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contrib.jl
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contrib.jl
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"""
```
contrib(s::Selection, atom_contributions::Array{Float64}, selection)
```
Extract the contribution of a given atom type selection from the
solute or solvent atomic contributions to the MDDF.
`s` here is the solute or solvent selection (type `ComplexMixtures.Selection`)
`atom_contributions` is the `R.solute_atom` or `R.solvent_atom` arrays of the `Result` structure,
and the last argument is the selection of atoms from the solute to be considered, given as a list
of indexes, list of atom names, vector of `PDBTools.Atom`s, or a `PDBTools.Residue`.
"""
function contrib(s::Selection, atom_contributions::Array{Float64}, indexes::Vector{Int})
nbins = size(atom_contributions, 1)
c = zeros(nbins)
# If the selection is a single molecule, the indexes are anything
if s.nmols == 1
for it in indexes
ind = findfirst(isequal(it),s.index)
if isnothing(ind)
error("Index $it of input list not found in selection indexes list.")
end
c += atom_contributions[:, ind]
end
# If more than one molecule, the index must correspond to an atom within one molecule
else
for it in indexes
if it > s.natomspermol
error(
"The index list contains atoms with indexes greater than the number of atoms of the molecule.",
)
end
c += atom_contributions[:, it]
end
end
return c
end
#
# If a list of atom names is provided
#
function contrib(s::Selection, atom_contributions::Array{Float64}, names::Vector{String})
indexes = Vector{Int}(undef, 0)
for name in names
index = findall(isequal(name), s.names)
if length(index) == 0
error(" Atom in input list is not part of solvent (or solute): $name")
end
append!(indexes, index)
end
return contrib(s, atom_contributions, indexes)
end
#
# If a list of atoms of PDBTools.Atom is provided
#
function contrib(
s::Selection,
atom_contributions::Array{Float64},
atoms::Vector{PDBTools.Atom};
warning = true,
)
(warning && s.nmols > 1) && warning_nmols_types()
indexes = [atom.index for atom in atoms]
# Check which types of atoms belong to this selection
selected_types = which_types(s, indexes, warning = warning)
return contrib(s, atom_contributions, selected_types)
end
#
# If a residue of type PDBTools.Residue is provided
#
function contrib(
s::Selection,
atom_contributions::Array{Float64},
residue::Residue;
warning = true,
)
(warning && s.nmols > 1) && warning_nmols_types()
indexes = collect(residue.range)
# Check which types of atoms belong to this selection
selected_types = which_types(s, indexes, warning = warning)
return contrib(s, atom_contributions, selected_types)
end
function warning_nmols_types()
println(
"WARNING: there is more than one molecule in this selection. " *
"Contributions are summed over all atoms of the same type.",
)
end