Info#

Displaying summary information about a molecular system and its elements

MolSysMT provides a function to display a concise summary of a molecular system and its elements: molsysmt.basic.info(). This function works at different levels depending on the selected element type — atom, group, component, molecule, chain, entity, or system. The output is a pandas.DataFrame.

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.info().

Let’s load a molecular system and explore a few examples of how this function works:

import molsysmt as msm

molsys = msm.convert('181L')

By default, molsysmt.basic.info() supplies a summary of the system as a Pandas dataframe:

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

Tip

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

But summary information on other elements such as atoms, groups, components, molecules, chains or entities can be obtained.

With atoms#

Example of how the function works at the atom level:

msm.info(molsys, element='atom', selection='molecule_type=="ion"')

index	id	name	type	group index	group id	group name	group type	component index	chain index	molecule index	molecule type	entity index	entity name
1289	1290	CL	CL	162	173	CL	ion	1	1	1	ion	1	CHLORIDE ION
1290	1291	CL	CL	163	178	CL	ion	2	2	2	ion	1	CHLORIDE ION

With groups#

Example of how the function works at the group level:

msm.info(molsys, element='group', selection=[9,10,11,12])

index	id	name	type	n atoms	molecule type	entity name
9	10	ASP	amino acid	8	protein	T4 LYSOZYME
10	11	GLU	amino acid	9	protein	T4 LYSOZYME
11	12	GLY	amino acid	4	protein	T4 LYSOZYME
12	13	LEU	amino acid	8	protein	T4 LYSOZYME

With components#

The function can also be applied to the component level, as shown below:

msm.info(molsys, element='component', selection='molecule_type=="small molecule"')

index	n atoms	n groups	chain index	molecule index	molecule type	entity index	entity name
3	8	1	3	3	small molecule	2	2-HYDROXYETHYL DISULFIDE
4	6	1	4	4	small molecule	3	BENZENE

With molecules#

Let’s see an example of how this function works with molecules:

msm.info(molsys, element='molecule',
         selection='molecule_type!=["water", "protein"] within 4.0 angstroms of molecule_type=="protein"')

index	name	type	n atoms	n groups	n components	chain index	entity index	entity name
1	CHLORIDE ION	ion	1	1	1	1	1	CHLORIDE ION
2	CHLORIDE ION	ion	1	1	1	2	1	CHLORIDE ION
3	2-HYDROXYETHYL DISULFIDE	small molecule	8	1	1	3	2	2-HYDROXYETHYL DISULFIDE
4	BENZENE	small molecule	6	1	1	4	3	BENZENE

With chains#

The function can also be applied to chain elements as shown below:

msm.info(molsys, element='chain', selection='molecule_type=="water"')

index	id	name	n atoms	n groups	n components	molecule index	molecule type	entity index	entity name
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']

With entities#

This example shows how to obtain a summary of entity elements:

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

index	name	type	n atoms	n groups	n components	n chains	n molecules
0	T4 LYSOZYME	protein	1289	162	1	1	1
1	CHLORIDE ION	ion	2	2	2	2	2
2	2-HYDROXYETHYL DISULFIDE	small molecule	8	1	1	1	1
3	BENZENE	small molecule	6	1	1	1	1
4	water	water	136	136	136	1	136

With system#

Let’s see an example of how this function works with the system (default option):

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