Add support to create dendrimers

[pm-blanco]

Notes from an online discussion with @pinedaps, ideas for adding a new feature to build dendrimers in pyMBE:

@mariusaarsten and @kosovan, we would appreciate your opinion on these ideas since you both have experience in building dendrimers! :smile:

Parameters of the dendrimer

Structure of the dendrimer

N1                                                          N1
    \                                                   /      
       branch                                   branch       
                 \                            /
                     N0 -- central_chain -- N0                    
                 /                            \
       branch                                   branch        
   /                                                     \      
N1                                                           N1  

Ideas

Case 1) have pre-defined models to set up symmetric dendrimers (like the one above)

• Use-cases: PAMAM dendrimer, glycogen and other homogenous-like dendrimers
• Users can define the composition of the central_chain, the branches and the nodes.
• All branches and nodes would have the same chemical identity
• If the user defines an empty central_chain, then the dendrimer would start from a central node.

define_dendrimer(name,
                 model="homogenous_dendrimer",
                 central_chain=[Res1, Res2, Res3, ...],
                 branch=[Res1, Res2, Res3, ...],
                 inner_nodes=particle_name,
                 outer_nodes=particle_name2,
                 branching_number=3 # number of branches per node
                 number_of_generations=4)

Case 2) Have a general framework to generate heterogenous dendrimer

• Use-cases: conjugated PAMAM dendrimer with peptide tails and other more complex dendrimers
• Load the topology from a JSON file
• Features: The user can specify the chemical composition of each branch and node for a given generation

  {
  {"building_block_type": "central_chain",  
  "residue_list" : ["Res1", "Res2", "Res3", ...] },
  {"building_block_type": "node",  
  "particle_name" : "N0", 
  "generation_number": 0, 
  "number_of_nodes": 2  },
  {"building_block_type": "node",  
  "particle_name" : "N1", 
  "generation_number": 1,
  "branching_number": 3, 
  "number_of_nodes": 4  },
  {"building_block_type": "branch",   
  "connecting_nodes": ["N0", "N1"]
  "residue_list" : ["Res1", "Res2", "Res3", ...], 
  "generation_number": 1,
  "number_of_branches": 4
  },
  }

Then, one would load the topology file directly.

define_dendrimer(name,
                 model="from_file",
                 path_to_topology_file="...")

and latter one would create it into espresso using pyMBE (with either case)

create_dendrimer(name, number_of_molecules)

[mariusaarsten]

@pm-blanco Based on my little experience working with PAMAM denrimer, I think this sounds like a great idea! In the homogenous case, you have labeled the the nodes N0 and N1, but based on the way you are planning to set up the function, these are really the same chemical identity if I understand correctly? And if one would like to distinguish between different chemical identites one would have to use option 2?

[pm-blanco]

Offline discussion with @mariusaarsten, we should also support a different particle type for the ending particles in case 1) because this is a fairly common case for dendrimers.

[pm-blanco]

suggestion by @davidbbeyer, check the BigSMILES project