Open florisvdf opened 1 year ago
Hi Leandro,
I'm trying to mutate a structure with the following code:
from pyfoldx.structure import Structure pdb_3dkm = Structure("3DKM") pdb_3dkm.mutate("RA1291L", number_of_runs=1)
But when I run this, I get:
--------------------------------------------------------------------------- IndexError Traceback (most recent call last) Cell In[30], line 1 ----> 1 pdb_3dkm.mutate("RA1291L", number_of_runs=5) File ~/work/phd/projects/APBSMeshCNN/conda_env/lib/python3.8/site-packages/pyfoldx/structure/structure.py:349, in Structure.mutate(self, mutations, number_of_runs, terms, verbose) 346 trajMut = Ensemble(self.code+"_Mut",working_path="") 347 trajWT = Ensemble(self.code+"_WT",working_path="") --> 349 ddGsDf, mutModels, wtModels = foldxHandler.getMutants(self, mutations, number_of_runs) 351 # if generate mutated ensemble, add models to the ensemples 352 for i in range(number_of_runs): File ~/work/phd/projects/APBSMeshCNN/conda_env/lib/python3.8/site-packages/pyfoldx/foldx/foldxHandler.py:248, in getMutants(st, mutations, number_of_runs, other_parameters) 246 for i in range(number_of_runs): 247 mut_line_number = number_of_runs*(-2) + i --> 248 dfData = raw_lines[mut_line_number].split("\t")[1:] 249 mutPdbs[i].totalEnergy = pd.DataFrame(data = [dfData], columns= ENERGY_TERMS, index=[mutPdbs[i].code]) 251 wt_line_number = -number_of_runs + i IndexError: list index out of range
I wondered if this had anything to do with pyfoldx not ocating the foldx binary, so I checked this with:
from pyfoldx.foldx.foldxHandler import FOLDX_LOCATION
Which is set to the correct path. Any clue what could be causing this?
Cheers, Floris
I faced a similar issue.
Hi Leandro,
I'm trying to mutate a structure with the following code:
But when I run this, I get:
I wondered if this had anything to do with pyfoldx not ocating the foldx binary, so I checked this with:
from pyfoldx.foldx.foldxHandler import FOLDX_LOCATION
Which is set to the correct path. Any clue what could be causing this?
Cheers, Floris