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
import sasmol.system as systemmolecule = 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 = 0molecule.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');