BUG: branched dextran no longer possible to produce directly

Working on latest master branch of polyply.

I was trying to roughly follow the tutorial at https://github.com/marrink-lab/polyply_regression_tests/blob/main/examples/liquid_liquid_phase_separation/PolyplyTutorial.ipynb

Then, I noticed that dextran.martini3.ff doesn't even have alpha 1->3 linkages anymore, they were deleted for some reason in 0a76a13 -- was that an accident? Perhaps a branched build regression test is needed there? It looks like you already have an unbranched dextran regression test at polyply/tests/test_data/library_tests/martini3/DEX/polyply/command.

PEO polymer construction seems to work just fine for me locally, and so does unbranched dextran. For reproducer, this could be pared down quite a lot, but you'll get the idea--need to generate a branched JSON file with DEX 1-3 linkages/branches, then the failure to gen_params can be reproduced. I can help you produce a smaller regression test if you really want, but fixing the parameters in a MARTINI-3 compliant way is probably beyond the scope of my expertise, though you may just need to restore some deleted lines to fix it?

# modified from: https://github.com/marrink-lab/polyply_regression_tests/blob/main/examples/liquid_liquid_phase_separation/PolyplyTutorial.ipynb

import sys
import random
import json
import numpy as np
import networkx as nx
from networkx.readwrite import json_graph
from plot_polymers import plot_graph_nicley
import matplotlib.pyplot as plt

def write_graph_to_json(graph, filename):
    g_json = json_graph.node_link_data(graph)
    with open(filename, "w") as file_handle:
        json.dump(g_json, file_handle, indent=2)

def random_linear_comb(n_mon_tot, max_mon_side, p_side_chain):
    """
    Generate a graph that consists of a backbone and branches coming off
    the backbone such that the total number of monomers is `n_mon_tot`.

    Parameters
    ----------
    n_mon_tot: int
        total number of monomers in the polymer
    max_mon_side:
        the maximum number of monomers per branched off arm
    p_side_chain: list[float]
        probabilities to add at a level corrsponding to the
        position in the list i.e. probability of adding a monomer
        to a side chain beyond the back-bone is list[0], adding a monomer branched
        off 2 level from the back-bone is list[1].

    Returns
    --------
    nx.Graph
    """
    G = nx.Graph()
    # add the first edge to get started
    G.add_edge(0, 1, **{"linktype": "a16"})
    # backbone-nodes
    bb_nodes = [0, 1]
    ndx = 1
    prev_node = "BB"
    while ndx < n_mon_tot:
        # then we make the choice back-bone or side-chain
        # but only if we did not add a side-chain before
        # because we build a comb which has only 1 side chain
        # per back-bone otherwise it's a tree
        if prev_node == "BB":
            choice = random.choices(["BB", "SC"], weights=[1-p_side_chain[0], p_side_chain[0]])[0]
        else:
            choice = "BB"

        # if choice is BB we append to the list of BB nodes and continue
        if choice == "BB":
            G.add_edge(bb_nodes[-1], ndx+1, **{"linktype": "a16"})
            ndx += 1
            bb_nodes.append(ndx)
            prev_node = "BB"

        # if choice is SC we start growing a arm
        else:
            # add the first node of the arm
            G.add_edge(bb_nodes[-1], ndx+1, **{"linktype": "a13"})
            ndx += 1
            prev_node = "SC"
            # an arm can have at most max_side_chains monomers beyond first level
            # we add them until we draw a stop
            for sc_idxs in range(1, max_mon_side):
                choice = random.choices(["stop", "add"], weights=[
                                        1-p_side_chain[sc_idxs], p_side_chain[sc_idxs]])[0]
                if choice == "stop":
                    break
                else:
                    G.add_edge(ndx, ndx+1, **{"linktype": "a16"})
                    ndx += 1
                prev_node = "SC"
                # if we exceed the max number of monomers we terminate
                if ndx >= n_mon_tot:
                    return G

        # if we exceed the max number of monomers we terminate
        if ndx >= n_mon_tot:
            return G

if __name__ == "__main__":
    graph = random_linear_comb(61, 2, [0.5, 0.95, 0.95, 0.1])
    nx.set_node_attributes(graph, "DEX", "resname")
    resids = {node: node+1 for node in graph.nodes}
    nx.set_node_attributes(graph, resids, "resid")
    fig = plt.figure()
    ax_dextran = fig.add_subplot(111)
    plot_graph_nicley(graph, link_labels=True, ax=ax_dextran)
    ax_dextran.set_title("polyply branched dextran (10 kg/mol) prototype residue graph")
    fig.set_size_inches(20, 8)
    fig.savefig("dextran_residue_graph.png", dpi=300)
    write_graph_to_json(graph, 'dextran_polymer_1.json')

polyply gen_params -lib martini3 -seqf dextran_polymer_1.json -name DEX_polymer_1 -o dex_polymer_1.itp

<snip>
WARNING - general - Missing a link between residue 56 DEX and residue 57 DEX.
WARNING - general - Missing a link between residue 57 DEX and residue 58 DEX.
WARNING - general - Missing a link between residue 58 DEX and residue 59 DEX.
WARNING - general - Missing a link between residue 58 DEX and residue 61 DEX.
WARNING - general - Missing a link between residue 59 DEX and residue 60 DEX.
WARNING - general - Missing a link between residue 61 DEX and residue 62 DEX.
WARNING - general - Missing a link between residue 62 DEX and residue 63 DEX.
<snip>

marrink-lab / polyply_1.0

BUG: branched dextran no longer possible to produce directly #351