Store a data item from within an SD file. Data items begin with a line of the form "> <ITEM_NAME>" (additional specifications are possible), end with a single blank line, and can contain customized format information. The information will be read as a series of raw strings, one per line and each representing a whole line. Once read, member functions of the class can extract specific integer, real, char4, or string coded data from within the item. More...

#include <mdlmol_dataitem.h>

Public Member Functions
bool	placeInternalRegnoInHeader () const
	Indicate whether to display the internal identification number (based on the position of the molecule in the SD file) in the header line.

bool	placeExternalRegnoInHeader () const
	Indicate whether to display the (user-supplied) external identification number in the header line.

bool	placeTitleInHeader () const
	Indicate whether to display the data item name (title) in the header line, between angular brackets.

bool	placeMaccsIIFieldInHeader () const
	Indicate whether to display the MACCS-II field number in the header.

bool	noteArchivesInHeader () const
	Indicate that the "FROM ARCHIVES" tag should go in the header line.

const std::string &	getItemName () const
	Get a const reference to the item name, if it exists. If there is no item name, a const reference to a blank string will be returned.

const std::string &	getOutputItemName () const
	Get a const reference to the output item name, if it exists. If there is no item name, a const reference to a blank string will be returned.

const std::string &	getExternalRegistryNumber () const
	Get the external registry number.

int	getInternalRegistryNumber () const
	Get the internal registry number. This will return -1 if no such registry number exists.

int	getMaccsFieldNumber () const
	Get the MACCS-II database field number.

StateVariable	getTrackedState () const
	Get the state variable enumeration for this data item. This is used in the case of a STATE_VARIABLE kind of data item, to signal that a particular component of the molecular mechanics energy, or some intensive or expansive system property, should be retrieved.

int	getDataLineCount () const
	Get the data line count.

const std::string &	getDataLine (const int line_index) const
	Get a particular data lines from the item body.

const std::vector< std::string > &	getBody () const
	Get all data lines.

MdlMolDataItemKind	getKind () const
	Get the custom data item type. Here, the "NATIVE" code indicates that no custom enumeration is present.

void	setItemName (const std::string &item_name_in, ModificationPolicy mpol=ModificationPolicy::DO_NOT_MODIFY, ExceptionResponse notify=ExceptionResponse::WARN)
	Set the item name and apply checks to the result.

void	addDataLine (const std::string &text)
	Add a line to the data item.


	MdlMolDataItem (const std::string &item_name_in=std::string(""), const std::string &external_regno_in=std::string(""), int internal_regno_in=-1, int maccs_ii_number_in=-1, uint header_info=0U, const std::vector< std::string > &body_in={}, ModificationPolicy mpol=ModificationPolicy::DO_NOT_MODIFY, ExceptionResponse notify=ExceptionResponse::WARN)
	The constructor takes the original text file and the number of the first line of the data item, or the information pertinent to the header line and a series of strings that will form the body of data in the item. Any information submitted as part of a string such as an atom or bond index, which could then go to an output file, must be in the Fortran array indexing (starting at 1). Integer information read from the data body can be adjusted to meet internal array indexing.

	MdlMolDataItem (const TextFile &tf, int line_number, int *line_advance, int compound_line_end=-1, const std::string &title=std::string(""), ModificationPolicy mpol=ModificationPolicy::DO_NOT_MODIFY, ExceptionResponse notify=ExceptionResponse::WARN)

	MdlMolDataItem (const MdlMolDataRequest &ask, const std::vector< std::string > &body_in, ModificationPolicy mpol=ModificationPolicy::DO_NOT_MODIFY, ExceptionResponse notify=ExceptionResponse::WARN)


	MdlMolDataItem (const MdlMolDataItem &original)=default
	The default copy and move constructors, as well as copy and move assignment operators, are applicable to this object which has no const members or pointers to repair.

	MdlMolDataItem (MdlMolDataItem &&original)=default

MdlMolDataItem &	operator= (const MdlMolDataItem &other)=default

MdlMolDataItem &	operator= (MdlMolDataItem &&other)=default


std::string	parseString (int element_number, int line_number) const
	Retrieve a string from the data lines of a data item, assuming that individual words on each line are separated by one or more white space characters and that the quotation marks "" and '' collect everything between them into a single word.

std::string	parseString (int start_pos, int length, int line_number) const


llint	parseInteger (int element_number, int line_number) const
	Retrieve a signed integer from the data lines of a data item. The assumptions of parseString() above apply, as do the overloads and descriptions of formal arguments.

llint	parseInteger (int start_pos, int length, int line_number) const


ullint	parseUnsigned (int element_number, int line_number) const
	Retrieve an unsigned integer from the data lines of a data item. The assumptions of parseString() above apply, as do the overloads and descriptions of formal arguments.

ullint	parseUnsigned (int start_pos, int length, int line_number) const


double	parseReal (int element_number, int line_number) const
	Retrieve a real number from the data lines of a data item. The assumptions of parseString() above apply, as do the overloads and descriptions of formal arguments.

double	parseReal (int start_pos, int length, int line_number) const


char4	parseChar4 (int element_number, int line_number) const
	Retrieve a tuple of four characters from the data lines of a data item. Assumptions from parseString() above apply, as do overloads and descriptions of formal arguments.

char4	parseChar4 (int start_pos, int length, int line_number) const


bool	matchItemName (const std::string &item_name_comp, const std::string &ext_regno_comp, int maccs_ii_no_comp=-1) const
	Match this data item with a series of identification tags.

bool	matchItemName (const std::string &item_name_comp, int maccs_ii_no_comp=-1) const

bool	matchRegistryNumber (const std::string &ext_regno_comp, int maccs_ii_no_comp=-1) const

bool	matchMaccsField (int maccs_ii_no_comp) const

Detailed Description

Store a data item from within an SD file. Data items begin with a line of the form "> <ITEM_NAME>" (additional specifications are possible), end with a single blank line, and can contain customized format information. The information will be read as a series of raw strings, one per line and each representing a whole line. Once read, member functions of the class can extract specific integer, real, char4, or string coded data from within the item.

