Merge pull request #75 from OMaraLab/hotfix-solver-errror-message

error message hotfix, made polyconf scripts executable

Author: recombinatrix

polyconf/polyconf/Polymer.py

@@ -192,9 +192,6 @@ def extend(self, monomer, n, nn, names, joins, ortho=[1,1,1],
             any dummy atoms.
 
         """
-        # TODO I renamed the atoms in the manuscript, so I guess I gotta fix that here
-        # cool.
-        # love that for me.
 
         Q = self.polymer.select_atoms(f"resid {n} and name {names['Q']}").positions[-1]
         S = self.polymer.select_atoms(f"resid {n} and name {names['S']}").positions[-1]
@@ -238,14 +235,6 @@ def extend(self, monomer, n, nn, names, joins, ortho=[1,1,1],
 
             u_r2 = u_r1.atoms.rotateby(theta,axis=k,point=V1)
 
-            # R= u_.select_atoms('resid '+str(nn)+' and name '+names['R']).positions[0]
-            # S= u_.select_atoms('resid '+str(nn)+' and name '+names['S']).positions[0]
-            # RS=S-R
-            # RS_n=np.linalg.norm(RS)
-            # ortho_n=np.linalg.norm(ortho)
-            # check = degrees(np.arccos(np.dot(RS,ortho)/(RS_n * ortho_n)))
-            # if abs(check)>1: print('linear check =' ,check)
-
             u_r1=u_r2
 
         # combine extended polymer into new universe
@@ -421,7 +410,6 @@ def dihedral_solver(self,pairlist,dummies='X*',cutoff=0.7,backwards_only=True):
                 resolved and no clashes detected
         :rtype: bool
         """
-        # TODO stepback isn't working right, it's not stepping back far enough
         steps=len(pairlist)
         tries={x:0 for x in range(0,steps)} # how many steps around the dihedral have we tried? resets to zero if you step backwards
         fails={x:0 for x in range(0,steps)} # how many times have we had to step backwards at this monomer?  the more times, the further back we step 
@@ -461,7 +449,7 @@ def dihedral_solver(self,pairlist,dummies='X*',cutoff=0.7,backwards_only=True):
                 done=True
         if failed or i<0: # hard coded to detect failure if you stop at i<=0 because detecting this automatically wasn't working
             print('Could not reach a valid conformation')
-            print('Perhaps you should try building a pseudolinear geometry with .extend(linearize=True) or randomising all dihedrals with shuffler(), and then try solving a conformation again')
+            print('Perhaps you should try building a pseudolinear geometry with .extend(linearise=True) or randomising a subset of the dihedrals with shuffler(), and then try solving a conformation again')
             return True
         else:
             return False

polyconf_examples/01a_build_PEI_with_extend.py

@@ -51,6 +51,8 @@
     dh += [sidechains[i]]
 
 print('attempting to solve initial conformation')
+print('the random seed in this example script has been chosen specifically so that this process fails')
+print('this is expected and is part of the tutorial')
 
 PMMA_atactic.dihedral_solver(dh,dummies=dummies,cutoff=1.1)