FeaturedMolecule

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Class Summary

class FeaturedMolecule
: public LigandMolecule
{
public:
class FeatureSetAttributes ;
// Constructors
FeaturedMolecule(unsigned int molId, ifstream& mol2FileStream, const string molName) ;
RigidGroup* createRigidGroup(int groupId);
// Inspectors
const vector< Feature*>& getFeatures() const ;
const Feature* getFeature(unsigned int featureID) const ;
unsigned int numberOfFeatures() const ;
string getFeaturesFileName() const;
string getPymolFileName() const;
void getFeatureAttributes(FeatureSetAttributes& attributes) const;
static void getFeatureAttributes(const vector< const Feature*>& someFeatures, FeatureSetAttributes& attributes);
static void getFeatureAttributes(const Feature* aFeature, FeatureSetAttributes& attributes);
void getFeaturesInBall(const Vector3& point, float radius, HashResult< Feature*>& result) const ;
float getFeatureRadiusForCenterFit(int featureID) const ;
float getFeatureWeight(int featureID) const ;
float calculateActualScoreByFeatures(int bitset) const;
int calculateActualNumOfFeatures(int bitset) const;
// Setters
void setFeatureValidity(int featureID, bool valid) ;
void setFeatureWeight(int featureID, float w) ;
void setFeatureRadiusForCenterFit(int featureID, float r) ;
void resetValidityAndWeight(int featureID) ;
void resetValidityAndWeight() ;
// Output
void dumpFeatures(ostream& output) const ;
void outputFeaturesMol2File(ostream& output) const;
void outputFeaturesMol2File(ostream& output, const RigidTrans3& trans) const;
void outputFeaturesMol2File(ostream& output, int bitSet) const;
void outputFeaturesMol2File(RigidGroupTrans3Map& transformations, ostream& output) const;
void outputFeaturesMol2File(RigidGroupTrans3Map& transformations, ostream& output, int bitSet) const;
void preparePymolScript() const;
// Destructors
~FeaturedMolecule() ;
static float SECONDARY_FEATURE_WEIGHT;
protected:
vector< Feature*> features_;
vector< vector< const Feature*> > atomIndex2FeaturesMap_;
GeomHash< Vector3, Feature*> featuresHash_;
hash_map< int, int> samePositionFeatures_;
vector< int> featuresToGroups_;
vector< int> featuresToGroupsIndex_;
vector< vector< int> > featuresGroups_;
}; // FeaturedMolecule

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KEYWORD

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AUTHORS

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CHANGES LOG

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GOALS

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USAGE

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class FeatureSetAttributes ;

  class FeatureSetAttributes {
  public:
    unsigned int numOfFeatures;
    unsigned int numOfSpatialFeatures;
    unsigned int numOfAromaticRings;
    unsigned int numOfHydrophobes;
    unsigned int numOfHbDonors;
    unsigned int numOfHbAcceptors;
    unsigned int numOfNegativeCharges;
    unsigned int numOfPositiveCharges;
    unsigned int numOfUserDefineFeatures;

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FeaturedMolecule(unsigned int molId, ifstream& mol2FileStream, const string molName) ;

Constructs a FeaturedMolecule object according to the given Mol2 file which describes the molecule. 

  FeaturedMolecule(unsigned int molId, ifstream& mol2FileStream, const string molName) ;

Function is currently defined inline.


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RigidGroup* createRigidGroup(int groupId);

virtual RigidGroup* createRigidGroup(int groupId);

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const vector< Feature*>& getFeatures() const ;

  const vector< Feature*>& getFeatures() const                      
;

Function is currently defined inline.


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const Feature* getFeature(unsigned int featureID) const ;

  const Feature* getFeature(unsigned int featureID) const                                                         ;

Function is currently defined inline.


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unsigned int numberOfFeatures() const ;

  unsigned int numberOfFeatures() const                             
;

Function is currently defined inline.


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string getFeaturesFileName() const;

  string getFeaturesFileName() const;

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string getPymolFileName() const;

  string getPymolFileName() const;

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void getFeatureAttributes(FeatureSetAttributes& attributes) const;

  void getFeatureAttributes(FeatureSetAttributes& attributes) const;

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void getFeatureAttributes(const vector< const Feature*>& someFeatures, FeatureSetAttributes& attributes);

  static void getFeatureAttributes(const vector< const Feature*>& someFeatures, FeatureSetAttributes& attributes);

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void getFeatureAttributes(const Feature* aFeature, FeatureSetAttributes& attributes);

  static void getFeatureAttributes(const Feature* aFeature, FeatureSetAttributes& attributes);

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void getFeaturesInBall(const Vector3& point, float radius, HashResult< Feature*>& result) const ;

  void getFeaturesInBall(const Vector3& point, float radius, HashResult< Feature*>& result) const                                                      
;

Function is currently defined inline.


