Remove `pdb` from init_from_file options for BuildingBlock

The minimum working example at the bottom shows clearly that if you write and then init_from_file, you will lose bond order information. This is because PDB files do not contain bond order information in their “CONECT” records.

Therefore, I suggest removing it as an init function (the with_structure_from_file method is completely fine because it just loads the coordinates). Perhaps a warning is added for 6 months before removing?

What do you think, @lukasturcani?

import stk
from collections import Counter

pdb_writer = stk.PdbWriter()

bb = stk.BuildingBlock(
    'CN(c1ccc(cc1)N=Cc2cccnc2)c3nc(nc(n3)N(C)c4ccc(cc4)N=Cc5ccccn5)'
    'N(C)c6ccc(cc6)N=Cc7ccccn7'
)

# Get bond order information.
orders = []
for bond in bb.get_bonds():
    orders.append(bond.get_order())

# Write to PDB.
bb.write(f'first.pdb')

# Read from PDB.
bb2 = stk.BuildingBlock.init_from_file('first.pdb')

# Get bond order information.
orders2 = []
for bond in bb2.get_bonds():
    orders2.append(bond.get_order())

print(Counter(orders), Counter(orders2)) ## >> Counter({1.0: 72, 2.0: 24}) Counter({1.0: 96})

# Write to PDB.
bb.write(f'second.pdb')

# Compare text of PDBs.
s1 = pdb_writer.to_string(bb)
s2 = pdb_writer.to_string(bb2)

print(s1 == s2)

[lukasturcani]

fair, we write XYZ files which do not preserve bond orders. so thats not too crazy

[andrewtarzia]

Can this be closed now? #449