BALL::MolDB Class Reference

#include <BALL/FORMAT/molDB.h>

Classes
struct	VendorInfo

Public Member Functions
int	getVersion ()
	MolDB (String hostname, String user, String password, String db, int port=3306)
virtual	~MolDB ()
void	getDatasetSummary (vector< String > &dataset_names, vector< Size > &no_isomers, vector< Size > &no_conformations)
void	searchMoleculesByUCK (String uck, list< LongSize > &conformation_IDs)
Molecule *	fetchMoleculeById (LongSize conformation_id)
vector< Molecule * >	fetchMoleculeById (vector< LongSize > &conformation_ids)
LongSize	storeMolecule (Molecule *mol, String *conformation_hash)
LongSize	storeMolecule (Molecule *mol)
void	deleteIsomer (LongSize isomer_id)
void	deleteConformation (LongSize conformation_id)
void	storeResult (Result *result, String &target_name)
vector< Result * >	fetchResults (list< String > &conformation_hashs, String target_name="")
void	searchMoleculesByLogP (const double &min_logP, const double &max_logP, list< LongSize > &conformation_IDs, const list< LongSize > *conformation_IDs_to_check, bool input_isomer_IDs=0, bool output_isomer_IDs=0)
void	searchMoleculesByMW (const double &min_MW, const double &max_MW, list< LongSize > &conformation_IDs, const list< LongSize > *conformation_IDs_to_check, bool input_isomer_IDs, bool output_isomer_IDs)
void	fetchDatasetConformationIDs (String &target_name, list< LongSize > &conformation_IDs, const list< LongSize > *conformation_IDs_to_check=0, bool input_isomer_IDs=0, bool output_isomer_IDs=0)
void	searchSimilarMoleculesByFingerprint (list< vector< bool > > &query_fingerprints, const float &minimal_similarity, const float &maximal_similarity, list< LongSize > &conformation_IDs, const list< LongSize > *conformation_IDs_to_check=0, bool input_isomer_IDs=0, bool output_isomer_IDs=0)
void	fetchVendorInformation (Molecule *mol, list< VendorInfo > &vendor_info)
bool	hasResults ()
void	disableFunctionalGroupCounting ()
void	setVendorPropertyNames (String vendor_name, String vendors_compound_id_tag, bool fetch_vendorname_from_prop, String vendor_version, String url)

Static Public Member Functions
static void	createNewDatabase (String &host, String &user, String &password, String &db_name, int port=0)
static void	buildTopology (Molecule &mol, QByteArray &data)
static void	getTopology (Molecule &mol, QDataStream &ds)
static void	buildCoordinates (Molecule &mol, QByteArray &data)
static void	getCoordinates (Molecule &mol, QDataStream &ds)
static void	buildCharges (Molecule &mol, QByteArray &data)
static void	getCharges (Molecule &mol, QDataStream &ds)

Detailed Description

Molecule database class.
This class is intended to store small molecules, information about them (fingerprint, smiles, etc.) and results of docking or (re-)scoring.
Topologies and conformations are stored separately in order to prevent waste of space. IDs will be automatically assigned to new topologies and conformations.

When a given molecule is to be stored in the database (by use of MolDB::storeMolecule()), it is automatically detected (by use of hash-keys for topologies and conformations) whether its topology and conformation need to be written to the database or whether they already exists in the database. This way, waste of disk space is automatically prevented.
Furthermore, all Properties of a given molecule will also be saved and will be restored when retrieving the molecule later.

Additionally, the following things that can be used for searching molecules later will be automatically calculated and stored in the database: – molecular weight – canonical smile (if OpenEye or OpenBabel is available) – logP (if OpenEye or OpenBabel is available; needed for SMARTS matching) – binary pathway-based fingerprint – functional group counts (if OpenEye or OpenBabel is available; needed for SMARTS matching).

Information about docking or (re-)scoring can be stored by use MolDB::storeResult() and retrieved later by MolDB::fetchResults().

Definition at line 48 of file molDB.h.

Constructor & Destructor Documentation

BALL::MolDB::MolDB	(	String	hostname,
		String	user,
		String	password,
		String	db,
		int	port = 3306
	)

Create MolDB instance with database connection parameters.

Parameters

hostname
username
password
dbname

virtual BALL::MolDB::~MolDB ( )

virtual

Member Function Documentation

static void BALL::MolDB::buildCharges ( Molecule &  mol, QByteArray &  data  )

static

Reconstruct molecule charges from binary data.

Parameters

target	molecule for building charges
binary	data fetched from database

static void BALL::MolDB::buildCoordinates ( Molecule &  mol, QByteArray &  data  )

static

Reconstruct molecule conformation from binary data.

