basic_usage.md

Basic Usage

This section highlights basic usage from reading in atomic information from a protein data bank (PDB) file, extracting information from the molecule, performing simple operations on the molecule and how to save the new coordinates to a new PDB file

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Import sasmol library

import sasmol.system as system

Define "molecule" an instance of the Molecule class. This is the "object" that will hold all information for the molecule

molecule = system.Molecule()

Read the contents of a PDB file into the molecule

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

Query the number of atoms

molecule.natoms()

6730

Determine the center of mass of the molecule for frame = 0

molecule.calculate_center_of_mass(0) 

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

Set the center of mass to [0, 0, 0] for frame = 0

molecule.center(0)

Check that the center of mass is indeed now at [0, 0, 0]

molecule.calculate_center_of_mass(0)

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

Save the coordinates to a new PDB file

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