Atom selection
Using TrjArray-type for storing MD trajectory data, users can flexibly select specific atoms and their trajectory data. Users can select atoms as like slicing arrays from the buit-in Array type in Julia.
using MDToolbox
ENV["COLUMNS"] = 130; # if you are using Jupyter, the column width should be set for the message width from MDToolbox.jl
t = mdload("examples/data/3gb1.pdb")
32x855 TrjArray{Float64, Int64}
| A | A | … A |
| 1MET | 1MET | … 56GLU |
| 1N | 2CA | … 855HG3 |
| -13.15 -1.71 5.51 | -12.20 -2.85 5.70 | … 10.24 2.24 -4.53 |
| -13.16 -2.75 4.19 | -12.38 -3.43 5.26 | 10.29 1.79 -3.20 |
| -13.26 -2.20 5.12 | -12.23 -3.26 5.29 | 11.09 3.24 -6.13 |
| -12.45 -4.30 6.28 | -12.25 -3.22 5.28 | 11.75 2.57 -3.31 |
| -13.05 -1.52 5.31 | -12.15 -2.68 5.56 | 10.46 1.51 -3.50 |
| -12.98 -3.74 6.65 | -12.43 -3.31 5.34 | … 11.26 3.06 -3.59 |
| -13.03 -2.10 3.64 | -12.47 -2.79 4.83 | 10.38 1.53 -3.30 |
| -13.00 -2.17 5.21 | -12.09 -3.19 5.78 | 11.32 3.37 -5.78 |
| -12.57 -2.96 3.87 | -12.12 -3.42 5.21 | 10.36 1.38 -3.53 |
| -12.60 -2.85 4.27 | -12.16 -3.02 5.68 | 10.44 1.40 -3.37 |
| -13.12 -1.61 4.72 | -12.34 -2.60 5.52 | … 10.96 3.58 -5.68 |
| ⋮ | ⋮ | ⋱ ⋮ |
| -13.46 -2.54 6.05 | -12.41 -3.14 5.18 | 10.33 1.63 -3.72 |
| -12.61 -4.31 6.34 | -12.22 -3.51 5.15 | 10.26 1.56 -3.59 |
| -13.24 -2.72 6.28 | -12.16 -3.34 5.45 | 11.30 2.91 -3.41 |
| -13.21 -2.29 5.61 | -12.13 -3.31 5.53 | 11.76 2.84 -5.65 |
| -12.75 -2.42 4.33 | -12.22 -2.96 5.61 | … 11.53 3.05 -5.67 |
| -13.32 -2.12 5.10 | -12.27 -3.17 5.25 | 10.38 1.88 -3.32 |
| -13.07 -2.31 4.32 | -12.27 -3.22 5.19 | 11.65 3.11 -5.90 |
| -12.76 -3.69 6.68 | -12.11 -3.33 5.38 | 11.51 2.97 -5.63 |
| -13.21 -2.55 5.53 | -12.06 -3.41 5.11 | 10.26 1.60 -3.20 |
| -13.13 -2.12 4.11 | -12.34 -3.00 5.02 | … 12.68 3.28 -4.88 |
| -12.81 -2.86 4.32 | -12.23 -3.33 5.62 | 9.98 2.33 -5.34 |First, specific frames of TrjArray variable can be selected by row indices. For example, the 3rd to 5th frames can be sliced by,
t[3:5, :]
3x855 TrjArray{Float64,Int64}
| A | A | … A |
| 1MET | 1MET | … 56GLU |
| 1N | 2CA | … 855HG3 |
| -13.26 -2.20 5.12 | -12.23 -3.26 5.29 | … 11.09 3.24 -6.13 |
| -12.45 -4.30 6.28 | -12.25 -3.22 5.28 | 11.75 2.57 -3.31 |
| -13.05 -1.52 5.31 | -12.15 -2.68 5.56 | 10.46 1.51 -3.50 |Next, specific atoms of TrjArray variable can be selected by column indices. For example, the 1st to 3rd atoms can be sliced by,
t[:, 1:3]
32x3 TrjArray{Float64,Int64}
| A | A | A |
| 1MET | 1MET | 1MET |
| 1N | 2CA | 3C |
| -13.15 -1.71 5.51 | -12.20 -2.85 5.70 | -10.79 -2.30 5.87 |
| -13.16 -2.75 4.19 | -12.38 -3.43 5.26 | -11.06 -2.70 5.50 |
| -13.26 -2.20 5.12 | -12.23 -3.26 5.29 | -10.88 -2.62 5.57 |
| ⋮ | ⋮ | ⋮ |
| -13.21 -2.55 5.53 | -12.06 -3.41 5.11 | -10.74 -2.72 5.46 |
| -13.13 -2.12 4.11 | -12.34 -3.00 5.02 | -11.00 -2.35 5.33 |
| -12.81 -2.86 4.32 | -12.23 -3.33 5.62 | -10.89 -2.63 5.85 |Of couse, both frame and atom selections can be specified together,
t[3:5, 1:3]
3x3 TrjArray{Float64,Int64}
| A | A | A |
| 1MET | 1MET | 1MET |
| 1N | 2CA | 3C |
| -13.26 -2.20 5.12 | -12.23 -3.26 5.29 | -10.88 -2.62 5.57 |
| -12.45 -4.30 6.28 | -12.25 -3.22 5.28 | -10.90 -2.54 5.53 |
| -13.05 -1.52 5.31 | -12.15 -2.68 5.56 | -10.73 -2.16 5.80 |Also, atoms can be selected by strings. For example, residue ID == 10 can be selected by
t[:, "resid 10"]
32x22 TrjArray{Float64,Int64}
| A | A | … A |
| 10LYS | 10LYS | … 10LYS |
