructures.MMCIFDictType
MMCIFDict(filepath; gzip=false)
MMCIFDict(io; gzip=false)
MMCIFDict()

A macromolecular Crystallographic Information File (mmCIF) dictionary.

Can be accessed using similar functions to a standard Dict. Keys are field names as a String and values are always Vector{String}, even for multiple components or numerical data. To directly access the underlying dictionary of MMCIFDict d, use d.dict. Call MMCIFDict with a filepath or stream to read the dictionary from that source. The keyword argument gzip (default false) determines if the input is gzipped.

BioStructures.MMTFDictType
MMTFDict(filepath; gzip=false)
MMTFDict(io; gzip=false)
MMTFDict()

A Macromolecular Transmission Format (MMTF) dictionary.

Can be accessed using similar functions to a standard Dict. Keys are field names as a String and values are various types. To directly access the underlying dictionary of MMTFDict d, use d.dict. Call MMTFDict with a filepath or stream to read the dictionary from that source. The keyword argument gzip (default false) determines if the file is gzipped.

BioStructures.TransformationType
Transformation(el1, el2, residue_selectors...)
Transformation(coords1, coords2)
Transformation(trans1, trans2, rot)

A 3D transformation to map one set of coordinates onto another, found using the Kabsch algorithm.

When called with structural elements, carries out a pairwise alignment and superimposes on atoms from aligned residues. In this case, keyword arguments for pairwise alignment can be given, see pairalign. The residue selectors determine which residues to do the pairwise alignment on. The keyword argument alignatoms is an atom selector that selects the atoms to calculate the superimposition on (default calphaselector). Can also be called with two sets of coordinates of the same size, with the number of dimensions in the first axis and the number of points in the second axis.

The returned Transformation object consists of the mean coordinates of the first set, the mean coordinates of the second set, the rotation to map the first centred set onto the second centred set, and the indices of the aligned residues in the first and second elements if relevant.

Base.collectMethod
collect(el)

Returns a Vector of the sub-elements in a StructuralElementOrList, e.g. AbstractAtoms in a Residue or AbstractResidues in a Chain.

Base.readMethod
read(filepath::AbstractString, format::Type; <keyword arguments>)
read(input::IO, format::Type; <keyword arguments>)

Read a Protein Data Bank (PDB) file and return a ProteinStructure.

Arguments

  • format::Type: the format of the PDB file; options are PDB, MMCIF and MMTF.
  • structure_name::AbstractString: the name given to the returned ProteinStructure; defaults to the file name.
  • remove_disorder::Bool=false: whether to remove atoms with alt loc ID not ' ' or 'A'.
  • read_std_atoms::Bool=true: whether to read standard ATOM records.
  • read_het_atoms::Bool=true: whether to read HETATOM records.
  • run_dssp::Bool=false: whether to run DSSP to assign secondary structure.
  • run_stride::Bool=false: whether to run STRIDE to assign secondary structure.
  • gzip::Bool=false: whether the input is gzipped, not available for PDB format.
BioAlignments.pairalignMethod
pairalign(el1, el2, residue_selectors...)

Carries out a pairwise sequence alignment between the sequences of two structural elements.

Additional arguments are residue selector functions - only residues that return true from all the functions are retained. The keyword arguments scoremodel (default AffineGapScoreModel(BLOSUM62, gap_open=-10, gap_extend=-1)) and aligntype (default GlobalAlignment()) determine the properties of the alignment. See BioAlignments.jl for more on how to use alignments.

BioGenerics.distanceMethod
distance(element_one, element_two, atom_selectors...)

Get the minimum distance in Å between two StructuralElementOrLists.

Additional arguments are atom selector functions - only atoms that return true from the functions are retained.

BioStructures.allselectorMethod
allselector(at)
allselector(res)

Trivial selector that returns true for any AbstractAtom or AbstractResidue. Use it to select all atoms or residues.

BioStructures.altlocidsMethod
altlocids(dis_at)

Get the list of alternative location IDs in an AbstractAtom as a Vector{Char}, sorted by atom serial.

BioStructures.applyselectors!Method
applyselectors!(els, selectors...)

Removes from a Vector of StructuralElements all elements that do not return true from all the selector functions.

BioStructures.applyselectorsMethod
applyselectors(els, selectors...)

Returns a copy of a Vector of StructuralElements with all elements that do not return true from all the selector functions removed.

