Atom mask selection¶

Residue selections¶

Examples of residue selections, accompanied by comments annotating what is being selected, is shown below:

:1,3,6-10    Select residues 1, 3, 6, 7, 8, 9, and 10
:ALA,LYS,10  Select all residues with names ALA or LYS, and residue 10
:1-3,6-10    Select residues 1, 2, 3, 6, 7, 8, 9, and 10

Atom selections¶

Examples of residue selections, accompanied by comments annotating what is being selected, is shown below:

@1-100,150-160   Select the first 100 atoms as well as the 11 atoms 150-160
@CA,C,10-15      Select all atoms whose names are CA or C, and 6 atoms 10-15

Atom type selections¶

In some cases, it is more succinct to select by atom type name, rather than atom name. Be careful though! Atom type names can change from force field to force field, and are considered an implementation detail. While atom names should never change (and are based on the PDB standard, typically), atom type names can be set and/or changed to whatever the force field developer wants.

You have been warned. If you wish to push on, though, you can use the @% characters to select from type names rather than atom names. Note, no indices (or index ranges) can be used, as atom types have no defined order. Examples are shown below:

@%CT,CX         Select all atoms whose types are CT or CX

Logical operators¶

You often want to select certain atoms from certain residues. You can use the & binary operator to do this, as shown in examples below:

(:1-100)&(@CA)      Selects atoms named CA in the first 100 residues
(:1-100)&(@CA,CB)   Selects atoms named CA or CB in the first 100 residues
(:ASP,GLU)&(@CA)    Selects atoms named CA in all ASP or GLU residues

This is so common, you can use a simple shortcut, demonstrated below, giving equivalent expressions to the examples above:

:1-100@CA
:1-100@CA,CB
:ASP,GLU@CA

You can also expand your selection using the | (or) operator. For example:

:1-100|@CA      Selects all atoms in the first 100 residues AND all atoms named CA

Don’t get confused between what the & (and) and | (or) operators do. The above example selects all atoms if it satisfies the criteria of being in the first 100 residues or if it satisfies the criteria of having the name CA, meaning it selects all atoms in the first 100 residues and all atoms named CA.

You can also select all atoms except a particular selection:

!(:LIG)         Selects all atoms that are NOT in a residue named LIG

Wild-cards¶

Let’s suppose you want to select all hydrogen atoms. These atoms usually have many names, but they almost always start with “H”, so we would like a way to select all atoms that start with the letter “H”. We can do this with wild-cards, which is the = character in Amber masks, and works for both atoms and residues. For example:

:AS=@H=   Select all atoms whose residue starts with AS AND atom name starts with H

Distance-based selections¶

Sometimes you also want to be able to select all atoms within a certain distance (or all atoms within a residue that is a certain distance) from a specific set of atoms. For this, the < and > operators are used to denote distances that are less than or greater than a particular value, respectively.

This is probably the most complex part of the Amber mask syntax, but it is also quite powerful. In addition to the < and > operators, you must use either @ or : to indicate whether you want to select individual atoms or whole residues satisfying the distance. When selecting residues, the whole residue is selected if any atom satisfies the distance criteria. The general syntax is SELECTION<:DISTANCE, where SELECTION is an Amber mask (: can also be @ to select only atoms), and DISTANCE is a floating point distance that defines the criteria. Examples are shown below with annotations:

:8<@5.0     All atoms that are LESS THAN 5 Angstroms away from any atom in residue 8
:1>:10.0    All atoms in any residue in which one atom is MORE THAN 10 angstroms away from residue 1

Get atom_indices¶

In [11]: top = traj.top

# Topology can be loaded alone by:
#top = pt.load_topology('data/tz2.ortho.parm7')
In [12]: top
Out[12]: <Topology: 5293 atoms, 1704 residues, 1692 mols, PBC with box type = ortho>

# Residue selections, return atom_indices (0-based)
In [13]: top.select(':1,3,6-10')
Out[13]: array([  0,   1,   2, ..., 168, 169, 170])

In [14]: top.select(':ALA,LYS,10')
Out[14]: array([111, 112, 113, ..., 214, 215, 216])

In [15]: top.select('@1-100,150-160')
Out[15]: array([  0,   1,   2, ..., 157, 158, 159])

In [16]: top.select('(:1-100)&(@CA)')
Out[16]: array([  4,  15,  39, ..., 159, 173, 197])

# select based on distance, need to set reference frame
In [17]: top.set_distance_mask_reference(traj[0])

# pick all atoms around residue 1, distance cutoff < 5.0 Angstrom
In [18]: top.select(':1 <:5.0')
Out[18]: array([   0,    1,    2, ..., 4732, 4733, 4734])

Get new Topology¶

In [19]: top[':1,3,6-10']
Out[19]: <Topology: 108 atoms, 7 residues, 3 mols, PBC with box type = ortho>

In [20]: top[':ALA,LYS,10']
Out[20]: <Topology: 58 atoms, 3 residues, 3 mols, PBC with box type = ortho>

In [21]: top['@1-100,150-160']
Out[21]: <Topology: 111 atoms, 8 residues, 4 mols, PBC with box type = ortho>

In [22]: top['(:1-100)&(@CA)']
Out[22]: <Topology: 12 atoms, 12 residues, 12 mols, PBC with box type = ortho>

In [23]: top[':1 <:5.0']
Out[23]: <Topology: 189 atoms, 32 residues, 27 mols, PBC with box type = ortho>