/* * File: codClassify.h * Author: flong * * Created on April 4, 2012, 5:48 PM * Last modified July 27, 2016 */ #ifndef CODCLASSIFY_H #define CODCLASSIFY_H #ifndef KERNEL_H #include "kernel.h" #endif #ifndef FILE_H #include "file.h" #endif #ifndef ATOM_H #include "atom.h" #endif #ifndef LIBG_ATOMASSEMBLY_H #include "atomAssembly.h" #endif #ifndef MOLECULE_H #include "molecule.h" #endif #ifndef BOND_H #include "bond.h" #endif #ifndef ANGLE_H #include "angle.h" #endif #ifndef TORSION_H #include "torsion.h" #endif #ifndef RESIDUE_H #include "residue.h" #endif #ifndef RING_H #include "ring.h" #endif #ifndef PLANE_H #include "plane.h" #endif #ifndef CHAIN_H #include "chain.h" #endif #ifndef LIBG_MODEL_H #include "libgmodel.h" #endif #ifndef SSBOND_H #include "ssbond.h" #endif #ifndef LIBG_LINK_H #include "libglink.h" #endif #ifndef CRYSTINFO_H #include "crystInfo.h" #endif #ifndef SECONDARYSTRUCTURES_H #include "secondaryStructures.h" #endif #ifndef ALLSYSTEM_H #include "AllSystem.h" #endif #ifndef UTILITY_H #include "utility.h" #endif #ifndef PERIODICTABLE_H #include "periodicTable.h" #endif #ifndef CIFFILE_H #include "DictCifFile.h" #endif #ifndef CHEMPROPSET_H #include "chemPropSet.h" #endif namespace LIBMOL { class AtomDict; class BondDict; class Ring; class RingDict; class Angle; class AngleDict; class Torsion; class TorsionDict; class Chiral; class Plane; class PlaneDict; class PeriodicTable; class DictCifFile; class DictPDBFile; class AllSystem; struct aValueSet { REAL value; REAL sigValue; int numCodValues; }; // an AtomTree is a representative of atom types class AtomTree { public: //Default constructor AtomTree(); // Copy constructor AtomTree(const AtomTree & tAtTree); //Constructor using a COD atom class AtomTree(ID & tCodClass); //Destructor ~AtomTree(); void sortedTree(); int scoreParents(); int scoreChilds(); int scoreTree(); ID root; std::map > family; }; class AtomForest { public: // Default constructor AtomForest(); // Copy Constructor AtomForest(const AtomForest & tAtForest); // Constructor using a vector of AtomTree AtomForest(std::vector & tAtoms); //Destructor ~AtomForest(); // }; struct NB1stFam { std::string name; std::vector NB2ndList; int repN; }; class CodClassify { public : // Default constructor CodClassify(); CodClassify(const std::vector & tAtoms); CodClassify(const std::vector & tAtoms, const std::vector & tHAtomIdx, const std::vector & tBonds, const std::vector & tAngles, const std::vector & tTorsions, const std::vector & tChirals, const std::vector & tPlans, const std::map > & tRings, std::string tLibmolTabDir); CodClassify(const std::vector & tAtoms, const std::vector & tHAtomIdx, const std::vector & tBonds, const std::vector & tAngles, const std::vector & tTorsions, const std::vector & tChirals, const std::vector & tPlans, const std::map > & tRings, std::string tLibmolTabDir, int nTM); CodClassify(const std::vector & tAtoms, const std::vector & tHAtomIdx, const std::vector & tBonds, const std::vector & tAngles, const std::vector & tTorsions, const std::vector & tChirals, const std::vector & tPlans, const std::map > & tRings, std::string tLibmolTabDir, int nTM, bool tMdPls); CodClassify(const std::vector & tAtoms, const std::vector & tHAtomIdx, const std::vector & tBonds, const std::vector & tAngles, const std::vector & tTorsions, const std::vector & tChirals, const std::vector & tPlans, const std::map > & tRings, std::string tLibmolTabDir, int nTM, const double tUBS, const double tLBS, const double tUAS, const double tLAS); // Constructor by a DictCifFile object CodClassify(const