added more groups, rearranged tutorials, started working on consisten…

…t 1-indexing

cctk/__init__.py

@@ -1,5 +1,5 @@
 from .file import File
-from .molecule import Molecule
+from .molecule import Molecule, OneIndexedArray
 from .ensemble import Ensemble, ConformationalEnsemble
 from .group import Group
 

cctk/ensemble.py

@@ -63,13 +63,6 @@ def batch_add(self, atomic_numbers, geometries, bonds=None, charges=None, multip
         if bonds is None:
             bonds = [None] * len(atomic_numbers)
 
-        print(len(geometries))
-        print(len(atomic_numbers))
-        print(len(bonds))
-        print(bonds)
-        print(len(charges))
-        print(charges)
-        print(len(multiplicities))
         assert all(
             len(x) == len(atomic_numbers) for x in [geometries, bonds, charges, multiplicities]
         ), "uneven list lengths -- cannot batch create molecules!"
@@ -78,7 +71,6 @@ def batch_add(self, atomic_numbers, geometries, bonds=None, charges=None, multip
             if len(numbers) != len(geometry):
                 raise TypeError("atoms and geometries must be the same length!")
 
-            print(charge)
             mol = Molecule(numbers, geometry, bonds=bond_edges, charge=charge, multiplicity=multiplicity)
             self.add_molecule(mol)
 

cctk/gaussian_file.py

@@ -238,8 +238,6 @@ def read_file(cls, filename, return_lines=False):
 
         #### parameters don't get printed every time for opt jobs
         if JobType.OPT in job_types:
-            print(bonds)
-            print(bonds[0])
             bonds = np.repeat(np.array([bonds[0]]), len(atomic_numbers)-1, axis=0).tolist() + [bonds[-1]]
             charge = list(np.tile(np.array(charge[0]), len(atomic_numbers)-1)) + [charge[-1]]
             multip = list(np.tile(np.array(multip[0]), len(atomic_numbers)-1)) + [multip[-1]]
@@ -387,13 +385,19 @@ def get_molecule(self, num=None):
         return self.molecules.molecules[num]
 
     @classmethod
-    def write_ensemble_to_file(cls, filename, ensemble, header, **kwargs):
+    def write_ensemble_to_file(cls, filename, ensemble, headers, kwargs):
         """
         Writes an Ensemble to a file using Link1 specification.
+
+        Args:
+            filename (str): where to write the file
+            ensemble (Ensemble): ``Ensemble`` object to write
+            headers (list): headers for each ``write_molecule_to_file`` call
+            kwargs (list of dict): arguments for each ``write_molecule_to_file`` call
         """
         for idx, molecule in enumerate(ensemble.molecules):
             if idx == 0:
-                self.write_molecule_to_file(filename, molecule, header, append=False, **kwargs)
+                cls.write_molecule_to_file(filename, molecule, headers[idx], append=False, **kwargs[idx])
             else:
-                self.write_molecule_to_file(filename, molecule, header, append=True, **kwargs)
+                cls.write_molecule_to_file(filename, molecule, headers[idx], append=True, **kwargs[idx])
 

cctk/group.py

@@ -128,9 +128,10 @@ def add_group_to_molecule(molecule, group, add_to):
         ), f"molecule has {len(molecule.atomic_numbers)} atoms but {len(molecule.geometry)} geometry elements!"
 
         #### now we want to find the "lowest" energy conformation, defined as the rotamer which minimizes the RMS distance between all atoms
-        adjacent_on_old_molecule = molecule.get_adjacent_atoms(adjacent_atom)[0]
-        adjacent_on_new_molecule = molecule.get_adjacent_atoms(add_to)[-1]
-        molecule.optimize_dihedral(adjacent_on_old_molecule, adjacent_atom, add_to, adjacent_on_new_molecule)
+        if group.num_atoms() > 3:
+            adjacent_on_old_molecule = molecule.get_adjacent_atoms(adjacent_atom)[0]
+            adjacent_on_new_molecule = molecule.get_adjacent_atoms(add_to)[-1]
+            molecule.optimize_dihedral(adjacent_on_old_molecule, adjacent_atom, add_to, adjacent_on_new_molecule)
 
         try:
             molecule.check_for_conflicts()

