Set#

Setting attribute values to a molecular system.

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

Hint

Visit the section Attributes for a detailed overview of attributes in MolSysMT.

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.set().

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)
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 component index chain index molecule index molecule type entity index entity name
248 249 N N 30 31 HIS amino acid 0 0 0 protein 0 T4 LYSOZYME
249 250 CA C 30 31 HIS amino acid 0 0 0 protein 0 T4 LYSOZYME
250 251 C C 30 31 HIS amino acid 0 0 0 protein 0 T4 LYSOZYME
251 252 O O 30 31 HIS amino acid 0 0 0 protein 0 T4 LYSOZYME
252 253 CB C 30 31 HIS amino acid 0 0 0 protein 0 T4 LYSOZYME
253 254 CG C 30 31 HIS amino acid 0 0 0 protein 0 T4 LYSOZYME
254 255 ND1 N 30 31 HIS amino acid 0 0 0 protein 0 T4 LYSOZYME
255 256 CD2 C 30 31 HIS amino acid 0 0 0 protein 0 T4 LYSOZYME
256 257 CE1 C 30 31 HIS amino acid 0 0 0 protein 0 T4 LYSOZYME
257 258 NE2 N 30 31 HIS amino acid 0 0 0 protein 0 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 also be invoked from the main level of the library. Hence, molsysmt.set() is the same function 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 component index chain index molecule index molecule type entity index entity name
248 249 N N 30 31 HSD amino acid 0 0 0 protein 0 T4 LYSOZYME
249 250 CA C 30 31 HSD amino acid 0 0 0 protein 0 T4 LYSOZYME
250 251 C C 30 31 HSD amino acid 0 0 0 protein 0 T4 LYSOZYME
251 252 O O 30 31 HSD amino acid 0 0 0 protein 0 T4 LYSOZYME
252 253 CB C 30 31 HSD amino acid 0 0 0 protein 0 T4 LYSOZYME
253 254 CG C 30 31 HSD amino acid 0 0 0 protein 0 T4 LYSOZYME
254 255 ND1 N 30 31 HSD amino acid 0 0 0 protein 0 T4 LYSOZYME
255 256 CD2 C 30 31 HSD amino acid 0 0 0 protein 0 T4 LYSOZYME
256 257 CE1 C 30 31 HSD amino acid 0 0 0 protein 0 T4 LYSOZYME
257 258 NE2 N 30 31 HSD amino acid 0 0 0 protein 0 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]]]
Unitsnanometer

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]]]
Unitsnanometer

See also

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