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Rosetta
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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 <core/select/util/SelectResiduesByLayer.hh>#include <core/pose/symmetry/util.hh>#include <protocols/parser/BluePrint.hh>#include <protocols/flxbb/utility.hh>#include <utility>#include <utility/string_util.hh>#include <utility/tag/Tag.hh>#include <utility/tag/XMLSchemaGeneration.hh>#include <core/pack/task/operation/task_op_schemas.hh>#include <utility/vector1.hh>#include <string>#include <algorithm>#include <boost/foreach.hpp>#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>Namespaces | |
| protocols | |
| The instance of Loops contained by AbrelaxApplication should be replaced by a LoopsOP. | |
| protocols::flxbb | |
Functions | |
| static basic::Tracer | TR ("protocols.flxbb.LayerDesignOperation") |
| template<class T > | |
| LayerDesignOperation::LayerDefinitions | protocols::flxbb::makeMap (T const &map_initializer) |
| std::string | protocols::flxbb::print_string_vector (utility::vector1< std::string > const &vect) |
| Utility function to convert a string vector into a comma-separated list of strings. More... | |
| std::string | protocols::flxbb::layer_design_ss_layer_naming_func (std::string const &element_name) |
| std::string | protocols::flxbb::layer_design_ss_layer_group () |
| std::string | protocols::flxbb::layer_design_ss_layer_or_taskop_group () |
| std::string | protocols::flxbb::unique_chars (std::string const &orig) |
| returns a string containing sorted, unique residue one-letter codes More... | |
| utility::vector1< std::string > | protocols::flxbb::unique_strs (utility::vector1< std::string > const &orig, utility::vector1< std::string > const &orig2) |
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.
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1.9.1