Molecule energy estimation ala Jankowski et al. More...

#include <MoleculeDecomposition.hh>

Inheritance diagram for ggl::chem::MoleculeDecomposition:

Data Structures
class	DecompositionReporter

class	MC_MC_RingNode

class	priority_order

class	RingDescriptor
	descriptor of a ring within the molecule More...

Public Types
typedef std::list< size_t >	RingList
	type of a list of node indices that form a ring More...

typedef std::set< size_t >	RingNodes
	type of a set of node indices that form a ring More...

Public Member Functions
double	getEnergy (const Molecule &mol)

	MoleculeDecomposition (sgm::GraphMatching &fullMatcher, sgm::SubGraphMatching &matcher)

	MoleculeDecomposition (sgm::GraphMatching &fullMatcher, sgm::SubGraphMatching &matcher, DecompositionReporter &reporter)

void	reportHit (const sgm::Pattern_Interface &componentPattern, const sgm::Graph_Interface &targetMol, const sgm::Match &match)

void	reportRing (const sgm::Graph_Interface &graph, const RingList &ringList)

virtual	~MoleculeDecomposition ()
	destruction More...

Static Public Member Functions
static RingNodes	toRing (const Graph_Interface &graph, const RingList &ringList)

Protected Types
typedef std::set < MoleculeComponent, priority_order >	ComponentContainer

typedef boost::property_map < Molecule, PropNodeIndex > ::const_type	NodeIndexMap
	node index map typedef for shorter parameter lists More...

typedef boost::property_map < Molecule, PropNodeLabel > ::type	NodeLabelMap
	node label map typedef for shorter parameter lists More...

Protected Member Functions
size_t	extendPolyphosphateChain (Molecule &m, NodeLabelMap &mNodeLabel, NodeIndexMap &mNodeIndex, const size_t idxNextP, const size_t compID)

bool	isValidRingFragment (const MoleculeComponent::RingFragment &ringFragment, const sgm::Match &match)

Static Protected Member Functions
static void	correctCyclicPhosphates (std::set< std::set< size_t > > &curMatchedIDs)

static void	correctEnclosedPhosphates (std::set< std::set< size_t > > &curMatchedIDs)

static size_t	getAmideNumber (sgm::SubGraphMatching &matcher, sgm::Graph_Interface &molGraph)

static const ComponentContainer &	getGroups (void) throw (std::logic_error)

static const ComponentContainer &	getInteractions (void) throw (std::logic_error)

static const ComponentContainer &	getSmallMolecules (void) throw (std::logic_error)

static size_t	getThioesterNumber (sgm::SubGraphMatching &matcher, sgm::Graph_Interface &molGraph)

Protected Attributes
const MoleculeComponent *	curComponent
	the currently matched MoleculeComponent More...

std::set< std::set< size_t > >	curMatchedIDs
	the matched set of node indices for current MoleculeComponent More...

RingNodes	curMolRingNodes

std::map < MoleculeComponent::RingFragmentType, std::vector< RingDescriptor > >	curMolRings

double	energy
	the energy of the currently parsed molecule More...

sgm::GraphMatching *	fullMatcher
	the graph matching implementation to be used More...

sgm::SubGraphMatching *	matcher
	the sub graph matching implementation to be used More...

DecompositionReporter *	reporter
	an optional decomposition reporter More...

Static Protected Attributes
static double	contributionMiddlePhosphate

static double	correctionHydroCarbon

static double	correctionPerAmide

static double	correctionPerHeteroaromaticRing
	correction term for each heteroaromatic ring within the molecule More...

static double	correctionPerThioester

static double	correctionPerThreeMemberedRing

static double	correctionVicinalChlorine
	correction term for vicinal chlorines within the molecule More...

static ComponentContainer	groups

static ComponentContainer	interactions
	set of all interaction patterns to be screened for More...

static ComponentContainer	smallMolecules
	set of all small molecules to be screened for More...

Detailed Description

   Molecule decomposition approach to analyze a molecules thermodynamics.
   The approach follows the paper by Jankowski et al. (2008)

   Group Contribution Method for Thermodynamic Analysis of Complex
    Metabolic Networks
   Matthew D. Jankowski, Christopher S. Henry, Linda J. Broadbelt
    and Vassily Hatzimanikatis
   Biophysical Journal, Volume 95, Issue 3, 1487-1499, 1 August 2008
   doi:10.1529/biophysj.107.124784

Author: Martin Mann - 2010 - http://www.bioinf.uni-freiburg.de/~mmann/

Definition at line 38 of file MoleculeDecomposition.hh.

Member Typedef Documentation

typedef std::set< MoleculeComponent, priority_order > ggl::chem::MoleculeDecomposition::ComponentContainer

protected

Definition at line 139 of file MoleculeDecomposition.hh.

typedef boost::property_map< Molecule, PropNodeIndex>::const_type ggl::chem::MoleculeDecomposition::NodeIndexMap

protected

Definition at line 444 of file MoleculeDecomposition.hh.

typedef boost::property_map< Molecule, PropNodeLabel>::type ggl::chem::MoleculeDecomposition::NodeLabelMap

protected

Definition at line 442 of file MoleculeDecomposition.hh.

typedef std::list<size_t> sgm::RingReporter::RingList

inherited

Definition at line 27 of file RingReporter.hh.

typedef std::set<size_t> sgm::RingReporter::RingNodes

inherited

Definition at line 25 of file RingReporter.hh.

