Where is attribute#

Identifying the item where a specific attribute is found in a molecular system.

In MolSysMT, molecular systems can be defined as a list of items, each of which may belong to a different form and contribute different attributes. For example, one item might provide structural data (coordinates, time), while another defines topology (bonds, atom types). If you wonder where a specific attribute resides within such a system, the function molsysmt.basic.where_is_attribute() can help.

Hint

Visit the section User guide > Introduction > Molecular System > Attributes in case you are not familiar with the concept of “attribute” in MolSysMT.

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.where_is_attribute().

Let’s illustrate how this function works with the following situation. Imagine we have a molecular system coming from the combination of two files: one with structural attributes and the other with topological ones.

import molsysmt as msm

structure = msm.systems['pentalanine']['pentalanine.inpcrd']
topology = msm.systems['pentalanine']['pentalanine.prmtop']

msm.info([topology, structure])

form	n_atoms	n_groups	n_components	n_chains	n_molecules	n_entities	n_waters	n_peptides	n_structures
['file:prmtop', 'file:inpcrd']	5207	1722	1716	1	1716	2	1715	1	1

The function molsysmt.basic.where_is_attribute() allows us to know where a given attribute is found in the list of items. Let’s see how {func}molsysmt.basic.where_is_attribute identifies the item holding a specific attribute:

msm.where_is_attribute([topology, structure], attribute='box')

('/home/diego/repos@uibcdf/molsysmt/molsysmt/data/inpcrd/pentalanine.inpcrd',
 'file:inpcrd')

msm.where_is_attribute([topology, structure], attribute='group_name')

('/home/diego/repos@uibcdf/molsysmt/molsysmt/data/prmtop/pentalanine.prmtop',
 'file:prmtop')

Tip

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