actions.write_structure() — write out the model coordinates

write_structure(skip, filepattern, write_all_atoms=True, first=False, last=False, start=0)

This action writes out a file containing the current optimizer structure, every skip steps during the optimization. It should be specified in the actions argument to an optimizer object (e.g., conjugate_gradients() or molecular_dynamics()).

filepattern is a C-style format string, used to construct filenames. It should contain a %d format, which is substituted with the model number (e.g., specifying 'file%d.pdb' would generate files called 'file0.pdb', 'file1.pdb', 'file2.pdb', etc). The model number will start with start (or 0, if not given).

If write_all_atoms is True (the default) then all atoms in the model are written out to the structure file, whether or not they are selected. If False, only selected atoms are written out.

If first is True, then the structure at step 0 (before the optimization) is also written out. If last is True, then the structure of the last step is written, regardless of whether it is a multiple of skip. By default, both are False.

Example: See conjugate_gradients() command.