Parameters

target	molecule for building conformation
binary	data fetched from database

static void BALL::MolDB::buildTopology ( Molecule &  mol, QByteArray &  data  )

static

Reconstruct molecule topology from binary data.

Parameters

target	molecule for building topology
binary	data fetched from database

static void BALL::MolDB::createNewDatabase ( String &  host, String &  user, String &  password, String &  db_name, int  port = 0  )

static

void BALL::MolDB::deleteConformation

(

LongSize

conformation_id

)

void BALL::MolDB::deleteIsomer

(

LongSize

isomer_id

)

void BALL::MolDB::disableFunctionalGroupCounting

(

)

Disable creation/filling of table 'functional_groups' during molecule import.

void BALL::MolDB::fetchDatasetConformationIDs	(	String &	target_name,
		list< LongSize > &	conformation_IDs,
		const list< LongSize > *	conformation_IDs_to_check = 0,
		bool	input_isomer_IDs = 0,
		bool	output_isomer_IDs = 0
	)

Fetch all conformation-IDs for a given target.

Molecule* BALL::MolDB::fetchMoleculeById

(

LongSize

conformation_id

)

vector<Molecule*> BALL::MolDB::fetchMoleculeById

(

vector< LongSize > &

conformation_ids

)

vector<Result*> BALL::MolDB::fetchResults	(	list< String > &	conformation_hashs,
		String	target_name = ""
	)

void BALL::MolDB::fetchVendorInformation	(	Molecule *	mol,
		list< VendorInfo > &	vendor_info
	)

Search for vendors for the given compound.

Parameters

mol	input compound
vendor_info	vendor-information found for this compound will be stored here.

static void BALL::MolDB::getCharges ( Molecule &  mol, QDataStream &  ds  )

static

Encode the molecule charge data into binary data.

Parameters

source	molecule for extracting charges
binary	data stream to output data

static void BALL::MolDB::getCoordinates ( Molecule &  mol, QDataStream &  ds  )

static

Encode the molecule conformation into binary data.

Parameters

source	molecule for extracting conformation
binary	data stream to output data

void BALL::MolDB::getDatasetSummary	(	vector< String > &	dataset_names,
		vector< Size > &	no_isomers,
		vector< Size > &	no_conformations
	)

Get a summary of all datasets currently stored in the data base.

Parameters

dataset_names	the name of each dataset will be stored here
no_isomers	the number of distinct isomers of each of the datasets
no_conformations	the number of distinct conformations of each of the datasets

static void BALL::MolDB::getTopology ( Molecule &  mol, QDataStream &  ds  )

static

Encode the molecule topology into binary data.

Parameters

source	molecule for extracting topology
binary	data stream to output data

int BALL::MolDB::getVersion

(

)

Get version number of MolDB.

bool BALL::MolDB::hasResults

(

)

Find out whether this database has a 'results' table or not. If it has such a table, the results of Docking/Scoring have been saved here.

void BALL::MolDB::searchMoleculesByLogP	(	const double &	min_logP,
		const double &	max_logP,
		list< LongSize > &	conformation_IDs,
		const list< LongSize > *	conformation_IDs_to_check,
		bool	input_isomer_IDs = 0,
		bool	output_isomer_IDs = 0
	)

Filter database according to specified logP thresholds.

void BALL::MolDB::searchMoleculesByMW	(	const double &	min_MW,
		const double &	max_MW,
		list< LongSize > &	conformation_IDs,
		const list< LongSize > *	conformation_IDs_to_check,
		bool	input_isomer_IDs,
		bool	output_isomer_IDs
	)

Filter database according to specified molecular weight thresholds.

void BALL::MolDB::searchMoleculesByUCK	(	String	uck,
		list< LongSize > &	conformation_IDs
	)

void BALL::MolDB::searchSimilarMoleculesByFingerprint	(	list< vector< bool > > &	query_fingerprints,
		const float &	minimal_similarity,
		const float &	maximal_similarity,
		list< LongSize > &	conformation_IDs,
		const list< LongSize > *	conformation_IDs_to_check = 0,
		bool	input_isomer_IDs = 0,
		bool	output_isomer_IDs = 0
	)

Fetch all conformation-IDs for those molecules that have a tanimoto coefficient larger or equal than the given cutoff to at least one of the query fingerprints.

void BALL::MolDB::setVendorPropertyNames	(	String	vendor_name,
		String	vendors_compound_id_tag,
		bool	fetch_vendorname_from_prop,
		String	vendor_version,
		String	url
	)

LongSize BALL::MolDB::storeMolecule	(	Molecule *	mol,
		String *	conformation_hash
	)

LongSize BALL::MolDB::storeMolecule ( Molecule *  mol )

inline

Definition at line 91 of file molDB.h.

void BALL::MolDB::storeResult	(	Result *	result,
		String &	target_name
	)