BALL: PDBdefs.h Source File

00001 // -*- Mode: C++; tab-width: 2; -*-
00002 // vi: set ts=2:
00003 //
00004 // $Id: PDBdefs.h,v 1.8 2005/12/23 17:01:45 amoll Exp $
00005 //
00006 
00007 #ifndef BALL_FORMAT_PDBDEFS_H
00008 #define BALL_FORMAT_PDBDEFS_H
00009 
00010 #ifndef BALL_COMMON_H
00011 # include <BALL/common.h>
00012 #endif
00013 
00014 #ifndef BALL_KERNEL_ATOM_H
00015 # include <BALL/KERNEL/atom.h>
00016 #endif
00017 
00018 #ifndef BALL_KERNEL_SECONDARYSTRUCTURE_H
00019 # include <BALL/KERNEL/secondaryStructure.h>
00020 #endif
00021 
00022 #ifndef BALL_KERNEL_CHAIN_H
00023 # include <BALL/KERNEL/chain.h>
00024 #endif
00025 
00026 #ifndef BALL_KERNEL_RESIDUE_H
00027 # include <BALL/KERNEL/residue.h>
00028 #endif
00029 
00030 #ifndef BALL_DATATYPES_HASHSET_H
00031 # include <BALL/DATATYPE/hashSet.h>
00032 #endif
00033 
00034 #ifndef BALL_MATHS_MATRIX44_H
00035 # include <BALL/MATHS/matrix44.h>
00036 #endif
00037 
00038 namespace BALL 
00039 {
00040 
00041 
00047   namespace PDB 
00048   {
00051     enum
00052     {
00053       SIZE_OF_PDB_RECORD_LINE      = 80,
00054       SIZE_OF_PDB_LINE_BUFFER      = 256,   
00055       SIZE_OF_FORMAT_STRING_BUFFER = 256
00056     };
00057 
00060     enum RecordType
00061     {
00062       RECORD_TYPE__UNKNOWN = 0,
00063       RECORD_TYPE__ANISOU,
00064       RECORD_TYPE__ATOM,
00065       RECORD_TYPE__AUTHOR,
00066       RECORD_TYPE__CAVEAT,
00067       RECORD_TYPE__CISPEP,
00068       RECORD_TYPE__COMPND,
00069       RECORD_TYPE__CONECT,
00070       RECORD_TYPE__CRYST1,
00071       RECORD_TYPE__DBREF,
00072       RECORD_TYPE__END,
00073       RECORD_TYPE__ENDMDL,
00074       RECORD_TYPE__EXPDTA,
00075       RECORD_TYPE__FORMUL,
00076       RECORD_TYPE__FTNOTE,
00077       RECORD_TYPE__HEADER,
00078       RECORD_TYPE__HELIX,
00079       RECORD_TYPE__HET,
00080       RECORD_TYPE__HETATM,
00081       RECORD_TYPE__HETNAM,
00082       RECORD_TYPE__HETSYN,
00083       RECORD_TYPE__HYDBND,
00084       RECORD_TYPE__JRNL,
00085       RECORD_TYPE__KEYWDS,
00086       RECORD_TYPE__LINK,
00087       RECORD_TYPE__MASTER,
00088       RECORD_TYPE__MODEL,
00089       RECORD_TYPE__MODRES,
00090       RECORD_TYPE__MTRIX1,
00091       RECORD_TYPE__MTRIX2,
00092       RECORD_TYPE__MTRIX3,
00093       RECORD_TYPE__OBSLTE,
00094       RECORD_TYPE__ORIGX1,
00095       RECORD_TYPE__ORIGX2,
00096       RECORD_TYPE__ORIGX3,
00097       RECORD_TYPE__REMARK,
00098       RECORD_TYPE__REVDAT,
00099       RECORD_TYPE__SCALE1,
00100       RECORD_TYPE__SCALE2,
00101       RECORD_TYPE__SCALE3,
00102       RECORD_TYPE__SEQADV,
00103       RECORD_TYPE__SEQRES,
00104       RECORD_TYPE__SHEET,
00105       RECORD_TYPE__SIGATM,
00106       RECORD_TYPE__SIGUIJ,
00107       RECORD_TYPE__SITE,
00108       RECORD_TYPE__SLTBRG,
00109       RECORD_TYPE__SOURCE,
00110       RECORD_TYPE__SPRSDE,
00111       RECORD_TYPE__SSBOND,
00112       RECORD_TYPE__TER,
00113       RECORD_TYPE__TITLE,
