Merge branch 'master' of github.com:ekwan/cctk

ekwan · Aug 9, 2020 · 1d5fc05 · 1d5fc05
2 parents 4e6bb8d + 7d2386c
commit 1d5fc05
Show file tree

Hide file tree

Showing 4 changed files with 6 additions and 5 deletions.
diff --git a/cctk/mol2_file.py b/cctk/mol2_file.py
@@ -305,7 +305,7 @@ def write_molecule_to_file(cls, filename, molecule, title=None, append=False):
         assert isinstance(molecule, Molecule), "molecule is not a valid Molecule object!"
 
         text = f"# {title}\n#\n#\n\n#\n#\n\n"
-        text += f"@<TRIPOS>MOLECULE\nMolecule Name\n{molecule.num_atoms()} {molecule.bonds.number_of_edges()}\nSMALL\nNO_CHARGES\n\n\n"
+        text += f"@<TRIPOS>MOLECULE\n{title}\n{molecule.num_atoms()} {molecule.bonds.number_of_edges()}\nSMALL\nNO_CHARGES\n\n\n"
         text += "@<TRIPOS>ATOM\n"
         for idx, z in enumerate(molecule.atomic_numbers, start=1):
             v = molecule.get_vector(idx)

diff --git a/docs/recipe_01.rst b/docs/recipe_01.rst
@@ -59,7 +59,7 @@ Reading a Gaussian Output File
 
     # following is equivalent to file.get_molecule()
     ensemble = file.ensemble
-    molecule = file.molecules[-1]
+    molecule = ensemble.molecules[-1]
 
     # get the molecular properties dictionary
     properties_dict = ensemble.get_properties_dict(molecule)

diff --git a/docs/recipe_03.rst b/docs/recipe_03.rst
@@ -95,6 +95,6 @@ Generating Non-Ground States
     import cctk.quasiclassical as qc
 
     # returns a new Molecule object and the energy above the ground state, sampled from the relevant Boltzmann distribution
-    perturbed_molecule, energy = qc.get_quasiclassical_perturbation(molecule, temp=350)
+    perturbed_molecule, energy = qc.get_quasiclassical_perturbation(molecule, temperature=350)
 
 
diff --git a/docs/recipe_07.rst b/docs/recipe_07.rst
@@ -58,11 +58,12 @@ MOL2 Files
     len(ensemble) == 597
 
     # write one structure
+    filename2 = "my_filename.mol2"
     cctk.MOL2File.write_molecule_to_file(filename2, molecule, title)
-    write_molecule_to_file(cls, filename, molecule, title=None):
 
     # write multiple structures
-    cctk.MOL2File.write_ensemble_to_file(filename2, ensemble)
+    filename3 = "your_filename.mol2"
+    cctk.MOL2File.write_ensemble_to_file(filename3, ensemble)
 
 - Setting ``print_status_messages`` to ``True`` will print progress to stdout.
 - For large files that contain only conformers, set ``contains_conformers`` to ``True``.