Constructor & Destructor Documentation

ggl::chem::MoleculeDecomposition::MoleculeDecomposition	(	sgm::GraphMatching &	fullMatcher,
		sgm::SubGraphMatching &	matcher
	)

construction

Parameters

fullMatcher	the graph matching implementation to be used
matcher	the sub graph matching implementation to be used

ggl::chem::MoleculeDecomposition::MoleculeDecomposition	(	sgm::GraphMatching &	fullMatcher,
		sgm::SubGraphMatching &	matcher,
		DecompositionReporter &	reporter
	)

construction with a given reporter

Parameters

fullMatcher	the graph matching implementation to be used
matcher	the sub graph matching implementation to be used
reporter	the decomposition reporter to be used

virtual ggl::chem::MoleculeDecomposition::~MoleculeDecomposition ( )

virtual

Member Function Documentation

static void ggl::chem::MoleculeDecomposition::correctCyclicPhosphates ( std::set< std::set< size_t > > & curMatchedIDs )

staticprotected

Corrects the mapping of cyclic phosphates. Due to their symmetric symmetric pattern they are matched twice. Thus, one oxygen is mapped too much.

Parameters

curMatchedIDs the node sets for each match that has to be corrected

static void ggl::chem::MoleculeDecomposition::correctEnclosedPhosphates ( std::set< std::set< size_t > > & curMatchedIDs )

staticprotected

Corrects the mapping of enclosed primary phosphates. Due to their symmetric symmetric pattern they are matched all along the phosphate fragment and not only at the ends.

Parameters

curMatchedIDs the node sets for each match that has to be corrected

size_t ggl::chem::MoleculeDecomposition::extendPolyphosphateChain	(	Molecule &	m,
		NodeLabelMap &	mNodeLabel,
		NodeIndexMap &	mNodeIndex,
		const size_t	idxNextP,
		const size_t	compID
	)

protected

Extend the labeling of a phosphate chain starting from a given phosphorus node using a specified component label.

Parameters

m	the molecule to label
mNodeLabel	the node label access for m
mNodeIndex	the node index access for m
idxNextP	the phosphorus node to start the labeling
compID	the label for the phosphate chain

Returns: the length of the chain

static size_t ggl::chem::MoleculeDecomposition::getAmideNumber	(	sgm::SubGraphMatching &	matcher,
		sgm::Graph_Interface &	molGraph
	)

staticprotected

Computes the number of amide matches within the molecule where for nitrogen atom involved in two amides only one occurrence is counted

Parameters

matcher	the sub graph matcher to be used
molGraph	the molecule graph to check

Returns: the number of amides within the molecule

double ggl::chem::MoleculeDecomposition::getEnergy ( const Molecule & mol )

Decomposes the given molecule into MoleculeComponents and derives an estimate of its energy in kcal/mol.

Parameters

mol	the molecule to be analyzed

Returns: an estimate of its energy in kcal/mol

static const ComponentContainer& ggl::chem::MoleculeDecomposition::getGroups ( void ) throw (std::logic_error)

staticprotected

Access to the groups member. This function initializes the container if not already done.

Returns: the groups container to be matched. std::logic_error in case the group initialization failed which should never happen

static const ComponentContainer& ggl::chem::MoleculeDecomposition::getInteractions ( void ) throw (std::logic_error)

staticprotected

Access to the interactions member. This function initializes the container if not already done.

Returns: the interactions container to be matched. std::logic_error in case the group initialization failed which should never happen

static const ComponentContainer& ggl::chem::MoleculeDecomposition::getSmallMolecules ( void ) throw (std::logic_error)

staticprotected

Access to the smallMolecules member. This function initializes the container if not already done.

Returns: the smallMolecules container to be matched. std::logic_error in case the group initialization failed which should never happen

static size_t ggl::chem::MoleculeDecomposition::getThioesterNumber	(	sgm::SubGraphMatching &	matcher,
		sgm::Graph_Interface &	molGraph
	)

staticprotected

Computes the number of thioester matches within the molecule where for sulfur atoms involved in two thioester only one occurrence is counted

Parameters

matcher	the sub graph matcher to be used
molGraph	the molecule graph to check

Returns: the number of thioester within the molecule

bool ggl::chem::MoleculeDecomposition::isValidRingFragment	(	const MoleculeComponent::RingFragment &	ringFragment,
		const sgm::Match &	match
	)

protected

Checks whether or not a given ring fragment is present in the molecule.

