Tutorial

import spyrmsd
from spyrmsd import io, rmsd

RDKit

spyrmsd natively supports RDKit to load molecules in order to work as a standalone tool. However, the API for RMSD calculations is extremely minimal and only needs the following information:

  • Atomic coordinates

  • Atomic numbers

  • Molecular adjacency matrix (for symmetry)

This means that spyrmsd can be used in combination with any library that can provide such information.

Loading Molecules

The spyrmsd.io module provides functions to easily load molecules from a file and to transform them into a spyrmsd.molecule.Molecule object:

ref = io.loadmol("molecules/1a4k_ligand.sdf")

io.loadmol load a single molecule from a file. In order to load all molecules we need to use io.loadallmols:

mols = io.loadallmols("molecules/1a4k_dock.sdf")

[22:16:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
[22:16:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
[22:16:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
[22:16:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
[22:16:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
[22:16:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
[22:16:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
[22:16:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
[22:16:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
[22:16:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.

Loading RDKit Molecules

spyrmsd natively supports RDKit (if installed). The Molecule class provides a from_rdkit() constructor.

from rdkit import Chem
from rdkit.Chem import AllChem

rdmol1 = Chem.MolFromSmiles("c1ccccc1")
rdmol2 = Chem.MolFromSmiles("c1ccccc1")
AllChem.EmbedMolecule(rdmol1)
AllChem.EmbedMolecule(rdmol2)

from spyrmsd.molecule import Molecule
from spyrmsd.rmsd import rmsdwrapper

mol1 = Molecule.from_rdkit(rdmol1)
mol2 = Molecule.from_rdkit(rdmol2)

rmsdwrapper(mol1, mol2)

[22:16:58] Molecule does not have explicit Hs. Consider calling AddHs()
[22:16:58] Molecule does not have explicit Hs. Consider calling AddHs()

[np.float64(0.12488387292807933)]

Removing Hydrogen Atoms

Hydrogen atoms can be removed with the strip() function:

ref.strip()

for mol in mols:
    mol.strip()

Symmetry-Corrected RMSD

spyrmsd only needs atomic coordinates, atomic number and the molecular adjacency matrix to compute the standard RMSD with spyrmsd.rmsd.symmrmsd. The spyrmsd.molecule.Molecule class provides easy access to such information:

coords_ref = ref.coordinates
anum_ref = ref.atomicnums
adj_ref = ref.adjacency_matrix

coords = [mol.coordinates for mol in mols]
anum = mols[0].atomicnums
adj = mols[0].adjacency_matrix

With this information we can easily compute the RMSD between the reference molecule and all other molecules:

RMSD = rmsd.symmrmsd(
    coords_ref,
    coords,
    anum_ref,
    anum,
    adj_ref,
    adj,
)

print(RMSD)

[np.float64(2.024608573240444), np.float64(1.4951562971486378), np.float64(10.028009301306854), np.float64(7.900570020309069), np.float64(7.578344354783399), np.float64(9.52999506817054), np.float64(4.952371789159666), np.float64(7.762808670066815), np.float64(9.996922964463582), np.float64(7.1732072690335755)]

Minimum RMSD

We can also compute the minimum RMSD obtained by superimposing the molecular structures:

RMSD = rmsd.symmrmsd(
    coords_ref,
    coords,
    anum_ref,
    anum,
    adj_ref,
    adj,
    minimize=True,
)

print(RMSD)

[np.float64(1.2012368667355466), np.float64(1.0533413220699535), np.float64(1.153253104575548), np.float64(1.036542688936588), np.float64(0.8407673221224143), np.float64(1.1758143217869736), np.float64(0.7817315189656703), np.float64(1.0933314311267779), np.float64(1.0260767175206498), np.float64(0.9586369647000478)]

Change Backend

spyrmsd supports multiple backends. You see which backends are available by looking at the available_backends attribute:

spyrmsd.available_backends

['rustworkx', 'networkx']

The available backends are a subset of the supported backends. Only the backends that are installed will be available.

You can check the current backend with

spyrmsd.get_backend()

'rustworkx'

You can switch the backend using

spyrmsd.set_backend("networkx")
spyrmsd.get_backend()

'networkx'