Fix hbonds path (#4286)

Co-authored-by: Rocco Meli <r.meli@bluemail.ch>

package/CHANGELOG

@@ -13,7 +13,8 @@ The rules for this file:
   * release numbers follow "Semantic Versioning" http://semver.org
 
 ------------------------------------------------------------------------------
-??/??/?? IAlibay, ianmkenney, PicoCentauri, pgbarletta, p-j-smith, richardjgowers
+??/??/?? IAlibay, ianmkenney, PicoCentauri, pgbarletta, p-j-smith, richardjgowers,
+         lilyminium
 
  * 2.7.0
 
@@ -24,6 +25,7 @@ Fixes
     their original type value (np.float64 and np.nan) (PR #4272)
   * Fixes a case where qcprot.CalcRMSDRotationalMatrix would return a
     RMSD of None
+  * Fixes hydrogenbonds tutorial path to point to hbonds (Issue #4285, PR #4286)
 
 Enhancements
   * Updated lib.qcprot.CalcRMSDRotationalMatrix to accept either float32 or float64

package/MDAnalysis/analysis/hydrogenbonds/hbond_autocorrel.py

@@ -87,11 +87,11 @@
 ::
 
   import MDAnalysis as mda
-  from MDAnalysis.analysis import hbonds
+  from MDAnalysis.analysis import hydrogenbonds
   from MDAnalysis.tests.datafiles import waterPSF, waterDCD
   u = mda.Universe(waterPSF, waterDCD)
   hydrogens = u.select_atoms('name H*')
-  donors = hbonds.find_hydrogen_donors(hydrogens)
+  donors = hydrogenbonds.find_hydrogen_donors(hydrogens)
 
 
 Note that this requires the Universe to have bond information.  If this isn't
@@ -101,7 +101,7 @@
 ::
 
   import MDAnalysis as mda
-  from MDAnalysis.analysis import hbonds
+  from MDAnalysis.analysis import hydrogenbonds
   from MDAnalysis.tests.datafiles import GRO
   # we could load the Universe with guess_bonds=True
   # but this would guess **all** bonds
@@ -112,7 +112,7 @@
   water.guess_bonds()
   hydrogens = water.select_atoms('type H')
   # this is now possible as we guessed the bonds
-  donors = hbonds.find_hydrogen_donors(hydrogens)
+  donors = hydrogenbonds.find_hydrogen_donors(hydrogens)
 
 
 The keyword **exclusions** allows a tuple of array addresses to be provided,
@@ -166,7 +166,7 @@
 ::
 
   import MDAnalysis as mda
-  from MDAnalysis.analysis import hbonds
+  from MDAnalysis.analysis import hydrogenbonds
   from MDAnalysis.tests.datafiles import TRZ_psf, TRZ
   import matplotlib.pyplot as plt
   # load system
@@ -176,7 +176,7 @@
   N = u.select_atoms('name N')
   O = u.select_atoms('name O')
   # create analysis object
-  hb_ac = hbonds.HydrogenBondAutoCorrel(u,
+  hb_ac = hydrogenbonds.HydrogenBondAutoCorrel(u,
               acceptors=O, hydrogens=H, donors=N,
               bond_type='continuous',
               sample_time=2.0, nsamples=1000, nruns=20)
@@ -216,7 +216,7 @@
 from MDAnalysis.due import due, Doi
 due.cite(Doi("10.1063/1.4922445"),
          description="Hydrogen bonding autocorrelation time",
-         path='MDAnalysis.analysis.hbonds.hbond_autocorrel',
+         path='MDAnalysis.analysis.hydrogenbonds.hbond_autocorrel',
 )
 del Doi
 

package/MDAnalysis/analysis/hydrogenbonds/wbridge_analysis.py

@@ -271,18 +271,16 @@ class WaterBridgeAnalysis_OtherFF(WaterBridgeAnalysis):
 All water bridges between arginine and aspartic acid can be analysed with ::
 
   import MDAnalysis
-  import MDAnalysis.analysis.hbonds
+  from MDAnalysis.analysis.hydrogenbonds import WaterBridgeAnalysis
 
   u = MDAnalysis.Universe('topology', 'trajectory')
-  w = MDAnalysis.analysis.hbonds.WaterBridgeAnalysis(u, 'resname ARG',
-                                                     'resname ASP')
+  w = WaterBridgeAnalysis(u, 'resname ARG', 'resname ASP')
   w.run()
 
 The maximum number of bridging waters detected can be changed using the order
 keyword. ::
 
-  w = MDAnalysis.analysis.hbonds.WaterBridgeAnalysis(u, 'resname ARG',
-                                                     'resname ASP', order=3)
+  w = WaterBridgeAnalysis(u, 'resname ARG', 'resname ASP', order=3)
 
 Thus, a maximum of three bridging waters will be detected.
 

testsuite/MDAnalysisTests/utils/test_duecredit.py

@@ -58,8 +58,8 @@ def test_duecredit_collector_primary(self, module, path, citekey):
         ("MDAnalysis.analysis.psa",
          "MDAnalysis.analysis.psa",
          "10.1371/journal.pcbi.1004568"),
-        ("MDAnalysis.analysis.hbonds.hbond_autocorrel",
-         "MDAnalysis.analysis.hbonds.hbond_autocorrel",
+        ("MDAnalysis.analysis.hydrogenbonds.hbond_autocorrel",
+         "MDAnalysis.analysis.hydrogenbonds.hbond_autocorrel",
          "10.1063/1.4922445"),
         ("MDAnalysis.analysis.leaflet",
          "MDAnalysis.analysis.leaflet",