core::chemical::sdf::MolWriter Class Reference

#include <mol_writer.hh>

Public Member Functions
	MolWriter ()
	MolWriter (std::string const &ctab_mode)
void	output_residue (std::ostream &output_stream, core::conformation::ResidueCOP residue)
void	output_residue (std::ostream &output_stream, core::chemical::ResidueTypeCOP residue_type)
void	output_residue (std::ostream &output_stream, core::chemical::MutableResidueTypeCOP residue_type)
void	output_residue (std::ostream &output_stream, core::conformation::Residue const &residue)
void	output_residue (std::ostream &output_stream, core::chemical::ResidueType const &residue_type)
void	output_residue (std::ostream &output_stream, core::chemical::MutableResidueType const &residue_type)
template<class Input_t >
void	output_residue (std::string const &file_name, Input_t &residue)
void	set_job_data (std::map< std::string, std::string > const &job_data)

Private Types
enum	CtabMode { V2000, V3000 }

Private Member Functions
std::ostream &	open_file (std::string const &file_name) const
void	output_residue_impl (std::ostream &output_stream, core::chemical::MutableResidueType const &residue_type, std::map< std::string, core::Vector > const &coords={})
std::list< std::string >	compose_metadata (core::chemical::MutableResidueType const &residue)
std::list< std::string >	compose_ctab (core::chemical::MutableResidueType const &residue, std::map< std::string, core::Vector > const &coords)
std::list< std::string >	compose_atoms (core::chemical::MutableResidueType const &residue, std::map< std::string, core::Vector > const &coords)
std::list< std::string >	compose_bonds (core::chemical::MutableResidueType const &residue)
std::list< std::string >	compose_properties (core::chemical::MutableResidueType const &residue)
std::list< std::string >	compose_atomnames (core::chemical::MutableResidueType const &residue)
std::list< std::string >	compose_typeinfo (core::chemical::MutableResidueType const &residue)
std::list< std::string >	compose_nbr_atom (core::chemical::MutableResidueType const &residue)
std::list< std::string >	compose_naming (core::chemical::MutableResidueType const &residue)
std::list< std::string >	compose_rosetta_properties (core::chemical::MutableResidueType const &residue)
std::list< std::string >	compose_job_info ()

Private Attributes
std::string const	line_header_
std::map< std::string, std::string >	job_data_
CtabMode	ctab_mode_

Member Enumeration Documentation

enum core::chemical::sdf::MolWriter::CtabMode

private

Enumerator
V2000
V3000

Constructor & Destructor Documentation

core::chemical::sdf::MolWriter::MolWriter

(

)

core::chemical::sdf::MolWriter::MolWriter

(

std::string const &

ctab_mode

)

References ctab_mode_, V2000, and V3000.

Member Function Documentation

std::list< std::string > core::chemical::sdf::MolWriter::compose_atomnames ( core::chemical::MutableResidueType const &  residue )

private

References core::chemical::MutableResidueType::all_atoms(), and core::chemical::MutableResidueType::atom_name().

Referenced by output_residue_impl().

std::list< std::string > core::chemical::sdf::MolWriter::compose_atoms ( core::chemical::MutableResidueType const &  residue, std::map< std::string, core::Vector > const &  coords  )

private

References core::chemical::MutableResidueType::all_atoms(), core::chemical::MutableResidueType::atom(), core::chemical::MutableResidueType::atom_index(), core::chemical::MutableResidueType::atom_name(), core::chemical::MutableResidueType::atom_type(), core::chemical::MutableResidueType::bonded_hydrogens(), core::chemical::MutableResidueType::bonded_neighbors(), core::chemical::Atom::charge(), ctab_mode_, core::chemical::AtomType::element(), core::chemical::Atom::ideal_xyz(), core::chemical::Atom::is_hydrogen(), core::sequence::left, line_header_, protocols::kinmatch::str(), core::id::to_string(), V2000, and V3000.

Referenced by compose_ctab().

std::list< std::string > core::chemical::sdf::MolWriter::compose_bonds ( core::chemical::MutableResidueType const &  residue )

private

References core::chemical::MutableResidueType::all_atoms(), core::chemical::MutableResidueType::atom_index(), core::chemical::MutableResidueType::bond(), core::chemical::Bond::bond_name(), core::chemical::MutableResidueType::bonded_neighbors(), ctab_mode_, line_header_, protocols::kinmatch::str(), V2000, and V3000.

Referenced by compose_ctab().

std::list< std::string > core::chemical::sdf::MolWriter::compose_ctab ( core::chemical::MutableResidueType const &  residue, std::map< std::string, core::Vector > const &  coords  )

private

References compose_atoms(), compose_bonds(), compose_properties(), ctab_mode_, line_header_, core::chemical::MutableResidueType::natoms(), core::chemical::MutableResidueType::nbonds(), and V3000.

Referenced by output_residue_impl().

std::list< std::string > core::chemical::sdf::MolWriter::compose_job_info ( )

private

References job_data_.

Referenced by output_residue_impl().

std::list< std::string > core::chemical::sdf::MolWriter::compose_metadata ( core::chemical::MutableResidueType const &  residue )

private

References ctab_mode_, core::chemical::ResidueTypeBase::name(), core::chemical::ResidueTypeBase::name3(), core::chemical::MutableResidueType::natoms(), core::chemical::MutableResidueType::nbonds(), protocols::kinmatch::str(), and V2000.

