correct doc links to moleuclekit

Author: stefdoerr

doc/source/tutorials/system-prep/04-stapled-peptide.md

@@ -19,7 +19,7 @@ kernelspec:
 - You've worked through {doc}`Build a protein with a ligand <02-protein-ligand>`.
 
 ```{note}
-The workflow below is **identical** to {doc}`Build a protein with a ligand <02-protein-ligand>` - the only change is the two extra SMILES strings you pass to `templateResidueFromSmiles` (one per NCAA). {py:func}`~moleculekit.tools.nonstandard_residues.detectNonStandardResidues` reads the staple bond from the input structure's connectivity on its own, and {py:func}`~htmd.builder.nonstandard.parameterizeFromSpecs` carries it through to the build without any extra wiring.
+The workflow below is **identical** to {doc}`Build a protein with a ligand <02-protein-ligand>` - the only change is the two extra SMILES strings you pass to {py:meth}`~moleculekit.molecule.Molecule.templateResidueFromSmiles` (one per NCAA). {py:func}`~moleculekit.tools.nonstandard_residues.detectNonStandardResidues` reads the staple bond from the input structure's connectivity on its own, and {py:func}`~htmd.builder.nonstandard.parameterizeFromSpecs` carries it through to the build without any extra wiring.
 ```
 
 ## What the staple is

doc/source/tutorials/system-prep/05-cyclic-peptide.md

@@ -19,7 +19,7 @@ kernelspec:
 - You've worked through {doc}`Build a protein with a ligand <02-protein-ligand>` - this tutorial builds on the same five-step flow.
 
 ```{note}
-The workflow below is **identical** to {doc}`Build a protein with a ligand <02-protein-ligand>` - the only change is the SMILES dictionary you pass to `templateResidueFromSmiles`. {py:func}`~moleculekit.tools.nonstandard_residues.detectNonStandardResidues` finds the non-canonical residues; the ring-closing peptide bond is added separately by `amber.build`'s cyclic-segment detector, which spots head-to-tail N-C distances under 1.35 Å in the input geometry and emits the closing `bond` directive itself.
+The workflow below is **identical** to {doc}`Build a protein with a ligand <02-protein-ligand>` - the only change is the SMILES dictionary you pass to {py:meth}`~moleculekit.molecule.Molecule.templateResidueFromSmiles`. {py:func}`~moleculekit.tools.nonstandard_residues.detectNonStandardResidues` finds the non-canonical residues; the ring-closing peptide bond is added separately by `amber.build`'s cyclic-segment detector, which spots head-to-tail N-C distances under 1.35 Å in the input geometry and emits the closing `bond` directive itself.
 ```
 
 ## What makes cyclic peptides interesting

doc/source/tutorials/system-prep/06-bicyclic-peptide.md

@@ -19,7 +19,7 @@ kernelspec:
 - You've worked through {doc}`Build a stapled peptide <04-stapled-peptide>` - this tutorial extends the same scaffolded-NCAA pattern.
 
 ```{note}
-The workflow below is **identical** to {doc}`Build a protein with a ligand <02-protein-ligand>` - the only change is the single SMILES you pass to `templateResidueFromSmiles` (for the LFI scaffold). {py:func}`~moleculekit.tools.nonstandard_residues.detectNonStandardResidues` reads the three `SG-Cn` thioether bonds and the three CYS chain-positions from the input structure's connectivity on its own, and {py:func}`~htmd.builder.nonstandard.parameterizeFromSpecs` emits a `custombonds` list and topology / parameter files which you still pass explicitly to {py:func}`~htmd.builder.amber.build` — same plumbing as tutorial 02.
+The workflow below is **identical** to {doc}`Build a protein with a ligand <02-protein-ligand>` - the only change is the single SMILES you pass to {py:meth}`~moleculekit.molecule.Molecule.templateResidueFromSmiles` (for the LFI scaffold). {py:func}`~moleculekit.tools.nonstandard_residues.detectNonStandardResidues` reads the three `SG-Cn` thioether bonds and the three CYS chain-positions from the input structure's connectivity on its own, and {py:func}`~htmd.builder.nonstandard.parameterizeFromSpecs` emits a `custombonds` list and topology / parameter files which you still pass explicitly to {py:func}`~htmd.builder.amber.build` — same plumbing as tutorial 02.
 ```
 
 ## What the bicycle is