Where is attribute#

Identifying the item holding a specific attribute in a molecular system.

In MolSysMT, a molecular system can be represented by a list of items, each belonging to a different form and contributing different attributes. For example, one item might provide structural data (coordinates, time), while another defines topology (bonds, atom names). The function molsysmt.basic.where_is_attribute() identifies which item in a composite molecular system provides a given attribute.

Hint

Visit the section Attributes for a detailed overview of attributes in MolSysMT.

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.where_is_attribute().

Basic usage#

Let’s show how this function works using a composite molecular system defined by two files: an AMBER topology file (pentalanine.prmtop) and an AMBER coordinate file (pentalanine.inpcrd):

import molsysmt as msm

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

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.

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 also be invoked from the main level of the library. Hence, molsysmt.where_is_attribute() is the same function as molsysmt.basic.where_is_attribute().