rings still not merging

HTPolyNet/__init__.py

@@ -1 +1 @@
-HTPOLYNET_VERSION='1.0.7.1'
+HTPOLYNET_VERSION='1.0.8'

HTPolyNet/coordinates.py

@@ -161,6 +161,7 @@ def read_gro(cls,filename,wrap_coords=True):
         #     logger.debug(ln)
         if wrap_coords:
             inst.wrap_coords()
+        logger.debug(inst.A.dtypes)
         return inst
 
     @classmethod
@@ -773,7 +774,14 @@ def get_R(self,idx):
         :rtype: numpy.ndarray(3,float)
         """
         df=self.A
-        return np.array(get_row_attribute(df,['posX','posY','posZ'],{'globalIdx':idx}))
+        assert df['posX'].dtypes==float
+        assert df['posY'].dtypes==float
+        assert df['posZ'].dtypes==float
+        res=get_row_attribute(df,['posX','posY','posZ'],{'globalIdx':idx})
+        # logger.debug(f'get_R result from get_row_attribute is {res} with type {type(res)} dtype {res.dtype}')
+        res=res.to_numpy(dtype=float)
+        # logger.debug(f'...and after to_numpy(), it is {res} type {type(res)} dtype {res.dtype}')
+        return res
 
     def get_atom_attribute(self,name,attributes):
         """get_atom_attribute return values of attributes listed in name from atoms specified by attribute:value pairs in attributes

HTPolyNet/dataframetools.py

@@ -19,6 +19,9 @@ def get_row(df:pd.DataFrame,attributes:dict):
     sdf=df
     for k,v in attributes.items():
         sdf=sdf[sdf[k]==v]
+    # res=pd.Series(sdf.iloc[0,:])
+    # logger.debug(f'sdf dtypes {sdf.dtypes}')
+    # logger.debug(f'get_row returns series {res.to_string()} with dtypes {res.dtypes}')
     return pd.Series(sdf.iloc[0,:])
 
 def get_row_attribute(df:pd.DataFrame,name,attributes):
@@ -35,6 +38,8 @@ def get_row_attribute(df:pd.DataFrame,name,attributes):
     :rtype: scalar
     """
     row=get_row(df,attributes)
+    # res=row[name]
+    # logger.debug(f'get_row_attribute of {name} returns {res} with type {type(res)}')
     return row[name]
 
 def get_row_as_string(df:pd.DataFrame,attributes):

HTPolyNet/molecule.py

@@ -284,7 +284,7 @@ def initialize_molecule_rings(self):
         """
         TC=self.TopoCoord
         TC.Topology.detect_rings()
-
+        logger.debug(f'Detected {len(TC.Topology.rings)} unique rings.')
         # TC.idx_lists['cycle']=[]
         # cycle_dict=TC.Topology.detect_cycles()
         # logger.debug(f'Cycle dict: {cycle_dict}')
@@ -362,7 +362,7 @@ def initialize_monomer_grx_attributes(self):
                     TC.idx_lists['chain'].append(entry)
         TC.reset_grx_attributes_from_idx_list('chain')
         # set cycle, cycle_idx
-        self.initialize_molecule_cycles()
+        self.initialize_molecule_rings()
 
     def previously_parameterized(self):
         """previously_parameterized if a gro file exists in the project molecule/parameterized directory for this molecule, return True
@@ -835,7 +835,7 @@ def make_bonds(self,bdf:pd.DataFrame,moldict,stage):
         else:
             template_source='internal'  # signals that a template molecule should be identified to parameterize this bond
         TC.update_topology_and_coordinates(bdf,moldict,explicit_sacH=explicit_sacrificial_Hs,template_source=template_source)
-        self.initialize_molecule_cycles()
+        self.initialize_molecule_rings()
 
     def transrot(self,at_idx,at_resid,from_idx,from_resid,connected_resids=[]):
         """transrot given a composite molecule, translate and rotate the piece downstream of the yet-to-be created bond specified by (at_idx,at_resid) and (from_idx,from_resid) to minimize steric overlaps and identify the best two sacrificial hydrogens
@@ -888,21 +888,25 @@ def transrot(self,at_idx,at_resid,from_idx,from_resid,connected_resids=[]):
 
