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Rosetta
2020.50
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#include <mol_writer.hh>
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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_ |
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core::chemical::sdf::MolWriter::MolWriter | ( | ) |
core::chemical::sdf::MolWriter::MolWriter | ( | std::string const & | ctab_mode | ) |
References ctab_mode_, V2000, and V3000.
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References core::chemical::MutableResidueType::all_atoms(), and core::chemical::MutableResidueType::atom_name().
Referenced by output_residue_impl().
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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().
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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().
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References job_data_.
Referenced by output_residue_impl().
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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().
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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().
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void core::chemical::sdf::MolWriter::output_residue | ( | std::ostream & | output_stream, |
core::conformation::ResidueCOP | residue | ||
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void core::chemical::sdf::MolWriter::output_residue | ( | std::ostream & | output_stream, |
core::chemical::ResidueTypeCOP | residue_type | ||
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References output_residue().
void core::chemical::sdf::MolWriter::output_residue | ( | std::ostream & | output_stream, |
core::chemical::MutableResidueTypeCOP | residue_type | ||
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References output_residue().
void core::chemical::sdf::MolWriter::output_residue | ( | std::ostream & | output_stream, |
core::conformation::Residue const & | residue | ||
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void core::chemical::sdf::MolWriter::output_residue | ( | std::ostream & | output_stream, |
core::chemical::ResidueType const & | residue_type | ||
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References output_residue_impl().
void core::chemical::sdf::MolWriter::output_residue | ( | std::ostream & | output_stream, |
core::chemical::MutableResidueType const & | residue_type | ||
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References output_residue_impl().
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References core::conformation::membrane::out, and output_residue().
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References job_data_.
Referenced by protocols::ligand_docking::WriteLigandMolFile::apply().
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Referenced by compose_atoms(), compose_bonds(), compose_ctab(), compose_metadata(), compose_properties(), MolWriter(), and output_residue_impl().
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Referenced by compose_job_info(), and set_job_data().
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Referenced by compose_atoms(), compose_bonds(), and compose_ctab().