Quick info#
When you load a new molecular system, it is helpful to get a quick overview before you start selecting, styling, or measuring.
MolSysViewer provides view.info(...), a small wrapper around MolSysMT’s info. It renders a readable summary table in Jupyter.
If you want a deeper explanation of what info can show (and how the output depends on the element level), see MolSysMT’s info documentation.
import molsysviewer as viewer
view = viewer.demo["181L"]
view.show()
A good first checklist#
These three calls are often enough to understand what you are looking at:
system overview (
element="system")entity overview (
element="entity")chain breakdown (
element="chain")
view.info(element="system")
| 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 |
view.info(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 |
view.info(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'] |
Scoping with selections#
You can also combine info with a selection, to restrict the table to a specific subset (for example, only small molecules and ions):
view.info(element="molecule", selection='molecule_type in ["ion", "small molecule"]')
| 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 |
If you want to learn how selection strings work, see Selecting elements.