Get#

Retrieving attribute values from a molecular system.

A molecular system is defined by its attributes and the attributes of its elements — such as the number of atoms, group names, bonded atoms, coordinates, box dimensions, and more. However, not all attributes are available in every representation (form) of a system. Molecular systems can take different forms, such as string identifiers, file paths, or Python objects. Each form includes a specific set of attributes and omits others. Regardless of the form, retrieving attribute values is a key operation in any workflow involving molecular models.

Hint

Visit the section The Molecular System in case you are not familiar with the concepts of “form” or “attribute” in MolSysMT.

The list of attributes defined in MolSysMT for a molecular system can be checked in the section Attributes. And the function molsysmt.basic.get() is the tool to get the attribute values of a molecular system in any supported form.

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.get().

Basic usage#

Let’s show how this function works using a PDB system (1TCD):

import molsysmt as msm

molsys = msm.convert('1TCD', to_form='molsysmt.MolSys')

msm.info(molsys)

form	n_atoms	n_groups	n_components	n_chains	n_molecules	n_entities	n_waters	n_proteins	n_structures
molsysmt.MolSys	3983	662	167	4	167	2	165	2	1

Let’s retrieve the names of atoms with indices 32, 33, and 34 (0-based). The function molsysmt.basic.get() uses the element argument to specify the type of element being queried (e.g., ‘atom’, ‘group’, ‘molecule’, etc.). To filter which elements to include, use the selection argument, which accepts a list of indices or a query string.

names = msm.get(molsys, element='atom', selection=[32,33,34], name=True)
print('Atom names:',names)

Atom names: ['N', 'CA', 'C']

Tip

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

We are not limited to retrieving just one attribute. Multiple attributes can be requested in a single call:

names, group_indices, group_names = msm.get(molsys, element='atom', selection=[32,33,34],
                                            name=True, group_index=True, group_name=True)
print('Atom names:', names)
print('Group indices:', group_indices)
print('Group names:', group_names)

Atom names: ['N', 'CA', 'C']
Group indices: [4, 4, 4]
Group names: ['ILE', 'ILE', 'ILE']

Let’s illustrate now how things can work with other elements:

n_atoms = msm.get(molsys, element='group', selection=[10,11,12], n_atoms=True)
print('Number of atoms:', n_atoms)

Number of atoms: [9, 6, 8]

msm.get(molsys, element='group', selection=[10,11,12], n_atoms=True)

[9, 6, 8]

names, atom_indices, atom_names = msm.get(molsys, element='group', selection=[10,11,12],
                                            name=True, atom_index=True, atom_name=True)
print('Group names:', names)
print('Atom indices:', atom_indices)
print('Atom names:', atom_names)

Group names: ['LYS', 'CYS', 'ASN']
Atom indices: [[77, 78, 79, 80, 81, 82, 83, 84, 85], [86, 87, 88, 89, 90, 91], [92, 93, 94, 95, 96, 97, 98, 99]]
Atom names: [['N', 'CA', 'C', 'O', 'CB', 'CG', 'CD', 'CE', 'NZ'], ['N', 'CA', 'C', 'O', 'CB', 'SG'], ['N', 'CA', 'C', 'O', 'CB', 'CG', 'OD1', 'ND2']]

indices, component_indices = msm.get(molsys, element='component', selection=[55, 56, 57],
                                    index=True, group_index=True)
print('Indices:', indices)
print('Component indices:', component_indices)

Indices: [55, 56, 57]
Component indices: [[550], [551], [552]]

If no selection is specified, the function applies to all elements of the chosen type by default. See for example:

msm.get(molsys, element='atom', n_atoms=True)

The function msm.basic.get() also supports selection strings using logical or spatial queries. If you’re not familiar with selection syntax, visit User guide > Tools > Basic > Select. Let’s see how selection works beyond indices lists with some examples:

msm.get(molsys, element='atom', selection='group_index==20', name=True, index=True)

