Merge#

Merging elements from multiple molecular systems.

Elements coming from different molecular systems can be merged into a new molecular system with the molsysmt.basic.merge() function.

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.merge().

Basic usage#

Let’s show how this function works using three peptides built as separate molecular systems: proline dipeptide (\(A\)), valine dipeptide (\(B\)), and lysine dipeptide (\(C\)):

import molsysmt as msm
import numpy as np

molsys_A = msm.build.build_peptide('AceProNme')
molsys_B = msm.build.build_peptide('AceValNme')
molsys_C = msm.build.build_peptide('AceLysNme')

To prevent overlaps when merging, the systems \(B\) and \(C\) are translated in space before being combined with \(A\).

molsys_B = msm.structure.translate(molsys_B, translation='[-1.0, 0.0, 0.0] nanometers')
molsys_C = msm.structure.translate(molsys_C, translation='[1.0, 0.0, 0.0] nanometers')

molsys_D = msm.merge([molsys_A, molsys_B, molsys_C])

Tip

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

Let’s now inspect the contents of the merged system \(D\):

msm.info(molsys_D)

form	n_atoms	n_groups	n_components	n_chains	n_molecules	n_entities	n_peptides	n_structures
molsysmt.MolSys	88	9	3	3	3	3	3	1

msm.view(molsys_D)