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core::chemical::mmCIF::mmCIFParser Class Reference

#include <mmCIFParser.hh>

Inheritance diagram for core::chemical::mmCIF::mmCIFParser:
Inheritance graph
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Public Member Functions

 mmCIFParser ()
 
 ~mmCIFParser () override
 
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::Sizebond_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...
 

Constructor & Destructor Documentation

core::chemical::mmCIF::mmCIFParser::mmCIFParser ( )
core::chemical::mmCIF::mmCIFParser::~mmCIFParser ( )
inlineoverride

Member Function Documentation

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().

Member Data Documentation

std::map< std::string, core::Size> core::chemical::mmCIF::mmCIFParser::bond_string_to_sdf_size_
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().


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