BioStructures.atomidMethod
atomid(at)

Get a descriptive atom ID for an AbstractAtom as a Tuple of the form (full residue ID, residue name, atom name).

BioStructures.atomnameMethod
atomname(at; strip=true)

Get the atom name of an AbstractAtom as a String. strip determines whether surrounding whitespace is stripped.

BioStructures.atomnamesMethod
atomnames(res; strip=true)

Get the sorted list of AbstractAtoms in an AbstractResidue. strip determines whether surrounding whitespace is stripped.

BioStructures.atomnameselectorMethod
atomnameselector(at, atom_names; strip=true)

Determines if an AbstractAtom has its atom name in a list of names. strip determines whether surrounding whitespace is stripped from the atom name before it is checked in the list.

BioStructures.atomsMethod
atoms(res)

Return the dictionary of AbstractAtoms in an AbstractResidue.

BioStructures.backboneselectorMethod
backboneselector(at)

Determines if an AbstractAtom is not a hetero-atom and corresponds to a protein backbone atom.

BioStructures.bondangleMethod
bondangle(atom_a, atom_b, atom_c)
bondangle(vec_ba, vec_bc)

Calculate the bond or pseudo-bond angle in radians between three AbstractAtoms or two vectors.

The angle between B→A and B→C is returned in the range 0 to π.

BioStructures.cbetaselectorMethod
cbetaselector(at)

Determines if an AbstractAtom is not a hetero-atom and corresponds to a Cβ atom, or a Cα atom in glycine.

BioStructures.chainMethod
chain(at)
chain(res)

Return the Chain that an AbstractAtom or AbstractResidue belongs to.

BioStructures.chainid!Method
chainid!(ch, id)
chainid!(res, id)

Set the chain ID of a Chain or an AbstractResidue to a new String.

If a chain with this ID already exists, it will be removed from its current chain and added to that chain. If a chain with this ID does not exist, a new chain will be added to the model and this residue will be added to it. If moving this residue from a chain to a new chain leaves the old chain without residues, the old chain will be removed from the Model.

BioStructures.chainidMethod
chainid(el)

Get the chain ID of an AbstractAtom, AbstractResidue or Chain as a String.

BioStructures.chainidsMethod
chainids(mod)
chainids(struc)

Get the sorted chain IDs of the chains in a Model, or the default Model of a ProteinStructure, as a Vector{String}.

BioStructures.chainsMethod
chains(mod)
chains(struc)

Return the dictionary of Chains in a Model, or the default Model of a ProteinStructure.

BioStructures.chargeMethod
charge(at; strip=true)

Get the charge on an AbstractAtom as a String. The charge is set to " " if not specified during atom creation. strip determines whether surrounding whitespace is stripped.

BioStructures.choosedefaultaltlocidMethod
choosedefaultaltlocid(at_one, at_two)

Determine which of two Atoms representing a disorered atom better qualifies as the default location.

The Atom with the highest occupancy is chosen; in the case of ties the Atom with the lowest alternative location ID in alphabetical order is chosen.

BioStructures.coilselectorMethod
coilselector(res)
coilselector(at)

Determines if an AbstractResidue or AbstractAtom is part of a coil, i.e. whether the secondary structure code is in coilsscodes.

BioStructures.collectatomsMethod
collectatoms(el)

Returns a Vector of the atoms in a StructuralElementOrList.

Additional arguments are atom selector functions - only atoms that return true from all the functions are retained. The keyword argument expand_disordered (default false) determines whether to return all copies of disordered atoms separately.

BioStructures.collectchainsMethod
collectchains(el)

Returns a Vector of the chains in a StructuralElementOrList.

Additional arguments are chain selector functions - only chains that return true from all the functions are retained.

BioStructures.collectmodelsMethod
collectmodels(el)

Returns a Vector of the models in a StructuralElementOrList.

Additional arguments are model selector functions - only models that return true from all the functions are retained.

BioStructures.collectresiduesMethod
collectresidues(el)

Returns a Vector of the residues in a StructuralElementOrList.

Additional arguments are residue selector functions - only residues that return true from all the functions are retained. The keyword argument expand_disordered (default false) determines whether to return all copies of disordered residues separately.

BioStructures.coordarrayMethod
coordarray(element, atom_selectors...)

Get the atomic coordinates in Å of a StructuralElementOrList as a 2D Array.

