def __init__(self):
Molecule.__init__(self, "WATER")
# print NANOCAD_PDB_DIR + "/Solvents/WATER.pdb" , NANOCAD_PDB_DIR + "/Solvents/WATER.psf"
#self.load(NANOCAD_PDB_DIR + "/Solvents/WATER.pdb" , NANOCAD_PDB_DIR + "/Solvents/WATER.psf")
# build water molecule
atr = AtomAttributes(WATER.otObj,
[4.01300001, 0.83099997, -9.08300018])
#print "----------------------->", str(atr)
self.add_atom(atr, [])
atr = AtomAttributes(WATER.htObj,
[4.94099998, 0.84399998, -8.83699989])
#print "----------------------->", str(atr)
self.add_atom(atr, [1])
atr = AtomAttributes(WATER.htObj, [3.75, -0.068, -9.29300022])
#print "----------------------->", str(atr)
self.add_atom(atr, [1])
if WATER._FORCE_FIELD == None:
print("WATER generating FF")
WATER._FORCE_FIELD = ForceField(
self, NANOCAD_FORCE_FIELDS + "/WATER.prm")
#print "WATER1", WATER._FORCE_FIELD._BONDS
self.setForceField(WATER._FORCE_FIELD)
#print "WATER2", self.getForceField()._BONDS
self.copyChargesToForceField()
def __init__(self, n):
# initialize base class
Homopolymer.__init__(self, n, "PMMA(" + str(n) + ")")
PMMA._FORCE_FIELD = ForceField(self,
NANOCAD_FORCE_FIELDS + "/PMMA.prm")
self.setForceField(PMMA._FORCE_FIELD)
self.copyChargesToForceField()
def __init__(self, n):
global _FORCE_FIELD
# initialize base class
Homopolymer.__init__(self, n, "Chitosan(" + str(n) + ")")
if Chitosan._FORCE_FIELD == None:
Chitosan._FORCE_FIELD = ForceField(
self, NANOCAD_FORCE_FIELDS + "/Chitosan.prm")
self.setForceField(Chitosan._FORCE_FIELD)
self.copyChargesToForceField()
def __init__(self,n):
# initialize base class
Homopolymer.__init__(self, n, "PolyTHY(" + str(n) +")")
global _FORCE_FIELD
#self.setForceField(_FORCE_FIELD)
#self.copyChargesToForceField()
if PolyTHY._FORCE_FIELD == None:
PolyTHY._FORCE_FIELD = ForceField(self, NANOCAD_FORCE_FIELDS + "/PolyTHY.prm")
self.setForceField(PolyTHY._FORCE_FIELD )
self.copyChargesToForceField()
def __init__(self):
Molecule.__init__(self, "AcetoneAllH")
#print NANOCAD_PDB_DIR + "/Solvents/Acetone-All-H.pdb" , NANOCAD_PDB_DIR + "/Solvents/Acetone-All-H.psf"
self.load(NANOCAD_PDB_DIR + "/Solvents/AcetoneAllH.pdb",
NANOCAD_PDB_DIR + "/Solvents/AcetoneAllH.psf")
if AcetoneAllH._FORCE_FIELD == None:
AcetoneAllH._FORCE_FIELD = ForceField(
self, NANOCAD_FORCE_FIELDS + "/AcetoneAllH.prm")
self.setForceField(AcetoneAllH._FORCE_FIELD)
self.copyChargesToForceField()
class Argon(Molecule):
_FORCE_FIELD = ForceField("Argon", NANOCAD_FORCE_FIELDS + "/Argon.prm")
def __init__(self):
Molecule.__init__(self, "Argon")
atr = AtomAttributes("AR", "AR", "AR", [0.0, 0.0, 0.0], 0.0, 39.9500,
0.0, 1.0, ' ', "OT ", "WAT", "A", 1)
#print "----------------------->", str(atr)
self.add_node(1, attrs=[atr])
self.setForceField(self._FORCE_FIELD)
self.copyChargesToForceField()
def on_loadButton_pressed(self):
if self.selectedMolecule == None:
errorgui = QtGui.QErrorMessage(self)
errorgui.setModal(True) # blocks Wolffia
errorgui.showMessage( "Please select a molecule by clicking on its name in the NONBONDED section.")