cctk/groups/AcH.mol2

@@ -0,0 +1,29 @@
+# Molecule Name
+# Created by GaussView 6.0.16
+#
+
+#
+#
+
+@<TRIPOS>MOLECULE
+Molecule Name
+7 6
+SMALL
+NO_CHARGES
+
+
+@<TRIPOS>ATOM
+1 C1    -1.0756    -1.3886     0.0424 C
+2 H2    -1.6678    -0.4492     0.0405 H
+3 O3     0.1828    -1.3886     0.0445 O
+4 C4    -1.8969    -2.6913     0.0425 C
+5 H5    -2.9404    -2.4551     0.0428 H
+6 H6    -1.6605    -3.2620    -0.8312 H
+7 H7    -1.6602    -3.2621     0.9161 H
+@<TRIPOS>BOND
+1 1 2 1
+2 1 3 2
+3 1 4 1
+4 4 5 1
+5 4 6 1
+6 4 7 1

cctk/groups/BrH.mol2

@@ -0,0 +1,19 @@
+# Molecule Name
+# Created by GaussView 6.0.16
+#
+
+#
+#
+
+@<TRIPOS>MOLECULE
+Molecule Name
+2 1
+SMALL
+NO_CHARGES
+
+
+@<TRIPOS>ATOM
+1 Br1     0.2861     0.4087     0.0000 Br
+2 H2    -1.1539     0.4087     0.0000 H
+@<TRIPOS>BOND
+1 1 2 1

cctk/groups/CHOH.mol2

@@ -0,0 +1,23 @@
+# Molecule Name
+# Created by GaussView 6.0.16
+#
+
+#
+#
+
+@<TRIPOS>MOLECULE
+Molecule Name
+4 3
+SMALL
+NO_CHARGES
+
+
+@<TRIPOS>ATOM
+1 C1    -1.0756    -1.3886     0.0424 C
+2 H2    -1.6678    -0.4492     0.0424 H
+3 H3    -1.6678    -2.3280     0.0425 H
+4 O4     0.1828    -1.3886     0.0424 O
+@<TRIPOS>BOND
+1 1 2 1
+2 1 3 1
+3 1 4 2

cctk/groups/ClH.mol2

@@ -0,0 +1,19 @@
+# Molecule Name
+# Created by GaussView 6.0.16
+#
+
+#
+#
+
+@<TRIPOS>MOLECULE
+Molecule Name
+2 1
+SMALL
+NO_CHARGES
+
+
+@<TRIPOS>ATOM
+1 Cl1     0.2861     0.4087     0.0000 Cl
+2 H2    -1.0039     0.4087     0.0000 H
+@<TRIPOS>BOND
+1 1 2 1

cctk/groups/FH.mol2

@@ -0,0 +1,19 @@
+# Title
+# Created by GaussView 6.0.16
+#
+
+#
+#
+
+@<TRIPOS>MOLECULE
+Molecule Name
+2 1
+SMALL
+NO_CHARGES
+
+
+@<TRIPOS>ATOM
+1 F1     0.2861     0.4087     0.0000 F
+2 H2    -0.5939     0.4087     0.0000 H
+@<TRIPOS>BOND
+1 1 2 1

cctk/groups/IH.mol2

@@ -0,0 +1,19 @@
+# Molecule Name
+# Created by GaussView 6.0.16
+#
+
+#
+#
+
+@<TRIPOS>MOLECULE
+Molecule Name
+2 1
+SMALL
+NO_CHARGES
+
+
+@<TRIPOS>ATOM
+1 I1     0.2861     0.4087     0.0000 I
+2 H2    -1.3439     0.4087     0.0000 H
+@<TRIPOS>BOND
+1 1 2 1

cctk/groups/NMe2H.mol2

@@ -13,23 +13,23 @@ NO_CHARGES
 
 
 @<TRIPOS>ATOM
-1 C1    -0.7671     1.9489     0.0000 C
-2 H2    -0.4107     2.4535    -0.8737 H
-3 H3    -1.8371     1.9483     0.0000 H
-4 H4    -0.4107     2.4535     0.8737 H
-5 N5    -0.2764     0.5632     0.0000 N
-6 H6     0.7236     0.5638    -0.0018 H
-7 C7    -0.7638    -0.1292     1.2016 C
-8 H8    -1.8338    -0.1294     1.2038 H
-9 H9    -0.4070    -1.1380     1.2014 H
-10 H10    -0.4054     0.3757     2.0743 H
+1 N1    -0.2764     0.5632     0.0000 N
+2 H2     0.7236     0.5638    -0.0018 H
+3 C3    -0.7638    -0.1292     1.2016 C
+4 H4    -1.8338    -0.1294     1.2038 H
+5 H5    -0.4054     0.3757     2.0743 H
+6 H6    -0.4070    -1.1380     1.2014 H
+7 C7    -0.7671     1.9489     0.0000 C
+8 H8    -0.4122     2.4529    -0.8746 H
+9 H9    -1.8371     1.9483     0.0019 H
+10 H10    -0.4091     2.4540     0.8727 H
 @<TRIPOS>BOND
 1 1 2 1
 2 1 3 1
-3 1 4 1
-4 1 5 1
-5 5 6 1
-6 5 7 1
+3 1 7 1
+4 3 4 1
+5 3 5 1
+6 3 6 1
 7 7 8 1
 8 7 9 1
 9 7 10 1

