API Build

add_bonds(molecular_system, bonded_atom_pairs)	Adding covalent bonds between atom pairs in a molecular system.
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_missing_terminal_cappings(molecular_system)	Adding terminal cappings to peptides and proteins.
build_peptide(molecular_system[, to_form, ...])	Building a peptide from a sequence.
define_new_chain(molecular_system[, ...])	Defining a new chain from selected atoms.
get_disulfide_bonds(molecular_system[, ...])	Identifying disulfide bonds between sulfur atoms.
get_missing_bonds(molecular_system[, ...])	To be written soon...
get_missing_heavy_atoms(molecular_system[, ...])	To be written soon...
get_missing_residues(molecular_system[, ...])	To be written soon...
get_missing_terminal_cappings(molecular_system)	To be written soon...
get_non_standard_residues(molecular_system)	To be written soon...
has_hydrogens(molecular_system[, selection, ...])	Check whether a molecular system (or selection) contains hydrogen atoms.
is_solvated(molecular_system[, skip_digestion])	To be written soon...
make_bioassembly(molecular_system[, ...])	To be written soon...
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, ...])	To be written soon...
remove_bonds(molecular_system[, ...])	Remove bonds from a molecular system by index.
remove_overlapping_molecules(...[, ...])	Removing molecules that overlap a reference selection within a distance threshold.
solvate(molecular_system[, box_shape, ...])	To be written soon...
solve_atoms_with_alternate_location(...[, ...])	To be written soon...