A molecular or atomic property read from an MDL .mol or SDF file. More...

#include <mdlmol_property.h>

Public Member Functions
MdlMolPropertyKind	getKind () const
	Get the kind of property according to the internal enumerator.

char4	getCode () const
	Get the property code. This will indicate whether to obliterate certain types of information from the atom block of the V2000 MDL MOL format entry.

int	getSubstrate () const
	Get the substrate atom or S-group. The nature of the property will indicate which type of substrate this is.

int	getPrintedSubstrate () const
	Get the substrate atom or S-group for the purposes of printing. The nature of the property will indicate which type of substrate this is, but all substrates' indices shift by -1 when being read and therefore shift by +1 when being written to the MDL MOL format.

bool	applyToExclusions () const
	Indicate whether the atom list encoded by this property is based on excluded elements (return TRUE) or included ones (return FALSE). If the property is not an "M ALS" entry, raise a runtime error.

char	getExclusionCode () const
	Get a code ('T' if TRUE, 'F' if FALSE) to indicate whether the atom list describes exclusions.

int	getEntryCount () const
	Get the number of entries for this property.

int	getDataLineCount () const
	Get the number of data lines for this property.

const std::string &	getDataLine (int index) const
	Get a const pointer to one of the data lines.

std::string	getMdlText () const
	Recompose the text string for this property as it would appear in an MDL MOL file.

void	setSubstrate (int index)
	Define the substrate to be used, whether an atom or an S-group.

void	setEntryFormat (const std::vector< MolObjPropField > &entry_detail_in, const std::vector< MolObjIndexKind > &entry_adjustment_in)
	Define the entry format for the property. If applied to an existing MdlMolProperty with nonzero depth, this will create an error.

void	addEntry (const std::vector< int > &int_data_in, const std::vector< char4 > &char4_data_in, const std::vector< double > &real_data_in, const std::vector< std::string > &str_data_in)
	Add an entry to the MDL MOL V2000 format property. The layout must match that established in the detail array. Adjustments will not be applied to the indexing for input originating within the program. Other methods will adjust the indexing of atoms, bonds, and S-groups named in auxiliary user input when making properties out of such information.


	MdlMolProperty (const char4 code_in={ ' ', ' ', ' ', ' ' }, int substrate_in=-1, int entry_count_in=0, int entry_depth_in=0, bool exclusions_in=false, int substrate_line_pos_in=-1, int entry_count_line_pos_in=-1, int entry_read_start_pos_in=0, const std::vector< int > &entry_data_bounds_in={}, const std::vector< MolObjPropField > &entry_detail_in={}, const std::vector< MolObjIndexKind > &entry_adjustment_in={}, const std::vector< int > &int_data_in={}, const std::vector< double > &real_data_in={}, const std::vector< std::string > &str_data_in={}, const std::vector< std::string > &data_lines_in={})
	The constructor takes all member variable inputs, or the original text and a line number within it.

	MdlMolProperty (const TextFile &tf, int line_number, int *line_advance, const std::string &title=std::string(""))


	MdlMolProperty (const MdlMolProperty &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.

	MdlMolProperty (MdlMolProperty &&original)=default

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

MdlMolProperty &	operator= (MdlMolProperty &&other)=default


int	getIntegerValue (int entry_index, int attribute_index) const
	Get a value from the property for a specific entry. Inputs to these functions will be checked by checkAttributeValidity().

int	getPrintedIntegerValue (int entry_index, int attribute_index) const

double	getRealValue (int entry_index, int attribute_index) const

char4	getChar4Value (int entry_index, int attribute_index) const

std::string	getStringValue (int entry_index, int attribute_index) const


void	setCode (char x, char y, char z, char major='M')
	Define the property code.

void	setCode (char4 code_in)

Detailed Description

A molecular or atomic property read from an MDL .mol or SDF file.

