markovmodel / PyEMMA

🚂 Python API for Emma's Markov Model Algorithms 🚂
http://pyemma.org
GNU Lesser General Public License v3.0
307 stars 118 forks source link

torsion feature for specific range #1543

Closed Bazzinga18 closed 2 years ago

Bazzinga18 commented 2 years ago

I want to define a feature in which i want to take backbone and sidechain torsions but for a specific residue range. lets say size of my protein is 120 aa, and i want to consider the above feature from residue number 111 to 120. How one can define the feature?? please help. I use the following code for whole sequence but i didnt know how to do for specific sequence range feat = pyemma.coordinates.featurizer(pdb) feat.add_backbone_torsions(cossin=True, periodic=False) feat.add_sidechain_torsions(which='chi1', cossin=True, periodic=False)

thempel commented 2 years ago

In the manual of the functions that you are copying, you see that you can pass a selection string, e.g. 'residue 111 to 120'.

http://www.emma-project.org/latest/api/generated/pyemma.coordinates.featurizer.html#pyemma.coordinates.data.featurization.featurizer.MDFeaturizer.add_backbone_torsions

http://www.emma-project.org/latest/api/generated/pyemma.coordinates.featurizer.html#pyemma.coordinates.data.featurization.featurizer.MDFeaturizer.add_sidechain_torsions

Bazzinga18 commented 2 years ago

thanks;)