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

#include <mmCIFParser.hh>

Inheritance diagram for core::chemical::mmCIF::mmCIFParser:

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::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...

Constructor & Destructor Documentation

core::chemical::mmCIF::mmCIFParser::mmCIFParser

(

)

References bond_string_to_sdf_size_.

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().

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

• src/core/chemical/mmCIF/mmCIFParser.hh
• src/core/chemical/mmCIF/mmCIFParser.cc