Each column corresponds to one atom, so the size is (3, natoms). Additional arguments are atom selector functions - only atoms that return true from all the functions are retained. The keyword argument `expanddisordered(defaultfalse`) determines whether to return coordinates for all copies of disordered atoms separately.

BioStructures.coords!Method
coords!(at, new_coords)

Set the coordinates of an AbstractAtom to a Vector of 3 numbers.

For DisorderedAtoms only the default atom is updated.

BioStructures.coordsMethod
coords(at)

Get the atomic coordinates of an AbstractAtom as a Vector{Float64}.

BioStructures.countatomsMethod
countatoms(el)

Return the number of atoms in a StructuralElementOrList as an Int.

Additional arguments are atom selector functions - only atoms that return true from all the functions are counted. The keyword argument expand_disordered (default false) determines whether to return all copies of disordered atoms separately.

BioStructures.countchainsMethod
countchains(el)

Return the number of Chains in a StructuralElementOrList as an Int.

Additional arguments are chain selector functions - only chains that return true from all the functions are counted.

BioStructures.countmodelsMethod
countmodels(el)

Return the number of Models in a StructuralElementOrList as an Int.

Additional arguments are model selector functions - only models that return true from all the functions are counted.

BioStructures.countresiduesMethod
countresidues(el)

Return the number of residues in a StructuralElementOrList as an Int.

Additional arguments are residue selector functions - only residues that return true from all the functions are counted. The keyword argument expand_disordered (default false) determines whether to return all copies of disordered residues separately.

BioStructures.defaultaltlocidMethod
defaultaltlocid(dis_at)

Get the alternative location ID of the default Atom in a DisorderedAtom as a Char.

The default is the highest occupancy, or lowest character alternative location ID for ties (i.e. 'A' beats 'B').

BioStructures.defaultatomMethod
defaultatom(dis_at)

Return the default Atom in a DisorderedAtom.

The default is the highest occupancy, or lowest character alternative location ID for ties (i.e. 'A' beats 'B').

BioStructures.defaultmodelMethod
defaultmodel(struc)

Get the default Model in a ProteinStructure.

This is the Model with the lowest model number.

BioStructures.defaultresidueMethod
defaultresidue(dis_res)

Return the default Residue in a DisorderedResidue.

The default is the first name read in.

BioStructures.defaultresnameMethod
defaultresname(dis_res)

Get the name of the default Residue in a DisorderedResidue as a String.

The default is the first name read in.

BioStructures.dihedralangleMethod
dihedralangle(atom_a, atom_b, atom_c, atom_d)
dihedralangle(vec_ab, vec_bc, vec_cd)

Calculate the dihedral angle in radians defined by four AbstractAtoms or three vectors.

The angle between the planes defined by atoms (A, B, C) and (B, C, D) is returned in the range -π to π.

BioStructures.disorderedresMethod
disorderedres(dis_res, res_name)

Return the Residue in a DisorderedResidue with a given residue name.

BioStructures.disorderselectorMethod
disorderselector(at)
disorderselector(res)

Determines whether an AbstractAtom or AbstractResidue is disordered, i.e. has multiple locations in the case of atoms or multiple residue names (point mutants) in the case of residues.

BioStructures.displacementsMethod
displacements(element_one, element_two, residue_selectors...)
displacements(element_one, element_two, superimpose=false)
displacements(coords_one, coords_two)

Get the displacements in Å between atomic coordinates from two StructuralElementOrLists or two coordinate Arrays.

If superimpose is true (the default), the elements are superimposed before calculation and the displacements are calculated on the superimposed residues. See Transformation for keyword arguments. If superimpose is false the elements are assumed to be superimposed and must be of the same length. The keyword argument dispatoms is an atom selector that selects the atoms to calculate displacements on (default calphaselector).

BioStructures.downloadallobsoletepdbMethod
downloadallobsoletepdb(; <keyword arguments>)

Download all obsolete Protein Data Bank (PDB) files from the RCSB server.

Returns the list of PDB IDs downloaded. Requires an internet connection.

Arguments

  • obsolete_dir::AbstractString=pwd(): the directory where the PDB files are downloaded; defaults to the current working directory.
  • format::Type=PDB: the format of the PDB file; options are PDB, PDBXML, MMCIF and MMTF.
  • overwrite::Bool=false: if set true, overwrites the PDB file if it exists in dir; by default skips downloading the PDB file if it exists.
BioStructures.downloadentirepdbMethod
downloadentirepdb(; <keyword arguments>)

Download the entire Protein Data Bank (PDB) from the RCSB server.