return
file1 = QtGui.QFileDialog.getOpenFileName(self, "Load a force field file", self.history.currentState().getBuildDirectory(), "*.prm")
#print file +"***file***"
if len(file1) > 0:
self.history.push()
for molName in self.history.currentState().mixture:
molecule = self.history.currentState().mixture.getMolecule(molName)
#print "on_loadButton_pressed changing ff of " , self.selectedMolecule , " ... checking ", molecule.molname()
if molecule.molname() == self.selectedMolecule:
#print " on_loadButton_pressed YES, changing ff of " , self.selectedMolecule
#molecule.getForceField().loadCHARMM(file1)
ff = ForceField()
ff.loadCHARMM(file1)
molecule.setForceField(ff)
#print " on_loadButton_pressed ", molecule.getForceField(),molecule.getForceField()._NONBONDED
self.update()
def __init__(self):
Mixture.__init__(self, "SDS")
#print NANOCAD_PDB_DIR + "/Solvents/THF.pdb" , NANOCAD_PDB_DIR + "/Solvents/THF.psf"
self.load(NANOCAD_PDB_DIR + "/Surfactant/SDS.pdb" , NANOCAD_PDB_DIR + "/Surfactant/SDS.psf")
#print "SDS ff", _FORCE_FIELD._NONBONDED
#print "SDS a", NANOCAD_FORCE_FIELDS + "/SDS.prm"
p1, p2 = [self.getMolecule(p) for p in self.molecules()]
if p1.order() == 1:
p1.rename("NA")
SDS._FORCE_FIELD_NA = ForceField(p1, NANOCAD_FORCE_FIELDS + "/SDS.prm")
p1.setForceField(SDS._FORCE_FIELD_NA )
SDS._FORCE_FIELD_SDS = ForceField(p2, NANOCAD_FORCE_FIELDS + "/SDS.prm")
p2.setForceField(SDS._FORCE_FIELD_SDS )
else:
p2.rename("NA")
SDS._FORCE_FIELD_NA = ForceField(p2, NANOCAD_FORCE_FIELDS + "/SDS.prm")
p2.setForceField(SDS._FORCE_FIELD_NA )
SDS._FORCE_FIELD_SDS = ForceField(p1, NANOCAD_FORCE_FIELDS + "/SDS.prm")
p1.setForceField(SDS._FORCE_FIELD_SDS )
p1.copyChargesToForceField()
p2.copyChargesToForceField()
def __init__(self, n, m, length):
Hexagonal2D.__init__(self,
n,
m,
length,
element="C",
bondLength=1.3350,
mass=12.011)
molname = "Graphene(" + str(n) + "," + str(n) + ")"
if Graphene._FORCE_FIELD == None:
Graphene._FORCE_FIELD = ForceField(
self, NANOCAD_FORCE_FIELDS + "/CNT.prm")
self.setForceField(Graphene._FORCE_FIELD)
def __init__(self):
Molecule.__init__(self, "Na")
atr = AtomAttributes(Na.ai, [0.0, 0.0, 0.0])
self.add_atom(atr, [])
#print NANOCAD_PDB_DIR + "/Solvents/THF.pdb" , NANOCAD_PDB_DIR + "/Solvents/THF.psf"
self.load(NANOCAD_PDB_DIR + "/Ions/Na.pdb",
NANOCAD_PDB_DIR + "/Ions/Na.psf")
if Na._FORCE_FIELD == None:
Na._FORCE_FIELD = ForceField(self)
Na._FORCE_FIELD.setNonBond("Na", -0.1153, NonBond._EPSILON)
Na._FORCE_FIELD.setNonBond("Na", 2.275, NonBond._SIGMA)
Na._FORCE_FIELD.setNonBond("Na", 1., NonBond._CHARGE)
self.setForceField(Na._FORCE_FIELD)
self.copyChargesToForceField()
def __init__(self):
Molecule.__init__(self, "CLF4")
atr = AtomAttributes(CLF4.ai1, [0., 0., 0.])
