def main():
Output = {}
Output[DENDRIMER] = Dendrimer
Output[POLYMER] = Polymer
mode = Utils.buildingMode
while mode != DENDRIMER and mode != POLYMER:
mode = raw_input(
'Choose 1 for Dendrimer or 2 for Polymer construction: ')
mode = int(mode)
top = Output[mode]()
# Read and create bb_factories dict. Ex: bb_factories[CCO] = factory do CCO
top.read_bbs()
# Read and create connections array
top.read_connections()
# connect building blocks
print("Connecting Building Blocks...")
top.connect_bbs()
for atom in top.get_atom_list():
atom.set_bond_list([])
atom.set_atom_list([])
for bond in top.get_bond_list():
bond.get_a_1().get_atom_list().append(
bond.get_other_atom(bond.get_a_1()))
bond.get_a_2().get_atom_list().append(
bond.get_other_atom(bond.get_a_2()))
top.generate_exclusions()
top.generate_pairs14()
# catch recursion error of deepcopy
if len(top.get_atom_list()) > 1000:
print(
"You are building a very large structure!\nYour topology will include {} atoms.\n"
"This will take a while.\n".format(len(top.get_atom_list())))
sys.setrecursionlimit(100000)
print("Increasing recursionlimit...\n\n")
print("Building Angles...")
top.set_angle_list(top.create_all_angles(top.get_bond_list()))
print("Building Dihedrals...")
if Utils.verbose:
print(
"Specfific information about specified dihedrals at branchpoints following, eventually: \n"
)
# ----------------------- dihedrals ### ###
top.set_dihedral_list(top.create_all_dihedrals(forzmatrix=False))
top.clear_repeated_dihedrals()
# ----------------------- angles ### ###
top.clear_repeated_angles()
print("Topology is done!\n")
# ----------------------- write topology ------------------------------ #
if Utils.outputFormat == GROMOS_FORMAT:
Printer.printGromos(top)
elif Utils.outputFormat == GROMACS_FORMAT:
Printer.printGromacs(top)
else:
print("Unkown Output format! Printing Gromacs format instead:")
Printer.printGromacs(top)
if Utils.nogeom:
quit() # test everything before torsion opt
# ----------------------- geom opt ------------------------------ #
print("Building initial structure...")
# angles
top.set_angle_list(top.create_all_angles(top.get_bond_list()))
# dihedrals
top.set_dihedral_list(top.create_all_dihedrals(forzmatrix=True))
top.clear_repeated_dihedrals()
top.clear_repeated_angles()
print("Optimizing Torsions...")
# quit()
optGeo = TorsionOpt(top)
optGeo.run()
print(
"Successfully performed optimization of torsional degrees of freedom!")
top.calculateAtomsNeighbors()
top.createPairList()
top.createNonBondedPairs()
top.standardPairList()
print("Trying to optimize geometry ...")
minGeo = OptimizeGeometry(top)
minGeo.run()
# ----------------------- write coordinates ------------------------------ #
if Utils.outputFormat == GROMOS_FORMAT:
Printer.printGROMOSCoordFile(top)
elif Utils.outputFormat == GROMACS_FORMAT:
Printer.printGROMACSCoordFile(top)
else:
print("Unknown Output format! Printing Gromacs format instead:")
Printer.printGROMACSCoordFile(top)
print("All Done! Please don't forget to\n")
print("***************************")
print("*!!!CHECK YOUR TOPOLOGY!!!*")
print("***************************\n")
print(
"If your system has any special feature that is not covered by pyPolyBuilder or"
)
print(
"If you encounter any bug, please, help us improve the code at www.github.xxx/pypolybuilder\n"
)
def main():
Output = {}
Output[DENDRIMER] = Dendrimer
Output[POLYMER] = Polymer
mode = Utils.buildingMode
while (mode != DENDRIMER and mode != POLYMER):
mode = raw_input(
'Choose 1 for Dendrimer or 2 for Polymer construction: ')
mode = int(mode)
top = Output[mode]()
# Read and create bb_factories dict. Ex: bb_factories[CCO] = factory do CCO
top.read_bbs()
# Read and create connections array
top.read_connections()
# connect building blocks
print("Connecting Building Blocks...")
top.connect_bbs()
for atom in top.get_atom_list():
atom.set_bond_list([])
atom.set_atom_list([])
for bond in top.get_bond_list():
bond.get_a_1().get_atom_list().append(
bond.get_other_atom(bond.get_a_1()))
bond.get_a_2().get_atom_list().append(
bond.get_other_atom(bond.get_a_2()))
top.generate_exclusions()
print("Building Angles...")
top.set_angle_list(top.create_all_angles(top.get_bond_list()))
print("Building Dihedrals...\n")
top.set_dihedral_list(top.create_all_dihedrals(top.get_bond_list()))
print("All Done! Please don't forget to\n")
print("***************************")
print("*!!!CHECK YOUR TOPOLOGY!!!*")
print("***************************\n")
print(
"If your system has any special feature that is not covered by pyPolyBuilder or"
)
print(
"If you encounter any bug, please, help us improve the code at www.github.xxx/pypolybuilder\n"
)
# top.calculateAtomsNeighbors()
#top.create_initial_coords()
if (Utils.optimizeGeometry):
#print("Calculating Atom Neighbors")
top.calculateAtomsNeighbors()
#print("Creating Pair List")
top.createPairList()
#print("Creating Non-bonded pairs")
top.createNonBondedPairs()
#print("Standard pair list")
top.standardPairList()
print("Trying to optimize geometry ...")
optGeo = OptimizeGeometry(top)
optGeo.run()
print("Done!")
print(
"\n***WARNING***: This geometry serves only as an initial guess for further geometry optimization using the MD code of your choice (e.g. GROMOS or GROMACS)"
)
top.clear_repeated_dihedrals()
top.clear_repeated_angles()
if (Utils.outputFormat == GROMOS_FORMAT):
Printer.printGromos(top)
Printer.printGROMOSCoordFile(top)
else:
Printer.printGromacs(top)
Printer.printGROMACSCoordFile(top)