Returns the list of PDB IDs downloaded. Ensure you have enough disk space and time before running. The function can be stopped any time and called again to resume downloading. Requires an internet connection.

Arguments

  • dir::AbstractString=pwd(): the directory to which the PDB files are downloaded; defaults to the current working directory.
  • format::Type=PDB: the format of the PDB file; options are PDB, PDBXML, MMCIF and MMTF.
  • overwrite::Bool=false: if set true, overwrites the PDB file if it exists in dir; by default skips downloading the PDB file if it exists.
BioStructures.downloadpdbMethod
downloadpdb(pdbid::AbstractString; <keyword arguments>)
downloadpdb(pdbid::Array{<:AbstractString, 1}; <keyword arguments>)
downloadpdb(f::Function, args...)

Download files from the Protein Data Bank (PDB) via RCSB.

When given an AbstractString, e.g. "1AKE", downloads the PDB file and returns the path to the file. When given an Array{<:AbstractString, 1}, downloads the PDB files in the array and returns an array of the paths to the files. When given a function as the first argument, runs the function with the downloaded filepath(s) as an argument then removes the file(s). Requires an internet connection.

Arguments

  • dir::AbstractString=pwd(): the directory to which the PDB file is downloaded; defaults to the current working directory.
  • format::Type=PDB: the format of the PDB file; options are PDB, PDBXML, MMCIF and MMTF.
  • obsolete::Bool=false: if set true, the PDB file is downloaded in the auto-generated "obsolete" directory inside the specified dir.
  • overwrite::Bool=false: if set true, overwrites the PDB file if it exists in dir; by default skips downloading the PDB file if it exists.
  • ba_number::Integer=0: if set > 0 downloads the respective biological assembly; by default downloads the PDB file.
BioStructures.elementMethod
element(at; strip=true)

Get the element of an AbstractAtom as a String.

The element is set to " " if not specified during atom creation. strip determines whether surrounding whitespace is stripped.

BioStructures.generatechainidMethod
generatechainid(entity_id)

Convert a positive Integer into a chain ID.

Goes A to Z, then AA to ZA, AB to ZB etc. This is in line with Protein Data Bank (PDB) conventions.

BioStructures.heavyatomselectorMethod
heavyatomselector(at)

Determines if an AbstractAtom corresponds to a heavy (non-hydrogen) atom and is not a hetero-atom.

BioStructures.helixselectorMethod
helixselector(res)
helixselector(at)

Determines if an AbstractResidue or AbstractAtom is part of an α-helix, i.e. whether the secondary structure code is in helixsscodes.

BioStructures.heteroselectorMethod
heteroselector(at)
heteroselector(res)

Determines if an AbstractAtom represents a hetero atom, e.g. came from a HETATM record in a Protein Data Bank (PDB) file, or if an AbstractResidue represents a hetero molecule, e.g. consists of HETATM records from a PDB file.

BioStructures.hydrogenselectorMethod
hydrogenselector(at)

Determines if an AbstractAtom represents hydrogen.

Uses the element field where possible, otherwise uses the atom name.

BioStructures.inscodeMethod
inscode(at)
inscode(res)

Get the insertion code of an AbstractAtom or AbstractResidue as a Char.

BioStructures.isdisorderedatomMethod
isdisorderedatom(at)

Determines if an AbstractAtom is a DisorderedAtom, i.e. if there are multiple locations present for an atom.

BioStructures.isdisorderedresMethod
isdisorderedres(res)

Determine if an AbstractResidue is a DisorderedResidue, i.e. there are multiple residue names with the same residue ID.

BioStructures.isheteroMethod
ishetero(at)
ishetero(res)

Determines if an AbstractAtom represents a hetero atom, e.g. came from a HETATM record in a Protein Data Bank (PDB) file, or if an AbstractResidue represents a hetero molecule, e.g. consists of HETATM records from a PDB file.

BioStructures.modelMethod
model(el)

Return the Model that an AbstractAtom, AbstractResidue or Chain belongs to.

BioStructures.modelnumberMethod
modelnumber(el)

Get the model number of a Model, Chain, AbstractResidue or AbstractAtom as an Int.

BioStructures.notwaterselectorMethod
notwaterselector(res)
notwaterselector(at)

Determines if an AbstractResidue or AbstractAtom does not represent a water molecule, i.e. whether the residue name is not in waterresnames.

