/* * File: atom.h * Author: flong * * Created on August 2, 2011, 6:38 PM */ #ifndef ATOM_H #define ATOM_H #ifndef KERNEL_H #include "kernel.h" #endif #ifndef RESTRAINTLISTS_H #include "restraintLists.h" #endif #ifndef RING_H #include "ring.h" #endif #ifndef CRYSTINFO_H #include "crystInfo.h" #endif namespace LIBMOL // temp { class NeighbList; class TreeSeg; class Bond; class BondDict; class BondList; class Angle; class AngleDict; class AngleList; class Torsion; class TorsionDict; class TorsionList; class Chiral; class ChiralList; class RestraintLists; class Ring; class RingDict; /* * Atom class describes the chemical entities, atoms etc. It derived publicly * from class Entity. * @Para: * (1) general properties * name; * elementName; * serNum-- the serial number in an assembly of atoms; * * (2) physical properties * type -- a parameter linked to bonding condition, used in * building molecules and forcefield optimization; * mass; * coordinates; * coordinate_exp--dictionary values of relative coordinates * coordinates_pre--coordinates in the previous moment; * force; * velocity; * acceleration; * * (3) PDB and x-ray related * * * * * */ enum hasType { UNDEFINED, DEFINED, NOTDETERMINED, DETERMINED }; class Atom { public: // default constructor Atom(); // copy constructor Atom(const Atom & tAtom); // destructor ~Atom(); std::string getName() const; void setName(std::string); int getSeriNum() const; void setSeriNum(int tN); Element getElementType() const; void setElementType(Element tElem); IDCode getID() const; void setIDCode(IDCode tID); ResName getResName() const; void setResName(ResName tName); SeriNumber getSeqNum() const; void setSeqNum(SeriNumber tN); InsCode getInsCode() const; void setInsCode(InsCode tID); SeriNumber getSegNum() const; void setSegNum(SeriNumber tN); IDCode getSegID() const; void setSegID(IDCode tID); ChainID getChainID() const; void setChainID(ChainID tID); SeriNumber getModSeriNum() const; void setModSeriNum(SeriNumber tN); REAL getMass() const; void setMass(REAL tMass); REAL getCharge() const; void setCharge(REAL tC); REAL getPartialCharge() const; void setPartialCharge(REAL tC); AltLoc getAltLoc() const; void setAltLoc(AltLoc tA); REAL getOccup() const; void setOccup(REAL tO); REAL getTempFact() const; void setTempFact(REAL tT); REAL getRadius() const; void setRadius(REAL tR); REAL getIonRadius() const; void setIonRadius (REAL tIR); // some data variables made public for efficiency //Cartesian coordinates of a atom in angstroms std::vector coords; // standard deviation of coordinates std::vector sigCoords; // the expected values of coordinates std::vector coords_exp; // the Cartesian velocities of the atom std::vector velos; // the Cartesian accelerations of the atom std::vector accels; // the forces acting on the atom std::vector forces; // sometime atom needs to remember the following std::vector coordsPre; std::vector velosPre; std::vector accelsPre; std::vector Uxx; // anisotropic temperature factors // U[0] = u11, U[1]=u22, U[2]=u33, // U[3] = u12, U[4]=u13, U[5]=u23 std::vector sigUxx; std::vector altLoc; std::list neighbAtoms; std::vector connectedAtoms; RestraintLists * allRestrLists; std::list treeSeg; // atom serial numbers only /* possible key-type for map types are * hydrogen bonding type * ligand type */ std::map types; std::map state; private : std::string itsName; int itsSeriNum; Element itsElementType; // the element type of an atom IDCode itsID; // atom role name. See PDB convention ResName itsResName; // amino acid abbreviation for an atom SeriNumber itsSeqNum; // Residue sequence number InsCode itsInsCode; // Code for insertion of residues SeriNumber itsSegNum; // segment serial number IDCode itsSegID; // segment identifier ChainID itsChainID; // the chain ID for an atom SeriNumber itsModNum; // the serial number of the model REAL itsMass; // the mass of an atom REAL itsCharge; // the charges linked with atomic number REAL itsPCharge; // the partial charge for