Build

Assign autodock atom types	Attaching named chemical type provenance to a detached single-state MolSys
Assign partial charges	Attaching a validated full-atom mechanical assignment to a detached MolSys
Add fixed-state ligand hydrogens	Materializing a prepared H inventory while retaining the source pose
Add terminal atoms	Appending declared atoms with full-frame coordinates and stable original indices
Add missing bonds	Adding the missing bonds in a molecular system
Add missing heavy atoms	Adding the missing heavy atoms in a molecular system
Add missing hydrogens	Adding the missing hydrogen atoms in a molecular system
Add missing terminal cappings	Adding the missing terminal cappings in a molecular system
Build peptide	Building a peptide
Editable	Creating an editable molecular system builder to modify or construct topologies
Get disulfide bonds	Identifying structure-specific disulfide candidates and using the build wrapper
Get covalent bond candidates	Inspecting exact heavy-group templates and explicit candidate coverage
Get peptide bond candidates	Reviewing adjacent source-group C–N evidence and exclusions
Infer covalent bonds	Applying supported native candidates with persisted historical provenance
Get missing bonds	Getting the missing bonds of a molecular system
Get missing heavy atoms	Getting the missing heavy atoms of a molecular system
Get missing residues	Getting the missing residues of a molecular system
Get missing terminal cappings	Getting the missing terminal cappings of a molecular system
Get non standard residues	Getting the non standard residues of a molecular system
Get residue chemical coverage	Comparing stored residue chemistry with exact supported templates
Has hydrogens	Checking if a molecular system has hydrogen atoms
Is solvated	Checking if a molecular system is solvated
Make bioassembly	Making a bioassembly of a molecular system
Make water box	Making a water box system
Mutate	Mutating residues in a molecular system
Remove overlapping molecules	Removing overlapping molecules in a molecular system
Solvate	Solvating of a molecular system
Solve atoms with alternate location	Solving the coordinates of atoms with alternate locations in a molecular system