5.26. Guessing unknown Topology information — `MDAnalysis.topology.guessers`

In general guess_atom_X returns the guessed value for a single value, while guess_Xs will work on an array of many atoms.

5.26.1. Example uses of guessers

5.26.1.1. Guessing elements from atom names

Currently, it is possible to guess elements from atom names using guess_atom_element() (or the synonymous guess_atom_type()). This can be done in the following manner:

import MDAnalysis as mda
from MDAnalysis.topology.guessers import guess_atom_element
from MDAnalysisTests.datafiles import PRM7

u = mda.Universe(PRM7)

print(u.atoms.names[1])  # returns the atom name H1

element = guess_atom_element(u.atoms.names[1])

print(element)  # returns element H

In the above example, we take an atom named H1 and use guess_atom_element() to guess the element hydrogen (i.e. H). It is important to note that element guessing is not always accurate. Indeed in cases where the atom type is not recognised, we may end up with the wrong element. For example:

import MDAnalysis as mda
from MDAnalysis.topology.guessers import guess_atom_element
from MDAnalysisTests.datafiles import PRM19SBOPC

u = mda.Universe(PRM19SBOPC)

print(u.atoms.names[-1])  # returns the atom name EPW

element = guess_atom_element(u.atoms.names[-1])

print(element)  # returns element P

Here we find that virtual site atom ‘EPW’ was given the element P, which would not be an expected result. We therefore always recommend that users carefully check the outcomes of any guessers.

In some cases, one may want to guess elements for an entire universe and add this guess as a topology attribute. This can be done using guess_types() in the following manner:

import MDAnalysis as mda
from MDAnalysis.topology.guessers import guess_types
from MDAnalysisTests.datafiles import PRM7

u = mda.Universe(PRM7)

guessed_elements = guess_types(u.atoms.names)

u.add_TopologyAttr('elements', guessed_elements)

print(u.atoms.elements)  # returns an array of guessed elements

More information on adding topology attributes can found in the user guide.

MDAnalysis.topology.guessers.get_atom_mass(element)[source]

Return the atomic mass in u for element.

Masses are looked up in MDAnalysis.topology.tables.masses.

Warning

Unknown masses are set to 0.0

Changed in version 0.20.0: Try uppercase atom type name as well

MDAnalysis.topology.guessers.guess_angles(bonds)[source]

Given a list of Bonds, find all angles that exist between atoms.

Works by assuming that if atoms 1 & 2 are bonded, and 2 & 3 are bonded, then (1,2,3) must be an angle.

Returns:: List of tuples defining the angles. Suitable for use in u._topology
Return type:: list of tuples

5.26. Guessing unknown Topology information — MDAnalysis.topology.guessers

5.26.1. Example uses of guessers

5.26.1.1. Guessing elements from atom names

5.26. Guessing unknown Topology information — `MDAnalysis.topology.guessers`