add code

mrdna/readers/segmentmodel_from_lists.py

@@ -234,7 +234,7 @@ def model_from_basepair_stack_3prime(coordinate, basepair, stack, three_prime,
                                      max_basepairs_per_bead = 5,
                                      max_nucleotides_per_bead = 5,
                                      local_twist = False,
-                                     dimensions=(5000,5000,5000),return_prop=False
+                                     dimensions=(5000,5000,5000)
                                      **model_parameters):
     """ 
     Creates a SegmentModel object from lists of each nucleotide's
@@ -475,11 +475,62 @@ def model_from_basepair_stack_3prime(coordinate, basepair, stack, three_prime,
     if sequence is None:
         for s in model.segments:
             s.randomize_unset_sequence()
-    if return_prop is True:
-        nt_prop=pd.DataFrame({"r":coordinate,"bp":basepair,"stack":stack,"fwd":fwd,"threeprime":three_prime,"seq":sequence,"orientation":orientation})
-        return model,nt_prop
+
+    return model
+
+def model_from_pandas(df,coordinate_col="r",bp_col="bp",stack_col="stack",three_prime_col="threeprime",
+                        seq_col=None,orientation_col=None,
+                        max_basepairs_per_bead = 5,
+                        max_nucleotides_per_bead = 5,
+                        local_twist = False,
+                        dimensions=(5000,5000,5000)
+                        **model_parameters):
+    try:
+        c=df[coordinate_col]
+    except:
+        print("cannot locate coordinate")
+    try:
+        bp=df[bp_col]
+    except:
+        print("cannot locate bp")
+    try:
+        stack=df[stack_col]
+    except:
+        print("cannot find stack")
+    try:
+        tprime=df[three_prime_col]
+    except:
+        print("cannot locate 3's")
+    if seq_col is not None:
+        try:
+            seq=df[seq_col]
+        except:
+            print("no sequence inputted")
+            seq=None
     else:
+        seq=None
+    
+    if orientation_col is not None:
+        try:
+            orient=df[orientation_col]
+        except:
+            print("no orientation inputted")
+            orient=None
+    else:
+        orient=None   
+    
+    try:
+        model=model_from_basepair_stack_3prime(c, bp, stack, tprime,
+                                        sequence=seq, orientation=orient,
+                                        max_basepairs_per_bead = max_basepairs_per_bead,
+                                        max_nucleotides_per_bead =max_nucleotides_per_bead ,
+                                        local_twist = local_twist,
+                                        dimensions=dimensions
+                                        **model_parameters)
+        model._dataframe=df
         return model
+    except:
+        print("cannot phrase DataFrame, aborted")
 
 def UNIT_circular():
     """ Make a circular DNA strand, with dsDNA in the middle """