nostrumbiodiscovery / msm_pele Goto Github PK

Two initial structures are missing, and additional initial structure called initial_80.pdb appears instead.
plasmin_bug.tar.zip

Quan troba la template ja existent el codi de main.py no té declarada la variable template

Després de correr l'adaptive i fer el clustering, em dona un error al construir la caixa per que intenta agafar els punts de la carpeta d'equilibració (dins la carpeta extractedCoordinates) però no existeixen ja que els extractCoords d'adaptive només agafa les carpetes que són output d'adaptive (i. e. que tenen digits com a nom)

Crec que és podria arreglar afegint una línea com ara

epochs = filter(lambda x: x.isdigit(), epochs)

al Helpers/best_structs, linea 86, però no sé si estic obviant algo més.

Et deixo també el traceback complert
Traceback (most recent call last):
File "/apps/PYTHON/2.7.13/INTEL/lib/python2.7/runpy.py", line 174, in _run_module_as_main
"main", fname, loader, pkg_name)
File "/apps/PYTHON/2.7.13/INTEL/lib/python2.7/runpy.py", line 72, in _run_code
exec code in run_globals
File "/gpfs/projects/bsc72/MSM_PELE/bin/MSM_PELE/main.py", line 180, in
run(args.input, args.residue, args.chain, args.charge_ter, args.forc, args.confile, args.native, args.cpus, args.core, args.mtor, args.n, args.mae_charges, args.clean, args.only_plop)
File "/gpfs/projects/bsc72/MSM_PELE/bin/MSM_PELE/main.py", line 142, in run
center, radius = bx.main(adap_ex_output, clusters, center_mass)
File "/gpfs/projects/bsc72/MSM_PELE/bin/MSM_PELE/Helpers/box.py", line 38, in main
sasa_points = get_sasa_points(path, sasa_info)
File "/gpfs/projects/bsc72/MSM_PELE/bin/MSM_PELE/Helpers/box.py", line 63, in get_sasa_points
with open(coord_file, 'r') as f:
IOError: [Errno 2] No such file or directory: '/gpfs/projects/bsc72/jgilabert/test_MSM_PELE/AMR_Pele/output_adaptive_exit/equilibration_1/extractedCoordinates/coord_91.dat'

If several epochs are present in the long adaptive (for example joining several simulations as one) the extractCoord script only runs the gather part for the first one, then since the allTraj folders exists it skips the rest. The test should be performed before the main loop, and it should probably check if all the extracedCoordinates, repeatedCoordinates and allTrajs are present and if so return and skip the work.

It would be a good idea to provide the option to specify the output folder name