Get form#

Identifying the form of a molecular system.

A single molecular system can be represented in different forms, such as a file, a string ID, or a Python object. These forms can be converted between one another depending on the attributes needed and the steps of a workflow. The form of a molecular system can be obtained with the function molsysmt.basic.get_form().

Hint

Visit the section Items and Forms if you are not familiar with the concept of “form” 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.get_form().

Basic usage#

Let’s show how this function works using different representations of molecular systems:

import molsysmt as msm

molsys = '181L'

msm.get_form(molsys)

'string:pdb_id'

Tip

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

Let’s try with other forms of this and other molecular systems:

molsys_B = msm.convert(molsys, to_form='openmm.Modeller')
msm.get_form(molsys_B)

'openmm.Modeller'

msm.get_form('AceAlaValTyrNme')

'string:amino_acids_3'

molsys = msm.systems['pentalanine']['pentalanine.inpcrd']
msm.get_form(molsys)

'file:inpcrd'

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.

import numpy as np
molsys = np.zeros(shape=[10,4,3])*msm.pyunitwizard.unit('angstroms')
msm.get_form(molsys)

'XYZ'

molsys = ('HETATM 3274  C1  BEN A 302      -9.410  30.002  12.405  1.00 61.32           C  \n'
          'HETATM 3275  C2  BEN A 302     -10.677  29.482  12.626  1.00 58.40           C  \n'
          'HETATM 3276  C3  BEN A 302     -10.836  28.180  13.091  1.00 49.12           C  \n'
          'HETATM 3277  C4  BEN A 302      -9.725  27.387  13.331  1.00 56.99           C  \n'
          'HETATM 3278  C5  BEN A 302      -8.454  27.906  13.109  1.00 53.41           C  \n'
          'HETATM 3279  C6  BEN A 302      -8.298  29.207  12.650  1.00 55.79           C  \n'
          'HETATM 3280  C   BEN A 302      -9.255  31.315  11.933  1.00 63.37           C  \n'
          'HETATM 3281  N1  BEN A 302      -8.925  31.552  10.675  1.00 73.79           N  \n'
          'HETATM 3282  N2  BEN A 302      -9.382  32.348  12.740  1.00 62.54           N  ')

msm.get_form(molsys)

'string:pdb_text'

view = msm.view(molsys)
msm.get_form(view)

'molsysviewer.MolSysView'