Selection functions
A simple selection syntax is provided. Use it with, for example:
atoms = select(atoms,"protein and resnum < 30")General selections
Accepted Boolean operators: and, or, and not.
The accepted keywords for the selection are:
| Keyword | Options | Input value | Example |
|---|---|---|---|
index | =,>,<,<=,>= | Integer | index <= 10 |
index_pdb | =,>,<,<=,>= | Integer | index_pdb <= 10 |
name | String | name CA | |
element | String | element N | |
resname | String | resname ALA | |
resnum | =,>,<,<=,>= | Integer | resnum = 10 |
residue | =,>,<,<=,>= | Integer | residue = 10 |
chain | String | chain A | |
model | Integer | model 1 | |
beta | =,>,<,<=,>= | Real | beta > 0.5 |
occup | =,>,<,<=,>= | Real | occup >= 0.3 |
segname | String | segname PROT | |
resnum is the residue number as written in the PDB file, while residue is the residue number counted sequentially in the file.
index_pdb is the number written in the "atom index" field of the PDB file, while index is the sequential index of the atom in the file.
Special macros: proteins, water
Just use these keywords to select the residues matching the properties desired.
Examples:
aromatic = select(atoms,"aromatic")
aromatic = select(atoms,"charged")
Available keywords:
| Keywords | ||
|---|---|---|
water | ||
protein | backbone | sidechain |
acidic | basic | |
aliphatic | aromatic | |
charged | neutral | |
polar | nonpolar | |
hydrophobic | ||
The properties refer to protein residues and will return false to every non-protein residue. Thus, be careful with the use of not with these selections, as they might retrieve non-protein atoms.
Retrieving indexes only
If only the indexes of the atoms are of interest, a specific function will directly return them:
indexes = selindex(atoms,"protein and name CA")
All indexing is 1-based. Thus, the first atom of the structure is atom 1.
Use Julia anonymous functions directly
Selections can be done using Julia anonymous functions directly, providing a greater control over the selection and, possibly, the use of user defined selection functions. For example:
atoms = select(atoms, by = atom -> atom.x < 10.)
With that, selections can become really complex, as:
sel = atom -> (atom.x < 10. && atom.resname == "GLY") || (atom.name == "CA")
atoms = select(atoms, by = sel )
Iterate over residues (or molecules)
The eachresidue iterator allows iteration over the resiudes of a structure (in PDB files distinct molecules are associated to different residues, thus this iterates similarly over the molecules of a structure). For example:
julia> protein = wget("1LBD")
Array{Atoms,1} with 1870 atoms with fields:
index name resname chain resnum residue x y z beta occup model segname index_pdb
1 N SER A 225 1 45.228 84.358 70.638 67.05 1.00 1 - 1
2 CA SER A 225 1 46.080 83.165 70.327 68.73 1.00 1 - 2
3 C SER A 225 1 45.257 81.872 70.236 67.90 1.00 1 - 3
⋮
1868 OG1 THR A 462 238 -27.462 74.325 48.885 79.98 1.00 1 - 1868
1869 CG2 THR A 462 238 -27.063 71.965 49.222 78.62 1.00 1 - 1869
1870 OXT THR A 462 238 -25.379 71.816 51.613 84.35 1.00 1 - 1870
julia> nALA = 0
for residue in eachresidue(protein)
if name(residue) == "ALA"
nALA += 1
end
end
nALA
22
The result of the iterator can also be collected, with:
julia> residues = collect(eachresidue(protein))
Array{Residue,1} with 238 residues.
julia> residues[1]
Residue of name SER with 6 atoms.
index name resname chain resnum residue x y z beta occup model segname index_pdb
1 N SER A 225 1 45.228 84.358 70.638 67.05 1.00 1 - 1
2 CA SER A 225 1 46.080 83.165 70.327 68.73 1.00 1 - 2
3 C SER A 225 1 45.257 81.872 70.236 67.90 1.00 1 - 3
4 O SER A 225 1 45.823 80.796 69.974 64.85 1.00 1 - 4
5 CB SER A 225 1 47.147 82.980 71.413 70.79 1.00 1 - 5
6 OG SER A 225 1 46.541 82.639 72.662 73.55 1.00 1 - 6
These residue vector do not copy the data from the original atom vector. Therefore, changes performed on these vectors will be reflected on the original data.
It is possible also to iterate over the atoms of one or more residue:
julia> m_ALA = 0.
for residue in eachresidue(protein)
if name(residue) == "ALA"
for atom in residue
m_ALA += mass(atom)
end
end
end
m_ALA
1452.8601999999983
Which, in this simple example, results in the same as:
julia> sum( mass(atom) for atom in protein if atom.resname == "ALA" )
1452.8601999999983