@@ -161,6 +161,50 @@ Returning a complete set if often not required, if you only want to have the fir
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@@ -161,6 +161,50 @@ Returning a complete set if often not required, if you only want to have the fir
There are cases when you really need exactly one result. The :cpp:func:`cif::category::find1` can be used in that case, it will throw an exception if the query does not result in exactly one row.
There are cases when you really need exactly one result. The :cpp:func:`cif::category::find1` can be used in that case, it will throw an exception if the query does not result in exactly one row.
NULL and ANY
------------
Sometimes items may be empty. The trouble is a bit that empty comes in two flavors: unknown and null. Null in *CIF* parlance means the item should not contain a value since it makes no sense in this case, the value stored in the file is a single dot character: ``'.'``. E.g. *atom_site* records may have a NULL value for label_seq_id for atoms that are part of a *non-polymer*.
The other empty value is indicated by a question mark character: ``'?'``. This means the value is simply unknown.
Both these are NULL in *libcifpp* conditions and can be searched for using :cpp:var:`cif::null`.
So you can search for:
.. code-block:: cpp
cif::condition c = "label_seq_id"_key == cif::null;
You might also want to look for a certain value and don't care in which item it is stored, in that case you can use :cpp:var:`cif::any`.
.. code-block:: cpp
cif::condition c = cif::any == "foo";
And in linked record you might have the items that have a value in both parent and child or both should be NULL. For that, you can request the value to return by find to be of type std::optional and then use that value to build the query. An example to explain this, let's find the location of the atom that is referenced as the first atom in a struct_conn record:
.. code-block:: cpp
// Take references to the two categories we need
auto struct_conn = db["struct_conn"];
auto atom_site = db["atom_site"];
// Loop over all rows in struct_conn taking only the values we need
// Note that the label_seq_id is returned as a std::optional<int>
// That means it may contain an integer or may be empty
for (const auto &[asym1, seqid1, authseqid1, atomid1] :
Although Quaternions are the preferred way of doing rotations, not every manipulation is a rotation and thus we need a matrix class as well. Matrices and their operations are encoded as matrix_expressions in *libcifpp* allowing the compiler to generate very fast code. See the :ref:`file_cif++_matrix.hpp` for what is on offer.
Although Quaternions are the preferred way of doing rotations, not every manipulation is a rotation and thus we need a matrix class as well. Matrices and their operations are encoded as matrix_expressions in *libcifpp* allowing the compiler to generate very fast code. See the :ref:`file_cif++_matrix.hpp` for what is on offer.
Crystals
--------
The *CIF* and *mmCIF* were initially developed to store crystallographic information on structures. Apart from coordinates and the chemical information the crystallographic information is important. This information can be split into two parts, a unit cell and a set of :ref:`symmetry-ops` making up a spacegroup. The spacegroup number and name are stored in the *symmetry* category. The corresponding symmetry operations can be obtained in *libcifpp* by using the :cpp:class:`cif::spacegroup`. The cell is stored in the category *cell* and likewise can be loaded using the :cpp:class:`cif::cell`. Together these two classes make up a crystal and so we have a :cpp:class:`cif::crystal` which contains both. You can easily create such a crystal object by passing the datablock containing the data to the constructor. As in:
.. code:: cpp
// Load the file
cif::file f("1cbs.cif.gz");
auto &db = f.front();
cif::crystal c(db);
.. _symmetry-ops:
Symmetry operations
Symmetry operations
-------------------
-------------------
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@@ -31,21 +45,28 @@ To give an idea how this works, here's a piece of code copied from one of the un
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@@ -31,21 +45,28 @@ To give an idea how this works, here's a piece of code copied from one of the un
.. code:: cpp
.. code:: cpp
using namespace cif::literals;
// Load the file
// Load the file
cif::file f(gTestDir / "2bi3.cif.gz");
cif::file f(gTestDir / "2bi3.cif.gz");
// Simply assume we can use the first datablock
auto &db = f.front();
auto &db = f.front();
cif::mm::structure s(db);
// Load the crystal information
cif::crystal c(db);
cif::crystal c(db);
// Take references to the two categories we need
auto struct_conn = db["struct_conn"];
auto struct_conn = db["struct_conn"];
auto atom_site = db["atom_site"];
// Loop over all rows in struct_conn taking only the values we need