| 1N | 2CA | … 22HZ3 |
| 14.51 1.47 -1.06 | 15.96 1.11 -0.95 | … 15.72 3.47 -6.83 |
| 14.34 0.95 -1.15 | 15.79 0.64 -1.11 | 18.17 4.93 -4.94 |
| 14.53 1.21 -1.25 | 15.98 0.88 -1.17 | 13.99 4.58 -3.58 |
| ⋮ | ⋮ | ⋱ ⋮ |
| 14.35 1.24 -1.20 | 15.81 0.95 -1.20 | 14.40 4.35 -5.36 |
| 14.48 1.14 -1.19 | 15.92 0.79 -1.15 | … 18.17 5.89 -5.06 |
| 14.56 1.13 -1.20 | 16.01 0.83 -1.11 | 14.94 2.44 -7.45 |The colon in the row can be omitted,
t["resid 10"]
32x22 TrjArray{Float64,Int64}
| A | A | … A |
| 10LYS | 10LYS | … 10LYS |
| 1N | 2CA | … 22HZ3 |
| 14.51 1.47 -1.06 | 15.96 1.11 -0.95 | … 15.72 3.47 -6.83 |
| 14.34 0.95 -1.15 | 15.79 0.64 -1.11 | 18.17 4.93 -4.94 |
| 14.53 1.21 -1.25 | 15.98 0.88 -1.17 | 13.99 4.58 -3.58 |
| ⋮ | ⋮ | ⋱ ⋮ |
| 14.35 1.24 -1.20 | 15.81 0.95 -1.20 | 14.40 4.35 -5.36 |
| 14.48 1.14 -1.19 | 15.92 0.79 -1.15 | … 18.17 5.89 -5.06 |
| 14.56 1.13 -1.20 | 16.01 0.83 -1.11 | 14.94 2.44 -7.45 |Ranges can be specified using colons. For example, residue IDs rom 10 to 13 can be selected by
t["resid 10:13"]
32x77 TrjArray{Float64,Int64}
| A | A | … A |
| 10LYS | 10LYS | … 13LYS |
| 1N | 2CA | … 77HZ3 |
| 14.51 1.47 -1.06 | 15.96 1.11 -0.95 | … 15.42 -3.79 2.49 |
| 14.34 0.95 -1.15 | 15.79 0.64 -1.11 | 16.92 -1.15 2.36 |
| 14.53 1.21 -1.25 | 15.98 0.88 -1.17 | 14.80 -0.42 7.32 |
| ⋮ | ⋮ | ⋱ ⋮ |
| 14.35 1.24 -1.20 | 15.81 0.95 -1.20 | 16.18 -2.37 2.19 |
| 14.48 1.14 -1.19 | 15.92 0.79 -1.15 | … 12.10 -4.45 4.27 |
| 14.56 1.13 -1.20 | 16.01 0.83 -1.11 | 16.27 -3.58 4.58 |Not only IDs, names can be specified. For example, residue name of GLU ASP can be selected by
t["resname GLU ASP"]
32x136 TrjArray{Float64,Int64}
| A | A | … A |
| 15GLU | 15GLU | … 56GLU |
| 1N | 2CA | … 136HG3 |
| 5.87 -0.14 7.35 | 4.52 -0.66 6.99 | … 10.24 2.24 -4.53 |
| 5.97 -0.41 7.47 | 4.59 -0.80 7.07 | 10.29 1.79 -3.20 |
| 5.82 -0.05 7.35 | 4.47 -0.58 6.99 | 11.09 3.24 -6.13 |
| ⋮ | ⋮ | ⋱ ⋮ |
| 5.95 -0.37 7.62 | 4.60 -0.89 7.26 | 10.26 1.60 -3.20 |
| 5.96 -0.12 7.34 | 4.61 -0.66 7.02 | … 12.68 3.28 -4.88 |
| 5.91 -0.11 7.29 | 4.54 -0.56 6.92 | 9.98 2.33 -5.34 |These can be combined by using and, or, and brackets (). For example, C_alpha atoms of residue IDs from 1 to 20 can be selected by,
t["atomname CA and resid 1:20"]
32x20 TrjArray{Float64,Int64}
| A | A | … A |
| 1MET | 2THR | … 20ALA |
| 1CA | 2CA | … 20CA |
| -12.20 -2.85 5.70 | -8.56 -2.53 6.83 | … -11.12 2.18 3.06 |
| -12.38 -3.43 5.26 | -8.87 -2.64 6.54 | -11.10 2.14 3.34 |
| -12.23 -3.26 5.29 | -8.72 -2.69 6.68 | -11.29 2.23 3.10 |
| ⋮ | ⋮ | ⋱ ⋮ |
| -12.06 -3.41 5.11 | -8.63 -2.73 6.65 | -11.07 2.11 3.15 |
| -12.34 -3.00 5.02 | -8.86 -2.42 6.49 | … -11.11 2.25 3.12 |
| -12.23 -3.33 5.62 | -8.71 -2.59 6.92 | -11.02 2.10 3.14 |The following keywords are avaiable for atom selections by strings
| keywords | description | examples |
|---|---|---|
| chainname | specify chain names | chainname A chainname A B |
| chainid | specify chain IDs | chainid 1 chainid 1:3 chainid 1:3 5 |
| resname | specify residue names | resname ARG resname GLU ASP |
| resid | specify residue IDs | resid 1 resid 1:3 resid 1:3 5 |
| atomname | specify atom names | atomname CA atomname C N O CA |
| atomid | specify atom IDs | atomid 1 atomid 1:3 atomid 1:3 5 |
| protein | select proteins | protein |
| solvent | select solvents | solvent |
| water | select water molecues | water |
| hydrogen | select hydrogens | hydrogen |