sampledoc

Source code for test_subStructure

#!/usr/bin/env python
import copy

# Old setup testing replace IDs
diagramBefore="""  
1--'b1'---2
 -        |
  -       'b2'
   'b4'   |
     -    |
       -  3---'b3'---4
"""

diagramAfter="""
5--'b1'---2
 -        |
  -       'b2'
   'b4'   |
     -    |
       -  3---'b3'---4
"""


import os, sys, math, random, time

from particles import Particle
from particles import ParticleContainer

from bonds import Bond
from bonds import BondContainer

from structureContainer import StructureContainer

[docs]def main(): """ This test shows how to set up Structure container with Particle/Bond-Containers and shows how IDs changed in StructureContainer propagate to values set in BondContainer for its held particle ID values Illustrates how a substructure method can return subgroup """ print "*****************************************************************************************************" print " This test shows how to set up Structure container with Particle/Bond-Containers \n" print " and shows how IDs changed in StructureContainer propagate to values set in BondContainer for its " print " held particle ID values \n" print " Illustrates how a substructure method can return subgroup" print "************************************************************************************ \n" p1 = Particle( [0.2, 1.3, 33.0], "Si", 2.0, 1.23) p2 = Particle( [5.0, 2.3, -22.1], "C", 1.0, 2.34) p3 = Particle( [5.0, 2.3, -20.1], "C", 1.0, 2.34) p4 = Particle( [0.0, 2.3, -20.1], "C", 1.0, 2.34) p5 = Particle( [0.2, 1.3, 33.0], "Si", 2.0, 1.23) b1 = Bond( 5, 2, 1.233, "hooke") # This setup mimics earlier state of test b2 = Bond( 2, 3, 0.500, "hooke") # Still matches with diagram b3 = Bond( 3, 4, 2.301, "hooke") b4 = Bond( 5, 3, 0.828, "hooke") atoms1 = ParticleContainer() atoms1.put(p1) atoms1.put(p2) atoms1.put(p3) atoms1.put(p4) atoms1.put(p5) del atoms1[1] # This is to mimic state of container for an older test bonds = BondContainer() bonds.put(b1) bonds.put(b2) bonds.put(b3) bonds.put(b4) del p1, p2, p3, p4, b1, b2, b3, b4 polymer1 = StructureContainer(atoms1, bonds) del atoms1, bonds print "********************************************************** \n" print polymer1 print diagramAfter print "********************************************************** \n" print "-------------------------------------------------------------------------------- \n" print "********************************************************** \n" print "Testing polymer1.getSubStructure([5,2])" print " currently ID's are reassigned in substructure \n" subpolymer = polymer1.getSubStructure([5,2]) print subpolymer print diagramAfter print "********************************************************** \n" print "********************************************************** \n" print "polymer1 Struture after returning sub-structure" print polymer1 print "********************************************************** \n" print "-------------------------------------------------------------------------------- \n" print "********************************************************** \n" print "Testing polymer1.getSubStructure([2,3,4])" print " currently ID's are reassigned in substructure \n" subpolymer = polymer1.getSubStructure([2,3,4]) print subpolymer print diagramAfter print "********************************************************** \n"
if __name__ == '__main__': main()