In [1]:

    

import sasmol.system as system


    

In [2]:

    

molecule = system.Molecule()


    

In [3]:

    

molecule.read_pdb('hiv1_gag.pdb')


    

    




reading filename:  hiv1_gag.pdb
num_atoms =  6730
>>> found  1  model(s) or frame(s)
finished reading frame =  1

In [4]:

    

molecule.natoms()


    

    
Out[4]:





6730

In [5]:

    

molecule.calculate_center_of_mass(0)


    

    
Out[5]:





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

In [6]:

    

molecule.center(0)


    

In [7]:

    

molecule.calculate_center_of_mass(0)


    

    
Out[7]:





array([  7.11544707e-13,   2.48159571e-12,  -8.45832820e-13])

In [8]:

    

molecule.write_pdb("centered_hiv1_gag.pdb", 0, "w");