core::io::mmcif Namespace Reference

Typedefs
typedef std::string	String

Functions
static basic::Tracer	TR ("core.io.mmcif.cif_reader")
StructFileRepOP	create_sfr_from_cif_file_op (CifFileOP cifFile, StructFileReaderOptions const &options)
bool	dump_cif (core::pose::Pose const &pose, std::string const &file_name, StructFileRepOptionsCOP options)
	Dump an mmCIF from a pose to a file. Return success or failure. More...
StructFileRepOP	dump_cif (core::pose::Pose const &pose, std::ostream &out, StructFileRepOptionsCOP options)
	Dump an mmCIF from a pose to an ostream. More...
std::string	dump_cif (core::pose::Pose const &pose)
	Return an mmCIF-format string from a pose. More...
StructFileRepOP	dump_cif (core::pose::Pose const &pose, std::string const &jd2_job_data, utility::io::ozstream &out)
	Dump an mmCIF from a pose, optionally extracting extra info. More...
bool	dump_cif (std::string const &file_name, StructFileRepOP sfr, StructFileRepOptions const &options)
	Main dump_cif function. Create the sfr from pose using the PoseToStructFileRepConverter class. Return success or failure. More...
std::string	dump_cif (StructFileRepOP sfr, StructFileRepOptions const &options)
	Main dump_cif function. Return a string with contents of a CIF file, extracted from a Pose to a StructFileRep via PoseToStructFileRepConverter. More...
void	dump_cif (std::ostream &out, StructFileRepOP sfr, StructFileRepOptions const &options)
	Main dump_cif function. Create the sfr from pose using the PoseToStructFileRepConverter class. More...

Typedef Documentation

typedef std::string core::io::mmcif::String

Function Documentation

StructFileRepOP core::io::mmcif::create_sfr_from_cif_file_op	(	CifFileOP	cifFile,
		StructFileReaderOptions const &	options
	)

References core::io::CrystInfo::A(), core::io::CrystInfo::alpha(), core::io::AtomInformation::altLoc, core::io::CrystInfo::B(), core::io::CrystInfo::beta(), core::io::CrystInfo::C(), core::io::AtomInformation::chainID, core::io::LinkInformation::chainID1, core::io::SSBondInformation::chainID1, core::io::LinkInformation::chainID2, core::io::SSBondInformation::chainID2, core::io::AtomInformation::element, core::io::CrystInfo::gamma(), core::io::AtomInformation::iCode, core::io::LinkInformation::iCode1, core::io::SSBondInformation::iCode1, core::io::LinkInformation::iCode2, core::io::SSBondInformation::iCode2, core::io::AtomInformation::isHet, core::io::LinkInformation::length, core::io::SSBondInformation::length, core::io::AtomInformation::name, core::io::LinkInformation::name1, core::io::LinkInformation::name2, core::io::StructFileReaderOptions::new_chain_order(), core::io::StructFileReaderOptions::obey_ENDMDL(), core::io::AtomInformation::occupancy, core::io::StructFileRepOptions::read_only_ATOM_entries(), core::io::StructFileReaderOptions::read_pdb_header(), core::io::LinkInformation::resID1, core::io::SSBondInformation::resID1, core::io::LinkInformation::resID2, core::io::SSBondInformation::resID2, core::io::AtomInformation::resName, core::io::LinkInformation::resName1, core::io::SSBondInformation::resName1, core::io::LinkInformation::resName2, core::io::SSBondInformation::resName2, core::io::AtomInformation::resSeq, core::io::LinkInformation::resSeq1, core::io::SSBondInformation::resSeq1, core::io::LinkInformation::resSeq2, core::io::SSBondInformation::resSeq2, core::io::AtomInformation::segmentID, core::io::AtomInformation::serial, core::io::CrystInfo::spacegroup(), core::io::pdb::store_base_residue_type_name_in_sfr(), core::chemical::orbitals::strip_whitespace(), core::io::AtomInformation::temperature, core::io::AtomInformation::terCount, core::io::AtomInformation::x, core::io::AtomInformation::y, and core::io::AtomInformation::z.