DictCifFile & tCifObj, std::string tLibmolTabDir); // Constructor by a Mol/Sdf molecules CodClassify(const std::vector & tMols, std::string tLibmolTabDir); // Constructor using a general system CodClassify(const AllSystem & tAllSys); // Destructor ~CodClassify(); void setupSystem(); void setupSystem2(); void setupSystem3(); // get CCP4 energy lib void getCCP4BondAndAngles(); // General functions int atomPosition(ID tID); // Transfering between atoms and COD classes void codAtomClassify(int dLev); void codAtomClassify2(int dLev); void codAtomClassifyNew(int dLev); void codAtomClassifyNew2(int dLev); void codAtomClassifyNew3(int dLev); void getSmallFamily(std::string tInStr, NB1stFam & aNBFam); void codClassToAtom(ID & tCC, AtomDict & tAt); void codClassToAtom2(ID & tCC, AtomDict & tAt); void codClassToAtomAng(ID & tCC, AtomDict & tAt); void codClassToAtomAng2(ID & tCC, AtomDict & tAt); void codNBProps(std::vector tarStrs, std::vector & tCTs, std::vector & tNB2s, std::vector & tRis, std::vector & tPls); // the "distances" (or dissimilarities) between two atom int codAtomsDist(std::vector tarStrs, std::vector tNBs, int tLev); int codAtomsChemTypeDist(std::vector & tarCTs, std::vector & tarRis, std::vector & tarPls, std::vector & bCTs, std::vector & bRis, std::vector & bPls); int codAtomsNumNBDist(std::vector & tNB2s, std::vector & bNB2s); // Ring detecting related methods void ringDetecting(); void ringDetecting2(); //a recursive function void checkOnePathSec(std::vector & seenAtoms, std::map & seenIDs, AtomDict & curAto, int iMax, std::vector::iterator iAto); void checkOnePathSec(AtomDict & curAto, int iMax, std::vector::iterator iOriAto, int SeriNumPreAto, int curLev, std::map & seenAtomIDs, std::map & atomIDsInPath); void checkOnePathSec2(AtomDict & curAto, int iMax, std::vector::iterator iOriAto, int SeriNumPreAto, int curLev, std::map & seenAtomIDs, std::map & atomIDsInPath); void setAtomCodClassName(AtomDict &tAtom, AtomDict &tOriAtom, int tLev); void setAtomCodClassName2(AtomDict &tAtom, AtomDict &tOriAtom, int tLev); void setAtomCodClassNameNew(AtomDict &tAtom, AtomDict &tOriAtom, int tLev); void setAtomCodClassNameNew2(AtomDict &tAtom, AtomDict &tOriAtom, int tLev); void setAtomCodClassNameNew3(AtomDict &tAtom, AtomDict &tOriAtom, int tLev); void outRingSec(AtomDict & tAtom); void outRingSec2(AtomDict & tAtom); void outRingSecNew(AtomDict & tAtom); void outRingSecNew2(std::string & tAtmCodStr, AtomDict & tAtom); std::string outRingSecStr(AtomDict &tAtom); // Methods related to planarity generation (depending // also on if rings have been detected //void setAtomsBondingAndChiralCenter(); // use the standalone function in chemPropSet // Plane-related void detectPlaneGroups(); void groupOrgAtomsToPlanes(); void groupMetAndLigandAtomsToPlanes(); // this could be use both early and late stage of a process void setSmallestPLs(std::vector & tSmaPls); void mergeLargePLGroups(std::vector & tSmaPls); bool checkATorsAtomsInPla(std::vector & tAtms); int checkATorsAtomsInAroRing(int tAtm1, int tAtm2); // Ring-related bool furtherM(std::vector &tV1, std::vector &tV2); bool isInSameRing(PlaneDict & tP1, PlaneDict & tP2); // Relations between torsion angles and ring // Atom hashing related void readTablesForHashing(std::map & tDigitKeys, std::map & tLinkedHA); void readTablesForHashing2(std::map & tDigitKeys, std::map & tLinkedHA); void hashingAtoms(); void hashingAtoms2(); void setAtomsNBSymb(); void setAtomsNBSymb2(); // void setAtomsNB1NB2_SP(); // Tree-related void setAtomsMST(); // Bonds relate void setDefaultOrgBonds(); void