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. Its output is a new molecular system with the elements and structures selected by the user. A composite input, such as a topology file paired with a coordinate trajectory, is materialized as a native molsysmt.MolSys before extraction so both domains remain aligned. For an H5MSM file input, provide a different output_filename to write a subset, or request to_form='molsysmt.MolSys' to keep the subset in memory.

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.basic.extract().

Basic usage#

Let’s show how this function works using a PDB structure (181L):

import molsysmt as msm

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	ion	2	2	2	2	2
2	2-HYDROXYETHYL DISULFIDE	small molecule	8	1	1	1	1
3	BENZENE	small molecule	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 also be invoked from the main level of the library. Hence, molsysmt.extract() is the same function 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