Library ligand_pharma

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Classes

AromaticRing

Implementation Note (Oranit): There are aromatic groups that are not rings. Currently, we ignore these groups. However, in the future we may consider adding a new class called AromaticGroup that will extend Feature and the current AromaticRing class will be its subclassL: AromaticRing extends AromaticGroup extends Feature

Assembly

BPEdge

the BPEdge keeps the source node, the BPEdge itself is stored inside target BPNode

BPNode

BestKSum

BestKTuples

BestKoutOfDBestK

BipartiteMatcher

BitVectors

Bond

CarboxyEsterFeature

Cell

Charge

ColorCoder

CompareCell

CompareMoleculesRigidGroupsNum

CompareMultipleResultNodes

CompareMultipleResults

ComparePairwiseResult

CompareTuples

CompareVotes

DBEvaluator

DBScreener

EvalData

Evaluator

FMatch

Defines a match object used to build and refine matches between Molecule type objects. Matches are build by matching pairs of Particles from each Molecule.

FastClusterer

This clustering technique is very coarse and therefore efficient in fast reduction of transformations number. FastClusterer first clusters transformations according to rotational parameters and after that applies RMSD clustering in each such cluster. TransT template should be like TransT in RMSDCluster class

Feature

FeatureBipartiteMatcher

FeaturedMolecule

FeaturedRigidGroup

GraphCircleFinder

This class implements an algorithm for finding inner circles in a given graph, namely circles that do not contain other circles.

GraphDFS

GraphUtils

GroupEdge

HB

HTMLWriter

Hydrophobe

JmolWriter

LigandLoader

LigandMolecule

MARepresentor

MatchLigands

Mol2

The Mol2 class defines a set of tools used for reading a file in Tripos Mol2 format.

Mol2Atom

This is a general class to hold an atom as it appears in a Mol2 file.

MultiAlg

MultiRes

MultipleResult

MultipleResultCluster

MultipleResultGraph

MultipleResultNode

MultipleResultPath

NTuple

PairwiseGenerator

PairwiseResult

PairwiseResultCompletion

Pharmacophore

PharmacophoreData

PharmacophoreSearcher

PivotRMSDEvaluator

RMSDCluster

Template intended to provide a good quality clustering of transformations, using the distance between two transformations as the RMSD of the picture on a set of points. (the set of points is given by the user in the preProcessing stage). RMSDCluster provides two clustering algorithms - one is faster and less accurate, while the other is more thorough but is limited by the number of transformations it can handle. The decision of which algorithm to use is left to the user, who can determine with the useFastClustering method to use the faster algorithm. The user is also required to supply the hash cube size for the fast clustering. The larger the cube size the more accurate the algorithm is, but also there will be more transformations in each bin and so the algorithm will be slower. Both algorithms are iterative trying to join pairs of close transformatins using a weighted average heuristic. The difference is that the thorough algorithm calculates the entire distance matrix of all the transformations at once and then continuessly contracts the smallest edge that connects vertices that were not used in this iteration, while the faster algorithm uses a hash table and at first only clusters transformations which put the centroid of the molecule in close locations. Calculation of the distance between any two rigid transformation is O(n) in complexity, where n is the number of points, given in the pre-processing stage.

RefMARepresentor

RigidGroup

RotatableBond

RotatableBondAngleMap

ScoredMatched

ScoredMatchedList

SubsetCut

UserDefFeature

UserDefineFeatureInput

VolumeGrid

Vote

VoteTable

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Data

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Global Functions

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bool reconstructTree(Cell& cell, PairwiseResult& result, vector< BPNode*>& orderedBPNodes, int treeNum);

bool reconstructTree(Cell& cell, PairwiseResult& result, vector< BPNode*>& orderedBPNodes, int treeNum);

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bool reconstructTrees(vector< PairwiseResult>&results, vector< BPNode*>& orderedBPNodes, unsigned int resultsNum, PairwiseResult templateRes);

returns true if ALL possible trees were constructed within the K we asked for

bool reconstructTrees(vector< PairwiseResult>&results, vector< BPNode*>& orderedBPNodes, unsigned int resultsNum, PairwiseResult templateRes);

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void bestKTrees(vector< BPNode*>& orderedBPNodes, int K);

void bestKTrees(vector< BPNode*>& orderedBPNodes, int K);

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enum CARBOXY_ESTER_TYPE ;

This enum defines the different types of a carboxy ester feature - Lactone: O=C-O-C where C-O-C are on a ring - Carboxy Aryl-Ester: O=C-O-C not on a ring - P Variant Carboxy Ester: 1. P connected to 4 oxygens in 3 single bonds and 1 double bond: O O-P=O O C 2. P connected to 3 oxygens in single bonds and 1 double bond to S O O-P=S O C - Thio Lactone: O=C-S-C where the C-S-C are on a ring - Thio Aryl Ester: O=C-S-C where the C-s-C are not on a ring

NOTE: The order of the different types is according to their priority, where lactone is the most important type. Also, the type values correspond to their score weights.

enum CARBOXY_ESTER_TYPE {LACTONE = 4, 
			 CARBOXY_ARYL_ESTER = 3,
			 P_VARIANT_CARBOXY_ESTER = 2,
			 THIO_LACTONE = 1,
			 THIO_ARYL_ESTER = 0};

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double calculateRMSD(const vector< Vector3>& mol1, const vector< Vector3>& mol2);

double calculateRMSD(const vector< Vector3>& mol1, const vector< Vector3>& mol2);

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enum FEATURE_TYPE ;

enum FEATURE_TYPE {HYDROPHOBIC = 0, AROMATIC = 1, hDONOR = 2, hACCEPTOR = 3, POSITIVE = 4, NEGATIVE = 5, USER_DEF = 6, NUM_OF_FEATURE_TYPES = 7};

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enum HYBRIDIZATION_TYPE ;

Different Hybridization types of an atom

enum HYBRIDIZATION_TYPE { SP, SP2, SP3, UNKNOWN_SP };

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enum ELEMENT ;

The periodic table elements

enum ELEMENT {CARBON, NITROGEN, PHOSPHORUS, HYDROGEN, FLUORINE, 
	      CHLORINE, BROMINE, IODINE, SILICON, OXYGEN, 
	      SULFUR, SODIUM, POTASSIUM, CALCIUM, LITHIUM, 
	      ALUMINUM, HALOGEN, IRON, FERRUM = IRON, 
	      MAGNESIUM, CHROMIUM, MANGANESE, COBALT, 
	      COPPER, ZINC, SELENIUM, MOLYBDENUM,
	      TIN,UNKNOWN_ELEMENT };

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define FEATURE_STAMP_LENGTH 20

#define FEATURE_STAMP_LENGTH 20

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typedef char FeatureStamp[FEATURE_STAMP_LENGTH];

typedef char FeatureStamp[FEATURE_STAMP_LENGTH];

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enum USER_FEATURE_TYPE ;

enum USER_FEATURE_TYPE {UNSPECIFIED_USER_FEATURE_TYPE, CARBOXY_ESTER};

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