cctk/groups/SF5H.mol2

@@ -0,0 +1,29 @@
+# Molecule Name
+# Created by GaussView 6.0.16
+#
+
+#
+#
+
+@<TRIPOS>MOLECULE
+Molecule Name
+7 6
+SMALL
+NO_CHARGES
+
+
+@<TRIPOS>ATOM
+1 S1     0.2861     0.4087     0.0000 S
+2 H2     1.5961     0.4087     0.0000 H
+3 F3     0.2861    -1.1813     0.0000 F
+4 F4    -1.3039     0.4087     0.0000 F
+5 F5     0.2861     0.4087     1.5900 F
+6 F6     0.2861     0.4087    -1.5900 F
+7 F7     0.2861     1.9987     0.0000 F
+@<TRIPOS>BOND
+1 1 2 1
+2 1 3 1
+3 1 4 1
+4 1 5 1
+5 1 6 1
+6 1 7 1

cctk/groups/SO3HH.mol2

@@ -0,0 +1,27 @@
+# Molecule Name
+# Created by GaussView 6.0.16
+#
+
+#
+#
+
+@<TRIPOS>MOLECULE
+Molecule Name
+6 5
+SMALL
+NO_CHARGES
+
+
+@<TRIPOS>ATOM
+1 S1     0.2861     0.4087     0.0000 S
+2 H2     1.4395     0.8503    -0.4367 H
+3 O3     0.0384    -1.1462    -0.5567 O
+4 O4     0.2861     0.4087     1.6700 O
+5 O5    -0.9366     1.4006    -0.5567 O
+6 H6    -0.5604     2.1046    -1.0901 H
+@<TRIPOS>BOND
+1 1 2 1
+2 1 3 1
+3 1 4 1
+4 1 5 1
+5 5 6 1

cctk/load_groups.py

@@ -24,28 +24,50 @@
     "HCN.mol2",
     "HNO2.mol2",
     "HCO2Me.mol2",
+    "FH.mol2",
+    "ClH.mol2",
+    "BrH.mol2",
+    "IH.mol2",
+    "SF5H.mol2",
+    "SO3HH.mol2",
+    "AcH.mol2",
+    "CHOH.mol2",
 ]
 
 names = [
-    "methyl",
-    "ethyl",
-    "isopropyl",
-    "tert-butyl",
-    "hydroxy",
-    "methoxy",
-    "acetamido",
-    "amino",
-    "dimethylamino",
-    "trifluoromethyl",
-    "cyano",
-    "nitro",
-    "carboxylmethyl",
+    ["methyl", "Me", "CH3",],
+    ["ethyl", "Et", "C2H5",],
+    ["isopropyl", "iPr", "iC3H7",],
+    ["tert-butyl", "tBu", "tC4H9",],
+    ["hydroxy", "OH",],
+    ["methoxy", "MeO", "OMe", "CH3O",],
+    ["acetamido", "NHAc",],
+    ["amino", "NH2",],
+    ["dimethylamino", "Me2N", "NMe2",],
+    ["trifluoromethyl", "CF3",],
+    ["cyano", "CN",],
+    ["nitro", "NO2",],
+    ["carboxylmethyl", "MeO2C", "CO2Me",],
+    ["fluoro", "F",],
+    ["chloro", "Cl",],
+    ["bromo", "Br",],
+    ["iodo", "I",],
+    ["pentafluorosulfanyl", "SF5",],
+    ["sulfonyl", "SO3H",],
+    ["acetyl", "Ac", "COMe",],
+    ["formyl", "CHO",],
 ]
 
 
 def load_group(name):
-    assert name in names, f"can't find group {name}!"
-    filename = filenames[names.index(name)]
+    filename = None
+
+    for row in names:
+        if name in row:
+            filename = filenames[names.index(row)]
+            break
+
+    assert filename is not None, f"can't find name {name}!"
 
     with pkg_resources.path(groups, filename) as file:
         mol = MOL2File.read_file(file).molecules[0]