Substitution function?

[sarahkha]

Hello,

I was wondering whether there is any function to substitute a line of coordinate by another line of coordinate?

Thank you Sarah

[mcocdawc]

What exactly do you want to do?

The general answer is probably just do use the loc or iloc selection methods with boolean indexing and assign to slices.

molecule.loc[index, :] = iterable

I strongly recommend to have a look at some pandas tutorials to understand boolean slicing etc.

Lets, assume you want to to move all carbon atoms in a molecule 1 Å into the x direction. This task becomes.

molecule.loc[molecule.atom == 'C', 'x'] = molecule.loc[molecule.atom == 'C', 'x'] + 1

[sarahkha]

I would like:

Frag1 C 0.000000 0.000000 0.000000 H 0.000000 0.000000 1.089000​ H -0.513360 -0.889165 -0.363000​ H -0.513360 0.889165 -0.363000 H 1.026720 0.000000 -0.362996 = substitute by Frag2 ?

Frag2 C 1.414215 0.000000 -0.499995​ H 1.414220 0.000000 -1.569995​ H 1.918617 0.873651 -0.143326​ H 1.918617 -0.873651 -0.143326

Final frag = frag1 substitute the last line by frag2 C 0.000000 0.000000 0.000000 H 0.000000 0.000000 1.089000 H -0.513360 -0.889165 -0.363000​ H -0.513360 0.889165 -0.363000 C 1.414215 0.000000 -0.499995​ H 1.414220 0.000000 -1.569995​ H 1.918617 0.873651 -0.143326​ H 1.918617 -0.873651 -0.143326​

---

De : Oskar Weser notifications@github.com Envoyé : mercredi 9 octobre 2019 18:20 À : mcocdawc/chemcoord chemcoord@noreply.github.com Cc : sarahkha sarahkha@mit.edu; Author author@noreply.github.com Objet : Re: [mcocdawc/chemcoord] Substitution function? (#60)

What exactly do you want to do?

The general answer is probably just do use the loc or iloc selection methods with boolean indexing and assign to slices.

molecule.loc[index, :] = iterable

I strongly recommend to have a look at some pandas tutorialshttps://pandas.pydata.org/pandas-docs/stable/getting_started/tutorials.html to understand boolean slicing etc.

Lets, assume you want to to move all carbon atoms in a molecule 1 Å into the x direction. This task becomes.

molecule.loc[molecule.atom == 'C', 'x'] = molecule.loc[molecule.atom == 'C', 'x'] + 1

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[sarahkha]

I would like:

Frag1 C 0.000000 0.000000 0.000000 H 0.000000 0.000000 1.089000​ H -0.513360 -0.889165 -0.363000​ H -0.513360 0.889165 -0.363000 H 1.026720 0.000000 -0.362996 = substitute by Frag2 ?

Frag2 C 1.414215 0.000000 -0.499995​ H 1.414220 0.000000 -1.569995​ H 1.918617 0.873651 -0.143326​ H 1.918617 -0.873651 -0.143326

Final frag = frag1 substitute the last line by frag2 C 0.000000 0.000000 0.000000 H 0.000000 0.000000 1.089000 H -0.513360 -0.889165 -0.363000​ H -0.513360 0.889165 -0.363000 C 1.414215 0.000000 -0.499995​ H 1.414220 0.000000 -1.569995​ H 1.918617 0.873651 -0.143326​ H 1.918617 -0.873651 -0.143326

[mcocdawc]

cc.xyz_functions.concat([frag1.iloc[:-1, :], frag2], ignore_index=True)

If you are working with fragments and want to change their relative position, I would use a Z-matrix.