def main():
"""
Read in gaussian fchk file and create an xyz file
"""
#
# Read options
#
options, args = get_options()
#
# Initialize blank system
#
struc_o = StructureContainer()
#struc_o.unset_verbose()
param_o = ParameterContainer()
struc_o.read_cply(options.in_cply)
search_i = dict()
search_i = create_search(search_i, options.symbol, options.label,
options.fftype, options.residue, options.resname,
options.chain, options.ring)
if (len(search_i) > 0):
if (options.verbose):
log_line = "\n Searching group i {} {} ".format(
search_i, len(search_i))
#log_out.write(log_line)
if (options.verbose): print log_line
list_i = struc_o.ptclC.getParticlesWithTags(search_i)
struc_i = struc_o.getSubStructure(list_i, particlesOnly=True)
else:
struc_i = struc_o
print struc_i
if (len(options.xyz) > 0):
log_line = " Setting types to {} ".format(options.xyz)
if (options.verbose):
print log_line
struc_i.set_type(options.xyz)
comment = " From data file {} ".format(options.in_cply)
append = False
struc_i.ptclC.write_xmol("{}".format(options.out_xyz), comment, append)
def main():
"""
Read in gaussian fchk file and create an xyz file
"""
#
# Read options
#
options, args = get_options()
#
# Initialize blank system
#
struc_o = StructureContainer()
#struc_o.unset_verbose()
param_o = ParameterContainer()
struc_o.read_cply(options.in_cply)
search_i = dict()
search_i = create_search(search_i,options.symbol,options.label,options.fftype,options.residue,options.resname,options.chain,options.ring)
if( len(search_i) > 0 ):
if( options.verbose ):
log_line = "\n Searching group i {} {} ".format(search_i,len(search_i))
#log_out.write(log_line)
if( options.verbose ): print log_line
list_i = struc_o.ptclC.getParticlesWithTags(search_i)
struc_i = struc_o.getSubStructure(list_i, particlesOnly=True )
else:
struc_i = struc_o
print struc_i
if( len( options.xyz) > 0 ):
log_line = " Setting types to {} ".format(options.xyz)
if( options.verbose ):
print log_line
struc_i.set_type(options.xyz)
comment = " From data file {} ".format( options.in_cply)
append = False
struc_i.ptclC.write_xmol("{}".format(options.out_xyz),comment,append)
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"
def main():
"""
Illustrates how a substructure method returns subgroup with ONLY particle container included
This is for speed considerations
"""
print "**********************************************************************************************"
print "Illustrates how a substructure method returns subgroup with ONLY particle container included"
print "This is for speed considerations"
print "**********************************************************************************************\n"
p1 = Particle([1.1, 1.1, 1.1], "Si", 2.0, 1.23)
p2 = Particle([2.2, 2.2, 2.2], "Si", 1.0, 2.34)
p3 = Particle([3.3, 3.3, 3.3], "Si", 1.0, 2.34)
p4 = Particle([4.4, 4.4, 4.4], "Si", 1.0, 2.34)
p5 = Particle([5.5, 5.5, 5.5], "C", 1.0, 2.34) # 1
p6 = Particle([6.6, 6.6, 6.6], "C", 1.0, 2.34) # 2
p7 = Particle([7.7, 7.7, 7.7], "C", 1.0, 2.34) # 3
p8 = Particle([8.8, 8.8, 8.8], "C", 1.0, 2.34) # 4
b1 = Bond(1, 2, 1.11, "hooke")
b2 = Bond(2, 3, 2.22, "hooke")
b3 = Bond(3, 4, 3.33, "hooke")
b4 = Bond(4, 5, 4.44, "hooke")
b5 = Bond(5, 6, 5.55, "hooke")
b6 = Bond(6, 7, 6.66, "hooke")
b7 = Bond(7, 8, 7.77, "hooke")
a1 = Angle(1, 2, 3, 1.11, "harmonic")
a2 = Angle(2, 3, 4, 2.22, "harmonic")
a3 = Angle(3, 4, 5, 3.33, "harmonic")
a4 = Angle(4, 5, 6, 4.44, "harmonic")
a5 = Angle(5, 6, 7, 5.55, "harmonic")
a6 = Angle(6, 7, 8, 6.66, "harmonic")
d1 = Dihedral(1, 2, 3, 4, 1.11, "stiff")
d2 = Dihedral(2, 3, 4, 5, 2.22, "stiff")
d3 = Dihedral(3, 4, 5, 6, 3.33, "stiff")
d4 = Dihedral(4, 5, 6, 7, 4.44, "stiff")
