Tools
These tools may call external programs to perform each task. Please verify the installation of the necessary tool for each case.
Check the stereochemistry of protein residues
PDBTools.zeta — Functionzeta(r::Residue)Computes the Cα chirality (zeta "virtual" torsion angle - Cα-N-C-Cβ).
Returns the torsion angle or NaN if the residue is not recognized a protein residue or if its a Gly residue. Expected values are 33.9 ± 3.5 degrees (for one standard deviation). Also see the zeta_check function.
Example
julia> using PDBTools
julia> protein = select(read_pdb(PDBTools.TESTPDB), "protein");
julia> residues = collect(eachresidue(protein));
julia> zeta(residues[1])
33.672016f0PDBTools.zeta_check — Functionzeta_check(r::Residue; nsigma=2)Checks if the Cα chirality falls into expected ranges. See the zeta function for further information. The expected mean is 33.9 degrees with a standard deviation of 3.5 degrees. By default, nsigma=2, implying that the function returns true if the torsion falls within two standard deviations from the mean.
See: https://www.ebi.ac.uk/thornton-srv/software/PROCHECK/manual/manappa.html
Example
julia> using PDBTools
julia> protein = select(read_pdb(PDBTools.TESTPDB), "protein");
julia> residues = collect(eachresidue(protein));
julia> zeta_check(residues[1])
trueAdd hydrogens with OpenBabel
PDBTools.add_hydrogens! — Functionadd_hydrogens!(atoms::AbstractVector{<:Atom}; pH=7.0, obabel="obabel", debug=false)Add hydrogens to a PDB file using Open Babel.
Arguments
atoms::AbstractVector{<:Atom}: structure (usually PDB file of a protein) to add hydrogens to.pH: the pH of the solution. Default is 7.0.obabel: path to the obabel executable. Default is "obabel".debug: if true, print the output message from obabel. Default is false.
This function requires the installation of OpenBabel. Please cite the corresponding reference if using it.
Example
julia> using PDBTools
julia> atoms = read_pdb(PDBTools.TESTPDB, "protein and not element H");
julia> add_hydrogens!(atoms)
Vector{Atom{Nothing}} with 1459 atoms with fields:
index name resname chain resnum residue x y z occup beta model segname index_pdb
1 N ALA A 1 1 -9.229 -14.861 -5.481 1.00 0.00 1 - 1
2 CA ALA A 1 1 -8.483 -14.912 -6.726 1.00 0.00 1 - 2
3 CB ALA A 1 1 -9.383 -14.465 -7.880 1.00 0.00 1 - 3
⋮
1457 H THR A 104 208 5.886 -10.722 -7.797 1.00 0.00 1 - 1457
1458 H THR A 104 208 5.871 -10.612 -9.541 1.00 0.00 1 - 1458
1459 H THR A 104 208 6.423 -12.076 -8.762 1.00 0.00 1 - 1459Custom protein residue types
It is possible to add to the list of protein residues, custom residue types. This can be done by simply adding to the PDBTools.protein_residues dictionary of residues a new PDBTools.ProteinResidue entry. For example, here we create a new resiude type NEW with the same properties of an ALA residue. To remove all custom protein residues, use remove_custom_protein_residues!().
julia> using PDBTools
julia> remove_custom_protein_residues!();
julia> add_protein_residue!("NEW", PDBTools.protein_residues["ALA"])
PDBTools.ProteinResidue("NEW", "ALA", "A", "Aliphatic", false, true, 71.037114, 71.0779, 0, true)
julia> atom = Atom(resname="NEW");
julia> isprotein(atom)
true
julia> remove_custom_protein_residues!();Here we repeteadly call remove_custom_residues!() to guarantee the proper execution of the test codes, without any custom residues in the list of protein residues.
PDBTools.add_protein_residue! — Functionadd_protein_residue!(resname::String, reference_residue::PDBTools.ProteinResidue)Function to add a custom protein residue to the list of protein residues. The function will return the ProteinResidue object that was added. To remove all custom protein residues use remove_custom_protein_residues!().