Parameters

ringFragment	the ring fragment to check
match	the node matching that triggered the check

Returns: true, if the ring fragment is matched; false otherwise

void ggl::chem::MoleculeDecomposition::reportHit	(	const sgm::Pattern_Interface &	componentPattern,
		const sgm::Graph_Interface &	targetMol,
		const sgm::Match &	match
	)

virtual

Handles the occurence of a MoleculeComponent within a decomposed molecule graph.

Parameters

componentPattern	the pattern of the MoleculeComponent to be matched.
targetMol	the molecule graph the pattern was found within
match	contains the indices of the matched pattern nodes in the target graph. match[i] corresponds to the mapping of the ith vertex in the pattern graph.

Implements sgm::Match_Reporter.

void ggl::chem::MoleculeDecomposition::reportRing	(	const sgm::Graph_Interface &	graph,
		const RingList &	ringList
	)

virtual

Is called to report a ring. The ring is stored for lookup of ring constraints of the MoleculeComponents matched.

Parameters

graph	the graph that contains the ring
ringList	the ring to report

Implements sgm::RingReporter.

static RingNodes sgm::RingReporter::toRing	(	const Graph_Interface &	graph,
		const RingList &	ringList
	)

staticinherited

Utility class that converts a RingList, i.e. a list of nodes when traversing a ring within a graph, into the set of nodes that form the ring.

Parameters

graph	the graph that contains the ring
ringList	the ring list to convert

Returns: the list of nodes traversing the ring

Field Documentation

double ggl::chem::MoleculeDecomposition::contributionMiddlePhosphate

staticprotected

energy contribution term for a middle phosphate within a phosphate chain

Definition at line 177 of file MoleculeDecomposition.hh.

double ggl::chem::MoleculeDecomposition::correctionHydroCarbon

staticprotected

correction term if a molecule is a hydrocarbon, i.e. it contains only H and C

Definition at line 153 of file MoleculeDecomposition.hh.

double ggl::chem::MoleculeDecomposition::correctionPerAmide

staticprotected

correction term for each amide within the molecule; note, for nitrogen atom involved in two amides only one occurrence is considered

Definition at line 165 of file MoleculeDecomposition.hh.

double ggl::chem::MoleculeDecomposition::correctionPerHeteroaromaticRing

staticprotected

Definition at line 156 of file MoleculeDecomposition.hh.

double ggl::chem::MoleculeDecomposition::correctionPerThioester

staticprotected

correction term for each thioester within the molecule; note, for sulfur atom involved in two amides only one occurrence is considered

Definition at line 170 of file MoleculeDecomposition.hh.

double ggl::chem::MoleculeDecomposition::correctionPerThreeMemberedRing

staticprotected

correction term for each three-membered ring independently of the atom labels

Definition at line 160 of file MoleculeDecomposition.hh.

double ggl::chem::MoleculeDecomposition::correctionVicinalChlorine

staticprotected

Definition at line 173 of file MoleculeDecomposition.hh.

const MoleculeComponent* ggl::chem::MoleculeDecomposition::curComponent

protected

Definition at line 251 of file MoleculeDecomposition.hh.

std::set< std::set<size_t> > ggl::chem::MoleculeDecomposition::curMatchedIDs

protected

Definition at line 253 of file MoleculeDecomposition.hh.

RingNodes ggl::chem::MoleculeDecomposition::curMolRingNodes

protected

set of all nodes participating in a ring within the current molecule handled

Definition at line 257 of file MoleculeDecomposition.hh.

std::map< MoleculeComponent::RingFragmentType, std::vector< RingDescriptor > > ggl::chem::MoleculeDecomposition::curMolRings

protected

string encoding of all rings within the current molecule grouped by their type

Definition at line 296 of file MoleculeDecomposition.hh.

double ggl::chem::MoleculeDecomposition::energy

protected

Definition at line 249 of file MoleculeDecomposition.hh.

sgm::GraphMatching* ggl::chem::MoleculeDecomposition::fullMatcher

protected

Definition at line 302 of file MoleculeDecomposition.hh.

ComponentContainer ggl::chem::MoleculeDecomposition::groups

staticprotected

set of all groups that are matched exclusively starting with the one with lowest priority value

Definition at line 143 of file MoleculeDecomposition.hh.

ComponentContainer ggl::chem::MoleculeDecomposition::interactions

staticprotected

Definition at line 146 of file MoleculeDecomposition.hh.

sgm::SubGraphMatching* ggl::chem::MoleculeDecomposition::matcher

protected

Definition at line 304 of file MoleculeDecomposition.hh.

DecompositionReporter* ggl::chem::MoleculeDecomposition::reporter

protected

Definition at line 299 of file MoleculeDecomposition.hh.

ComponentContainer ggl::chem::MoleculeDecomposition::smallMolecules

staticprotected

Definition at line 149 of file MoleculeDecomposition.hh.

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

src/ggl/chem/MoleculeDecomposition.hh

Data Structures

Public Types

Public Member Functions

Static Public Member Functions

Protected Types

Protected Member Functions

Static Protected Member Functions

Protected Attributes

Static Protected Attributes

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Field Documentation