00114       RECORD_TYPE__TURN,
00115       RECORD_TYPE__TVECT,
00116         
00117       NUMBER_OF_REGISTERED_RECORD_TYPES,
00118       
00119       ALL_RECORD_TYPES
00120     };
00121 
00124     BALL_EXPORT extern const char* FORMAT_UNKNOWN;
00125     BALL_EXPORT extern const char* FORMAT_ANISOU;
00126     BALL_EXPORT extern const char* FORMAT_ATOM;
00127     BALL_EXPORT extern const char* FORMAT_ATOM_PARTIAL_CRG;
00128     BALL_EXPORT extern const char* FORMAT_AUTHOR;
00129     BALL_EXPORT extern const char* FORMAT_CAVEAT;
00130     BALL_EXPORT extern const char* FORMAT_CISPEP;
00131     BALL_EXPORT extern const char* FORMAT_COMPND;
00132     BALL_EXPORT extern const char* FORMAT_CONECT;
00133     BALL_EXPORT extern const char* FORMAT_CRYST1;
00134     BALL_EXPORT extern const char* FORMAT_DBREF;
00135     BALL_EXPORT extern const char* FORMAT_END;
00136     BALL_EXPORT extern const char* FORMAT_ENDMDL;
00137     BALL_EXPORT extern const char* FORMAT_EXPDTA;
00138     BALL_EXPORT extern const char* FORMAT_FORMUL;
00139     BALL_EXPORT extern const char* FORMAT_FTNOTE;
00140     BALL_EXPORT extern const char* FORMAT_HEADER;
00141     BALL_EXPORT extern const char* FORMAT_HELIX;
00142     BALL_EXPORT extern const char* FORMAT_HET;
00143     BALL_EXPORT extern const char* FORMAT_HETATM;
00144     BALL_EXPORT extern const char* FORMAT_HETNAM;
00145     BALL_EXPORT extern const char* FORMAT_HETSYN;
00146     BALL_EXPORT extern const char* FORMAT_HYDBND;
00147     BALL_EXPORT extern const char* FORMAT_JRNL;
00148     BALL_EXPORT extern const char* FORMAT_KEYWDS;
00149     BALL_EXPORT extern const char* FORMAT_LINK;
00150     BALL_EXPORT extern const char* FORMAT_MASTER;
00151     BALL_EXPORT extern const char* FORMAT_MODEL;
00152     BALL_EXPORT extern const char* FORMAT_MODRES;
00153     BALL_EXPORT extern const char* FORMAT_MTRIX1;
00154     BALL_EXPORT extern const char* FORMAT_MTRIX2;
00155     BALL_EXPORT extern const char* FORMAT_MTRIX3;
00156     BALL_EXPORT extern const char* FORMAT_OBSLTE;
00157     BALL_EXPORT extern const char* FORMAT_ORIGX1;
00158     BALL_EXPORT extern const char* FORMAT_ORIGX2;
00159     BALL_EXPORT extern const char* FORMAT_ORIGX3;
00160     BALL_EXPORT extern const char* FORMAT_REMARK;
00161     BALL_EXPORT extern const char* FORMAT_REVDAT;
00162     BALL_EXPORT extern const char* FORMAT_SCALE1;
00163     BALL_EXPORT extern const char* FORMAT_SCALE2;
00164     BALL_EXPORT extern const char* FORMAT_SCALE3;
00165     BALL_EXPORT extern const char* FORMAT_SEQADV;
00166     BALL_EXPORT extern const char* FORMAT_SEQRES;
00167     BALL_EXPORT extern const char* FORMAT_SHEET;
00168     BALL_EXPORT extern const char* FORMAT_SIGATM;
00169     BALL_EXPORT extern const char* FORMAT_SIGUIJ;
00170     BALL_EXPORT extern const char* FORMAT_SITE;
00171     BALL_EXPORT extern const char* FORMAT_SLTBRG;
00172     BALL_EXPORT extern const char* FORMAT_SOURCE;
00173     BALL_EXPORT extern const char* FORMAT_SPRSDE;