[['N', 'CA', 'C', 'O', 'CB', 'CG', 'CD'], [148, 149, 150, 151, 152, 153, 154]]

msm.get(molsys, element='atom', selection='molecule_type=="protein"', n_groups=True)

msm.get(molsys, element='molecule', selection='molecule_type=="water"', n_molecules=True)

msm.get(molsys, element='atom', selection='all within 7.0 angstroms of atom_index==0', n_atoms=True)

Finally, not all molecular system forms include all attributes. For example, an openmm.Topology object has no atom coordinates, and a file:inpcrd system may not contain chain names. When an attribute is unavailable, the function returns None.

inpcrd_file = msm.systems['pentalanine']['pentalanine.inpcrd']
msm.get(inpcrd_file, n_groups=True) is None

True

Note

Demo Systems Catalog

This tutorial uses demonstration datasets provided by MolSysMT. To explore the full catalog of bundled systems, forms, and file paths, visit the Demo Systems guide.

Examples with topological attributes#

Here you can find some additional examples where msm.basic.get() works over atoms, groups, components, chains, molecules, entities, bonds or system.

With atoms#

# Group id of atoms with index 0, 1 or 2
msm.get(molsys, element='atom', selection='atom_index in [0,1,2]', group_id=True)

['4', '4', '4']

# Number of groups in atoms with index 0, 1 or 2
msm.get(molsys, element='atom', selection='atom_index in [0,1,2]', n_groups=True)

# Index of groups in atoms with index 0 to 15
msm.get(molsys, element='atom', selection=range(5,10), group_index=True)

[0, 0, 0, 0, 1]

With groups#

# Id of groups with index 0, 1 or 2
msm.get(molsys, element='group', selection=[0,1,2], id=True)

['4', '5', '6']

# Index of atoms in groups with index 0 or 1
msm.get(molsys, element='group', selection=[0,1], atom_index=True)

[[0, 1, 2, 3, 4, 5, 6, 7, 8], [9, 10, 11, 12, 13, 14, 15]]

# Number of groups in molecules of type water
msm.get(molsys, element='group', selection='molecule_type=="water"', n_groups=True)

# Number of groups of type aminoacid
msm.get(molsys, element='group', selection='group_type=="amino acid"', n_groups=True)

With components#

msm.get(molsys, element='component', selection='molecule_type=="water"', index=True)

msm.get(molsys, element='component', selection=[0,1,2,3], n_waters=True)

[0, 0, 1, 1]

