Rosetta
2019.12
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#include <mmCIFParser.hh>
Public Member Functions | |
mmCIFParser () | |
virtual | ~mmCIFParser () |
utility::vector1 < sdf::MolFileIOMoleculeOP > | parse (std::string const &filename) |
parse the mmCIF file. This is generally used with the command line option -extra_res_mmCIF_fa. The mmCIF can contain multiple blocks that contain different residue paramaters. This will read each block and pushback to the MolFileIO object More... | |
sdf::MolFileIOMoleculeOP | parse (std::string const &lines, std::string const &pdb_id) |
parse a concatenated string (line) and create a MolFileIO object from the stream. Specificaly pull out the block from the pdb_id. This is used in conjection with streamed mmCIF files, ie, the lazy loader. More... | |
sdf::MolFileIOMoleculeOP | get_molfile_molecule (Block &block) |
-the secret sauce. Pull tables form the block segment to construct parameters return a MolFileIOMolecule More... | |
Private Attributes | |
std::map< std::string, core::Size > | bond_string_to_sdf_size_ |
When you are lazy, create a map of strings and sizes to convert the string for bonds found in the mmCIF file to the sdf version. More... | |
core::chemical::mmCIF::mmCIFParser::mmCIFParser | ( | ) |
References bond_string_to_sdf_size_.
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inlinevirtual |
sdf::MolFileIOMoleculeOP core::chemical::mmCIF::mmCIFParser::get_molfile_molecule | ( | Block & | block | ) |
-the secret sauce. Pull tables form the block segment to construct parameters return a MolFileIOMolecule
References bond_string_to_sdf_size_.
Referenced by parse().
utility::vector1< sdf::MolFileIOMoleculeOP > core::chemical::mmCIF::mmCIFParser::parse | ( | std::string const & | filename | ) |
parse the mmCIF file. This is generally used with the command line option -extra_res_mmCIF_fa. The mmCIF can contain multiple blocks that contain different residue paramaters. This will read each block and pushback to the MolFileIO object
References get_molfile_molecule().
Referenced by core::chemical::GlobalResidueTypeSet::attempt_readin(), and core::chemical::GlobalResidueTypeSet::extra_nonparam_restypes_from_commandline().
sdf::MolFileIOMoleculeOP core::chemical::mmCIF::mmCIFParser::parse | ( | std::string const & | lines, |
std::string const & | pdb_id | ||
) |
parse a concatenated string (line) and create a MolFileIO object from the stream. Specificaly pull out the block from the pdb_id. This is used in conjection with streamed mmCIF files, ie, the lazy loader.
References get_molfile_molecule().
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private |
When you are lazy, create a map of strings and sizes to convert the string for bonds found in the mmCIF file to the sdf version.
Referenced by get_molfile_molecule(), and mmCIFParser().