"Fossies" - the Fresh Open Source Software Archive  

Source code changes of the file "examples/chempy/generate_amber.py" between
pymol-v1.8.6.0.tar.bz2 and pymol-v2.1.0.tar.bz2

About: PyMOL is a Python-enhanced molecular graphics tool. It excels at 3D visualization of proteins, small molecules, density, surfaces, and trajectories. It also includes molecular editing, ray tracing, and movies. Open Source version.

generate_amber.py  (pymol-v1.8.6.0.tar.bz2)	:	generate_amber.py  (pymol-v2.1.0.tar.bz2)
skipping to change at line 15		skipping to change at line 15
from chempy import protein_amber99		from chempy import protein_amber99
model= io.pdb.fromFile("../../test/dat/pept.pdb")		model= io.pdb.fromFile("../../test/dat/pept.pdb")
model= protein.generate(model,forcefield=protein_amber99)		model= protein.generate(model,forcefield=protein_amber99)
sm = 0		sm = 0
for a in model.atom:		for a in model.atom:
sm = sm + a.partial_charge		sm = sm + a.partial_charge
print " prot: net partial charge on protein is %8.4f" % sm		print(" prot: net partial charge on protein is %8.4f" % sm)
print " prot: (this should be integral)!"		print(" prot: (this should be integral)!")
io.pkl.toFile(model,"generate_amber.pkl")		io.pkl.toFile(model,"generate_amber.pkl")
End of changes. 1 change blocks.
2 lines changed or deleted		2 lines changed or added

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