#!/usr/bin/env python import os, sys, glob sys.path.append("/home/ctk3b") import simtk.unit as units from mmtools.Topology.System import * print '##########################################' print '# Tests of the Topology.System methods #' print '##########################################' print "Create a System object from file ...", s = System() print "Done." print "Set the name of the System object to Frank ..." s.setName('Frank') print 'New name:', t.getName() print "Done." print "Add a molecule to the System object ..." s.addMolecule() print "There are now", s.getNumMolecules(), "molelcules in the Topology." print "Done." print "Insert a molecule at position 1 ..." s.insertMolecule(1) print "There are now", s.getNumMolecules(), "molecules in the Topology." print "Done." print "Delete molecule 0 from the Topology...",
import pdb import profile from mmtools.Topology.System import * print "Reading in a system ...\n", structureList = ['LG2-0-eq.gro'] topologyList = ['LG2.top'] sys = System("Test", structureList, topologyList, "Gromacs") print "Done.\n" # Test a simplified structure and topology #print "Reading a structure and preprocessed topology ...", #structureList = 'FullStructure.gro' #topologyList = 'FullTopology.top' #sys = System("Test", structureList, topologyList, "Gromacs") #print "Done." # Test, join, and split multiple structures and topologies #print "Adding multiple structures and topologies ...", #structureList = ['Protein.gro', 'Ligand.gro', 'Solvent.gro'] #topologyList = ['Protein.top', 'Ligand.top', 'Solvent.top'] #sys = System("Test", structureList, topologyList, "Gromacs") #print "Done." #print "Adding a molecule to a system ...", #sys.addMolecule('Ion.gro', 'Ion.gro', "Gromacs") #print "Done." # Test a single topology and multiple structures #print "Reading multiple structures and a single topology ...",