adding in_mol2 to amber

rinikerlab · Mar 18, 2022 · 51c602e · 51c602e
1 parent a58de3f
commit 51c602e
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Showing 2 changed files with 17 additions and 6 deletions.
diff --git a/pygromos/files/forcefield/_generic_force_field.py b/pygromos/files/forcefield/_generic_force_field.py
@@ -28,11 +28,11 @@ def __init__(
         if auto_import:
             self.auto_import_ff()
 
-    def auto_import_ff(self):
+    def auto_import_ff(self, **kwargs):
         raise NotImplementedError("This is a template class! It'should be used as a super class for all forcefields!")
 
-    def create_top(self, mol: str, in_top: Top = None) -> Top:
+    def create_top(self, mol: str, in_top: Top = None, **kwargs) -> Top:
         raise NotImplementedError("This is a template class! It'should be used as a super class for all forcefields!")
 
-    def create_cnf(self, mol: str, in_cnf: Cnf = None) -> Cnf:
+    def create_cnf(self, mol: str, in_cnf: Cnf = None, **kwargs) -> Cnf:
         raise NotImplementedError("This is a template class! It'should be used as a super class for all forcefields!")
diff --git a/pygromos/files/forcefield/amber/amberff.py b/pygromos/files/forcefield/amber/amberff.py
@@ -46,17 +46,28 @@ def auto_import_ff(self):
             if not os.path.isfile(frcmod):
                 raise ImportError("could not find ff file " + frcmod)
 
-    def create_top(self, mol: str, in_top: Top = None) -> Top:
+    def create_top(self, mol: str, in_top: Top = None, in_mol2_file: str = None) -> Top:
+        self.mol = mol
+        self.in_mol2_file = in_mol2_file
+
         if self.amber is None:
-            self.create_mol2()
+            if in_mol2_file is None:
+                self.create_mol2()
             self.amber = amber2gromos(
                 in_mol2_file=self.in_mol2_file,
                 mol=self.mol,
                 forcefield=self.Forcefield,
                 gromosPP=self.gromosPP,
                 work_folder=self.work_folder,
             )
-        self.top = Top(self.amber.get_gromos_topology())
+        if in_top is None:
+            self.top = Top(self.amber.get_gromos_topology())
+        elif isinstance(in_top, Top):
+            self.top = in_top + Top(self.amber.get_gromos_topology())
+        elif isinstance(in_top, str):
+            self.top = Top(in_top) + Top(self.amber.get_gromos_topology())
+        else:
+            raise TypeError("in_top is of wrong type")
 
     def create_cnf(self, mol: str, in_cnf: Top = None) -> Cnf:
         if self.amber is None: