zinc1_homodimer_setup.cc File Reference

Grafts a 2-residue + zinc match onto the match's scaffold, duplicates the pose, then performs two discrete flips (rollmoves) to the second chain that generates a symmetric pose with a tetrahedral metal binding site. More...

#include <devel/init.hh>
#include <protocols/metal_interface/MatchGrafter.hh>
#include <protocols/metal_interface/FindClosestAtom.hh>
#include <protocols/rigid/RollMover.hh>
#include <protocols/moves/Mover.hh>
#include <core/pose/Pose.hh>
#include <core/pose/PDBInfo.hh>
#include <core/import_pose/import_pose.hh>
#include <core/conformation/Conformation.hh>
#include <basic/Tracer.hh>
#include <utility/vector1.hh>
#include <utility/file/FileName.hh>
#include <numeric/xyzVector.hh>
#include <numeric/conversions.hh>
#include <numeric/xyz.io.hh>
#include <core/kinematics/FoldTree.hh>
#include <core/kinematics/Jump.hh>
#include <core/io/pdb/pose_io.hh>
#include <core/conformation/Residue.hh>
#include <core/chemical/util.hh>
#include <core/chemical/VariantType.hh>
#include <basic/options/util.hh>
#include <basic/options/option.hh>
#include <protocols/jd2/JobDistributor.hh>

Go to the source code of this file.

Classes
class	zinc1_homodimer_setup

Typedefs
typedef numeric::xyzVector < core::Real >	point
typedef point	axis
typedef utility::pointer::owning_ptr < zinc1_homodimer_setup >	zinc1_homodimer_setupOP

Functions
static THREAD_LOCAL basic::Tracer	TR ("apps.public.design.zinc1_homodimer_setup")
int	main (int argc, char *argv[])

Variables
basic::options::StringOptionKey const	scaffold_pdb ("scaffold_pdb")

Detailed Description

Grafts a 2-residue + zinc match onto the match's scaffold, duplicates the pose, then performs two discrete flips (rollmoves) to the second chain that generates a symmetric pose with a tetrahedral metal binding site.

Takes a 2-residue + zinc match as -s or -l, requires the scaffold pdb indicated as an option. The first flip (rollmove) is along the axis that connects p1 with p2 (p1 is an xyzVector one zinc-coordinating atom), and zinc is translated to the origin at the time of the flip. The second rollmove is along the axis that bisects the p1:p2 and p3:p4. This protocol preceeds SymMetalInterface_OneZN_design.cc

Definition in file zinc1_homodimer_setup.cc.

Typedef Documentation

typedef point axis

Definition at line 55 of file zinc1_homodimer_setup.cc.

typedef numeric::xyzVector<core::Real> point

Definition at line 54 of file zinc1_homodimer_setup.cc.

typedef utility::pointer::owning_ptr< zinc1_homodimer_setup > zinc1_homodimer_setupOP

Definition at line 173 of file zinc1_homodimer_setup.cc.

Function Documentation

int main	(	int	argc,
		char *	argv[]
	)

Definition at line 175 of file zinc1_homodimer_setup.cc.

References utility::options::OptionCollection::add(), utility::io::oc::cout, utility::options::ScalarOption_T_< K, T >::def(), devel::init(), utility::excn::EXCN_Base::msg(), basic::options::option, scaffold_pdb, and TR().

static THREAD_LOCAL basic::Tracer TR ( "apps.public.design.zinc1_homodimer_setup"  )

static

Referenced by zinc1_homodimer_setup::apply(), and main().

Variable Documentation

basic::options::StringOptionKey const scaffold_pdb("scaffold_pdb")

Referenced by APDBCMover::APDBCMover(), zinc1_homodimer_setup::apply(), and main().