Module build

Perform a connect between the atoms in the CT "st" based on the heavy atoms in atomlist1 and those in atomlist2. Usually each list will contain one atom each, from different molecules. Hydrogens bound to the specified atoms are removed as necessary.

Returns a dictionary of atom renumbering. Keys are old atom numbers, values are new atom numbers (or None if the atom was deleted, i.e. a hydrogen).

Attach fragment <fragname> of group <fraggroup> to <fromatom> in place of atom <toatom> Will use growbond atom labels in the incoming fragment.

Optionally specify a <direction> string. Usually one of the following: 'forward', 'backward', 'forward(N-to-C)', 'backward(C-to-N)'.

Returns a dictionary of atom renumbering. Keys are old atom numbers, values are new atom numbers (or None if the atom was deleted, i.e. a hydrogen).

Similar to attach_fragment(), but takes a fragment CT instead of name. From and to atoms in the fragment must also be specified.

Returns a dictionary of renumbered atoms. Keys are old atom numbers, values are new atom numbers or None if the atom was deleted.

Mutate the residue containing atom number 'atom_in_res' in Structure object 'st' to be of residue type 'res_type'. The residue type must be one of the 20 amino acids (HIS/HIP/HIE variants are allowed). It's not an error if the residue is already of that type

Returns a dictionary of renumbered atoms. Keys are old atom numbers, values are new atom numbers or None if the atom was deleted.

Adds hydrogens to the Structure 'st'. 

Default treatment is suitable for nearly all purposes. Hydrogens are
added in standard geometry and no attempt is made to optimize the
treatment in order to maximize hydrogen bonds, etc. 

Parameters

atom_list
    A list of atom indices (or _StructureAtom objects) to add hydrogens to
    (default all atoms).

Create a new structure from the provided one, with atoms reordered as specified in the new_order list.

Parameters:

• new_order (list of ints) - The new_order list must be the same size as the number atoms in the provided structure, and atom indices begin at one.