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 getpartblist(partmono, monomer, newatoms, add):
partmonobonds = []
for i in range(len(partmono)):
for j in range(len(monomer.bonds)):
if monomer.bonds[j].bond_master == partmono[i]:
bondscopy = copy.deepcopy(monomer.bonds[j])
newmast = atom.get_atombyid(newatoms, int(monomer.bonds[j].bond_master.atom_id) + add)
newslave = atom.get_atombyid(newatoms, int(monomer.bonds[j].bond_slave.atom_id) + add)
bondscopy.bond_master = newmast
bondscopy.bond_slave = newslave
partmonobonds.append(bondscopy)
return partmonobonds
