How to set and get properties#

Goal#

Read or write per-atom attributes (such as residue name, chain, or charge) for a selection of atoms.

Minimal example#

from moleculekit.molecule import Molecule

mol = Molecule("3PTB")

# Read the residue names of all Cα atoms
names = mol.get("resname", sel="protein and name CA")

# Set the chain of all atoms with resid 100 to "B"
mol.set("chain", "B", sel=mol.resid == 100)

Parameters that matter#

Parameter

Type

Default

What it does

field

str

required

The atom attribute to read or write

sel

str, boolean np.ndarray, or None

None (all)

Which atoms to read/write

fileBonds

bool

True

Use file bonds for bond-dependent selectors (get only)

guessBonds

bool

True

Fall back to guessed bonds for bond-dependent selectors (get only)

Common variations#

# Read a field for the entire molecule
all_resnames = mol.get("resname")

# Read with a boolean mask — direct array indexing is equivalent to .get
ala_mask = mol.resname == "ALA"
ala_names = mol.name[ala_mask]          # equivalent to mol.get("name", sel=ala_mask)
ala_coords = mol.coords[ala_mask]       # full (n_ALA, 3, numFrames) — note .get returns one frame

# Write with a boolean mask — direct assignment is equivalent to .set
mol.charge[ala_mask] = 0.0              # equivalent to mol.set("charge", 0.0, sel=ala_mask)

When you already hold a mask, the direct-indexing form is shorter and skips the field lookup string. Reach for get/set when the natural form of your selection is a string (atomselect syntax) you want re-parsed at call time.

Gotchas#

  • Common public fields: name, resname, resid, chain, segid, element, charge, masses, coords.

  • For coords, get returns the coordinates of the current active frame (mol.frame), not all frames. Direct indexing (mol.coords[mask]) returns the full (n_sel, 3, numFrames) slice.

  • Setting coords via set only updates the current frame; direct indexing again gives you the whole trajectory.

See also#