Referenced by core::import_pose::pose_from_file().

bool core::io::mmcif::dump_cif	(	core::pose::Pose const &	pose,
		std::string const &	file_name,
		StructFileRepOptionsCOP	options
	)

Dump an mmCIF from a pose to a file. Return success or failure.

References core::io::pose_to_sfr::PoseToStructFileRepConverter::init_from_pose(), core::conformation::membrane::out, core::io::pose_to_sfr::PoseToStructFileRepConverter::sfr(), and TR().

Referenced by dump_cif(), core::pose::Pose::dump_cif(), core::pose::Pose::dump_file(), and protocols::jd2::mmCIFJobOutputter::dump_pose().

StructFileRepOP core::io::mmcif::dump_cif	(	core::pose::Pose const &	pose,
		std::ostream &	out,
		StructFileRepOptionsCOP	options
	)

Dump an mmCIF from a pose to an ostream.

Dump cif to an outstream, optionally passing options and returning a StructFileRep for further processing.

References dump_cif(), core::io::pose_to_sfr::PoseToStructFileRepConverter::init_from_pose(), and core::io::pose_to_sfr::PoseToStructFileRepConverter::sfr().

std::string core::io::mmcif::dump_cif

(

core::pose::Pose const &

pose

)

Return an mmCIF-format string from a pose.

Return an mmCIF-format string from a pose with defaults.

References dump_cif(), and core::conformation::membrane::out.

StructFileRepOP core::io::mmcif::dump_cif	(	core::pose::Pose const &	pose,
		std::string const &	jd2_job_data,
		utility::io::ozstream &	out
	)

Dump an mmCIF from a pose, optionally extracting extra info.

Dump an mmCIF from a pose, optionally extracting extra info. NOTE: DEPRECATED. LEGACY JD2 function to use JOB data, which we no longer use in JD3.

References dump_cif().

bool core::io::mmcif::dump_cif	(	std::string const &	file_name,
		StructFileRepOP	sfr,
		StructFileRepOptions const &	options
	)

Main dump_cif function. Create the sfr from pose using the PoseToStructFileRepConverter class. Return success or failure.

References dump_cif(), core::conformation::membrane::out, and TR().

std::string core::io::mmcif::dump_cif	(	StructFileRepOP	sfr,
		StructFileRepOptions const &	options
	)

Main dump_cif function. Return a string with contents of a CIF file, extracted from a Pose to a StructFileRep via PoseToStructFileRepConverter.

References dump_cif(), and core::conformation::membrane::out.

void core::io::mmcif::dump_cif	(	std::ostream &	out,
		StructFileRepOP	sfr,
		StructFileRepOptions const &	options
	)

Main dump_cif function. Create the sfr from pose using the PoseToStructFileRepConverter class.

References core::io::AtomInformation::altLoc, core::io::AtomInformation::chainID, core::io::AtomInformation::element, core::sequence::end, core::io::rcsb::experimental_technique_to_string(), core::io::AtomInformation::iCode, core::io::AtomInformation::isHet, core::io::AtomInformation::name, core::io::AtomInformation::occupancy, core::io::StructFileRepOptions::output_pose_cache(), core::io::StructFileRepOptions::output_pose_energies_table(), core::io::StructFileRepOptions::pdb_comments(), core::io::StructFileRepOptions::preserve_header(), core::io::AtomInformation::resName, core::io::AtomInformation::resSeq, core::io::AtomInformation::serial, core::io::AtomInformation::temperature, core::id::to_string(), core::io::AtomInformation::x, core::io::AtomInformation::y, and core::io::AtomInformation::z.

static basic::Tracer core::io::mmcif::TR ( "core.io.mmcif.cif_reader"  )

static

Referenced by dump_cif().