DomainAssemblerNDocker Class Reference

Public Member Functions
	DomainAssemblerNDocker ()
	Constructor parses command line and sets up the job. More...
void	run ()
	DomainAssemblerNDocker ()
	Constructor parses command line and sets up the job. More...
void	run ()

Private Member Functions
void	setup_cen_domains (std::istream &input)
	reads PDB files for domains and copies dihedrals onto a blank pose More...

Private Attributes
core::io::silent::SilentFileData	sfd_out
std::string	sequence_
core::pose::Pose	cen_pose_
core::kinematics::MoveMapOP	movemap_
core::fragment::FragSetOP	fragset_large_
core::fragment::FragSetOP	fragset_small_
core::pose::Pose	native_pose_
bool	has_native_
utility::vector1< Size >	loop_pos_
utility::vector1< Size >	loop_len_
core::pose::Pose	fa_pose_

Constructor & Destructor Documentation

DomainAssemblerNDocker() [1/2]

DomainAssemblerNDocker::DomainAssemblerNDocker ( )

inline

Constructor parses command line and sets up the job.

References in::file::fasta(), in::file::frag3(), in::file::frag9(), in::file::fragA(), in::file::fragB(), in::file::native(), basic::options::OptionKeys::abinitio::number_3mer_frags, basic::options::OptionKeys::abinitio::number_9mer_frags, option, pyrosetta.distributed.io::pose_from_file, basic::options::OptionKeys::inout::dbms::user, and utility_exit_with_message.

DomainAssemblerNDocker() [2/2]

DomainAssemblerNDocker::DomainAssemblerNDocker ( )

inline

Constructor parses command line and sets up the job.

References in::file::frag3(), in::file::frag9(), in::file::fragA(), in::file::fragB(), in::file::native(), basic::options::OptionKeys::abinitio::number_3mer_frags, basic::options::OptionKeys::abinitio::number_9mer_frags, option, pyrosetta.distributed.io::pose_from_file, in::file::s(), and basic::options::OptionKeys::inout::dbms::user.

Member Function Documentation

run() [1/2]

void DomainAssemblerNDocker::run ( )

inline

References basic::options::OptionKeys::abinitio::abinitio, create_a3b_hbs::i, out::nooutput(), out::nstruct(), option, out::file::silent(), and challenge::ss.

run() [2/2]

void DomainAssemblerNDocker::run ( )

inline

References basic::options::OptionKeys::abinitio::abinitio, basic::options::OptionKeys::dna::specificity::fast, create_a3b_hbs::i, create_a3b_hbs::j, ObjexxFCL::lead_zero_string_of(), ObjexxFCL::len(), out::nooutput(), out::nstruct(), option, make_symmdef_file_denovo::pos, out::file::silent(), challenge::ss, and basic::options::OptionKeys::inout::dbms::user.

setup_cen_domains()

void DomainAssemblerNDocker::setup_cen_domains ( std::istream &  input )

inlineprivate

reads PDB files for domains and copies dihedrals onto a blank pose

References basic::Tracer::Debug, PREcst::fname, getline(), gaussian-sampling::input, line, make_symmdef_file_denovo::pos, pyrosetta.distributed.io::pose_from_file, pna::resi, basic::options::OptionKeys::cmiles::jumping::resj, and TR.

Member Data Documentation

cen_pose_

core::pose::Pose DomainAssemblerNDocker::cen_pose_

private

fa_pose_

core::pose::Pose DomainAssemblerNDocker::fa_pose_

private

fragset_large_

core::fragment::FragSetOP DomainAssemblerNDocker::fragset_large_

private

fragset_small_

core::fragment::FragSetOP DomainAssemblerNDocker::fragset_small_

private

has_native_

bool DomainAssemblerNDocker::has_native_

private

loop_len_

utility::vector1<Size> DomainAssemblerNDocker::loop_len_

private

loop_pos_

utility::vector1<Size> DomainAssemblerNDocker::loop_pos_

private

movemap_

core::kinematics::MoveMapOP DomainAssemblerNDocker::movemap_

private

native_pose_

core::pose::Pose DomainAssemblerNDocker::native_pose_

private

sequence_

std::string DomainAssemblerNDocker::sequence_

private

sfd_out

core::io::silent::SilentFileData DomainAssemblerNDocker::sfd_out

private

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The documentation for this class was generated from the following files:

• src/apps/pilot/dgront/DomainAssemblerNDocker.cc
• src/apps/pilot/dgront/saxs/linker_sampler.cc