00174     BALL_EXPORT extern const char* FORMAT_SSBOND;
00175     BALL_EXPORT extern const char* FORMAT_TER;
00176     BALL_EXPORT extern const char* FORMAT_TITLE;
00177     BALL_EXPORT extern const char* FORMAT_TURN;
00178     BALL_EXPORT extern const char* FORMAT_TVECT;
00180 
00183     BALL_EXPORT extern const char* RECORD_TAG_ANISOU;
00184     BALL_EXPORT extern const char* RECORD_TAG_ATOM;
00185     BALL_EXPORT extern const char* RECORD_TAG_AUTHOR;
00186     BALL_EXPORT extern const char* RECORD_TAG_CAVEAT;
00187     BALL_EXPORT extern const char* RECORD_TAG_CISPEP;
00188     BALL_EXPORT extern const char* RECORD_TAG_COMPND;
00189     BALL_EXPORT extern const char* RECORD_TAG_CONECT;
00190     BALL_EXPORT extern const char* RECORD_TAG_CRYST1;
00191     BALL_EXPORT extern const char* RECORD_TAG_DBREF;
00192     BALL_EXPORT extern const char* RECORD_TAG_END;
00193     BALL_EXPORT extern const char* RECORD_TAG_ENDMDL;
00194     BALL_EXPORT extern const char* RECORD_TAG_EXPDTA;
00195     BALL_EXPORT extern const char* RECORD_TAG_FORMUL;
00196     BALL_EXPORT extern const char* RECORD_TAG_FTNOTE;
00197     BALL_EXPORT extern const char* RECORD_TAG_HEADER;
00198     BALL_EXPORT extern const char* RECORD_TAG_HELIX;
00199     BALL_EXPORT extern const char* RECORD_TAG_HET;
00200     BALL_EXPORT extern const char* RECORD_TAG_HETATM;
00201     BALL_EXPORT extern const char* RECORD_TAG_HETNAM;
00202     BALL_EXPORT extern const char* RECORD_TAG_HETSYN;
00203     BALL_EXPORT extern const char* RECORD_TAG_HYDBND;
00204     BALL_EXPORT extern const char* RECORD_TAG_JRNL;
00205     BALL_EXPORT extern const char* RECORD_TAG_KEYWDS;
00206     BALL_EXPORT extern const char* RECORD_TAG_LINK;
00207     BALL_EXPORT extern const char* RECORD_TAG_MASTER;
00208     BALL_EXPORT extern const char* RECORD_TAG_MODEL;
00209     BALL_EXPORT extern const char* RECORD_TAG_MODRES;
00210     BALL_EXPORT extern const char* RECORD_TAG_MTRIX1;
00211     BALL_EXPORT extern const char* RECORD_TAG_MTRIX2;
00212     BALL_EXPORT extern const char* RECORD_TAG_MTRIX3;
00213     BALL_EXPORT extern const char* RECORD_TAG_OBSLTE;
00214     BALL_EXPORT extern const char* RECORD_TAG_ORIGX1;
00215     BALL_EXPORT extern const char* RECORD_TAG_ORIGX2;
00216     BALL_EXPORT extern const char* RECORD_TAG_ORIGX3;
00217     BALL_EXPORT extern const char* RECORD_TAG_REMARK;
00218     BALL_EXPORT extern const char* RECORD_TAG_REVDAT;
00219     BALL_EXPORT extern const char* RECORD_TAG_SCALE1;
00220     BALL_EXPORT extern const char* RECORD_TAG_SCALE2;
00221     BALL_EXPORT extern const char* RECORD_TAG_SCALE3;
00222     BALL_EXPORT extern const char* RECORD_TAG_SEQADV;
00223     BALL_EXPORT extern const char* RECORD_TAG_SEQRES;
00224     BALL_EXPORT extern const char* RECORD_TAG_SHEET;
00225     BALL_EXPORT extern const char* RECORD_TAG_SIGATM;
00226     BALL_EXPORT extern const char* RECORD_TAG_SIGUIJ;
00227     BALL_EXPORT extern const char* RECORD_TAG_SITE;
