Suppose we have the following .magres file for an ethanol molecule in a box:
#$magres-abinitio-v1.0
[atoms]
units lattice Angstrom
lattice 6.0000000000000009E+00 0.0000000000000000E+00 0.0000000000000000E+00 0.0000000000000000E+00 6.0000000000000009E+00 0.0000000000000000E+00 0.0000000000000000E+00 0.0000000000000000E+00 6.0000000000000009E+00
units atom Angstrom
atom H H 1 3.9805990000000007E+00 4.1783420000000007E+00 3.2950789999999999E+00
atom H H 2 5.0333940000000004E+00 3.4304300000000003E+00 4.5047590000000008E+00
atom H H 3 5.7190700000000012E+00 4.5522570000000000E+00 3.3153530000000009E+00
atom H H 4 3.7202350000000006E+00 5.3295050000000010E+00 5.5099090000000004E+00
atom H H 5 4.4121710000000007E+00 6.4335720000000007E+00 4.3170010000000012E+00
atom H H 6 5.9116109999999997E+00 5.0322839999999998E+00 6.2422020000000007E+00
atom C C 1 4.8469400000000009E+00 4.3506309999999999E+00 3.9411360000000002E+00
atom C C 2 4.6030250000000006E+00 5.5187379999999999E+00 4.8825320000000012E+00
atom O O 1 5.7462540000000013E+00 5.8127050000000011E+00 5.6871000000000009E+00
[/atoms]
[magres]
units ms ppm
ms H 1 3.0275414382832704E+01 1.2343176147963255E+00 3.8055347702168261E+00 1.9319927686201195E+00 2.7549852274727169E+01 2.4936355990438019E+00 4.1246695670194242E+00 2.2382434391773800E+00 3.0854546259833729E+01
ms H 2 2.6965983864643054E+01 -3.8585624895769854E-01 7.4285824854937599E-01 -4.1196902839127542E-01 3.5292668226256616E+01 -1.8802552393259337E+00 -6.7122267950404291E-01 -1.3639578313254843E+00 2.8419907854724499E+01
ms H 3 2.9971223084896938E+01 8.3477502779773927E-01 -3.2689438749161925E+00 -5.7219252176672120E-01 2.7791184879829256E+01 -2.1461997294113141E-01 -3.6440239128383367E+00 3.7767506813290157E-02 3.2454355403489878E+01
ms H 4 3.2261642842180500E+01 6.2520948574546298E-01 -1.4918313319633616E+00 7.5053965528921041E-01 2.2658737518918223E+01 1.7257630753650515E+00 -1.6495892494737605E-01 2.0870476890698075E+00 2.5941592095402918E+01
ms H 5 2.5948305588592422E+01 -2.7316306883849486E+00 3.8807548928060029E+00 -1.8011484678760228E+00 2.9698619245848839E+01 -4.6789512034172942E-01 2.9480868200872661E+00 -1.3677707067034952E+00 2.6474915442944035E+01
ms H 6 2.8536732593448992E+01 -2.0217790318703996E+00 4.8738962044242289E+00 -3.4947137896321606E-01 3.2849570358829844E+01 -6.5479198378162398E+00 4.6010039021206746E+00 -5.8146999362447280E+00 3.4278055161276548E+01
ms C 1 1.4998628033046998E+02 -1.0199071049759386E+01 -8.4736870826874103E-02 2.3362956476235755E-01 1.6059638213098884E+02 2.3169348644807837E+01 7.5564002686506901E+00 1.5878380496240151E+01 1.5778608358849078E+02
ms C 2 1.3326536661448372E+02 3.2787517370578650E-01 3.0641881628898851E+01 3.6408749419944675E+00 8.6537759377111740E+01 1.3720991423773526E+01 3.3471610166046347E+01 1.2743115987611173E+01 1.0826946534305428E+02
ms O 1 2.4574869953866229E+02 4.8677155199684901E+00 2.3843699230434890E+01 -2.5684198667080988E+01 2.8842353056750665E+02 -2.1091258283138934E+01 1.8346324157049754E+01 -3.9130135989063421E+00 2.6686459969143857E+02
[/magres]
You can run all these Python commands from the interpreter, supposing that you have saved the above data into a file called ethanol.magres in the same directory.
We can load this into an magres.atoms.MagresAtoms object using the load_magres() method.
>>> from magres.atoms import MagresAtoms
>>> atoms = MagresAtoms.load_magres('ethanol.magres')
If we run this code, atoms now contains a list of all the atoms in the system, plus a bunch of helpful functions as documented in magres.atoms.MagresAtomsView. Each atom will have a ms attribute, corresponding to a magres.atoms.MagresAtomMs object. This object contains lots of different ways to process the sigma tensor, including a number of different conventions.
For example, supposing that we want to iterate over each atom and print its name and isotropic shielding (iso) we can simply do
>>> for atom in atoms:
>>> print atom, atom.ms.iso
1H1 29.5599376391
1H2 30.2261866485
1H3 30.0722544561
1H4 26.9539908188
1H5 27.3739467591
1H6 31.8881193712
13C1 156.12291535
13C2 109.357530445
17O1 267.012276599
Maybe we want to print out the spans and skews for all the protons. To do this we select all atoms with the ‘H’ species with species() and then access the span and skew attributes.
>>> for atom in atoms.species('H'):
>>> print atom, atom.ms.span, atom.ms.skew
1H1 9.38562488256 0.818487161614
1H2 8.72896735943 0.7449106712
1H3 7.36075836882 0.925944171311
1H4 10.6945028349 0.0495013823109
1H5 9.32371700876 -0.0606983834955
1H6 16.2585008574 0.471974409294
Or perhaps we want to print out all isotropic and anisotropic shieldings for all atoms within 2 Angstrom of the C1 atom.
>>> for atom in atoms.within(atoms.get_species('C', 1), 2.0):
>>> print atom, atom.ms.iso, atom.ms.aniso
1H1 29.5599376391 8.95972202944
1H2 30.2261866485 8.17230075322
1H3 30.0722544561 7.22448160362
13C1 156.12291535 34.0294598396
13C2 109.357530445 70.540995898
You can also directly access the tensor, eigenvectors and eigenvaleus via the sigma, evecs and evals attributes. The eigenvectors and eigenvalues are by default ordered according to the Haeberlen convention. Let’s print out these for the C1 atom:
>>> atom = atoms.get_species('C', 1)
>>> print atom
13C1
>>> print atom.ms.sigma
[[ 1.49986280e+02 -1.01990710e+01 -8.47368708e-02]
[ 2.33629565e-01 1.60596382e+02 2.31693486e+01]
[ 7.55640027e+00 1.58783805e+01 1.57786084e+02]]
>>> print atom.ms.evecs
[array([-0.42141732, -0.9060046 , -0.03953616]), array([-0.62585978, 0.25900804, 0.73567273]), array([ 0.65628269, -0.33476933, 0.67618232])]
>>> print atom.ms.evals
[136.76839422482036, 152.79112991538537, 178.809221909744]
Note that we’re using numpy for array support.