Constructor & Destructor Documentation

◆ MdlMolDataItem()

stormm::structure::MdlMolDataItem::MdlMolDataItem	(	const std::string &	item_name_in = std::string(""),
		const std::string &	external_regno_in = std::string(""),
		int	internal_regno_in = -1,
		int	maccs_ii_number_in = -1,
		uint	header_info = 0U,
		const std::vector< std::string > &	body_in = {},
		ModificationPolicy	mpol = ModificationPolicy::DO_NOT_MODIFY,
		ExceptionResponse	notify = ExceptionResponse::WARN )

The constructor takes the original text file and the number of the first line of the data item, or the information pertinent to the header line and a series of strings that will form the body of data in the item. Any information submitted as part of a string such as an atom or bond index, which could then go to an output file, must be in the Fortran array indexing (starting at 1). Integer information read from the data body can be adjusted to meet internal array indexing.

Parameters

item_name_in	Name of the data item (an item_name of "ABCD" will appear as "<ABCD>" on the data item's first line)
external_regno_in	An identification number for the compound referencing an external database. An external identification number of "PD-3647" will be represented as "(PD-3647)" on the data item's header line.
maccs_ii_number_in	An integer representing the corresponding field in a MACCS-II database. A field number such as "6519" will be represented as "DT6519" in the data item header line.
header_info	A bit-packed unsigned integer containing, in its low to high bits, whether to display the internal identification number (based on the order in the SD file), the external identification number, the item name, the field number, and finally a "FROM ARCHIVES" declaration.
tf	The original text of the SD file, committed to RAM
line_number	Line of the file at which to begin reading the data item
line_advance	Line of the file that the construction of the data item leads to (after taking in lines of the item)
compound_line_end	Index of the last line of the compound within the SD file (the line contains $$$$)
title	The title of the structure, if known, for error tracing purposes
mpol	Policy about modifying details of the data items that may not conform to the Biovia standard
notify	Policy on whether to notify the user if modifications to certain details of the data item take place

Member Function Documentation

◆ addDataLine()

void stormm::structure::MdlMolDataItem::addDataLine ( const std::string & text )

Add a line to the data item.

Parameters

text	The text of the line to add. This should not include carriage returns, but if it does then it will all be taken as one "data line" to be printed.

◆ getDataLine()

const std::string & stormm::structure::MdlMolDataItem::getDataLine ( const int line_index ) const

Get a particular data lines from the item body.

Parameters

line_index The data line of interest

◆ matchItemName()

bool stormm::structure::MdlMolDataItem::matchItemName	(	const std::string &	item_name_comp,
		const std::string &	ext_regno_comp,
		int	maccs_ii_no_comp = -1 ) const

Match this data item with a series of identification tags.

Parameters

item_name_comp	Item name for comparison
ext_regno_comp	External registry number for comparison
maccs_ii_no_comp	MACCS-II database field number for comparison (omit leading "DT")

◆ parseString()

std::string stormm::structure::MdlMolDataItem::parseString	(	int	element_number,
		int	line_number ) const

Retrieve a string from the data lines of a data item, assuming that individual words on each line are separated by one or more white space characters and that the quotation marks "" and '' collect everything between them into a single word.

Overloaded:

Extract a free-format string based on words separated by white space, assuming that individual words on each line are separated by one or more white space characters and that the quotation marks "" and '' collect everything between them into a single word.
Extract a column-formatted string based on strict character indices

Parameters

element_number	Number of the word on the line (words are separated by white space)
start_pos	The starting position within the line at which to begin reading
start_pos	Length of the fixed-column reading to perform
line_number	Number of the data line on which to find the string

◆ setItemName()

void stormm::structure::MdlMolDataItem::setItemName	(	const std::string &	item_name_in,
		ModificationPolicy	mpol = ModificationPolicy::DO_NOT_MODIFY,
		ExceptionResponse	notify = ExceptionResponse::WARN )

Set the item name and apply checks to the result.

Parameters

item_name_in	The item name to assign
mpol	Indicate what to do if the proposed name does not meet strict Biovia SD file standards but is otherwise salvageable.
notify	Indicate what to do if modifications are made to the proposed name.

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

src/MoleculeFormat/mdlmol_dataitem.h
src/MoleculeFormat/mdlmol_dataitem.cpp

Public Member Functions

Detailed Description

Constructor & Destructor Documentation

◆ MdlMolDataItem()

Member Function Documentation

◆ addDataLine()

◆ getDataLine()

◆ matchItemName()

◆ parseString()

◆ setItemName()