API Build

add_missing_bonds(molecular_system[, ...])	Adding missing covalent bonds based on atomic distances and types.
add_missing_heavy_atoms(molecular_system[, ...])	Adding missing non-hydrogen atoms to a molecular system.
add_missing_hydrogens(molecular_system[, ...])	Adding missing hydrogen atoms to a molecular system.
add_terminal_atoms(molecular_system, ...[, ...])	Adding terminal atoms to existing groups in a new native system.
add_missing_terminal_cappings(molecular_system)	Adding terminal cappings to peptides and proteins.
assign_autodock_atom_types(molecular_system, ...)	Assigning full named AutoDock labels to a detached single-state MolSys.
assign_partial_charges(molecular_system, method)	Assigning validated full-atom charges to a detached single-state MolSys.
build_peptide(molecular_system[, to_form, ...])	Building a peptide from a sequence.
editable([molecular_system, skip_digestion])	Creating an editable molecular-system builder.
get_disulfide_bonds(molecular_system[, ...])	Identifying candidate disulfide bonds between sulfur atoms.
get_covalent_bond_candidates(molecular_system)	Getting bounded covalent candidates from exact group templates.
get_peptide_bond_candidates(molecular_system)	Getting bounded backbone C-N distance candidates without changing chemistry.
get_missing_bonds(molecular_system[, ...])	Identifying candidate missing covalent bonds.
get_missing_heavy_atoms(molecular_system[, ...])	Identify heavy (non-hydrogen) atoms that are missing from residues in a molecular system.
get_missing_residues(molecular_system[, ...])	Identify residues that are missing from a molecular system relative to a reference sequence.
get_missing_terminal_cappings(molecular_system)	Identify terminal capping atoms that are missing from chain termini in a molecular system.
get_non_standard_residues(molecular_system)	Identify non-standard residues in a molecular system and suggest standard replacements.
get_residue_chemical_coverage(molecular_system)	Assessing stored residue chemistry against exact supported templates.
has_hydrogens(molecular_system[, selection, ...])	Checking if a molecular system or selected subset contains hydrogen atoms.
is_solvated(molecular_system[, skip_digestion])	Check whether a molecular system is solvated with an explicit solvent box.
make_bioassembly(molecular_system[, ...])	Construct the biological assembly of a molecular system from its asymmetric unit.
make_water_box(box[, form, skip_digestion])	Building an SPC/E water box from a reference tile, supporting triclinic cells.
mutate(molecular_system[, mutations, keys, ...])	Applying amino-acid substitutions with explicit reconstruction limits.
remove_overlapping_molecules(...[, ...])	Removing molecules that overlap a reference selection within a distance threshold.
solvate(molecular_system[, box_shape, ...])	Solvate a molecular system by surrounding it with explicit water molecules and ions.
solve_atoms_with_alternate_location(...[, ...])	Resolving alternate-location atoms in selected structures.