With molecules#

# Names of groups in molecule of index 0
msm.get(molsys, element='molecule', selection=[0,1], group_name=True)

[['LYS',
  'PRO',
  'GLN',
  'PRO',
  'ILE',
  'ALA',
  'ALA',
  'ALA',
  'ASN',
  'TRP',
  'LYS',
  'CYS',
  'ASN',
  'GLY',
  'SER',
  'GLU',
  'SER',
  'LEU',
  'LEU',
  'VAL',
  'PRO',
  'LEU',
  'ILE',
  'GLU',
  'THR',
  'LEU',
  'ASN',
  'ALA',
  'ALA',
  'THR',
  'PHE',
  'ASP',
  'HIS',
  'ASP',
  'VAL',
  'GLN',
  'CYS',
  'VAL',
  'VAL',
  'ALA',
  'PRO',
  'THR',
  'PHE',
  'LEU',
  'HIS',
  'ILE',
  'PRO',
  'MET',
  'THR',
  'LYS',
  'ALA',
  'ARG',
  'LEU',
  'THR',
  'ASN',
  'PRO',
  'LYS',
  'PHE',
  'GLN',
  'ILE',
  'ALA',
  'ALA',
  'GLN',
  'ASN',
  'ALA',
  'ILE',
  'THR',
  'ARG',
  'SER',
  'GLY',
  'ALA',
  'PHE',
  'THR',
  'GLY',
  'GLU',
  'VAL',
  'SER',
  'LEU',
  'GLN',
  'ILE',
  'LEU',
  'LYS',
  'ASP',
  'TYR',
  'GLY',
  'ILE',
  'SER',
  'TRP',
  'VAL',
  'VAL',
  'LEU',
  'GLY',
  'HIS',
  'SER',
  'GLU',
  'ARG',
  'ARG',
  'LEU',
  'TYR',
  'TYR',
  'GLY',
  'GLU',
  'THR',
  'ASN',
  'GLU',
  'ILE',
  'VAL',
  'ALA',
  'GLU',
  'LYS',
  'VAL',
  'ALA',
  'GLN',
  'ALA',
  'CYS',
  'ALA',
  'ALA',
  'GLY',
  'PHE',
  'HIS',
  'VAL',
  'ILE',
  'VAL',
  'CYS',
  'VAL',
  'GLY',
  'GLU',
  'THR',
  'ASN',
  'GLU',
  'GLU',
  'ARG',
  'GLU',
  'ALA',
  'GLY',
  'ARG',
  'THR',
  'ALA',
  'ALA',
  'VAL',
  'VAL',
  'LEU',
  'THR',
  'GLN',
  'LEU',
  'ALA',
  'ALA',
  'VAL',
  'ALA',
  'GLN',
  'LYS',
  'LEU',
  'SER',
  'LYS',
  'GLU',
  'ALA',
  'TRP',
  'SER',
  'ARG',
  'VAL',
  'VAL',
  'ILE',
  'ALA',
  'TYR',
  'GLU',
  'PRO',
  'VAL',
  'TRP',
  'ALA',
  'ILE',
  'GLY',
  'THR',
  'GLY',
  'LYS',
  'VAL',
  'ALA',
  'THR',
  'PRO',
  'GLN',
  'GLN',
  'ALA',
  'GLN',
  'GLU',
  'VAL',
  'HIS',
  'GLU',
  'LEU',
  'LEU',
  'ARG',
  'ARG',
  'TRP',
  'VAL',
  'ARG',
  'SER',
  'LYS',
  'LEU',
  'GLY',
  'THR',
  'ASP',
  'ILE',
  'ALA',
  'ALA',
  'GLN',
  'LEU',
  'ARG',
  'ILE',
  'LEU',
  'TYR',
  'GLY',
  'GLY',
  'SER',
  'VAL',
  'THR',
  'ALA',
  'LYS',
  'ASN',
  'ALA',
  'ARG',
  'THR',
  'LEU',
  'TYR',
  'GLN',
  'MET',
  'ARG',
  'ASP',
  'ILE',
  'ASN',
  'GLY',
  'PHE',
  'LEU',
  'VAL',
  'GLY',
  'GLY',
  'ALA',
  'SER',
  'LEU',
  'LYS',
  'PRO',
  'GLU',
  'PHE',
  'VAL',
