hailiangzhang / zazmol

Library for defining molecular objects to create simulation and analysis programs To install: python setup.py install dependencies: numpy, mocker

ZAZMOL

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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:

numpy, mocker

---

basic usage

library documentation

developer notes

---

import sasmol.system as system

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_principle_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');