SASMOL

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import sasmol.system as system This is the unstable developer branch of sasmol

Library for defining molecular objects to create simulation and analysis programs

To install:

python setup.py install

dependencies:

• Python
• NumPy

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basic usage

library documentation

developer notes

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molecule = system.Molecule('hiv1_gag.pdb')

reading filename: hiv1_gag.pdb num_atoms = 6730

found 1 model(s) or frame(s) finished reading frame = 1

molecule.natoms()

6730

molecule.number_of_frames()

1

frame = 0

molecule.calculate_center_of_mass(frame)

array([-6.79114736, -23.71577133, 8.06558513])

molecule.translate(frame, [88.3, 19.6, 14.7], point=True)

molecule.calculate_center_of_mass(frame)

array([88.3, 19.6, 14.7])

molecule.rotate(frame, 'x', 45*3.1515927/180.0)

molecule.calculate_center_of_mass(frame)

array([88.3, 3.40417778, 24.26234889])

molecule.calculate_principal_moments_of_inertia(frame)

(array([1.30834716e+07, 1.91993314e+08, 1.85015201e+08]), array([[-0.08711655, -0.97104917, 0.22242802], [-0.9670572, 0.13604234, 0.21515775], [0.23918838, 0.19635682, 0.95091162]]), array([[1.90290278e+08, -1.54065145e+07, 2.25205595e+06], [-1.54065145e+07, 2.43538600e+07, 3.99557354e+07], [2.25205595e+06, 3.99557354e+07, 1.75447849e+08]]))

molecule.write_pdb('rotated_hiv1_gag.pdb', frame, 'w')