an atom REAL itsRadius; // atom radius REAL itsIonRadius; // ionic radius for the atom // atoms in macromolecules from x-ray ( e.g. from PDB) AltLoc itsAltLoc; // alternate location indicator REAL itsOccup; // Occupancy for an atom REAL itsTempFact; // B value or temperature factor // standard deviations for some member variables REAL itsSigOcc; // standard deviation of occupancy REAL itsSigTemp; // standard deviation of temperature factor }; class AtomDict { public: //Default constructor AtomDict(); // Copy constructor AtomDict(const AtomDict & tAtom); // Initiate from class Atom AtomDict(const Atom & tAtom); // Destructor ~AtomDict(); int getNumAtomsWithin2stNB(std::vector & tAllAtoms); int getNum1stNbHave2edNb(std::vector & tAllAtoms); void setCodClass(); void outRingSec(); int getMinRing(); int getMinRing2(); void setBaseRingProps(); void setCodChemType(); void fromCodClassToEnerType(); void outNeighBAtoms(); int atomPosition(std::vector & tAtoms); // These are from Dictionary cif file int seriNum; ID resName; ID id; ID altId; ID chemType; Name enerType; REAL charge; REAL parCharge; REAL formalCharge; int formalChargeI; REAL radius; REAL ionRadius; int inChiralIdx; int chiralIdx; int bondingIdx; ID hybrid; int matType; // 0:org; 1:metal; 2:metalloid bool isMetal; ID metalGeo; REAL isoB; REAL ocp; int symmMult; int excessElec; // These are CCP4 related ID ccp4Type; // These are COD related ID cChemType; // COD element ID with sp2 info ID codClass; int codMolIdx; ID codCifName; ID codAtmRoot; ID codNBSymb; ID codNB2Symb; ID codNB3Symb; ID codAtmMain; ID codNB1NB2_SP; ID codNB1NB2_ExElec; int hashingValue; bool coordExist; int numPi; bool isCChemTypeSet; bool isInPreCell; bool chiralChecked; bool isInAromRing; bool isInSP2Ring; bool fromCalc; // symmetry-related ID sId; ID symmOp; int fromOrig; // int bondingIdx; /* meaning of curBondingIdx * 0 undetermined * 1 sp1 * 2 sp2 * 3 sp3 * 4 sp3d * * int chiralIdx; * -1 a plane center * 0 undetermined * 1 chiral center */ // atom type in small molecule cif ID sMolType; std::vector codClassV; std::map existProps; // existProps may have the following keys // 1. Coords // 2. ChemType // 3. EnerType; // 4. ParCharge; std::vector coords; std::vector fracCoords; std::vector forces; std::vector connAtoms; std::vector connHAtoms; // H atoms connected to this atom std::vector connMAtoms; // Metal atoms connected to this atom std::vector neighbAtoms; std::map NBAtomMap; std::vector inBonds; std::vector bondLengths; std::vector inAngles; std::vector inRings; std::vector inRingsFull; std::vector inChirals; std::vector< std::string > nbRep; std::map ringRep; std::map ringRepS; std::map ringRepBySeriNum; std::map baseRingProp; std::map > tree; REAL treeBond; REAL treeAngle; REAL treeTorsion; // element 1: immediate neighbor // element 2: include neighbor of // of neighbor atoms // => codClass // element 3: one more neighbor layers // than key 2 std::vector formType; }; class metalCluster { public: // Default constructor metalCluster(); // Copy constructor metalCluster(const metalCluster & tMC); // Default destructor ~metalCluster(); void setMetClusterFormu(std::vector & tAtoms); std::string setOneAtomFormu(std::vector & tAtoms, int tCenSerial); void buildBondAndAngleMap(std::vector & tAtoms, std::vector::iterator tCryst); void setOrgRingsInMetalCluster(std::vector & tAtoms, int tCenSerial); void projectCoordsToUnitSph(std::vector & tAtoms); int metSeril; std::vector ligandSerilSet; std::string formu; std::string coordGeoID; std::map > > ligandNBs; std::map ligandForma; // or use atom types // of the acedrg style std::map > uniqBondsMap; std::map > > uniqAngsMap; std::map > > secondNBAngsMap; std::map > > allAngs; std::map > angVect; std::vector > unitCoords; std::vector allRings; }; extern int getAtom(std::string tId, int tSeri, std::vector & tAtoms); extern void setAtomsAltId(std::vector & tAtoms); extern void setMetalConnAtm(std::vector & tAtom); } #endif /* ATOM_H */