35 lines
1.1 KiB
Python
35 lines
1.1 KiB
Python
from plip.basic import config
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from plip.exchange.webservices import fetch_pdb
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from plip.structure.preparation import create_folder_if_not_exists, extract_pdbid
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from plip.structure.preparation import tilde_expansion, PDBComplex
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pdbId = "6LU7"
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print("Downloading PDB:",pdbId)
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pdbfile, pdbid = fetch_pdb(pdbId.lower())
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pdbpath = tilde_expansion('%s/%s.pdb' % (config.BASEPATH.rstrip('/'), pdbid))
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create_folder_if_not_exists(config.BASEPATH)
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with open(pdbpath, 'w') as g:
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g.write(pdbfile)
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print("Adding Charges")
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import oddt
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from oddt.docking.AutodockVina import write_vina_pdbqt
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receptor = next(oddt.toolkit.readfile("pdb",pdbpath.split("./")[1]))
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receptor.calccharges()
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#receptor = next(oddt.toolkits.rdk.readfile("pdb",pdbpath.split("./")[1]))
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#receptor.calccharges()
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print("Writing PDBQT")
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path = write_vina_pdbqt(receptor,'.',flexible=False)
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smiles = 'CCC(CC)COC(=O)C(C)NP(=O)(OCC1C(C(C(O1)(C#N)C2=CC=C3N2N=CN=C3N)O)O)OC4=CC=CC=C4'
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print("Generating Strucutre")
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mol = oddt.toolkit.readstring('smi', smiles)
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mol.make3D()
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print("Adding Charges")
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mol.calccharges()
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path2 = write_vina_pdbqt(mol,'.',flexible=False) |