# python from chempy import io from chempy import protein from chempy import protein_amber99 model= io.pdb.fromFile("../../test/dat/pept.pdb") model= protein.generate(model,forcefield=protein_amber99) sm = 0 for a in model.atom: sm = sm + a.partial_charge print " prot: net partial charge on protein is %8.4f" % sm print " prot: (this should be integral)!" io.pkl.toFile(model,"generate_amber.pkl")
from chempy import io from chempy import protein from chempy import protein_mmff from chempy import bond_mmff # #print 'normal' #protein_mmff.check_sum(protein_mmff.normal) #print 'n_terminal' #protein_mmff.check_sum(protein_mmff.n_terminal) #print 'c_terminal' #protein_mmff.check_sum(protein_mmff.c_terminal) model= io.pdb.fromFile("../../test/dat/pept.pdb") model= protein.generate(model,forcefield=protein_mmff,bondfield=bond_mmff) for a in model.atom: a.numeric_type = protein_mmff.alpha_map[a.text_type] sm = 0 for a in model.atom: sm = sm + a.partial_charge print " prot: net partial charge on protein is %8.3f" % sm print " prot: (this should be integral)!" io.pkl.toFile(model,"generate_mmff.pkl")
# python from chempy import io from chempy import protein from chempy import protein_amber99 model= io.pdb.fromFile("../../test/dat/pept.pdb") model= protein.generate(model,forcefield=protein_amber99) sm = 0 for a in model.atom: sm = sm + a.partial_charge print(" prot: net partial charge on protein is %8.4f" % sm) print(" prot: (this should be integral)!") io.pkl.toFile(model,"generate_amber.pkl")