@@ -10,3 +10,24 @@ Information about compounds is captured in the :cpp:class:`cif::compound`. An in
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@@ -10,3 +10,24 @@ Information about compounds is captured in the :cpp:class:`cif::compound`. An in
If the compound you want to use is not available in the CCD or in CCP4, you can add that information yourself. For this you can use the method :cpp:func:`cif::compound_factory::push_dictionary`.
If the compound you want to use is not available in the CCD or in CCP4, you can add that information yourself. For this you can use the method :cpp:func:`cif::compound_factory::push_dictionary`.
So, given that we have CCD, CCP4 monomer library and used defined compound definitions, what will you get when you try to retrieve such a compound by ID? The answer is, the factory has a stack of compound generators. The first thrown on the stack is the one for a CCD file (*components.cif*) if it can be found. Then, if the *CLIBD_MON* environmental variable is defined, a generator for monomer library files is added to the stack. And then all generators for files you added using *push_dictionary* are added in order. The generators are searched in the reverse order in which they were added to see if it creates a compound object for the ID. If no compound was created at all, nullptr is returned.
So, given that we have CCD, CCP4 monomer library and used defined compound definitions, what will you get when you try to retrieve such a compound by ID? The answer is, the factory has a stack of compound generators. The first thrown on the stack is the one for a CCD file (*components.cif*) if it can be found. Then, if the *CLIBD_MON* environmental variable is defined, a generator for monomer library files is added to the stack. And then all generators for files you added using *push_dictionary* are added in order. The generators are searched in the reverse order in which they were added to see if it creates a compound object for the ID. If no compound was created at all, nullptr is returned.
Updating CCD
------------
The CCD data is stored in a single file called *components.cif* and can be downloaded from `CCD <https://www.wwpdb.org/data/ccd>`_.
As can be read in the section on resources (:doc:`/resources`) files in libcifpp are loaded in a specific order. If the CCD datafile was downloaded during installation, a copy can be found in the directory */usr/share/libcifpp/* (if you installed in */usr*). This is a static file and will not be updated until the next installation of libcifpp.
When configuring libcifpp, you can specify the *CIFPP_INSTALL_UPDATE_SCRIPT* option, as in:
.. code-block:: console
cmake -S . -B build -DCIFPP_INSTALL_UPDATE_SCRIPT=ON # ... more options?
This will install a script named *update-libcifpp-data* in */etc/cron.weekly* or */etc/periodic/weekly*. This file uses a config file named */etc/libcifpp.conf* which you then need to edit. In this config file the following line needs to be uncommented:
.. code-block:: console
# update=true
After that, the update script will weekly download the latest components.cif file to */var/cache/libcifpp*.
