geometry and topology tested version for AA and CG resolution

Author: mbrosz

data/martini300C-ff/aminoacids.ff

@@ -116,11 +116,10 @@ L5Y                1
   BB   SC1    1       0.360     8000      
  SC1   SC2    1       0.365     7000  
 
-[angles]
+[ angles ]
 #meta {"group": "Side chain angles"}
 ;  i     j    k     funct   angle  force.c.
-  BB   SC1  SC2       2   140    100     
-
+  BB   SC1  SC2     2   140    100     
 
 ;;;; TRIVALENT - CROSSLINK - PART LY2
 
@@ -1138,6 +1137,106 @@ collagen
 [ dihedrals ]
 -BB BB  +BB ++BB 1 77  19 1
 
+[ link ]
+resname $protein_resnames
+cgsecstruct "F"
+[ features ]
+collagen
+[ angles ]
+-BB BB SC1 1 40 152 {"group": "BBS angles L4Y"}
+[ patterns ]
+-BB BB {"cgsecstruct": "F","resname": "L4Y"} SC1 
+
+[ link ]
+resname $protein_resnames
+cgsecstruct "F"
+[ features ]
+collagen
+[ angles ]
+SC1 BB +BB 1 95 152 {"group": "BBS angles L4Y"}
+[ patterns ]
+SC1 BB {"cgsecstruct": "F","resname": "L4Y"} +BB
+
+[ link ]
+resname $protein_resnames
+cgsecstruct "F"
+[ features ]
+collagen
+[ angles ]
+-BB BB SC1 1 70 152 {"group": "BBS angles L5Y"}
+[ patterns ]
+-BB BB {"cgsecstruct": "F","resname": "L5Y"} SC1 
+
+[ link ]
+resname $protein_resnames
+cgsecstruct "F"
+[ features ]
+collagen
+[ angles ]
+SC1 BB +BB 1 110 152 {"group": "BBS angles L5Y"}
+[ patterns ]
+SC1 BB {"cgsecstruct": "F","resname": "L5Y"} +BB
+
+[ link ]
+resname $protein_resnames
+cgsecstruct "F"
+[ features ]
+collagen
+[ angles ]
+-BB BB SC1 1 70 152 {"group": "BBS angles LY2"}
+[ patterns ]
+-BB BB {"cgsecstruct": "F","resname": "LY2"} SC1 
+
+[ link ]
+resname $protein_resnames
+cgsecstruct "F"
+[ features ]
+collagen
+[ angles ]
+SC1 BB +BB 1 95 152 {"group": "BBS angles LY2"}
+[ patterns ]
+SC1 BB {"cgsecstruct": "F","resname": "LY2"} +BB
+
+[ link ]
+resname $protein_resnames
+cgsecstruct "F"
+[ features ]
+collagen
+[ angles ]
+-BB BB SC1 1 75 152 {"group": "BBS angles LY3"}
+[ patterns ]
+-BB BB {"cgsecstruct": "F","resname": "LY3"} SC1 
+
+[ link ]
+resname $protein_resnames
+cgsecstruct "F"
+[ features ]
+collagen
+[ angles ]
+SC1 BB +BB 1 77 152 {"group": "BBS angles LY3"}
+[ patterns ]
+SC1 BB {"cgsecstruct": "F","resname": "LY3"} +BB
+
+[ link ]
+resname $protein_resnames
+cgsecstruct "F"
+[ features ]
+collagen
+[ angles ]
+-BB BB SC1 1 140 152 {"group": "BBS angles LYX"}
+[ patterns ]
+-BB BB {"cgsecstruct": "F","resname": "LYX"} SC1 
+
+[ link ]
+resname $protein_resnames
+cgsecstruct "F"
+[ features ]
+collagen
+[ angles ]
+SC1 BB +BB 1 140 152 {"group": "BBS angles LYX"}
+[ patterns ]
+SC1 BB {"cgsecstruct": "F","resname": "LYX"} +BB
+
 [ link ]
 resname $protein_resnames
 [ constraints ]

src/colbuilder/geometry/caps.py

@@ -10,7 +10,7 @@ class Caps:
     
     Obarska-Kosinska A, Rennekamp B, Ünal A, Gräter F. 
     ColBuilder: A server to build collagen fibril models.
-    Viophys J. 2021 Sep 7;120(17):3544-3549. 
+    Biophys J. 2021 Sep 7;120(17):3544-3549. 
     doi: 10.1016/j.bpj.2021.07.009. 
     Epub 2021 Jul 13. PMID: 34265261; PMCID: PMC8456305.
 
@@ -79,7 +79,7 @@ def add_caps(self,pdb_id=None):
                 if cap=='N' and int(line_cap.split(' ')[1])!=1:
                     cmd.edit(line_cap)
                     editor.attach_amino_acid('pk1','ace',ss=0)
-                if cap=='C' and int(line_cap.split(' ')[1])!=int(self.chain_length[cap]): 
+                if cap=='C' and int(line_cap.split(' ')[1])!=int(self.chain_length[chain]): 
                     cmd.edit(line_cap)
                     editor.attach_amino_acid('pk1','nme',ss=0)
         cmd.save('tmp.pdb')

src/colbuilder/geometry/system.py

@@ -75,7 +75,7 @@ def get_connect(self,connect=None):
         get crystal contacts for a model in system
         
         """
-        self.connect={ self.get_model(model_id=key).id : [] for key in self.get_models() } # TODO: Why transform here? not needed
+        self.connect={ self.get_model(model_id=key).id : [] for key in self.get_models() } 
         for idx in self.get_models():
             self.connect[self.get_model(model_id=idx).id]=self.get_model(model_id=idx).connect
         return self.connect