Remove#

Removing atoms or structures from a molecular system

The function molsysmt.basic.remove() allows atoms or structures from a molecular system.

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.remove().

Removing atoms#

The function molsysmt.basic.remove() removes atoms from a molecular system. The input argument selection allows us to define the elements to be removed. Let’s see a basic example:

import molsysmt as msm

molsys = msm.convert('181L')

msm.info(molsys, element='chain')

index	id	name	n atoms	n groups	n components	molecule index	molecule type	entity index	entity name
0	A	A	1289	162	1	[0]	['protein']	[0]	['T4 LYSOZYME']
1	B	A	1	1	1	[1]	['ion']	[1]	['CHLORIDE ION']
2	C	A	1	1	1	[2]	['ion']	[1]	['CHLORIDE ION']
3	D	A	8	1	1	[3]	['small molecule']	[2]	['2-HYDROXYETHYL DISULFIDE']
4	E	A	6	1	1	[4]	['small molecule']	[3]	['BENZENE']
5	F	A	136	136	136	[5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140]	['water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water']	[4]	['water']

molsys_trimmed = msm.remove(molsys, selection='chain_index==[1,2,3,4,5]')

Tip

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

msm.info(molsys_trimmed, element='chain')

index	id	name	n atoms	n groups	n components	molecule index	molecule type	entity index	entity name
0	A	A	1289	162	1	[0]	['protein']	[0]	['T4 LYSOZYME']

Removing structures#

The function molsysmt.basic.remove() can also remove structures from a molecular system. The input argument structure_indices can be used to choose the structures to be removed. The following example shows how to remove structures using this argument:

pdbfile = msm.systems['Trp-Cage']['1l2y.pdb']
molsys = msm.convert(pdbfile, to_form='molsysmt.Structures')

msm.info(molsys)

form	n_atoms	n_groups	n_components	n_chains	n_molecules	n_entities	n_structures
molsysmt.Structures	304	None	None	None	None	None	38

molsys_trimmed = msm.remove(molsys, structure_indices=range(1,38))

msm.info(molsys_trimmed)

form	n_atoms	n_groups	n_components	n_chains	n_molecules	n_entities	n_structures
molsysmt.Structures	304	None	None	None	None	None	1