Constructor & Destructor Documentation

◆ MdlMolProperty()

stormm::structure::MdlMolProperty::MdlMolProperty	(	const char4	code_in = { ' ', ' ', ' ', ' ' },
		int	substrate_in = -1,
		int	entry_count_in = 0,
		int	entry_depth_in = 0,
		bool	exclusions_in = false,
		int	substrate_line_pos_in = -1,
		int	entry_count_line_pos_in = -1,
		int	entry_read_start_pos_in = 0,
		const std::vector< int > &	entry_data_bounds_in = {},
		const std::vector< MolObjPropField > &	entry_detail_in = {},
		const std::vector< MolObjIndexKind > &	entry_adjustment_in = {},
		const std::vector< int > &	int_data_in = {},
		const std::vector< double > &	real_data_in = {},
		const std::vector< std::string > &	str_data_in = {},
		const std::vector< std::string > &	data_lines_in = {} )

The constructor takes all member variable inputs, or the original text and a line number within it.

Parameters

tf	Text of the original .sdf or .mol file, read into RAM
line_number	Number of the line on which to read the data
line_advance	The line advancement position, which will account for data lines in some properties
title	The title of the structure, if known, for error tracing purposes

Member Function Documentation

◆ addEntry()

void stormm::structure::MdlMolProperty::addEntry	(	const std::vector< int > &	int_data_in,
		const std::vector< char4 > &	char4_data_in,
		const std::vector< double > &	real_data_in,
		const std::vector< std::string > &	str_data_in )

Add an entry to the MDL MOL V2000 format property. The layout must match that established in the detail array. Adjustments will not be applied to the indexing for input originating within the program. Other methods will adjust the indexing of atoms, bonds, and S-groups named in auxiliary user input when making properties out of such information.

int_data_in All integer data, given in the order that INTEGER MolObjPropField types appear in the detail array. No char4, real or string data indices are included in this array.

Parameters

char4_data_in	List of char4 data elements, given back-to-back in the order that CHAR4 MolObjPropField types appear in the detail array.
real_data_in	List of real data, ordered as the other arrays in this input.
string_data_in	List of string data, ordered as the other arrays in this input.

◆ getIntegerValue()

int stormm::structure::MdlMolProperty::getIntegerValue	(	int	entry_index,
		int	attribute_index ) const

Get a value from the property for a specific entry. Inputs to these functions will be checked by checkAttributeValidity().

Parameters

entry_index	The index of the entry to access
attribute_index	The index of the attribute to retrieve

◆ setCode()

void stormm::structure::MdlMolProperty::setCode	(	char	x,
		char	y,
		char	z,
		char	major = 'M' )

Define the property code.

Overloaded:

Provide the first letter and the final three
Provide all four letters as a pre-made char tuple

Parameters

x	The first letter of the three-letter tuple in the property code
y	The second letter of the three-letter tuple defining the property code
z	The last letter of the three-letter tuple defining the property code
major	The first letter that will appear on the line if the property is written to a file
code_in	A pre-made code to apply, ordered 3-4-5-0 in terms of the indices that each character would occupy on a property line of an MDL MOL format entry

◆ setEntryFormat()

void stormm::structure::MdlMolProperty::setEntryFormat	(	const std::vector< MolObjPropField > &	entry_detail_in,
		const std::vector< MolObjIndexKind > &	entry_adjustment_in )

Define the entry format for the property. If applied to an existing MdlMolProperty with nonzero depth, this will create an error.

Parameters

entry_detail_in	List of data types of the entry elements
entry_adjustment_in	List of index adjustments for each element of the entry. Atom and bond elements will have their indices adjusted by -1, but only if the information is read from a file–programmatic input is still expected to occur in the C / C++ array numbering.

◆ setSubstrate()

void stormm::structure::MdlMolProperty::setSubstrate ( int index )

Define the substrate to be used, whether an atom or an S-group.

Parameters

index Atom or S-group index of the substrate. This should be provided for the C / C++ array element, not the file format (+1 will be added if and when the information is committed to a file).

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

src/MoleculeFormat/mdlmol_property.h
src/MoleculeFormat/mdlmol_property.cpp

Public Member Functions

Detailed Description

Constructor & Destructor Documentation

◆ MdlMolProperty()

Member Function Documentation

◆ addEntry()

◆ getIntegerValue()

◆ setCode()

◆ setEntryFormat()

◆ setSubstrate()