<jupyter_start><jupyter_text>Docking Parameters used to perform the Ensemble Docking Procedure1. EGFR conformations were aligned using the $\alpha$ Carbons of pocket residues.<jupyter_code>import sys
sys.path.insert(0, '../..')
from helper_modules.get_cocristalized_ligands \
     import get_pocket_ligand, PocketResidues<jupyter_output><empty_output><jupyter_text>2. All conformations were aligned to the same reference structure: [7a2a](https://www.rcsb.org/structure/7A2A).<jupyter_code>ref_struc_id    = '7a2a'
ref_ligand_name_1 = '57N'
ref_ligand_name_2 = '7G9'

pkt_info_1 = PocketResidues(ref_struc_id, ref_ligand_name_1)
pkt_info_2 = PocketResidues(ref_struc_id, ref_ligand_name_2)

pocket_residues_str_1 = pkt_info_1.get_pocket_residues_as_list().split(' ')
pocket_residues_str_2 = pkt_info_2.get_pocket_residues_as_list()
pocket_residues_str_2 = pocket_residues_str_2.split(' ')

# Merge the values
pocket_residues_str = sorted(list(set(pocket_residues_str_1 + pocket_residues_str_2)))
pocket_residues_str = ' '.join(pocket_residues_str)

print('Indices of pocket redsidues:', pocket_residues_str)
import pytraj as pyt
import nglview as nv
ens_traj = pyt.load('../3_Protein_Ensembles_Analysis/PDB_175_egfr_POCKET_ALL.dcd',
                    top = '../1_Download_and_prepare_protein_ensembles/pdb_structures/pdb_prepared/7a2a_ENS.pdb')
nv.show_pytraj(ens_traj)<jupyter_output><empty_output>
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{'chain_length': '2', 'dir': 'jupyter-structured-clean-dedup', 'id': '606216', 'license': 'MIT', 'n_tokens_mistral': 575, 'n_tokens_neox': 542, 'n_words': 80, 'path': 'egfr/4_Ensemble_docking_results/1_Docking_Parameters_used.ipynb', 'repo_name': 'jRicciL/ml_and_ensemble_docking', 'size': '1401'}