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_missing_terminal_cappings(molecular_system)

Adding terminal cappings to peptides and proteins.

build_peptide(molecular_system[, to_form, ...])

Building a peptide from a sequence.

get_disulfide_bonds(molecular_system[, ...])

Identifying disulfide bonds between sulfur atoms.

get_missing_bonds(molecular_system[, ...])

Identify bonds that are present in the chemical structure but absent from the topology.

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.

has_hydrogens(molecular_system[, selection, ...])

Check whether a molecular system (or selection) 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, ...])

Apply point mutations to one or more residues of a molecular system.

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.