Is solvated#

Checking whether a molecular system contains solvent molecules.

The function molsysmt.build.is_solvated() evaluates whether a molecular system contains solvent molecules (such as water or ions), returning True if solvent is present and False otherwise.

Added in version 1.0.0.

API documentation

Follow this link for a detailed description of the input arguments, raised errors, and returned objects of this function: molsysmt.build.is_solvated().

Basic usage#

Let’s show how this function works using Met-enkephalin:

import molsysmt as msm

molsys = msm.convert(msm.systems['Met-enkephalin']['met_enkephalin.h5msm'], to_form='molsysmt.MolSys')

Note

Demo Systems Catalog

This tutorial uses demonstration datasets provided by MolSysMT. To explore the full catalog of bundled systems, forms, and file paths, visit the Demo Systems guide.

First, let’s complete terminal cappings and hydrogens for the peptide:

molsys = msm.build.add_missing_terminal_cappings(molsys)
molsys = msm.build.add_missing_hydrogens(molsys)

We check if the system is solvated using molsysmt.build.is_solvated():

msm.build.is_solvated(molsys)

False

Now we solvate the system in a cubic water box using molsysmt.build.solvate():

molsys = msm.build.solvate(molsys, box_shape='cubic', clearance='14.0 angstroms', water_model='TIP3P')

We check again to confirm that the system is now solvated:

msm.build.is_solvated(molsys)

True

msm.get(molsys, n_waters=True)