FDB: Allow for the addition of fragments to the fragment database

[jeleclaire]

After reading a pdb-file, next steps would be adding bonds and reconstructing fragments by using the fragment data base. When the complex structure contains non-standard fragments, the possibility of adding fragments to the FDB would be extremely helpful.

Example:
PDB-ID 1IEP contains a ligand named Imatinib (STI-571) for which the FDB does not contain a reference fragment. PubChem does contain the required information about bonds (Pubchem ID: 5291), that can be loaded in BiochemicalAlgorithms as JSON.
Here is the output, when build_bonds is called on 1IEP.pdb (contains chloride ions which are not part of the FDB as well):

build_bonds!(sys, fdb)
┌ Warning: build_bonds!(): could not find reference fragment for  CL.
└ @ BiochemicalAlgorithms C:\Users\Leclaire\.julia\packages\BiochemicalAlgorithms\4zORk\src\preprocessing\build_bonds.jl:14
┌ Warning: build_bonds!(): could not find reference fragment for  CL.
└ @ BiochemicalAlgorithms C:\Users\Leclaire\.julia\packages\BiochemicalAlgorithms\4zORk\src\preprocessing\build_bonds.jl:14
┌ Warning: build_bonds!(): could not find reference fragment for  CL.
└ @ BiochemicalAlgorithms C:\Users\Leclaire\.julia\packages\BiochemicalAlgorithms\4zORk\src\preprocessing\build_bonds.jl:14
┌ Warning: build_bonds!(): could not find reference fragment for  CL.
└ @ BiochemicalAlgorithms C:\Users\Leclaire\.julia\packages\BiochemicalAlgorithms\4zORk\src\preprocessing\build_bonds.jl:14
┌ Warning: build_bonds!(): could not find reference fragment for STI.
└ @ BiochemicalAlgorithms C:\Users\Leclaire\.julia\packages\BiochemicalAlgorithms\4zORk\src\preprocessing\build_bonds.jl:14
┌ Warning: build_bonds!(): could not find reference fragment for  CL.
└ @ BiochemicalAlgorithms C:\Users\Leclaire\.julia\packages\BiochemicalAlgorithms\4zORk\src\preprocessing\build_bonds.jl:14
┌ Warning: build_bonds!(): could not find reference fragment for  CL.
└ @ BiochemicalAlgorithms C:\Users\Leclaire\.julia\packages\BiochemicalAlgorithms\4zORk\src\preprocessing\build_bonds.jl:14
┌ Warning: build_bonds!(): could not find reference fragment for STI.
└ @ BiochemicalAlgorithms C:\Users\Leclaire\.julia\packages\BiochemicalAlgorithms\4zORk\src\preprocessing\build_bonds.jl:14
[ Info: build_bonds!(): built 4576 bonds

We need an adapter transferring the JSON to a FDB Fragment.