self.add_atom(atr, [])
atr = AtomAttributes(CLF4.ai2, [0.58099997, -1.07599998, -1.27499998])
self.add_atom(atr, [1])
atr = AtomAttributes(CLF4.ai3, [1.29900002, 0.29100001, 1.16199994])
self.add_atom(atr, [1])
atr = AtomAttributes(CLF4.ai4, [-0.509, 1.53499997, -0.71100003])
self.add_atom(atr, [1])
if CLF4._FORCE_FIELD == None:
CLF4._FORCE_FIELD = ForceField(self,
NANOCAD_FORCE_FIELDS + "/CLF4.prm")
self.setForceField(CLF4._FORCE_FIELD)
self.copyChargesToForceField()
def __init__(self):
Molecule.__init__(self, "DMF")
#print NANOCAD_PDB_DIR + "/Solvents/DMF.pdb" , NANOCAD_PDB_DIR + "/Solvents/DMF.psf"
#self.load(NANOCAD_PDB_DIR + "/Solvents/DMF.pdb" , NANOCAD_PDB_DIR + "/Solvents/DMF.psf")
atr = AtomAttributes(DMF.ai1, [0.045, -0.12800001, 0.038])
self.add_atom(atr, [])
atr = AtomAttributes(DMF.ai2, [-0.38, 1.09099996, -0.31900001])
self.add_atom(atr, [1])
atr = AtomAttributes(DMF.ai3, [0.45500001, 2.171, -0.19499999])
self.add_atom(atr, [2])
atr = AtomAttributes(DMF.ai4, [1.38699996, -0.30599999, 0.55500001])
self.add_atom(atr, [1])
atr = AtomAttributes(DMF.ai5, [-0.838, -1.26999998, -0.094])
self.add_atom(atr, [1])
atr = AtomAttributes(DMF.ai6, [-1.38, 1.22399998, -0.70499998])
self.add_atom(atr, [2])
atr = AtomAttributes(DMF.ai7, [1.37600005, -0.192, 1.63900006])
self.add_atom(atr, [4])
atr = AtomAttributes(DMF.ai8, [2.04699993, 0.442, 0.117])
self.add_atom(atr, [4])
atr = AtomAttributes(DMF.ai9, [1.74600005, -1.30299997, 0.29800001])
self.add_atom(atr, [4])
atr = AtomAttributes(DMF.ai10, [-1.12800002, -1.38699996, -1.13800001])
self.add_atom(atr, [5])
atr = AtomAttributes(DMF.ai11, [-1.72899997, -1.11199999, 0.51499999])
self.add_atom(atr, [5])
atr = AtomAttributes(DMF.ai12, [-0.322, -2.16899991, 0.243])
self.add_atom(atr, [5])
if DMF._FORCE_FIELD == None:
DMF._FORCE_FIELD = ForceField(self,
NANOCAD_FORCE_FIELDS + "/DMF.prm")
self.setForceField(DMF._FORCE_FIELD)
self.copyChargesToForceField()
def __init__(self, symbol):
try:
symbol = symbol.upper()
nbParameters = Element._FORCE_FIELD_PARAMETERS[symbol]
except:
import logging
logger = logging.getLogger(self.__class__.__name__)
logger.error("Invalid element symbol \"" + str(symbol) + "\"")
print("Invalid element symbol \"" + str(symbol) + "\"")
return
Molecule.__init__(self, symbol)
self.add_node(1, attrs=[copy.deepcopy(Element._ATTRIBUTES[symbol])])
ff = ForceField(self)
ff.setNonBond(symbol, nbParameters[NonBond._EPSILON], NonBond._EPSILON)
ff.setNonBond(symbol, nbParameters[NonBond._SIGMA] / 2.,
NonBond._SIGMA) # VDw DISTANCE DIVIDED BY 2!!!!!
self.setForceField(ff)
along with this program (gpl.txt). If not, see <http://www.gnu.org/licenses/>.