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float getFeatureRadiusForCenterFit(int featureID) const ;

  float getFeatureRadiusForCenterFit(int featureID) const                                                                
;

Function is currently defined inline.


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float getFeatureWeight(int featureID) const ;

  float getFeatureWeight(int featureID) const                                                 
;

Function is currently defined inline.


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float calculateActualScoreByFeatures(int bitset) const;

  float calculateActualScoreByFeatures(int bitset) const;

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int calculateActualNumOfFeatures(int bitset) const;

  int calculateActualNumOfFeatures(int bitset) const;

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void setFeatureValidity(int featureID, bool valid) ;

  void setFeatureValidity(int featureID, bool valid)                                                    
;

Function is currently defined inline.


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void setFeatureWeight(int featureID, float w) ;

  void setFeatureWeight(int featureID, float w)                                              
;

Function is currently defined inline.


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void setFeatureRadiusForCenterFit(int featureID, float r) ;

  void setFeatureRadiusForCenterFit(int featureID, float r)                                                          
;

Function is currently defined inline.


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void resetValidityAndWeight(int featureID) ;

  void resetValidityAndWeight(int featureID)                                                          
;

Function is currently defined inline.


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void resetValidityAndWeight() ;

  void resetValidityAndWeight()                                                                                                       
;

Function is currently defined inline.


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void dumpFeatures(ostream& output) const ;

  void dumpFeatures(ostream& output) const                                                                                                                                
;

Function is currently defined inline.


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void outputFeaturesMol2File(ostream& output) const;

  void outputFeaturesMol2File(ostream& output) const;

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void outputFeaturesMol2File(ostream& output, const RigidTrans3& trans) const;

  void outputFeaturesMol2File(ostream& output, const RigidTrans3& trans) const;

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void outputFeaturesMol2File(ostream& output, int bitSet) const;

  void outputFeaturesMol2File(ostream& output, int bitSet) const;

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void outputFeaturesMol2File(RigidGroupTrans3Map& transformations, ostream& output) const;

Transform the features of the molecule according to the given rigid transformations and output the result to a file in Mol2 format 

  void outputFeaturesMol2File(RigidGroupTrans3Map& transformations, ostream& output) const;

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void outputFeaturesMol2File(RigidGroupTrans3Map& transformations, ostream& output, int bitSet) const;

  void outputFeaturesMol2File(RigidGroupTrans3Map& transformations, ostream& output, int bitSet) const;

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void preparePymolScript() const;

prepares pymol script that loads molecule with features 

  void preparePymolScript() const;

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~FeaturedMolecule() ;

  ~FeaturedMolecule()                                                                                                  
;

Function is currently defined inline.


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vector< Feature*> features_;

  vector< Feature*> features_;

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vector< vector< const Feature*> > atomIndex2FeaturesMap_;

Store for each atom the set of his features 

  vector< vector< const Feature*> > atomIndex2FeaturesMap_;

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GeomHash< Vector3, Feature*> featuresHash_;

  GeomHash< Vector3, Feature*> featuresHash_;

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hash_map< int, int> samePositionFeatures_;

  hash_map< int, int> samePositionFeatures_;

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vector< int> featuresToGroups_;

  vector< int> featuresToGroups_;

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vector< int> featuresToGroupsIndex_;

  vector< int> featuresToGroupsIndex_;

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vector< vector< int> > featuresGroups_;

  vector< vector< int> > featuresGroups_;

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float SECONDARY_FEATURE_WEIGHT;

  static float SECONDARY_FEATURE_WEIGHT;

