Improved writing for LigninBuilder

ligning/monomer.py

@@ -276,8 +276,8 @@ def create(self) -> nxgraph:
         self.G = G_m
 
         # Initialize a big graph for monomer
-        bigG = nx.Graph()
+        bigG = nx.DiGraph()
         bigG.add_node(self.mi, mtype = self.type, color = default_color[self.type])
         self.bigG = bigG
 
-        return G_m
+        return G_m

ligning/polymer.py

@@ -2,7 +2,7 @@
 Build lignin polymers
 """
 import networkx as nx
-
+import os
 from typing import Optional, TypeVar, Union, Tuple, List
 from copy import copy
 import warnings
@@ -131,7 +131,6 @@ def find_available_C2_in_monomer(self, C1_index_in_polymer: int, ring: Optional[
 
         if ring:
             C2_indices_in_monmer = [ci for ci in C2_indices_in_monmer if ci != 1]
-        #print(C2_indices_in_monmer)
 
         return C2_indices_in_monmer
 
@@ -422,7 +421,10 @@ def update_units(
         M2_index = self.G.nodes[C2_index_in_polymer]['mi']
 
         # Add the edges to monomer nodes
-        self.bigG.add_edges_from([(M1_index, M2_index)], btype=linkage_new_name)
+        if linkage_index[0] <= linkage_index[1]:
+            self.bigG.add_edges_from([(M1_index, M2_index)], btype=linkage_new_name)
+        else:
+            self.bigG.add_edges_from([(M2_index, M1_index)], btype=linkage_new_name)
 
 
     def try_adding_new(
@@ -463,10 +465,8 @@ def try_adding_new(
         if monomer_new is not None:
             monomer_new.create()
             PG_temp.G = ut.join_two(PG_temp.G, monomer_new.G)
-
         # Add the linkage
         new_linkage_flag = PG_temp.connect_C1_C2(linkage_index, C1_index_in_polymer, C2_index_in_polymer)
-
         # If a new linakge does form
         if new_linkage_flag: 
             # Update the polymer graph
@@ -891,6 +891,66 @@ def add_specific_ring(
 
         return new_linkage_flag
 
+    def write_LigninBuilder(self,
+        name: Optional[str]='test',
+        segname: Optional[str]='L',
+        save_path: Optional[str]=os.getcwd()) -> None:
+        """Convert this polymer to a Tcl script that VMD and LigninBuilder can convert to a 3D structure
+
+        Parameters
+        ----------
+        name : Optional[str], optional
+            name of the file to be written without the .tcl extension, by default 'test', creating a 'test.tcl' file
+        segname : Optional[str], optional
+            segment name created. Default is "L"
+        save_path : Optional[str], optional
+            path to save the figure, by default os.getcwd()
+        """ 
+        H = self.bigG
+        if not os.path.exists(save_path):
+            os.mkdir(save_path)
+        filename = os.path.join(save_path, name+'.tcl')
+        with open(filename, 'w') as fout:
+            fout.write("package require psfgen\ntopology toppar/top_all36_cgenff.rtf\ntopology toppar/top_lignin.top\n"
+               "topology toppar/top_spirodienone.top\n")
+            # Write monomers
+            fout.write("resetpsf\nsegment %s {\n" % segname)
+            for i in range(len(H.nodes)):
+                if H.nodes[i]['mtype'] == 'G':
+                    monomer = "GUAI"
+                elif H.nodes[i]['mtype'] == 'C':
+                    monomer = "CAT"
+                elif H.nodes[i]['mtype'] == 'H':
+                    monomer = "PHP"
+                elif H.nodes[i]['mtype'] == 'S':
+                    monomer = "SYR"
+                else:
+                    raise ValueError("Monomer type not allowed. Must input C, H, G or S.")
+                fout.write("residue %d %s\n" % (i+1, monomer))
+            fout.write("}\n")
+            #Write linkages
+            for ei in list(H.edges):
+                #ei will be the tuple describing the nodes that are connected.
+                #The order is important! The first node is the residue with the lower numbered carbon involved in the linkage.
+                #Based on the patches used by LigninBuilder, sometimes the "first" residue in the patch is the first residue in the graph, and sometimes its the second.
+                if H.edges[ei]['btype'] == '4-O-5':
+                    fout.write("patch 4O5 %s:%s %s:%s\n" % (segname, ei[0]+1, segname, ei[1]+1))
+                elif H.edges[ei]['btype'] == 'alpha-O-4':
+                    fout.write("patch AO4 %s:%s %s:%s\n" % (segname, ei[1]+1, segname, ei[0]+1))
+                elif H.edges[ei]['btype'] == 'beta-O-4':
+                    fout.write("patch BO4 %s:%s %s:%s\n" % (segname, ei[1]+1, segname, ei[0]+1))
+                elif H.edges[ei]['btype'] == '5-5':
+                    fout.write("patch 55 %s:%s %s:%s\n" % (segname, ei[0]+1, segname, ei[1]+1))
+                elif H.edges[ei]['btype'] == 'beta-5':
+                    if H.nodes[ei[0]]['mtype'] == 'H':
+                        fout.write("patch B5P %s:%s %s:%s\n" % (segname, ei[1]+1, segname, ei[0]+1))
+                    else:
+                        fout.write("patch B5%s %s:%s %s:%s\n" % (H.nodes[ei[0]]['mtype'], segname, ei[1]+1, segname, ei[0]+1))
+                elif H.edges[ei]['btype'] == 'beta-beta':
+                    fout.write("patch BB %s:%s %s:%s\n" % (segname, ei[0]+1, segname, ei[1]+1))
+                elif H.edges[ei]['btype'] == 'beta-1':
+                    fout.write("patch B1 %s:%s %s:%s\n" % (segname, ei[1]+1, segname, ei[0]+1))
+            fout.write("writepsf %s.psf\n" % segname)
 
 
 

ligning/utils.py

@@ -34,7 +34,7 @@
 import matplotlib
 if platform.system() == 'Linux':
     matplotlib.use('Agg')
-    print('switched')
+    #print('switched')
 import matplotlib.pyplot as plt   
 # if platform.system() == 'Linux':
 #     plt.switch_backend('agg')
@@ -93,7 +93,6 @@ def draw_big_graph(G: nxgraph) -> None:
     # big graph is marked by hexagons 
     draw_graph(G, node_labels, node_shape = 'h', node_size=1000)
 
-
 def draw_atomic_graph(G: nxgraph) -> None:
     """Plot the atomic graph
 
@@ -163,8 +162,6 @@ def graph_to_mol(
         Chem.Draw.MolToFile(mol, filename, size=(500, 500))
 
     return mol
-
-
 
 def smiles_to_formula(smiles: str) -> str:
     """Convert the smiles to the chemical formula in C, H and O