Path A - Module 53: Capability Matrix & Config#

MolSysMT is a multi-library framework. Some features depend on which external libraries (MDTraj, OpenMM, RDKit) you have installed.

In this module, you will learn to navigate the Capability Matrix to know exactly what is possible in your current environment and how to fine-tune the framework using the Config system.

import molsysmt as msm
from molsysmt import systems

1. The Interoperability Matrix#

Not every form is equal. A trajectory file (.xtc) does not store atom names, and a topology file (.prmtop) does not store coordinates.

You can generate a table of supported attributes for any form using msm.supported.forms().

# Let's see what the 'file:xtc' form can do
msm.supported.forms(form='file:xtc')

2. Supported Conversions#

Can I convert an OpenMM Topology directly into an MDTraj object? You can check the conversion paths available.

# See a summary of possible conversions
msm.supported.conversions()

3. The msm.configure System#

You can change the global behavior of MolSysMT. For example, you can tell the framework to be silent and not emit warnings during a loop.

# Check current configuration
print(f"Current logging level: {msm.configure.logging_level}")

# Change a setting (e.g., quiet mode)
msm.configure.logging_level = 'ERROR'
print("Logging level updated to ERROR only.")

🏆 Path A Challenge: The System Admin#

  1. Use msm.supported.forms() to find which forms support the ‘charge’ attribute.

  2. Check if your current environment has ‘MDTraj’ installed as a hard dependency.

  3. Use msm.configure to change the default units from ‘nm’ to ‘angstroms’ (if possible in the current version) or just explore the available settings.

  4. Find out if the form 'molsysmt.MolSysDict' supports ‘bonds’.

You are now in total control of the MolSysMT environment. In Module 54, we will finish your training with the Final Project: From Sequence to Analysis.