Example
julia> using PDBTools
julia> remove_custom_protein_residues!();
julia> add_protein_residue!("sA", PDBTools.protein_residues["ALA"])
PDBTools.ProteinResidue("sA", "ALA", "A", "Aliphatic", false, true, 71.037114, 71.0779, 0, true)
julia> isprotein(Atom(resname="sA"))
true
julia> remove_custom_protein_residues!(); # clean upHere we repeteadly call remove_custom_residues!() to guarantee the proper execution of the test codes, without any custom residues in the list of protein residues.
PDBTools.remove_custom_protein_residues! — Functionremove_custom_protein_residues!()Function to remove all custom protein residues from the list of protein residues.
Example
julia> using PDBTools
julia> remove_custom_protein_residues!(); # clean up
julia> add_protein_residue!("sA", PDBTools.protein_residues["ALA"])
PDBTools.ProteinResidue("sA", "ALA", "A", "Aliphatic", false, true, 71.037114, 71.0779, 0, true)
julia> isprotein(Atom(resname="sA"))
true
julia> remove_custom_protein_residues!();
julia> isprotein(Atom(resname="sA"))
falseHere we repeteadly call remove_custom_residues!() to guarantee the proper execution of the test codes, without any custom residues in the list of protein residues.
The SIRAH force-field residues and element types
Conveniencie functions can be created to add sets of new types of residues and atom types to the list of residues and elements. This is illustrated in the custom_types.jl file of the source code, in this case for the residues and atom types of the SIRAH force field for Coarse-Grained protein simulations.
With those definitions, adding all SIRAH protein residue types and element names can be done with:
julia> using PDBTools
julia> remove_custom_protein_residues!(); remove_custom_elements!();
julia> custom_protein_residues!(SIRAH)
┌ Warning:
│
│ Residue `sX` will be interpreted as bridged Cysteine.
│
└ @ PDBTools
julia> custom_elements!(SIRAH)
┌ Warning:
│
│ The element masses are not the coarse-grained ones. This must be fixed in the future.
│
└ @ PDBTools
julia> sirah_pdb = read_pdb(PDBTools.SIRAHPDB);
julia> resname.(eachresidue(sirah_pdb))
5-element Vector{InlineStrings.String7}:
"sI"
"sR"
"sX"
"sI"
"sG"
julia> getseq(sirah_pdb)
5-element Vector{String}:
"I"
"R"
"C"
"I"
"G"
julia> all(isprotein.(sirah_pdb))
true
julia> remove_custom_protein_residues!(); remove_custom_elements!();Note that the residue names of the SIRAH force-field are non-standard (sI, sR, etc.), but the sequence is properly retrieved with standard one-letter codes, and all the atoms of the structure are recognized as being "protein" atoms.
Here we repeteadly call remove_custom_residues!() and remove_custom_elements!() to guarantee the proper execution of the test codes.
Move atoms and center of mass
The center_of_mass function can be used to compute the center of mass of set of atoms, and the moveto! function can be used to move the center of mass of the atoms to the origin (by default) or to a specified position:
MolSimToolkitShared.center_of_mass — Functioncenter_of_mass(atoms::AbstractVector{<:Atom})Calculate the center of mass of the atoms.
Example
julia> using PDBTools
julia> atoms = read_pdb(PDBTools.SMALLPDB);
julia> center_of_mass(atoms)
3-element StaticArraysCore.SVector{3, Float64} with indices SOneTo(3):
-5.584422772707132
-13.110413081059928
-7.139970851058855PDBTools.moveto! — Functionmoveto!(atoms::AbstractVector{<:Atom}; center::AbstractVector{<:Real}=SVector(0.0, 0.0, 0.0))Move the center of mass of the atoms to the specified center position, which defaults to the origin.
Example
julia> using PDBTools
julia> atoms = read_pdb(PDBTools.SMALLPDB);
julia> center_of_mass(atoms)
3-element StaticArraysCore.SVector{3, Float64} with indices SOneTo(3):
-5.584422772707132
-13.110413081059928
-7.139970851058855
julia> moveto!(atoms; center = [1.0, 2.0, 3.0]);
julia> center_of_mass(atoms)
3-element StaticArraysCore.SVector{3, Float64} with indices SOneTo(3):
1.0000000263619948
1.9999999934852166
2.9999999509668918