setOrgBondHeadHashList(); void setOrgBondHeadHashList2(); void groupHashAndSpAndRingBonds(); void groupHashAndSpBonds(); void groupCodOrgBonds(); void groupCodOrgBonds2(); void groupCodOrgBonds3(); void searchCodOrgBonds(std::vector::iterator iOB); void searchCodOrgBonds2(std::vector::iterator iB); void searchCodOrgBonds2_2(std::vector::iterator iB); void levelSearchBonds(std::vector & tKeySet1, std::vector & tKeySet2, int tLev, int tNumTh, std::vector::iterator iB); void levelSearchBondsT(std::vector & tKeySet1, std::vector & tKeySet2, int tLev, int tNumTh, std::vector::iterator iB); void interLevelSearchBonds( std::vector & tKeySet1, std::vector & tKeySet2, int tStartLev, int tNumTh, std::vector::iterator iB); void exchangeSearch(std::vector & tKeySet1, std::vector & tKeySet2, std::string & tSKey, int tLev, std::vector::iterator iB); void groupCodMetBonds(); void searchCodMetBonds(std::vector::iterator iMB); void setupTargetMetBondsUsingMean(std::vector > tSkeys, std::vector::iterator tB); void searchCodBonds(); void searchBondHashAndSP(std::vector::iterator iB); void getCCP4Bonds(std::vector::iterator tB, ID tAtm1, ID tAtm2); // TEMP, should replace getCCP4Bonds before committing it void getCCP4Bonds2(std::vector::iterator tB, ID tAtm1, ID tAtm2); void setCCP4BondByMode(std::vector::iterator tB, ID tAtm1, ID tAtm2, ID tOrdS, std::map & tPosM); void setCCP4Mix(std::vector::iterator tB, ID tAtm1, ID tAtm2, ID tOrdS, int tMode); // !!!!!!! These are newly added for using sqlite3 search engine //void searchCodBondsUsingSqlite3(); //void searchOneOrgBondFromCodUsingSqlite(sqlite3 * tCombDB, // std::vector::iterator tB); // bool searchOneOrgBondUsingSqliteL(sqlite3 * tCombDB, // std::vector::iterator tB, // int & tLev, // std::map tPropNB, // std::map tPropHash); void setQueStr(std::string & tQue, int tLev, std::map tPropNB, std::map tPropHash); void setOneBondByMean(std::vector > & tResults, std::vector::iterator tB); void setOneBondByDist(std::vector > & tResults, std::vector::iterator tB); //End !!!!!!! void setupTargetBondsUsingSymblDist(std::vector & tBonds, std::vector::iterator tB, int tLev); void setupTargetBondsUsingSymblDist2(std::vector & tBonds, std::vector::iterator tB, int tAs0, int tAs1, int tLev); void constrBondSigmas(); // Using meaning values when secondary NBs have the same "space" // such as "c[6,6]-3:n[5,6]-3:N[5]-2:" void setupTargetBondsUsingMean(std::vector & tBonds, std::vector::iterator tB); void setupTargetBondsUsingValueSetMean(std::vector & tSets, std::vector::iterator tB); void setValueSet(aValueSet & tVs, std::vector & tVecVs); void setupTargetBonds(); void setupTargetBonds2(); void setupTargetBondsUsingSqlite(); void addAtomClassToBonds(std::vector & tBonds); // Bond angles related void setDefaultOrgAngle(); void addAtomClassToAngles(std::vector &tAngles); void initTargetAngles(); // generate target angles based on atoms and bonds void setDefaultCoordGeos(); void setOrgAngleHeadHashList(); void setOrgAngleHeadHashList2(); void setOrgAngleHeadHashList22(); void groupHashAndSpAngles(); void groupCodOrgAngles(); void groupCodOrgAngles2(); void groupCodOrgAngles22(); void searchCodOrgAngles(std::vector::iterator iAN); void searchCodOrgAngles2(std::vector::iterator iAN); void searchCodOrgAngles22(std::vector::iterator iAN); void levelSearchAngles( std::vector & tKeySet, std::vector & tKeySet2, int tLev, int tNumTh, std::vector::iterator iAN); void levelSearchAnglesENG( std::vector & tKeySet, std::vector & tKeySet2, int tLev, std::vector::iterator iAN); std::string matchRandCenterA(std::string & tR, std::string tCen, std::map > tDictAngs); bool searchCodOrgAnglesCen(std::vector::iterator iAN, int tHa1, int tHal2, int tHa3); bool getCCP4Angle(std::vector::iterator tAN); // bond-angles involving metal atoms as NB atoms void groupCodMetAngles(); void getIdealCNGeoAngles(std::vector::iterator iAN); void getCN10PentAntiPros(std::vector::iterator iAN); REAL getOnebond(ID aID1, ID aID2); void searchCodMetAngles(std::vector::iterator iAN); void groupCodAnglesWithNonCenteredMetal(); ID getMatchedKey(std::vector tKeys, ID tTarget, std::vector tIdxs); void getMatched2dVect(std::vector >tPairs, std::vector aPair, std::vector tIdxs, int & rIdx); void getMatched3dVect(std::vector >tPairs, std::vector aPair, std::vector tIdxs, int & rIdx); void getMatched4dVect(std::vector >tPairs, std::vector aPair, std::vector tIdxs, int & rIdx); void getMatched5dVect(std::vector >tPairs, std::vector aPair, std::vector tIdxs, int & rIdx); void searchCodAnglesWithNonCenteredMetal(std::vector::iterator iAN); void searchCodAngles(); void searchCodAngles2(); void setupTargetAngleUsingdist(std::vector & tAngles, std::vector::iterator tA, int tLev); void setupTargetAngleUsingdist2(std::vector & tAngles, std::vector::iterator tA, int as2, int as3, int tLev); void setupTargetAngleUsingdistAng(std::vector & tAngles, std::vector::iterator tA, int tLev); void setupTargetAngleUsingMean(std::vector & tAngles, std::vector::iterator tA); void setupTargetAngleUsingMean2(std::vector & tAngles, std::vector::iterator tA, int tHa1, int tHa2, int tHa3, ID tR3A, ID tA1NB2, ID tA2NB2, ID tA3NB2); void setupTargetAngleUsingMean3(std::vector & tAngValues, std::vector & tAngNums, std::vector::iterator tA); void setupTargetAngles(); void setupTargetAngles2(); // angles using sqlite3 //void setupTargetAnglesUsingSqlite(); //void searchCodAnglesUsingSqlite(); //void searchOneOrgAngleFromCodUsingSqlite(sqlite3 * tCombDB, // std::vector::iterator tA); //bool searchOneOrgAngleUsingSqliteL(sqlite3 * tCombDB, // std::vector::iterator tA, // int & tLev, // std::map tPropNB, // std::string tA1C); void setQueStrAn(std::string & tQue, int tLev, std::map tPropNB, std::string tA1C); void setOneAngleByMean(std::vector >& tResults, std::vector::iterator tA); void checkAngConstraints(); void checkSP2Constraints(std::vector tAngIdxs); void checkSP3Constraints(std::vector tAngIdxs); void checkRingAngleConstraints(std::vector::iterator iRv); bool checkSpeAng(std::vector::iterator tA); void setSpecialAngles(std::map > & tAngs); void setOneSetBoronAngles(std::map >::iterator tAs); void setOneSetCarbonAngles(std::map >::iterator tAs); // Torsion angles related void setupMiniTorsions(); void selectOneTorFromOneBond(ID tS, std::vector & tTors); void setupTargetTorsions(); void fixTorIDs(); // void setupAllTargetValues(); void setupAllTargetValues2(); void setupAllStdValues(); // Initiate a set of dummy atoms for (the torsion space) void initDummyAtoms(); // int checkNumInLevel(); void goToLeveL(int tLev); // Output void initRoughCoords(); void initRoughCoordsTor(); void outRestraintCif(FileName tFName); void outRestraintCif(FileName tFName, ID tMonoRootName); // temporally for outRestraintCif2 void outRestraintCif2(FileName tFName, ID tMonoRootName); void outPDB(FileName tFName); void outPDB(FileName tFName, ID tMonoRootName); void outAtomTypes(ID tMonoRootName); void getAnglesFromPDB(ID tFName); void setSpecial3NBSymb(std::vector::iterator tAt); void setSpecial3NBSymb2(std::vector::iterator tAt); // This should be moved into another specifically designed sqlite3 class //void