6.1.2.2. Default Guesser

DefaultGuesser is a generic guesser class that has basic guessing methods. This class is a general purpose guesser that can be used with most topologies, but being generic makes it the least accurate among all guessers.

6.1.2.2.1. Guessing behavior

This section describes how each attribute is guessed by the DefaultGuesser.

6.1.2.2.1.1. Masses

We first attempt to look up the mass of an atom based on its element if the element TopologyAttr is available. If not, we attempt to lookup the mass based on the atom type (type) TopologyAttr. If neither of these is available, we attempt to guess the atom type based on the atom name (name) and then lookup the mass based on the guessed atom type.

6.1.2.2.1.2. Types

We attempt to guess the atom type based on the atom name (name). The name is first stripped of any numbers and symbols, and then looked up in the MDAnalysis.guesser.tables.atomelements table. If the name is not found, we continue checking variations of the name following the logic in DefaultGuesser.guess_atom_element(). Ultimately, if no match is found, the first character of the stripped name is returned.

6.1.2.2.1.3. Elements

This follows the same method as guessing atom types.

6.1.2.2.1.4. Bonds

Bonds are guessed based on the distance between atoms. See DefaultGuesser.guess_bonds() for more details.

6.1.2.2.1.5. Angles

Angles are guessed based on the bonds between atoms. See DefaultGuesser.guess_angles() for more details.

6.1.2.2.1.6. Dihedrals

Dihedrals are guessed based on the angles between atoms. See DefaultGuesser.guess_dihedrals() for more details.

6.1.2.2.1.7. Improper Dihedrals

Improper dihedrals are guessed based on the angles between atoms. See DefaultGuesser.guess_improper_dihedrals() for more details.

6.1.2.2.1.8. Aromaticities

Aromaticity is guessed using RDKit’s GetIsAromatic method. See DefaultGuesser.guess_aromaticities() for more details.

6.1.2.2.2. Classes

class MDAnalysis.guesser.default_guesser.DefaultGuesser(universe, box=None, vdwradii=None, fudge_factor=0.55, lower_bound=0.1, **kwargs)[source]

This guesser holds generic methods (not directed to specific contexts) for guessing different topology attribute. It has the same methods which where originally found in Topology.guesser.py. The attributes that can be guessed by this class are:

masses

types

elements

angles

dihedrals

bonds

improper dihedrals

aromaticities

You can use this guesser either directly through an instance, or through the guess_TopologyAttrs() method.

Parameters:

universe (Universe) – The Universe to apply the guesser on
box (np.ndarray, optional) – The box of the Universe. This is used for bond guessing.
vdwradii (dict, optional) – Dict relating atom types: vdw radii. This is used for bond guessing
fudge_factor (float, optional) – The factor by which atoms must overlap each other to be considered a bond. Larger values will increase the number of bonds found. [0.55]
lower_bound (float, optional) – The minimum bond length. All bonds found shorter than this length will be ignored. This is useful for parsing PDB with altloc records where atoms with altloc A and B may be very close together and there should be no chemical bond between them. [0.1]

Examples

to guess bonds for a universe:

import MDAnalysis as mda
from MDAnalysisTests.datafiles import two_water_gro

u = mda.Universe(two_water_gro, context='default', to_guess=['bonds'])

Added in version 2.8.0.

copy(): Return a copy of this Guesser

get_atom_mass(element)[source]: Return the atomic mass in u for element. Masses are looked up in MDAnalysis.guesser.tables.masses.

Warning

Until version 3.0.0 unknown masses are set to 0.0

guess_angles(bonds=None)[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.

Parameters:: bonds (Bonds) – from which angles should be guessed
Returns:: List of tuples defining the angles. Suitable for use in u._topology
Return type:: list of tuples