LayerDesignOperation.cc File Reference

Design residues with selected amino acids depending on the enviroment: layer. The layer of each residue is assigned as core, boundary, or surface, which are defined by accessible surface of mainchain + CB. More...

#include <protocols/flxbb/LayerDesignOperation.hh>
#include <protocols/flxbb/LayerDesignOperationCreator.hh>
#include <core/pose/Pose.hh>
#include <core/conformation/Residue.hh>
#include <core/pack/task/PackerTask_.hh>
#include <core/pack/task/PackerTask.hh>
#include <core/scoring/dssp/Dssp.hh>
#include <core/pack/task/operation/TaskOperationFactory.hh>
#include <basic/Tracer.hh>
#include <protocols/toolbox/SelectResiduesByLayer.hh>
#include <core/pose/symmetry/util.hh>
#include <basic/datacache/DataMap.hh>
#include <protocols/jd2/parser/BluePrint.hh>
#include <protocols/flxbb/utility.hh>
#include <utility/string_util.hh>
#include <utility/tag/Tag.hh>
#include <utility/vector1.hh>
#include <algorithm>
#include <utility/vector0.hh>
#include <utility/io/ozstream.hh>
#include <utility/file/file_sys_util.hh>
#include <ObjexxFCL/format.hh>
#include <basic/options/keys/OptionKeys.hh>
#include <boost/assign/list_inserter.hpp>
#include <boost/assign/list_of.hpp>
#include <boost/foreach.hpp>
#include <boost/lexical_cast.hpp>

Namespaces
	protocols
	The instance of Loops contained by AbrelaxApplication should be replaced by a LoopsOP.
	protocols::flxbb

Functions
static thread_local basic::Tracer	TR ("protocols.flxbb.LayerDesignOperation")
template<class T >
LayerDesignOperation::LayerDefinitions	protocols::flxbb::makeMap (T const &map_initializer)

Detailed Description

Design residues with selected amino acids depending on the enviroment: layer. The layer of each residue is assigned as core, boundary, or surface, which are defined by accessible surface of mainchain + CB.

If ignore_pikaa_natro(true) is invoked, then if a resfile is read before calling this operation, this operation is not applied for the residues defined by PIKAA. Note that this breaks TaskOperation commutativity, so it is NOT the default behaviour. In RosettaScripts, the option ignore_pikaa_natro=true can be added to the <LayerDesign> tag to turn this on.

Author

Nobuyasu Koga ( nobuy.nosp@m.asu@.nosp@m.uw.ed.nosp@m.u ) Javier Castellanos (javie.nosp@m.rcv@.nosp@m.uw.ed.nosp@m.u ) Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu) – support for noncanonicals.

Function Documentation

static thread_local basic::Tracer TR ( "protocols.flxbb.LayerDesignOperation"  )

static