sqlite3Query(sqlite3 * tDB, // SqliteStatment tQue, // std::vector > & tResult); int wSize; std::string libmolTabDir; double upperBondSig; double lowBondSig; double upperAngleSig; double lowAngleSig; bool lMdPls; PeriodicTable * pPeriodictable; std::vector allAtoms; std::vector allHAtomIdx; // bonds std::vector allBonds; std::vector allDictBonds; std::map > > > > > > >allDictBondsIdx; std::map > > > > > > allDictBondsIdx1; std::map > > > > allDictBondsIdx2; std::map > > allDictBondsIdx3; std::map > > > > allDictPreMetBonds; std::map > > > > > allDictMetBonds; //DB3 std::vector allDictBondsD; std::map > > > > > > > > > > >allDictBondsIdxD; std::map > > > > > > > > > >allDictBondsIdx1D; std::map > > > > > > > > allDictBondsIdx2D; std::map > > > > allENBonds; std::map > > > > allHaAndSpBonds; std::map > > > allHaAndSpBonds1D; std::map > > allHaAndSpBonds2D; // std::vector allDictAnglesD; //std::map > > > > > > > > > > > > > > > > > > allDictAnglesIdxD; std::map > > > > > > > > > > > > > > > > allDictAnglesIdx1D; std::map > > > > > > > > > > > > > allDictAnglesIdx2D; std::map > > > > > > > > > > allDictAnglesIdx3D; std::map > > > > > > > allDictAnglesIdx4D; std::map > > > > allDictAnglesIdx5D; // angles std::vector allAngles; std::map > > allAnglesIdxs; std::vector allDictAngles; std::map > > > > > > > allHaAndSpAngles; std::map > > > allHaAndSpAngles1D; /* std::map > > > > > > > > > > > allDictAnglesIdx; std::map > > > > > > > > > allDictAnglesIdx1; std::map > > > > > > allDictAnglesIdx2; std::map > > > allDictAnglesIdx3; */ std::map DefaultOrgAngles; std::map DefaultCoordGeos; std::map > DefaultCoordGeos2; std::map > > allDictCoordGeoAngs; std::map > > > > > allDictNonCenMetAnglesIdx; std::vector allTorsions; std::vector miniTorsions; std::vector allChirals; std::vector allPlanes; std::map > allRings; std::vector allRingsV; std::vector allHydroAtoms; std::vector allDummyAtoms; std::map codOrgBondFiles; std::map codOrgBondFiles2; std::map codOrgAngleFiles; std::map codOrgAngleFiles2; std::map > > ccp4Bonds; std::map > > > ccp4BondsA; std::map > > ccp4Angles; }; class CodBonds { public: // Default constructor CodBonds(); // Copy constructor CodBonds(const CodBonds & tCBonds); // Constructor with an input file name CodBonds(FileName tFname, std::ios_base::openmode tOpenMode); // Destructor ~CodBonds(); void setupSystem(); void sortCodTable(FileName tFname, std::vector & allSortLines); void setupSystem(std::vector & tAllLines); void getTargetBonds(std::vector & targetBs); std::vector allBonds; std::map > allBondsMap; // May use this one. // instead of allBonds std::ofstream outFile; std::ifstream inFile; }; class CodAngles { public: // Default constructor CodAngles(); //Copy constructor CodAngles(const CodAngles & tCAngles); //Constructor using with an input file name CodAngles(FileName tFname, std::ios_base::openmode tOpenMode); // Destructor ~CodAngles(); void setupSystem(); void getTargetAngles(std::vector & targetAs); std::vector allAngles; std::ofstream outFile; std::ifstream inFile; }; class CodTorsions { public : //Default constructor CodTorsions(); //Copy constructor CodTorsions(const CodTorsions & tCT); // Constructor using a file name CodTorsions(FileName tFname, std::ios_base::openmode tOpenMode); // Destructor ~CodTorsions(); void setupSystem(); void getTargetTorsions(std::vector & targetTs); std::vector allTorsions; std::ofstream outFile; std::ifstream inFile; }; extern void outB_and_A_Levels(FileName tFName, std::vector & tAtoms, std::vector & tBonds, std::vector & tAngles); } #endif /* CODCLASSIFY_H */