The most basic operations in the MagresPython library are to select groups of atoms in a molecule or crystal. This tutorial will go through a few common operations.
First, we import the
MagresAtoms class from the library. This is a container
for a bunch of atoms.
from magres.atoms import MagresAtoms
Then, using the
MagresAtoms class, we load and parse an output file.
atoms = MagresAtoms.load_magres('../samples/ethanol-all.magres')
atoms is now a collection containing all the atoms in the system
<magres.atom.MagresAtoms - 9 atoms>
MagresPython has been designed to be pythonic, meaning that it behaves as
similarly to native Python as possible.
MagresAtoms behaves like a
can use standard builtin functions like
len on it, which returns the number of
And, like a
list, you can iterate over all the atoms
for atom in atoms: print atom
1H1 1H2 1H3 1H4 1H5 1H6 13C1 13C2 17O1
There are shortcuts for selecting a particular atom of a particular species. The following code picks out the first carbon atom
<magres.atom.MagresAtom - 13C1>
Atoms are objects and have properties, such as
position, which is returned as
a numpy array
[-0.004 -0.004 -0.004]
You can select subsets of atoms, which also behave like lists. For example, to select all hydrogen atoms in the system
<magres.atom.MagresAtomsView - 6 atoms>
You can select all atoms within a certain distance of each other. The following code selects all atoms within 2 Angstrom of the H1 atom.
<magres.atom.MagresAtomsView - 4 atoms>