Merge#

Merging elements from multiple molecular systems.

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

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.merge().

Let’s demonstrate how this function works using three peptides, each defined as a separate molecular system: proline dipeptide (\(A\)), valine dipeptide (\(B\)), and lysine dipeptide (\(C\)).

import molsysmt as msm

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 be invoked also from the main level of the library. Thus, molsysmt.merge() is simply an alias of 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	1	3	1

msm.view(molsys_D, standard=True)