def attach(partmono, attach1, monomer, number): # needs more work, very specific right now
monomernew = monomer
num = int(number)
for run in range(0, num):
add = int(monomernew.atoms[-1].atom_id)
newalist = []
newblist = []
# remove bonds in old attach and remove the hydrogen as well
for i in range(len(attach1.atom_bonds)):
if attach1.atom_bonds[i].atom_type == "H": # this has to do in a specific manner, may have to change
oldh = attach1.atom_bonds[i]
attachid = attach1.atom_id
abond = bond.get_bond(attach1, oldh, monomernew.bonds)
monomernew.bonds.remove(abond)
monomernew.atoms.remove(oldh)
# take partmono and offset all of its atoms to create a good atomlist
for i in range(len(partmono)):
newalist.append(copy.deepcopy(partmono[i]))
newalist[i].atom_id = int(partmono[i].atom_id) + add
newalist[i].x_pos = float(newalist[i].x_pos) + (run + 1) * -4.000
print (run + 1) * 5.000
# generate new alist, put this kind of stuff into one big method or something
for i in range(len(newalist)):
for j in range(len(newalist[i].atom_bonds)):
newalist[i].atom_bonds[j] = atom.get_atombyid(newalist, int(newalist[i].atom_bonds[j].atom_id) + add)
# generate new blist
newblist = getpartblist(partmono, monomer, newalist, add)
for i in range(len(newblist)):
if newblist[i].bond_slave == None:
newblist.remove(newblist[i])
break
a5add = atom.get_atombyid(newalist, 5 + add)
a37add = atom.get_atombyid(newalist, 37 + add)
newblist.append(bond.Bond(1, a5add, a37add))
# remove the nonetype from addloc so it doesnt f**k shit up
# add this to newmonomer
for i in range(len(newalist)):
monomernew.atoms.append(newalist[i])
for i in range(len(newblist)):
monomernew.bonds.append(newblist[i])
print newalist[0].atom_id
print monomer.atoms[0].atom_id
print newalist[0].atom_bonds[1].atom_id
print newblist[0].bond_master.atom_id
print newalist[0].x_pos
print monomer.atoms[0].x_pos
attach1 = atom.get_atombyid(newalist, int(attachid) + add)
return monomernew
def set_dft(dihedral,bonds):
""" Given a list of dihedrals find if you should set dft values for those dihedrals or not.
Sets a boolean on the list of dihedrals that need dft calculations done to them.
Probably should return a list instead for speed optimization
Keyword Arguments:
dihedral - The list of dihedrals you want to check
bonds - The list of bonds you want to check
"""
for i in range(len(dihedral)):
mb1 = bond.get_bond(dihedral[i].dihedral_master1,dihedral[i].dihedral_master2,bonds)
if mb1.bond_type == '1':
ob1 = bond.get_bond(dihedral[i].dihedral_master1,dihedral[i].dihedral_slave1,bonds)
ob2 = bond.get_bond(dihedral[i].dihedral_master2,dihedral[i].dihedral_slave2,bonds)
if ob1 == None or ob2 == None:
continue
if ob1.bond_type == '2' and ob2.bond_type == '2':
dihedral[i].dft = True
def create_polymer_cml(filename, partmono, attach, monomer, number):
""" Basically a test for writing a cml from data and creating a 3rd attach"""
new_cml = open("%s_new.cml" % filename, "w")
sys.stdout = new_cml
usedbonds = []
bondscopy = []
for i in range(len(monomer.bonds)):
bondscopy.append(monomer.bonds[i])
for i in range(len(attach.atom_bonds)):
if attach.atom_bonds[i].atom_type == "H":
attach2 = attach.atom_bonds[i]
abond = bond.get_bond(attach, attach2, monomer.bonds)
monomer.bonds.remove(abond)
monomer.atoms.remove(attach2) # find the hydrogen its attached to and remove instead
add = len(monomer.atoms) + 1
newattach = ""
anglelist = monomer.angles
# THIS SHIT IS USELESS. DONT USE FOR ATTACH MODULE
for i in range(len(anglelist)):
if (
anglelist[i].Angle_master.atom_type == "C"
and anglelist[i].Angle_slave1.atom_type == "C"
and anglelist[i].Angle_slave2.atom_type == "S"
and anglelist[i].Angle_master in partmono
and anglelist[i].Angle_slave1 in partmono
and anglelist[i].Angle_slave2 in partmono
):
newattach = anglelist[i].Angle_master
elif (
anglelist[i].Angle_master.atom_type == "C"
and anglelist[i].Angle_slave1.atom_type == "S"
and anglelist[i].Angle_slave2.atom_type == "C"
and anglelist[i].Angle_master in partmono
and anglelist[i].Angle_slave1 in partmono
and anglelist[i].Angle_slave2 in partmono
):
newattach = anglelist[i].Angle_master
print "<molecule>"
print " <atomArray>"
for i in range(len(monomer.atoms)):
print ' <atom id="a%s" elementType="%s" x3="%s" y3="%s" z3="%s"/>' % (
monomer.atoms[i].atom_id,
monomer.atoms[i].atom_type,
monomer.atoms[i].x_pos,
monomer.atoms[i].y_pos,
monomer.atoms[i].z_pos,
)
for i in range(len(partmono)):
print ' <atom id="a%s" elementType="%s" x3="%s" y3="%s" z3="%s"/>' % (
int(partmono[i].atom_id) + add,
partmono[i].atom_type,
float(partmono[i].x_pos) - 5.00,
float(partmono[i].y_pos),
float(partmono[i].z_pos),
)
print " </atomArray>"
print " <bondArray>"
for i in range(len(monomer.bonds)):
print ' <bond atomRefs2="a%s a%s" order="%s"/>' % (
monomer.bonds[i].bond_master.atom_id,
monomer.bonds[i].bond_slave.atom_id,
monomer.bonds[i].bond_type,
)
for i in range(len(partmono)):
for j in range(len(partmono[i].atom_bonds)):
if partmono[i].atom_bonds[j] in partmono:
bondid = bond.get_bond(partmono[i], partmono[i].atom_bonds[j], bondscopy)
if bondid in usedbonds:
continue
usedbonds.append(bondid)
print ' <bond atomRefs2="a%s a%s" order="%s"/>' % (
int(partmono[i].atom_id) + add,
int(partmono[i].atom_bonds[j].atom_id) + add,
bondid.bond_type,
)
else:
continue
print ' <bond atomRefs2="a%s a%s" order="1"/>' % (attach.atom_id, int(newattach.atom_id) + add - 2)
print " </bondArray>"
print "</molecule>"
new_cml.close()