Acknowledgements: The main funding source for this project has been provided
by the UPR-Penn Partnership for Research and Education in Materials program,
USA National Science Foundation grant number DMR-0934195.
"""
import sys, os
sys.path.append(
os.path.dirname(os.path.realpath(__file__)) + '/../../../../conf')
from conf.Wolffia_conf import NANOCAD_PDB_DIR, NANOCAD_FORCE_FIELDS
from lib.chemicalGraph.molecule.Molecule import Molecule
from lib.chemicalGraph.molecule.ForceField import ForceField
from lib.chemicalGraph.molecule.AtomAttributes import AtomAttributes
#=========================================================================
_FORCE_FIELD = ForceField("SDSplusNA", NANOCAD_FORCE_FIELDS + "/SDSplusNA.prm")
class SDSplusNA(Molecule):
def __init__(self):
Molecule.__init__(self, "SDSplusNA")
#print NANOCAD_PDB_DIR + "/Solvents/THF.pdb" , NANOCAD_PDB_DIR + "/Solvents/THF.psf"
self.load(NANOCAD_PDB_DIR + "/Surfactant/SDSplusNA.pdb",
NANOCAD_PDB_DIR + "/Surfactant/SDSplusNA.psf")
self.setForceField(_FORCE_FIELD)
#==========================================================================
if __name__ == '__main__':
You should have received a copy of the GNU General Public License
along with this program (gpl.txt). If not, see <http://www.gnu.org/licenses/>.
Acknowledgements: The main funding source for this project has been provided
by the UPR-Penn Partnership for Research and Education in Materials program,
USA National Science Foundation grant number DMR-0934195.
"""
import sys, os
sys.path.append(os.path.dirname(os.path.realpath(__file__))+'/../../../../conf')
from conf.Wolffia_conf import NANOCAD_PDB_DIR, NANOCAD_FORCE_FIELDS
from lib.chemicalGraph.molecule.Molecule import Molecule
from lib.chemicalGraph.molecule.ForceField import ForceField
from lib.chemicalGraph.molecule.AtomAttributes import AtomAttributes
#=========================================================================
_FORCE_FIELD = ForceField("H2O2", NANOCAD_FORCE_FIELDS + "/H2O2.prm")
class H2O2(Molecule):
def __init__(self):
Molecule.__init__(self, "H2O2")
# print NANOCAD_PDB_DIR + "/Solvents/WATER.pdb" , NANOCAD_PDB_DIR + "/Solvents/WATER.psf"
#self.load(NANOCAD_PDB_DIR + "/Solvents/WATER.pdb" , NANOCAD_PDB_DIR + "/Solvents/WATER.psf")
# build water H2O2
atr = AtomAttributes("OT1", "O", "OT", [ -0.077, 0.000, 0.730 ], 0.834, 15.9994, 0.0, 1.0, ' ', "OT ", "XXX", "A", 1)
#print "----------------------->", str(atr)
self.add_node(1, attrs=[atr])
atr = AtomAttributes("OT2", "O", "OT", [ 0.077, 0.000, -0.730], 0.834, 15.9994, 0.0, 1.0, ' ', "OT ", "XXX", "A", 1)
#print "----------------------->", str(atr)
self.add_node(2, attrs=[atr])
Acknowledgements: The main funding source for this project has been provided
by the UPR-Penn Partnership for Research and Education in Materials program,
USA National Science Foundation grant number DMR-0934195.