Referenced by output_residue_impl().

std::list< std::string > core::chemical::sdf::MolWriter::compose_naming ( core::chemical::MutableResidueType const &  residue )

private

References protocols::cluster::calibur::aa, core::chemical::ResidueTypeBase::aa(), core::chemical::aa_unk, core::chemical::ResidueTypeBase::interchangeability_group(), core::chemical::ResidueTypeBase::name(), core::chemical::ResidueTypeBase::name1(), and core::chemical::ResidueTypeBase::name3().

Referenced by output_residue_impl().

std::list< std::string > core::chemical::sdf::MolWriter::compose_nbr_atom ( core::chemical::MutableResidueType const &  residue )

private

References core::chemical::MutableResidueType::atom_index(), core::chemical::MutableResidueType::nbr_radius(), core::chemical::MutableResidueType::nbr_vertex(), and core::id::to_string().

Referenced by output_residue_impl().

std::list< std::string > core::chemical::sdf::MolWriter::compose_properties ( core::chemical::MutableResidueType const &  residue )

private

References core::chemical::MutableResidueType::all_atoms(), core::chemical::MutableResidueType::atom(), core::chemical::MutableResidueType::atom_index(), protocols::match::upstream::b, ctab_mode_, core::sequence::end, core::chemical::Atom::formal_charge(), protocols::kinmatch::str(), and V3000.

Referenced by compose_ctab().

std::list< std::string > core::chemical::sdf::MolWriter::compose_rosetta_properties ( core::chemical::MutableResidueType const &  residue )

private

References core::chemical::ResidueProperties::get_list_of_properties(), core::chemical::ResidueTypeBase::properties(), and update_ResidueType_enum_files::properties.

Referenced by output_residue_impl().

std::list< std::string > core::chemical::sdf::MolWriter::compose_typeinfo ( core::chemical::MutableResidueType const &  residue )

private

References core::chemical::MutableResidueType::all_atoms(), core::chemical::MutableResidueType::atom_index(), core::chemical::MutableResidueType::atom_type(), and core::chemical::AtomType::name().

Referenced by output_residue_impl().

std::ostream& core::chemical::sdf::MolWriter::open_file ( std::string const &  file_name ) const

private

void core::chemical::sdf::MolWriter::output_residue	(	std::ostream &	output_stream,
		core::conformation::ResidueCOP	residue
	)

Referenced by protocols::ligand_docking::WriteLigandMolFile::apply(), output_residue(), and core::chemical::sdf::output_residue().

void core::chemical::sdf::MolWriter::output_residue	(	std::ostream &	output_stream,
		core::chemical::ResidueTypeCOP	residue_type
	)

References output_residue().

void core::chemical::sdf::MolWriter::output_residue	(	std::ostream &	output_stream,
		core::chemical::MutableResidueTypeCOP	residue_type
	)

References output_residue().

void core::chemical::sdf::MolWriter::output_residue	(	std::ostream &	output_stream,
		core::conformation::Residue const &	residue
	)

References core::conformation::Residue::atom_name(), protocols::simple_filters::coords(), core::conformation::Residue::natoms(), output_residue_impl(), core::conformation::Residue::type(), and core::conformation::Residue::xyz().

void core::chemical::sdf::MolWriter::output_residue	(	std::ostream &	output_stream,
		core::chemical::ResidueType const &	residue_type
	)

References output_residue_impl().

void core::chemical::sdf::MolWriter::output_residue	(	std::ostream &	output_stream,
		core::chemical::MutableResidueType const &	residue_type
	)

References output_residue_impl().

template<class Input_t >

void core::chemical::sdf::MolWriter::output_residue ( std::string const &  file_name, Input_t &  residue  )

inline

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

void core::chemical::sdf::MolWriter::output_residue_impl ( std::ostream &  output_stream, core::chemical::MutableResidueType const &  residue_type, std::map< std::string, core::Vector > const &  coords = {}  )

private

References compose_atomnames(), compose_ctab(), compose_job_info(), compose_metadata(), compose_naming(), compose_nbr_atom(), compose_rosetta_properties(), compose_typeinfo(), ctab_mode_, update_ResidueType_enum_files::properties, and V2000.

Referenced by output_residue().

void core::chemical::sdf::MolWriter::set_job_data ( std::map< std::string, std::string > const &  job_data )

inline

References job_data_.

Referenced by protocols::ligand_docking::WriteLigandMolFile::apply().

Member Data Documentation

CtabMode core::chemical::sdf::MolWriter::ctab_mode_

private

Referenced by compose_atoms(), compose_bonds(), compose_ctab(), compose_metadata(), compose_properties(), MolWriter(), and output_residue_impl().

std::map<std::string,std::string> core::chemical::sdf::MolWriter::job_data_

private

Referenced by compose_job_info(), and set_job_data().

std::string const core::chemical::sdf::MolWriter::line_header_

private

Referenced by compose_atoms(), compose_bonds(), and compose_ctab().

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

• src/core/chemical/sdf/mol_writer.hh
• src/core/chemical/sdf/mol_writer.cc