  'GLU',
  'ILE',
  'ILE',
  'GLU',
  'ALA',
  'THR',
  'LYS'],
 ['SER',
  'LYS',
  'PRO',
  'GLN',
  'PRO',
  'ILE',
  'ALA',
  'ALA',
  'ALA',
  'ASN',
  'TRP',
  'LYS',
  'CYS',
  'ASN',
  'GLY',
  'SER',
  'GLU',
  'SER',
  'LEU',
  'LEU',
  'VAL',
  'PRO',
  'LEU',
  'ILE',
  'GLU',
  'THR',
  'LEU',
  'ASN',
  'ALA',
  'ALA',
  'THR',
  'PHE',
  'ASP',
  'HIS',
  'ASP',
  'VAL',
  'GLN',
  'CYS',
  'VAL',
  'VAL',
  'ALA',
  'PRO',
  'THR',
  'PHE',
  'LEU',
  'HIS',
  'ILE',
  'PRO',
  'MET',
  'THR',
  'LYS',
  'ALA',
  'ARG',
  'LEU',
  'THR',
  'ASN',
  'PRO',
  'LYS',
  'PHE',
  'GLN',
  'ILE',
  'ALA',
  'ALA',
  'GLN',
  'ASN',
  'ALA',
  'ILE',
  'THR',
  'ARG',
  'SER',
  'GLY',
  'ALA',
  'PHE',
  'THR',
  'GLY',
  'GLU',
  'VAL',
  'SER',
  'LEU',
  'GLN',
  'ILE',
  'LEU',
  'LYS',
  'ASP',
  'TYR',
  'GLY',
  'ILE',
  'SER',
  'TRP',
  'VAL',
  'VAL',
  'LEU',
  'GLY',
  'HIS',
  'SER',
  'GLU',
  'ARG',
  'ARG',
  'LEU',
  'TYR',
  'TYR',
  'GLY',
  'GLU',
  'THR',
  'ASN',
  'GLU',
  'ILE',
  'VAL',
  'ALA',
  'GLU',
  'LYS',
  'VAL',
  'ALA',
  'GLN',
  'ALA',
  'CYS',
  'ALA',
  'ALA',
  'GLY',
  'PHE',
  'HIS',
  'VAL',
  'ILE',
  'VAL',
  'CYS',
  'VAL',
  'GLY',
  'GLU',
  'THR',
  'ASN',
  'GLU',
  'GLU',
  'ARG',
  'GLU',
  'ALA',
  'GLY',
  'ARG',
  'THR',
  'ALA',
  'ALA',
  'VAL',
  'VAL',
  'LEU',
  'THR',
  'GLN',
  'LEU',
  'ALA',
  'ALA',
  'VAL',
  'ALA',
  'GLN',
  'LYS',
  'LEU',
  'SER',
  'LYS',
  'GLU',
  'ALA',
  'TRP',
  'SER',
  'ARG',
  'VAL',
  'VAL',
  'ILE',
  'ALA',
  'TYR',
  'GLU',
  'PRO',
  'VAL',
  'TRP',
  'ALA',
  'ILE',
  'GLY',
  'THR',
  'GLY',
  'LYS',
  'VAL',
  'ALA',
  'THR',
  'PRO',
  'GLN',
  'GLN',
  'ALA',
  'GLN',
  'GLU',
  'VAL',
  'HIS',
  'GLU',
  'LEU',
  'LEU',
  'ARG',
  'ARG',
  'TRP',
  'VAL',
  'ARG',
  'SER',
  'LYS',
  'LEU',
  'GLY',
  'THR',
  'ASP',
  'ILE',
  'ALA',
  'ALA',
  'GLN',
  'LEU',
  'ARG',
  'ILE',
  'LEU',
  'TYR',
  'GLY',
  'GLY',
  'SER',
  'VAL',
  'THR',
  'ALA',
  'LYS',
  'ASN',
  'ALA',
  'ARG',
  'THR',
  'LEU',
  'TYR',
  'GLN',
  'MET',
  'ARG',
  'ASP',
  'ILE',
  'ASN',
  'GLY',
  'PHE',
  'LEU',
  'VAL',
  'GLY',
  'GLY',
  'ALA',
  'SER',
  'LEU',
  'LYS',
  'PRO',
  'GLU',
  'PHE',
  'VAL',
  'GLU',
  'ILE',
  'ILE',
  'GLU',
  'ALA',
  'THR',
  'LYS']]

