32 lines
759 B
Python
32 lines
759 B
Python
# python
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from chempy import io
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from chempy import protein
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from chempy import protein_mmff
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from chempy import bond_mmff
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#
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#print 'normal'
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#protein_mmff.check_sum(protein_mmff.normal)
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#print 'n_terminal'
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#protein_mmff.check_sum(protein_mmff.n_terminal)
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#print 'c_terminal'
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#protein_mmff.check_sum(protein_mmff.c_terminal)
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model= io.pdb.fromFile("../../test/dat/pept.pdb")
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model= protein.generate(model,forcefield=protein_mmff,bondfield=bond_mmff)
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for a in model.atom:
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a.numeric_type = protein_mmff.alpha_map[a.text_type]
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sm = 0
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for a in model.atom:
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sm = sm + a.partial_charge
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print(" prot: net partial charge on protein is %8.3f" % sm)
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print(" prot: (this should be integral)!")
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io.pkl.toFile(model,"generate_mmff.pkl")
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