BioStructures.occupancyMethod
occupancy(at)

Get the occupancy of an AbstractAtom as a Float64.

The occupancy is set to 1.0 if not specified during atom creation.

BioStructures.omegaangleMethod
omegaangle(res, res_previous)
omegaangle(chain, res_id)

Calculate the omega angle in radians for an AbstractResidue.

Arguments can either be a residue and the previous residue or a chain and the position as a residue ID. The first residue (or one at the given index) requires the atoms "N" and "CA" and the previous residue requires the atoms "CA" and "C". The angle is in the range -π to π.

BioStructures.omegaanglesMethod
omegaangles(element, residue_selectors...)

Calculate the Vector of omega angles of a StructuralElementOrList.

The vectors have NaN for residues where an angle cannot be calculated, e.g. due to missing atoms or lack of an adjacent residue. The angle is in the range -π to π. Additional arguments are residue selector functions - only residues that return true from the functions are retained.

BioStructures.pdbentrylistMethod
pdbentrylist()

Obtain the list of all Protein Data Bank (PDB) entries from the RCSB server.

Requires an internet connection.

BioStructures.pdblineMethod
pdbline(at::Atom)
pdbline(at::DisorderedAtom)
pdbline(at::AtomRecord)

Form a Protein Data Bank (PDB) format ATOM or HETATM record as a String from an Atom, DisorderedAtom or AtomRecord.

This will throw an ArgumentError if a value cannot fit into the allocated space, e.g. the chain ID is longer than one character or the atom serial is greater than 99999. In this case consider using writemmcif or writemmtf to write a mmCIF file or a MMTF file.

BioStructures.pdbobsoletelistMethod
pdbobsoletelist()

Obtain the list of all obsolete Protein Data Bank (PDB) entries from the RCSB server.

Requires an internet connection.

BioStructures.pdbrecentchangesMethod
pdbrecentchanges()

Obtain three lists giving the added, modified and obsolete Protein Data Bank (PDB) entries from the recent RCSB weekly status files.

Requires an internet connection.

BioStructures.pdbstatuslistMethod
pdbstatuslist(url::AbstractString)

Obtain the list of Protein Data Bank (PDB) entries from a RCSB weekly status file by specifying its URL.

An example URL is ftp://ftp.wwpdb.org/pub/pdb/data/status/latest/added.pdb. Requires an internet connection.

BioStructures.phiangleMethod
phiangle(res, res_previous)
phiangle(chain, res_id)

Calculate the phi angle in radians for an AbstractResidue.

Arguments can either be a residue and the previous residue or a chain and the position as a residue ID. The first residue (or one at the given index) requires the atoms "N", "CA" and "C" and the previous residue requires the atom "C". The angle is in the range -π to π.

BioStructures.phianglesMethod
phiangles(element, residue_selectors...)

Calculate the Vector of phi angles of a StructuralElementOrList.

The vectors have NaN for residues where an angle cannot be calculated, e.g. due to missing atoms or lack of an adjacent residue. The angle is in the range -π to π. Additional arguments are residue selector functions - only residues that return true from the functions are retained.

BioStructures.psiangleMethod
psiangle(res, res_next)
psiangle(chain, res_id)

Calculate the psi angle in radians for an AbstractResidue.

Arguments can either be a residue and the next residue or a chain and the position as a residue ID. The first residue (or one at the given index) requires the atoms "N", "CA" and "C" and the next residue requires the atom "N". The angle is in the range -π to π.

BioStructures.psianglesMethod
psiangles(element, residue_selectors...)

Calculate the Vector of psi angles of a StructuralElementOrList.

The vectors have NaN for residues where an angle cannot be calculated, e.g. due to missing atoms or lack of an adjacent residue. The angle is in the range -π to π. Additional arguments are residue selector functions - only residues that return true from the functions are retained.

BioStructures.ramachandrananglesMethod
ramachandranangles(element, residue_selectors...)

Calculate the Vectors of phi and psi angles of a StructuralElementOrList.

The vectors have NaN for residues where an angle cannot be calculated, e.g. due to missing atoms or lack of an adjacent residue. The angles are in the range -π to π. Additional arguments are residue selector functions - only residues that return true from the functions are retained.