# Number of molecules of type protein
msm.get(molsys, element='molecule', selection='molecule_type=="protein"', n_molecules=True)

# Molecule type of molecules with index 1 to 9
msm.get(molsys, element='molecule', selection=range(1,10), molecule_type=True)

['protein',
 'water',
 'water',
 'water',
 'water',
 'water',
 'water',
 'water',
 'water']

With chains#

# Molecule type of molecules with index 1 to 9
msm.get(molsys, element='chain', selection='all', name=True)

['A', 'B', 'A', 'B']

# Molecule type of molecules with index 1 to 9
msm.get(molsys, element='chain', selection='all', id=True)

['A', 'B', 'C', 'D']

# Molecule type of molecules with index 1 to 9
msm.get(molsys, element='chain', selection='molecule_type=="protein"', id=True)

['A', 'B']

With entities#

# Name of entity with index 0
msm.get(molsys, element='entity', selection=0, name=True)

['TRIOSEPHOSPHATE ISOMERASE']

# Number of molecules in entity with index 1
msm.get(molsys, element='entity', selection=1, n_molecules=True)

[165]

# Index of molecules in entity with index 1
msm.get(molsys, element='entity', selection=1, molecule_index=True)

With bonds#

msm.get(molsys, element='atom', selection=[0,1,2,3,4,5], bonded_atoms=True)

[[1], [0, 2, 4], [1, 3, 9], [2], [1, 5], [4, 6]]

msm.get(molsys, element='atom', selection=[0,1,2,3,4,5], inner_bonded_atoms=True)

[[1], [0, 2, 4], [1, 3], [2], [1, 5], [4]]

msm.get(molsys, element='atom', selection=[0,1,2,3,4,5], bonded_atoms_pairs=True)

[[0, 1], [1, 2], [1, 4], [2, 3], [2, 9], [4, 5], [5, 6]]

msm.get(molsys, element='atom', selection=[0,1,2,3,4,5], inner_bonded_atoms_pairs=True)

[[0, 1], [1, 2], [1, 4], [2, 3], [4, 5]]

msm.get(molsys, element='atom', selection=[0,1,2,3,4,5], bond_index=True)

[[0], [0, 1, 2], [1, 3, 4], [3], [2, 5], [5, 6]]

msm.get(molsys, element='atom', selection=[0,1,2,3,4,5], n_bonds=True)

[1, 3, 3, 1, 2, 2]

msm.get(molsys, element='atom', selection=[0,1,2,3,4,5], inner_bond_index=True)

[[0], [0, 1, 2], [1, 3], [3], [2, 5], [5]]

msm.get(molsys, element='atom', selection=[0,1,2,3,4,5], n_inner_bonds=True)

[1, 3, 2, 1, 2, 1]

msm.select(molsys, element='bond', selection='group_index==3')

[26, 27, 28, 29, 30, 32, 33]

msm.get(molsys, element='bond', selection='group_index==3', index=True)

[26, 27, 28, 29, 30, 32, 33]

msm.get(molsys, element='bond', selection=[0,1,2,3,4], bonded_atoms=True)

[0, 1, 2, 3, 4, 9]

msm.get(molsys, element='bond', selection='group_index==3', bonded_atoms=True)

[25, 26, 27, 28, 29, 30, 31]

With the system#

The element system has some specific observables accounting for the amount of type of elements such as the number of aminoacid groups, ion molecules or protein molecules:

# Number of aminoacids and number of waters in the system
msm.get(molsys, element='system', n_amino_acids=True, n_waters=True)

[497, 165]

msm.get(molsys, element='system', n_bonds=True)

Examples with structural attributes#

msm.get(molsys, element='system', n_structures=True)

msm.get(molsys, element='atom', selection=100, structure_indices=0, coordinates=True)

Magnitude	[[[1.8835 3.8270999999999997 5.0365]]]
Units	nanometer

msm.get(molsys, element='system', coordinates=True)

Magnitude

[[[1.8466999999999998 2.7638 8.3661]  [1.8580999999999999 2.8457 8.2415]  [1.7231 2.8536999999999995 8.1751]  ...  [2.685 6.2692 5.3171]  [0.0135 4.6709 3.6203]  [0.5324 6.512399999999999 5.142499999999999]]]

Units

nanometer

msm.get(molsys, element='system', structure_indices=0, box=True)

Magnitude	[[[4.3709999999999996 0.0 0.0] [0.0 7.765 0.0] [0.0 0.0 14.953999999999997]]]
Units	nanometer

box_lengths, box_angles, box_volume = msm.get(molsys, element='system', structure_indices=0,
                                              box_lengths=True, box_angles=True, box_volume=True)

box_lengths

Magnitude	[[4.371 7.765 14.954]]
Units	nanometer

box_angles

Magnitude	[[1.570796 1.570796 1.570796]]
Units	radian

box_volume

Magnitude	[507.55094750999984]
Units	nanometer³