Set#

Setting attribute values (topological or structural) to a molecular system.

Some attributes of a molecular system can be changed without altering its identity — for example, modifying the box dimensions, coordinates, or forcefield information. In other cases, attribute corrections may be required, such as fixing a wrong residue name or atom type. MolSysMT provides the molsysmt.basic.set() function to assist with these tasks.

The list of attributes defined in MolSysMT for a molecular system can be checked in the section User guide > Introduction > Molecular system > Attributes.

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.set().

To illustrate how this function works, lets load a molecular system:

import molsysmt as msm

molsys = msm.convert('181L')

msm.info(molsys)

form	n_atoms	n_groups	n_components	n_chains	n_molecules	n_entities	n_waters	n_ions	n_small_molecules	n_proteins	n_structures
molsysmt.MolSys	1441	302	141	6	141	5	136	2	2	1	1

Suppose that the name of the group at index 30 is incorrect in our system:

msm.info(molsys, element='atom', selection='group_index==30')

index	id	name	type	group index	group id	group name	group type	molecule type	entity name
248	249	N	N	30	31	HIS	amino acid	protein	T4 LYSOZYME
249	250	CA	C	30	31	HIS	amino acid	protein	T4 LYSOZYME
250	251	C	C	30	31	HIS	amino acid	protein	T4 LYSOZYME
251	252	O	O	30	31	HIS	amino acid	protein	T4 LYSOZYME
252	253	CB	C	30	31	HIS	amino acid	protein	T4 LYSOZYME
253	254	CG	C	30	31	HIS	amino acid	protein	T4 LYSOZYME
254	255	ND1	N	30	31	HIS	amino acid	protein	T4 LYSOZYME
255	256	CD2	C	30	31	HIS	amino acid	protein	T4 LYSOZYME
256	257	CE1	C	30	31	HIS	amino acid	protein	T4 LYSOZYME
257	258	NE2	N	30	31	HIS	amino acid	protein	T4 LYSOZYME

Let’s now assume that the histidine residue should be labeled as “HSD” instead of “HIS”. This can be easily updated using the function molsysmt.basic.set():

msm.set(molsys, selection='group_index==30', group_name='HSD')

Tip

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

Let’s check that the group name changed in deed:

msm.info(molsys, element='atom', selection='group_index==30')

index	id	name	type	group index	group id	group name	group type	molecule type	entity name
248	249	N	N	30	31	HSD	amino acid	protein	T4 LYSOZYME
249	250	CA	C	30	31	HSD	amino acid	protein	T4 LYSOZYME
250	251	C	C	30	31	HSD	amino acid	protein	T4 LYSOZYME
251	252	O	O	30	31	HSD	amino acid	protein	T4 LYSOZYME
252	253	CB	C	30	31	HSD	amino acid	protein	T4 LYSOZYME
253	254	CG	C	30	31	HSD	amino acid	protein	T4 LYSOZYME
254	255	ND1	N	30	31	HSD	amino acid	protein	T4 LYSOZYME
255	256	CD2	C	30	31	HSD	amino acid	protein	T4 LYSOZYME
256	257	CE1	C	30	31	HSD	amino acid	protein	T4 LYSOZYME
257	258	NE2	N	30	31	HSD	amino acid	protein	T4 LYSOZYME

Let’s explore another example, this time modifying a structural attribute. We will look at the coordinates of the “CA” atom in the “HSD” group:

msm.get(molsys, element='atom', selection='group_name=="HSD" and atom_name=="CA"', coordinates=True)

Magnitude	[[[3.7278 1.6327 1.7646999999999997]]]
Units	nanometer

There is only a single structure in the system, let’s change the coordinates of this former atom to a new value:

msm.set(molsys, selection='group_name=="HSD" and atom_name=="CA"', structure_indices=0, coordinates='[0,0,0] nm')

Finally, let’s verify that the coordinates of the “CA” atom in the “HSD” group were updated correctly:

msm.get(molsys, element='atom', selection='group_name=="HSD" and atom_name=="CA"', coordinates=True)

Magnitude	[[[0.0 0.0 0.0]]]
Units	nanometer