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/*! \page p_develop Developing using Clipper
\section s_fftexam An FFT example
Most crystallographic calculations are based upon the observed data,
i.e structure factors, phase probability estimates, and associated
data. This page describes how to read observed structure factors and
phases from an MTZ file, and perform a Fourier transformation to obtain
an electron density map.
For reflection data to be meaningful, a cell, spacegroup, and
resolution limit must first be defined. This can be achieved by
defining a Spacegroup object (clipper::Spacegroup), a Cell object
(clipper::Cell), and a resolution object (clipper::Resolution), and
using them to create a reflection list (clipper::HKL_info). However,
in this case the cell, spacegroup and resolution will be imported from
the MTZ file, so it is not necessary to set their values. Therefore an
uninitialised clipper::HKL_info object is created using the null
constructor.
\code
clipper::HKL_info myhkl();
\endcode
If we want to calculate a map, we need a structure factor and
phase. So we'll create a data list of type \c F_phi . The data list
must refer to a reflection list, so we pass our clipper::HKL_info
object to the constructor.
\code
clipper::HKL_data<clipper::data32::F_phi> fphidata( myhkl );
\endcode
Next, we want to open an MTZ file. I'll assume it is called \c my.mtz
. To do this we create an \c clipper::MTZfile object. This is an i/o
object which can be linked to an MTZ file by an open command, and can
then fill Clipper data objects using the information from that file.
\code
clipper::CCP4MTZfile mtzin;
mtzin.open_read( "my.mtz" ); // open new file
\endcode
When we created the reflection list object, we did not provide a cell
or spacegroup, or generate a reflection list. So we'll get those from
the file now.
\code
mtzin.import_hkl_info( myhkl ); // read sg, cell, reso, hkls
\endcode
Now we want some actual data. We read a couple of MTZ columns into the
data list we created earlier.
\code
mtzin.import_hkl_data( fphidata, "/native/CuKa/[FCAL,PHICAL]" );
\endcode
Note that we create the data-list as a child of the reflection list \c
myhkl . (Actually, any descendent will do). The import operation will
actually move it, by inserting the appropriate \c CCrystal and \c
CDataset objects, according to the information on the file.
Note also that we give specify the MTZ columns by giving the full
path: crystal, dataset, and column names. The column names are grouped
in square brackets. (For older MTZ files, which do not have crystal
and dataset entries, the dummy names "unnamed_crystal" and
"unnamed_dataset" are used.)
Now we close the MTZ file. \b NOTE: No data is actually read until you
close the file!
\code
mtzin.close_read();
\endcode
Next, we create a map. For this we need to provide a grid. The grid
depends on the spacegroup, cell, and resolution, which we get from the
reflection list:
\code
clipper::Grid_sampling mygrid( myhkl.spacegroup(), myhkl.cell(), myhkl.resolution() ); // define grid
\endcode
Now we make the map itself, using the spacegroup, cell, and grid.
\code
clipper::Xmap<float> mymap( myhkl.spacegroup(), myhkl.cell(), mygrid ); // define map
\endcode
Next, we calculate the map by FFT.
\code
mymap.fft_from( fphidata ); // generate map
\endcode
Finally, then map is written out to an output file.
\code
clipper::CCP4MAPfile mapout;
mapout.open_write( "my.map" ); // write map
mapout.export_xmap( mymap );
mapout.close_write();
\endcode
To summarise, here is the complete program:
\code
clipper::HKL_info myhkl;
clipper::HKL_data<clipper::data32::F_phi> fphidata( myhkl );
clipper::CCP4MTZfile mtzin;
mtzin.open_read( "my.mtz" ); // open new file
mtzin.import_hkl_info( myhkl ); // read sg, cell, reso, hkls
mtzin.import_hkl_data( fphidata, "/native/CuKa/[FCAL,PHICAL]" );
mtzin.close_read();
clipper::Grid_sampling mygrid( myhkl.spacegroup(), myhkl.cell(), myhkl.resolution() ); // define grid
clipper::Xmap<float> mymap( myhkl.spacegroup(), myhkl.cell(), mygrid ); // define map
mymap.fft_from( fphidata ); // generate map
clipper::CCP4MAPfile mapout;
mapout.open_write( "my.map" ); // write map
mapout.export_xmap( mymap );
mapout.close_write();
\endcode
\section s_incl Libraries and Include files
Which header and library files should you include in your application?
The libraries are as follows, and there is an aggregated header file
for each library.
<table>
<tr>
<td> <b>Contents</b>
<td> <b>Library</b>
<td> <b>Include</b>
<tr>
<td> Reflection, maps, models
<td> $PREFIX/lib/libclipper.a
<td> $PREFIX/include/clipper/clipper.h
<tr>
<td> Function objects (e.g. SFcalc)
<td> $PREFIX/lib/libclipper-contrib.a
<td> $PREFIX/include/clipper/clipper-contrib.h
<tr>
<td> CCP4 mtz/map i/o
<td> $PREFIX/lib/libclipper-ccp4.a
<td> $PREFIX/include/clipper/clipper-ccp4.h
<tr>
<td> SHELX phs i/o
<td> $PREFIX/lib/libclipper-phs.a
<td> $PREFIX/include/clipper/clipper-phs.h
<tr>
<td> cctbx interface
<td> $PREFIX/lib/libclipper-cctbx.a
<td> $PREFIX/include/clipper/clipper-cctbx.h
</table>
Alternatively, you can include individual header files from the
subdirectories of include/clipper/. The precise header files can be
identified by the following include tree:
\image html include.png
\image latex include.eps \width=10cm
*/
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