| Molecular Model |
| =============== |
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| Theoretically it is possible to get along with only the classes *cif::file*, *cif::datablock* and *cif::category*. But to keep your data complete and valid you then have to update lots of categories for all but the simplest manipulations. For this *libcifpp* comes with a higher level API modelling atoms, residues, monomers, polymers and complete structures in their respective classes. |
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| Note that these classes only work properly if you are using *mmCIF* files and have an mmcif_pdbx dictionary available, either compiled in using `mrc <https://github.com/mhekkel/mrc.git>`_ or installed in the proper location. |
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| .. note:: |
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| This part of *libcifpp* is the least developed part. What is available should work but functionality should eventually be extended. |
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| Atom |
| ---- |
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| The :cpp:class:`cif::mm::atom` is a lightweight proxy class giving access to the data stored in *atom_site* and *atom_site_anisotrop*. It only caches the most often used item data and every modification is directly written back into the *mmCIF* categories. |
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| Atoms can be copied by value with low cost. The atom class only contains a pointer to an implementation that is reference counted. |
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| Residue, Monomer and Polymer |
| ---------------------------- |
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| The :cpp:class:`cif::mm::residue`, :cpp:class:`cif::mm::monomer` and :cpp:class:`cif::mm::polymer` implement what you'd expect. A monomer is a residue that is part of a polymer and thus has a sequence number and siblings. |
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| Sugars & Branches |
| ----------------- |
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| There are also classes for modelling sugars and sugar branches. You can create sugar branches |
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| Structure |
| --------- |
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| The :cpp:class:`cif::mm::structure` can be used to load one of the models from an *mmCIF* file. By default the first model is loaded. (Multiple models are often only available files containing structures defined using NMR). |
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| A structure holds a reference to a *cif::datablock* and retrieves its data from this datablock and writes any modification back into that datablock. |
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| One of the most useful parts of the structure class is the ability to create and modify residues. This updates related *chem_comp* and *entity* categories as well. |
