Extract#

Extracting a subset of atoms and structures from a molecular system.

The function molsysmt.basic.extract() allows you to extract a subset of a molecular system based on atom selections and structure indices. It’s output is a new molecular system with the elements and structures selected by the user.

Added in version 1.0.0.

How this function works#

API documentation

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

Let’s see molsysmt.basic.extract() in action with a simple example:

import molsysmt as msm

/home/diego/Myopt/miniconda3/envs/MolSysMT@uibcdf_3.12/lib/python3.12/site-packages/nglview/__init__.py:12: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.
  import pkg_resources

molsys = msm.convert('181L')

msm.info(molsys, element='entity')

index	name	type	n atoms	n groups	n components	n chains	n molecules
0	T4 LYSOZYME	protein	1289	162	1	1	1
1	CHLORIDE ION	unknown	2	2	2	2	2
2	2-HYDROXYETHYL DISULFIDE	unknown	8	1	1	1	1
3	BENZENE	unknown	6	1	1	1	1
4	water	water	136	136	136	1	136

We will extract only the protein and benzene entities from the system by using a selection based on entity_name.

molsubsys = msm.extract(molsys, selection='entity_name in ["T4 LYSOZYME", "BENZENE"]')

Tip

All methods defined in the molsysmt.basic module can be invoked also from the main level of the library. Hence, molsysmt.extract() is the same method as molsysmt.basic.extract().

msm.info(molsubsys, element='entity')

index	name	type	n atoms	n groups	n components	n chains	n molecules
0	T4 LYSOZYME	protein	1289	162	1	1	1
1	BENZENE	small molecule	6	1	1	1	1