d5 = Dihedral(5, 6, 7, 8, 5.55, "stiff")
atoms1 = ParticleContainer()
atoms1.put(p1)
atoms1.put(p2)
atoms1.put(p3)
atoms1.put(p4)
atoms1.put(p5)
atoms1.put(p6)
atoms1.put(p7)
atoms1.put(p8)
bonds = BondContainer()
bonds.put(b1)
bonds.put(b2)
bonds.put(b3)
bonds.put(b4)
bonds.put(b5)
bonds.put(b6)
bonds.put(b7)
angles = AngleContainer()
angles.put(a1)
angles.put(a2)
angles.put(a3)
angles.put(a4)
angles.put(a5)
angles.put(a6)
dihedrals = DihedralContainer()
dihedrals.put(d1)
dihedrals.put(d2)
dihedrals.put(d3)
dihedrals.put(d4)
dihedrals.put(d5)
del p1, p2, p3, p4, p5, p6, p7, p8
del b1, b2, b3, b4, b5, b6, b7
del a1, a2, a3, a4, a5, a6
del d1, d2, d3, d4, d5
polymer1 = StructureContainer(atoms1, bonds, angles, dihedrals)
del atoms1, bonds, angles, dihedrals
print "********************************************************** \n"
print "polymer1 Structure before returning sub-structure"
print polymer1
print "********************************************************** \n"
print "-------------------------------------------------------------------------------- \n"
print "********************************************************** \n"
print "Testing polymer1.getSubParticleContainer([2,3,4])"
print " currently ID's are reassigned in substructure \n"
subPtclC = polymer1.getSubStructure([2, 3, 4], particlesOnly=True)
print subPtclC
print "********************************************************** \n"
def main():
"""
This shows operations on empty StructureContainer objects for 'robustness'
"""
print "************************************************************************************"
print " This shows operations on empty StructureContainer objects for 'robustness'"
print "************************************************************************************ \n"
atoms1 = ParticleContainer()
bonds1 = BondContainer()
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)
b1 = Bond(1, 2, 1.233, "hooke")
b2 = Bond(2, 3, 0.500, "hooke")
atoms1.put(p1)
atoms1.put(p2)
atoms1.put(p3)
bonds1.put(b1)
bonds1.put(b2)
atoms2 = ParticleContainer()
bonds2 = BondContainer()
polymer1 = StructureContainer(atoms1, bonds1) # Non-empty structure 1
polymer2 = StructureContainer(atoms2, bonds2) # Empty structure 2
# ------------------------------------------------------------------------------------------------------------------------
print "Non-empty container", polymer1
print "Empty container", polymer2
print "Testing empty dump"
polymer2.dump("empty")
print "Testing empty compressPtclIDs"
polymer2.compressPtclIDs()
print "Testing empty getSubStructure"
subStruc = polymer2.getSubStructure([])
print "subStruc = ", subStruc
print "Testing empty getPtclPositions"
posList = polymer2.getPtclPositions()
print "posList = ", posList
print "------------------------------------------------------------------------------------ \n"
print "Testing struc add --> non-empty (polymer1) += empty (polymer2)"
polymer1 += polymer2
print "polymer1 = ", polymer1
print "------------------------------------------------------------------------------------ \n"
print "polymer2 = ", polymer2
print "------------------------------------------------------------------------------------ \n"
print "Testing struc add --> empty (polymer2) += non-empty (polymer1)"
polymer2 += polymer1
print "polymer2 = ", polymer2
print "------------------------------------------------------------------------------------ \n"
print "polymer1 = ", polymer1
print "------------------------------------------------------------------------------------ \n"
print "Testing empty getSubStructure with non-zero id list (should return ERROR)"
polymer3 = StructureContainer()
subStruc = polymer3.getSubStructure([1, 2])
print "subStruc = ", subStruc