BioStructures.readmultimmcifMethod
readmultimmcif(filepath; gzip=false)
readmultimmcif(io; gzip=false)

Read multiple MMCIFDicts from a filepath or stream. Each MMCIFDict in the returned Dict{String, MMCIFDict} corresponds to an mmCIF data block from the input. An example of such a file is the chemical component dictionary from the Protein Data Bank. The keyword argument gzip (default false) determines if the input is gzipped.

BioStructures.residMethod
resid(res; full=true)

Get a descriptive residue ID String for an AbstractAtom or AbstractResidue.

Format is residue number then insertion code with "H" in front for hetero residues. If full equals true the chain ID is also added after a colon. Examples are "50A", "H20" and "10:A".

BioStructures.resnameMethod
resname(at; strip=true)
resname(res; strip=true)

Get the residue name of an AbstractAtom or AbstractResidue as a String.

strip determines whether surrounding whitespace is stripped.

BioStructures.resnamesMethod
resnames(dis_res)

Get the residue names in an AbstractResidue as a Vector{String}.

For a DisorderedResidue there will be multiple residue names - in this case the default residue name is placed first, then the others are ordered alphabetically.

BioStructures.resnameselectorMethod
resnameselector(res, res_names)
resnameselector(at, res_names)

Determines if an AbstractResidue or AbstractAtom has its residue name in a list of names.

BioStructures.resnumberMethod
resnumber(at)
resnumber(res)

Get the residue number of an AbstractAtom or AbstractResidue as an Int.

BioStructures.retrievepdbMethod
retrievepdb(pdbid::AbstractString; <keyword arguments>)

Download and read a Protein Data Bank (PDB) file or biological assembly from the RCSB server, returning a ProteinStructure.

Requires an internet connection.

Arguments

  • pdbid::AbstractString: the PDB ID to be downloaded and read.
  • dir::AbstractString=pwd(): the directory to which the PDB file is downloaded; defaults to the current working directory.
  • obsolete::Bool=false: if set true, the PDB file is downloaded in the auto-generated "obsolete" directory inside the specified dir.
  • overwrite::Bool=false: if set true, overwrites the PDB file if it exists in dir; by default skips downloading the PDB file if it exists.
  • ba_number::Integer=0: if set > 0 downloads the respective biological assembly; by default downloads the PDB file.
  • structure_name::AbstractString="$pdbid.pdb": the name given to the returned ProteinStructure; defaults to the PDB ID.
  • remove_disorder::Bool=false: whether to remove atoms with alt loc ID not ' ' or 'A'.
  • read_std_atoms::Bool=true: whether to read standard ATOM records.
  • read_het_atoms::Bool=true: whether to read HETATOM records.
  • run_dssp::Bool=false: whether to run DSSP to assign secondary structure.
  • run_stride::Bool=false: whether to run STRIDE to assign secondary structure.
BioStructures.rmsdMethod
rmsd(element_one, element_two, residue_selectors...)
rmsd(element_one, element_two, superimpose=false)
rmsd(coords_one, coords_two)

Get the root-mean-square deviation (RMSD) in Å between two StructuralElementOrLists or two coordinate Arrays.

If superimpose is true (the default), the elements are superimposed before RMSD calculation and the RMSD is calculated on the superimposed residues. See Transformation for keyword arguments. If superimpose is false the elements are assumed to be superimposed and must be of the same length. The keyword argument rmsdatoms is an atom selector that selects the atoms to calculate RMSD on (default calphaselector).

BioStructures.rundssp!Method
rundssp!(struc)
rundssp!(mod)

Run DSSP (Define Secondary Structure of Proteins) on the given structural element to assign secondary structure.

A temporary PDB file is written, so this will fail if the structural element cannot be written to a PDB file, for example if there are two-letter chain IDs.

BioStructures.rundsspMethod
rundssp(struc)
rundssp(mod)
rundssp(filepath_in, dssp_filepath_out)

Return a copy of the structural element with DSSP (Define Secondary Structure of Proteins) run to assign secondary structure, or run DSSP directly on a PDB or mmCIF file.

BioStructures.runstride!Method
runstride!(struc)
runstride!(mod)

Run STRIDE on the given structural element to assign secondary structure.

A temporary PDB file is written, so this will fail if the structural element cannot be written to a PDB file, for example if there are two-letter chain IDs.

BioStructures.runstrideMethod
runstride(struc)
runstride(mod)
runstride(filepath_in, stride_filepath_out)

Return a copy of the structural element with STRIDE run to assign secondary structure, or run STRIDE directly on a PDB file.

