update dox

ekwan · Jul 13, 2020 · d772a03 · d772a03
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diff --git a/docs/recipe_01.rst b/docs/recipe_01.rst
@@ -133,7 +133,7 @@ Writing Multiple Molecules to One Gaussian Input File
 Using Custom Basis Sets from the Basis Set Exchange
 """"""""""""""""""""""""""""""""""""""""""""""""""""
 
-- Bespoke basis sets can be downloaded automatically from the `Basis Set Exchange <https://www.basissetexchange.org/>`.
+- Bespoke basis sets can be downloaded automatically from the `Basis Set Exchange <https://www.basissetexchange.org/>` _.
 - By default, the ``add_custom_basis_set`` method appends the basis set to the footer. However, 
   passing the ``return_string`` option allows for increased control over formatting (e.g. for combination with ``opt=modredundant``).
 - The ``gen`` keyword should be used in combination with these basis sets.
@@ -149,3 +149,14 @@ Using Custom Basis Sets from the Basis Set Exchange
     basis = file2.add_custom_basis_set("pcseg-2", return_string=True)
     file2.footer = f"B 1 10 F\n\n{basis}"
 
+"""""""""""""""""""""""""""
+Creating Molecules By Name
+""""""""""""""""""""""""""
+
+- If ``rdkit`` is installed, then molecules can be created from a name or SMILES string. Structures should be checked for sanity!
+
+::
+
+    imatinib = cctk.Molecule.new_from_name("imatinib")
+
+    phcf3 = cctk.Molecule.new_from_smiles("C1=CC=C(C=C1)C(F)(F)F")
diff --git a/docs/recipe_03.rst b/docs/recipe_03.rst
@@ -1,7 +1,7 @@
 .. _recipe_03:
 
 ==========================================
-Measuring and Setting Internal Coordinates
+Manipulating Molecule Objects
 ==========================================
 
 - ``import cctk`` is assumed
@@ -29,6 +29,10 @@ Measuring Distances and Angles
     # alternately, all get_ or set_ methods will also take a list of atom numbers
     dihedral_angle = molecule.get_dihedral(atoms=[1, 2, 3, 4])
 
+
+    # you can also get the volume!
+    vol = molecule.volume()
+
 """"""""""""""""""""""""""""
 Setting Distances and Angles
 """"""""""""""""""""""""""""
@@ -80,4 +84,17 @@ Checking For Clashes
 
         no_clashes_present = molecule.check_for_conflicts()
         
+""""""""""""""""""""""""""""
+Generating Non-Ground States
+""""""""""""""""""""""""""""
+
+- The output of a frequency job can be used to generate molecules with realistic non-equilibrium geometries.
+
+::
+
+    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)
+
 
diff --git a/docs/recipe_04.rst b/docs/recipe_04.rst
@@ -57,5 +57,7 @@ Renumbering Molecules
     assert isinstance(mol1, cctk.Molecule)
     assert isinstance(mol2, cctk.Molecule)
 
+    assert cctk.Molecule.are_isomorphic(mol1, mol2)
+
     mol2 = mol2.renumber_to_match(mol1)
 
diff --git a/docs/recipe_06.rst b/docs/recipe_06.rst
@@ -41,9 +41,17 @@ Chemical Shifts
     # note: 1-indexed
     shieldings = ensemble[:,"isotropic_shielding"]
 
+    # can automatically detect symmetric atoms from methyl, isopropyl, or tert-butyl groups
+    molecule = ensemble.molecules[-1].assign_connectivity()
+    symmetric = molecule.get_symmetric_atoms() # [[32, 33, 34], [37, 38, 39]]
+
     # linearly scale to get shifts
-    scaled_shifts, shift_labels = cctk.helper_functions.scale_nmr_shifts(ensemble,
-                                  symmetrical_atom_numbers=[[37,38,39],[32,33,34]], scaling_factors="default")
+    scaled_shifts, shift_labels = cctk.helper_functions.scale_nmr_shifts(
+        ensemble,
+        symmetrical_atom_numbers=symmetric, 
+        scaling_factors="default"
+    )
+
     expected_shifts = [6.52352,6.6285,6.51045,6.53005,6.22303,2.11021,2.7025,2.73022,2.38541,2.35172,3.1467,5.82979,
                        3.29202,1.92326,114.924,98.3836,107.641,94.3333,104.421,109.795,95.1041,112.168,121.346,
                        45.4898,14.1014,26.7028,36.3779,29.4323,104.708,155.804,38.0661,109.579,22.7099]

diff --git a/docs/recipe_08.rst b/docs/recipe_08.rst
@@ -95,3 +95,24 @@ Epimerization
 
     # exchanges substituent atoms sub1 and sub2 (and attached groups) around atom center
     enantiomer = molecule.epimerize(center, sub1, sub2)
+
+
+"""""""""""""""""
+Detecting Groups
+""""""""""""""""
+
+- *cctk* can search within existing molecules for groups and return the relevant atom numbers.
+
+::
+
+    import cctk.topology as top
+    from cctk.load_groups import load_group
+
+    methyl = cctk.load_group("methyl")
+    camphor = cctk.Molecule.new_from_name("camphor").assign_connectivity()
+
+    top.find_group(camphor, methyl)
+    # returns a list of dictionaries
+    # each element is a mapping from atomic numbers of camphor (keys) to atomic numbers of the group (values)
+    # in this case, camphor contains 3 methyl groups, so there are 3 matches
+    # [{1: 1, 12: 3, 13: 4, 14: 5}, {3: 1, 16: 3, 17: 4, 15: 5}, {8: 1, 24: 3, 25: 4, 23: 5}]
diff --git a/setup.py b/setup.py
@@ -11,13 +11,13 @@
     packages=["cctk", "cctk.data", "cctk.groups"],
 #    include_package_data=True,
     package_data={"cctk.data": ["*"], "cctk.groups": ["*"],},
-    version="v0.2.4",
+    version="v0.2.5",
     license="Apache 2.O",
     description="computational chemistry toolkit",
     author="Corin Wagen and Eugene Kwan",
     author_email="corin.wagen@gmail.com",
     url="https://github.com/ekwan/cctk",
-    download_url="https://github.com/ekwan/cctk/archive/v0.2.4.tar.gz",
+    download_url="https://github.com/ekwan/cctk/archive/v0.2.5.tar.gz",
     install_requires=["numpy", "networkx", "importlib_resources", "scipy", "pyahocorasick", "basis_set_exchange"],
     long_description=long_description,
     long_description_content_type='text/markdown',