"""
import sys, os
sys.path.append(os.path.dirname(os.path.realpath(__file__))+'/../../../../conf')
from conf.Wolffia_conf import NANOCAD_FORCE_FIELDS
from lib.chemicalGraph.molecule.ForceField import ForceField
from lib.chemicalGraph.molecule.Molecule import Molecule
from lib.chemicalGraph.molecule.polymer.Homopolymer import Homopolymer
import math
#-----------------------------------------------------------------------------------
_FORCE_FIELD = ForceField("PVP", NANOCAD_FORCE_FIELDS + "/PVP.prm")
class PVP(Homopolymer):
BACKBONE_MONOMER_PDB = '/Polymers/PVP/backbonePVP.pdb'
START_MONOMER_PDB = '/Polymers/PVP/startPVP.pdb'
END_MONOMER_PDB = '/Polymers/PVP/endPVP.pdb'
ONE_MONOMER_PDB = '/Polymers/PVP/onePVP.pdb'
BACKBONE_MONOMER_PSF = '/Polymers/PVP/backbonePVP.psf'
START_MONOMER_PSF = '/Polymers/PVP/startPVP.psf'
END_MONOMER_PSF = '/Polymers/PVP/endPVP.psf'
ONE_MONOMER_PSF = '/Polymers/PVP/endPVP.psf'
NUM_ATOMS_BACKBONE_MONOMER = 15
NUM_ATOMS_START_MONOMER = 16
NUM_ATOMS_LAST_MONOMER = 4
def __init__(self,
n,
m,
length,
element="C",
bondLength=1.421,
mass=12.011):
self.coords = []
self._n = n
self._m = m
self._length = length
self._mass = mass
self._bondLength = bondLength
self._element = element
self.EPSILON = bondLength / 2.
sheet = Hexagonal2D(n, m, length, element, bondLength, mass)
unitVectLength = self._bondLength * math.sqrt(
2. - 2. * math.cos(2. * math.pi / 3.))
#tubePerimeter = unitVectLength * math.sqrt(n*n+m*m)
tubePerimeter = sheet.getWidth() + self._bondLength
#print tubePerimeter
radius = tubePerimeter / 2. / math.pi
xToAngleFactor = 2. * math.pi / tubePerimeter
atoms = sheet.atoms()
for atom in atoms:
attr = sheet.getAtomAttributes(atom)
coords = attr.getCoord()
angle = coords[0] * xToAngleFactor
attr.setCoord([
radius * math.cos(angle), radius * math.sin(angle), coords[2]
])
sheet.setAtomAttributes(atom, attr)
# close tube
incomplete = []
#print "degree:",
for atom in atoms:
#print sheet.degree(atom),
if sheet.degree(atom) < 3:
incomplete.append(atom)
for atom1 in incomplete:
for atom2 in incomplete:
if atom1 != atom2 and not sheet.has_edge(
atom1, atom2) and sheet.distance(
atom1, atom2) < bondLength + self.EPSILON:
sheet.addBond(atom1, atom2)
#print "sheet.addBond(",atom1,", ",atom2
# remove redundant atoms and bonds
#for i in range(len(atoms)):
# for j in range(i+1,len(atoms)):
# if sheet.distance(atoms[i], atoms[j]) < self.EPSILON:
# print "caca",sheet.distance(atoms[i], atoms[j])
# sheet.removeAtom(atoms[i])
# break
molname = element + "_Tube(" + str(m) + "," + str(n) + ")"
Molecule.__init__(self, molname, sheet)
if Tube._FORCE_FIELD == None:
Tube._FORCE_FIELD = ForceField(self,
NANOCAD_FORCE_FIELDS + "/CNT.prm")
self.setForceField(Tube._FORCE_FIELD)
Acknowledgements: The main funding source for this project has been provided
by the UPR-Penn Partnership for Research and Education in Materials program,
USA National Science Foundation grant number DMR-0934195.