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All Members

public:
typedef hash_map< unsigned int, RigidTrans3, hash< unsigned int> > RigidGroupTrans3Map;
// Constructors
void init(ifstream& mol2FileStream) ;
void addDummyPoints();
// Inspectors
const Mol2Atom& getAtomById(int id) const ;
unsigned int getAtomIndexById(int id) const ;
const Vector3& getDummyPoint(unsigned int dummyPointIndex) const ;
const vector< Vector3>& getDummyPoints() const ;
void getCriticalPoints(vector< Vector3>& points) const;
unsigned int getID() const ;
const string& getFileName() const ;
const string& getMol2Name() const ;
const string& getName() const ;
HYBRIDIZATION_TYPE getHybridizationType(unsigned int atomIndex) const;
const vector< RigidGroup*>& getRigidGroups() const ;
unsigned int getNumOfRigidGroups() const ;
unsigned int numberOfHeavyAtoms() const ;
const RigidGroup& getRigidGroup(int groupId) const ;
const vector< Vector3> getCoordinates(int groupId) const ;
int getCommonRigidGroup(unsigned int atomIndex1, unsigned int atomIndex2, unsigned int atomIndex3) const;
void getNeighborsForAtom(unsigned int atomIndex, vector< unsigned int>& atomNeighbors) const;
unsigned int getNumOfNeighbors(unsigned int atomIndex) const;
void getNeighborsForBondAtom(unsigned int atomIndex1, unsigned int atomIndex2, vector< unsigned int>& atom1Neighbors) const;
int readMol2file(istream& mol2stream);
Molecule< Mol2Atom> transformAtoms(RigidGroupTrans3Map& rigidGroupTransformations) const;
void updateTransformations(RigidGroupTrans3Map& rigidGroupTransformations) const;
const vector< const RigidGroup*> getRigidGroups(unsigned int atomIndex) const;
bool isClose(const Vector3& point) const;
void outputMol2File(ostream& output) const;
void outputMol2File(ostream& output, const RigidTrans3& trans) const;
void outputMol2File(RigidGroupTrans3Map& transformations, ostream& output) const;
class FeatureSetAttributes ;
// Constructors
RigidGroup* createRigidGroup(int groupId);
// Inspectors
const vector< Feature*>& getFeatures() const ;
const Feature* getFeature(unsigned int featureID) const ;
unsigned int numberOfFeatures() const ;
string getFeaturesFileName() const;
string getPymolFileName() const;
void getFeatureAttributes(FeatureSetAttributes& attributes) const;
static void getFeatureAttributes(const vector< const Feature*>& someFeatures, FeatureSetAttributes& attributes);
static void getFeatureAttributes(const Feature* aFeature, FeatureSetAttributes& attributes);
void getFeaturesInBall(const Vector3& point, float radius, HashResult< Feature*>& result) const ;
float getFeatureRadiusForCenterFit(int featureID) const ;
float getFeatureWeight(int featureID) const ;
float calculateActualScoreByFeatures(int bitset) const;
int calculateActualNumOfFeatures(int bitset) const;
// Setters
void setFeatureValidity(int featureID, bool valid) ;
void setFeatureWeight(int featureID, float w) ;
void setFeatureRadiusForCenterFit(int featureID, float r) ;
void resetValidityAndWeight(int featureID) ;
void resetValidityAndWeight() ;
// Output
void dumpFeatures(ostream& output) const ;
void outputFeaturesMol2File(ostream& output) const;
void outputFeaturesMol2File(ostream& output, const RigidTrans3& trans) const;
void outputFeaturesMol2File(ostream& output, int bitSet) const;
void outputFeaturesMol2File(RigidGroupTrans3Map& transformations, ostream& output) const;
void outputFeaturesMol2File(RigidGroupTrans3Map& transformations, ostream& output, int bitSet) const;
void preparePymolScript() const;
// Destructors
static float SECONDARY_FEATURE_WEIGHT;
protected:
void initAtomHash() ;
void prepareAtomIdMapping() ;
void markHinges();
void buildRigidGroups();
void orderRigidGroups();
void addHydrogensToRigidGroups();
void markCyclicBonds();
void markPeptideBonds();
void addDummyPointsOnRings();
void addDummyPointsOnTriangles();
bool isConnectedToElement(const leda::node u, const ELEMENT element) const;
unsigned int numberOfNeighboursWithElement(const leda::node u, const ELEMENT element) const;
unsigned int numberOfNeighboursWithAtomType(const leda::node u, const string atomType) const;
int numberOfBonds(const leda::node u) const ;
bool isConnectedToAtom(const leda::node u, const string atomName) const;
void outputMol2Header(ostream& output) const;
void outputMol2Bonds(ostream& output) const;
vector< RigidGroup*> rigidGroups_;
leda::UGRAPH< unsigned int, Bond> ligandGraphWithHydrogens;
leda::UGRAPH< unsigned int, Bond> ligandGraphWithoutHydrogens;
map< unsigned int, leda::node> atomId2NodeWithoutHydrogens_, atomId2NodeWithHydrogens_;
unsigned int id;
string name;
string mol2name_;
hash_map< unsigned int, unsigned int> atomId2Index_;
GeomHash< Vector3, const Mol2Atom*> atomHash_;
vector< Vector3> dummyPoints_;
static float maxAtomDistance2_;
vector< Feature*> features_;
vector< vector< const Feature*> > atomIndex2FeaturesMap_;
GeomHash< Vector3, Feature*> featuresHash_;
hash_map< int, int> samePositionFeatures_;
vector< int> featuresToGroups_;
vector< int> featuresToGroupsIndex_;
vector< vector< int> > featuresGroups_;

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Ancestors

Inheritance chain for FeaturedMolecule:

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Descendants

Class is not inherited by any others.

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