BioStructures.sequentialresiduesMethod
sequentialresidues(res_first, res_second)

Determine if the second residue follows the first in sequence.

For this to be true the residues need to have the same chain ID, both need to be standard/hetero residues and the residue number of the second needs to be one greater than that of the first (or the residue numbers the same and the insertion code of the second greater than the first).

BioStructures.sheetselectorMethod
sheetselector(res)
sheetselector(at)

Determines if an AbstractResidue or AbstractAtom is part of a β-sheet, i.e. whether the secondary structure code is in sheetsscodes.

BioStructures.showcontactmapMethod
showcontactmap(contact_map)
showcontactmap(io, contact_map)

Print a representation of a ContactMap to stdout, or a specified IO instance.

A fully plotted version can be obtained with plot(contact_map) but that requires Plots.jl; showcontactmap works without that dependency.

BioStructures.spaceatomnameMethod
spaceatomname(at::Atom)

Space an Atom name such that the last element letter (generally) appears in the second column.

If the element property of the Atom is set it is used to get the element, otherwise the name starts from the second column where possible. This function is generally not required as spacing is recorded when atom names are read in from a Protein Data Bank (PDB) file. However this spacing can be important, for example distinguising between Cα and calcium atoms.

BioStructures.sqdistanceMethod
sqdistance(element_one, element_two, atom_selectors...)

Get the minimum square distance in Å between two StructuralElementOrLists.

Additional arguments are atom selector functions - only atoms that return true from the functions are retained.

BioStructures.sscode!Method
sscode!(res, ss_code)

Set the secondary structure code of an AbstractResidue to a Char.

BioStructures.sscodeMethod
sscode(res)
sscode(at)

Get the secondary structure code of an AbstractResidue or AbstractAtom as a Char.

'-' represents unassigned secondary structure. Secondary structure can be assigned using rundssp! or runstride!.

BioStructures.sscodeselectorMethod
sscodeselector(res, ss_codes)
sscodeselector(at, ss_codes)

Determines if an AbstractResidue or AbstractAtom has its secondary structure code in a list of secondary structure codes.

BioStructures.standardselectorMethod
standardselector(at)
standardselector(res)

Determines if an AbstractAtom represents a standard atom, e.g. came from a ATOM record in a Protein Data Bank (PDB) file, or if an AbstractResidue represents a standard molecule, e.g. consists of ATOM records from a PDB file.

BioStructures.structureMethod
structure(el)

Return the ProteinStructure that an AbstractAtom, AbstractResidue, Chain or Model belongs to.

BioStructures.structurenameMethod
structurename(el)

Get the name of the ProteinStructure that a StructuralElement belongs to as a String.

BioStructures.superimpose!Method
superimpose!(el1, el2, residue_selectors...)

Calculate the Transformation that maps the first element onto the second, and modify all coordinates in the first element according to the transformation.

See Transformation for keyword arguments.

BioStructures.tempfactorMethod
tempfactor(at)

Get the temperature factor of an AbstractAtom as a Float64.

The temperature factor is set to 0.0 if not specified during atom creation.

BioStructures.updatelocalpdbMethod
updatelocalpdb(; dir::AbstractString=pwd(), format::Type=PDB)

Update a local copy of the Protein Data Bank (PDB).

Obtains the recent weekly lists of new, modified and obsolete PDB entries and automatically updates the PDB files of the given format inside the local dir directory. Requires an internet connection.

BioStructures.waterselectorMethod
waterselector(res)
waterselector(at)

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

BioStructures.writemmcifMethod
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.

BioStructures.writemultimmcifMethod
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.

BioStructures.writepdbMethod
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.

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

Set the x coordinate of an AbstractAtom to val.

For DisorderedAtoms only the default atom is updated.

BioStructures.xMethod
x(at)

Get the x coordinate of an AbstractAtom as a Float64.

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

Set the y coordinate of an AbstractAtom to val.

For DisorderedAtoms only the default atom is updated.

BioStructures.yMethod
y(at)

Get the y coordinate of an AbstractAtom as a Float64.

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

Set the z coordinate of an AbstractAtom to val.

For DisorderedAtoms only the default atom is updated.

BioStructures.zMethod
z(at)

Get the z coordinate of an AbstractAtom as a Float64.

MMTF.writemmtfMethod
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.