"""
import sys, os
sys.path.append(
os.path.dirname(os.path.realpath(__file__)) + '/../../../../conf')
from conf.Wolffia_conf import NANOCAD_PDB_DIR, NANOCAD_FORCE_FIELDS
from lib.chemicalGraph.molecule.ForceField import ForceField
from lib.chemicalGraph.molecule.Molecule import Molecule
from lib.chemicalGraph.molecule.polymer.Polymer import Polymer
import math
#-----------------------------------------------------------------------------------
_FORCE_FIELD = ForceField(None, NANOCAD_FORCE_FIELDS + "/PANI.prm")
class PANI(Polymer):
DISPL = 5.68
ANGLE = 0
MONOMERS_PDBS={ 'Rs':'/Polymers/PANI/startPANIred.pdb',\
'Rb':'/Polymers/PANI/backbonePANIred.pdb',\
'Re': '/Polymers/PANI/endPANIred.pdb',\
'Os':'/Polymers/PANI/startPANIoxi.pdb',\
'Ob':'/Polymers/PANI/backbonePANIoxi.pdb',\
'Oe':'/Polymers/PANI/endPANIoxi.pdb'}
MONOMERS_PSFS={ 'Rs':'/Polymers/PANI/startPANIred.psf',\
'Rb':'/Polymers/PANI/backbonePANIred.psf',\
def __init__(self):
Molecule.__init__(self, "THF")
#print NANOCAD_PDB_DIR + "/Solvents/THF.pdb" , NANOCAD_PDB_DIR + "/Solvents/THF.psf"
#self.load(NANOCAD_PDB_DIR + "/Solvents/THF.pdb" , NANOCAD_PDB_DIR + "/Solvents/THF.psf")
atr = AtomAttributes(THF.atr1, [0.180, 0.300, -2.690])
self.add_atom(atr, [])
atr = AtomAttributes(THF.atr2, [1.084, 0.909, -2.675])
self.add_atom(atr, [1])
atr = AtomAttributes(THF.atr3, [-0.637, 0.671, -3.309])
self.add_atom(atr, [1])
atr = AtomAttributes(THF.atr4, [-0.350, 0.030, -1.310])
self.add_atom(atr, [1])
atr = AtomAttributes(THF.atr5, [-1.282, -0.535, -1.328])
self.add_atom(atr, [4])
atr = AtomAttributes(THF.atr6, [-0.371, 0.969, -0.757])
self.add_atom(atr, [4])
atr = AtomAttributes(THF.atr7, [0.820, -0.800, -0.800])
self.add_atom(atr, [4])
atr = AtomAttributes(THF.atr8, [0.539, -1.361, 0.091])
self.add_atom(atr, [7])
atr = AtomAttributes(THF.atr9, [1.667, -0.126, -0.669])
self.add_atom(atr, [7])
atr = AtomAttributes(THF.atr10, [1.110, -1.690, -1.900])
self.add_atom(atr, [7])
atr = AtomAttributes(THF.atr11, [0.460, -1.140, -3.080])
self.add_atom(atr, [1, 10])
atr = AtomAttributes(THF.atr12, [-0.501, -1.639, -3.207])
self.add_atom(atr, [11])
atr = AtomAttributes(THF.atr13, [1.120, -1.188, -3.946])
self.add_atom(atr, [11])
'''
self.addBond(1,2)
self.addBond(1,3)
self.addBond(1,4)
self.addBond(1,11)
self.addBond(4,5)
self.addBond(4,6)
self.addBond(4,7)
self.addBond(7,8)
self.addBond(7,9)
self.addBond(7,10)
self.addBond(10,11)
self.addBond(11,12)
self.addBond(11,13)
'''
#self.add_angle()
#self.add_angle()
#self.add_angle()
#self.add_angle()
#self.add_dihedrals ()
#self.add_dihedrals ()
if THF._FORCE_FIELD == None:
THF._FORCE_FIELD = ForceField(self,
NANOCAD_FORCE_FIELDS + "/THF.prm")
self.setForceField(THF._FORCE_FIELD)
self.copyChargesToForceField()