         Ri=TC.get_R(at_idx)
         Rj=TC.get_R(from_idx)
+        logger.debug(f'Ri {at_idx} {Ri} {type(Ri)} {Ri.dtype}')
+        logger.debug(f'Rj {from_idx} {Rj} {type(Rj)} {Rj.dtype}')
         overall_maximum=(-1.e9,-1,-1)
         coord_trials={}
         for myH,myHnm in myHpartners.items():  # keys are globalIdx's, values are names
             coord_trials[myH]:dict[TopoCoord]={}
             Rh=TC.get_R(myH)
+            logger.debug(f'  Rh {myH} {Rh} {Rh.dtype}')
             Rih=Ri-Rh
             Rih*=1.0/np.linalg.norm(Rih)
             for otH,otHnm in otHpartners.items():
-                # logger.debug(f'{self.name}: Considering {myH} {otH}')
+                logger.debug(f'{self.name}: Considering {myH} {otH}')
                 coord_trials[myH][otH]=deepcopy(BTC)
-                # logger.debug(f'\n{coord_trials[myH][otH].Coordinates.A.to_string()}')
+                logger.debug(f'\n{coord_trials[myH][otH].Coordinates.A.to_string()}')
                 Rk=coord_trials[myH][otH].get_R(otH)
-                # logger.debug(f'{self.name}:    otH {otH} Rk {Rk}')
+                logger.debug(f'{self.name}:    otH {otH} Rk {Rk} {Rk.dtype}')
                 Rkj=Rk-Rj
                 Rkj*=1.0/np.linalg.norm(Rkj)
+                logger.debug(f'Rkj {Rkj} {Rkj.dtype} Rih {Rih} {Rih.dtype}')
                 #Rhk=Rh-Rk
                 #rhk=np.linalg.norm(Rhk)
                 cp=np.cross(Rkj,Rih)

HTPolyNet/runtime.py

@@ -517,7 +517,7 @@ def _initialize_topology(self,inpfnm='init'):
         logger.info(f'Topology "{inpfnm}.top" in {pfs.cwd()}')
         TC.write_top(f'{inpfnm}.top')
         TC.write_tpx(f'{inpfnm}.tpx')
-        return f'{inpfnm}.top'
+        return f'{inpfnm}.top',f'{inpfnm}.tpx'
 
     def _initialize_coordinates(self,inpfnm='init'):
         """_initialize_coordinates builds initial top and gro files for initial liquid simulation

HTPolyNet/topocoord.py

@@ -599,7 +599,7 @@ def write_top(self,topfilename):
 
     def write_tpx(self,tpxfilename):
         self.Topology.write_tpx(tpxfilename)
-        self.files['tpx']=os.path.apbspath(tpxfilename)
+        self.files['tpx']=os.path.abspath(tpxfilename)
 
     def write_gro(self,grofilename,grotitle=''):
         """write_gro Write a Gromacs-format coordinate file; wrapper for Coordinates.write_gro()

README.md

@@ -25,7 +25,7 @@ The programs ``antechamber``, ``parmchk2`` and ``tleap`` from AmberTools must be
 ## Release History
 
 * 1.0.8
-    * uses `chordless_cycles` to find rings
+    * uses `chordless_cycles` to find rings; ringidx no long unique atom attribute; improved ring-pierce detection
 * 1.0.7.2
     * moved Library package to resources subpackage of HTPolyNet.HTPolyNet
 * 1.0.6

pyproject.toml

@@ -26,7 +26,7 @@ dependencies = [
     "pandas>=2",
     "scipy>=1.10",
     "parmed>=4",
-    "networkx>=3.2s",
+    "networkx>=3.2",
     "gputil>=1.4"
 ]