00228     BALL_EXPORT extern const char* RECORD_TAG_SLTBRG;
00229     BALL_EXPORT extern const char* RECORD_TAG_SOURCE;
00230     BALL_EXPORT extern const char* RECORD_TAG_SPRSDE;
00231     BALL_EXPORT extern const char* RECORD_TAG_SSBOND;
00232     BALL_EXPORT extern const char* RECORD_TAG_TER;
00233     BALL_EXPORT extern const char* RECORD_TAG_TITLE;
00234     BALL_EXPORT extern const char* RECORD_TAG_TURN;
00235     BALL_EXPORT extern const char* RECORD_TAG_TVECT;
00237 
00241 
00242     typedef char   AChar;
00244     typedef char   Atom[5];
00246     typedef char   Character;
00248     typedef long   Continuation;
00250     typedef char   Date[10];
00252     typedef char   IDcode[5];
00254     typedef long   Integer;
00256     typedef char   PDBList[SIZE_OF_PDB_RECORD_LINE + 1];
00258     typedef char   LString[SIZE_OF_PDB_RECORD_LINE + 1];
00260     typedef char   LString2[3];
00262     typedef char   LString3[4];
00264     typedef char   LString4[5];
00266     typedef char   LString5[6];
00268     typedef char   LString6[7];
00270     typedef char   LString7[8];
00272     typedef char   LString8[9];
00274     typedef char   LString9[10];
00276     typedef char   LString10[11];
00278     typedef char   LString11[12];
00280     typedef char   LString12[13];
00282     typedef char   LString13[14];
00284     typedef char   LString21[22];
00286     typedef double Real;
00288     typedef char   RecordName[7];
00290     typedef char   ResidueName[4];
00292     typedef char   SList[SIZE_OF_PDB_RECORD_LINE + 1];
00294     typedef char   Specification[SIZE_OF_PDB_RECORD_LINE + 1];
00296     typedef char   SpecificationList[SIZE_OF_PDB_RECORD_LINE + 1];
00298     typedef char   PDBString[SIZE_OF_PDB_RECORD_LINE + 1];
00300     typedef char   String2[3];
00302     typedef char   String3[4];
00304     typedef char   String4[5];
00306     typedef char   String5[6];
00308     typedef char   String40[41];
00310     typedef long   SymmetryOperator;
00312 
00316 
00319     struct BALL_EXPORT RecordTypeFormat
00320     {
00321       public:
00322       RecordType    record_type;
00323       char          string[7];
00324       const char*   format_string;
00325     };
00326 
00327     struct BALL_EXPORT Residue
00328     {
00329       ResidueName name;
00330       Character   chain_ID;
00331       Integer     sequence_number;
00332       AChar       insertion_code;
00333       
00334       Residue() { clear(); }
00335       void clear()
00336       {
00337         name[0] = '\0';
00338         chain_ID = ' ';
00339         sequence_number = 0;
00340         insertion_code = ' ';
00341       }
00342       void set(const ::BALL::Residue& residue)
00343       {
00344         strncpy(name, residue.getName().c_str(), 3);
00345         sequence_number = residue.getID().toInt();
00346         const Chain* chain = residue.getChain();
00347         chain_ID = (chain == 0 ? ' ' : chain->getName().c_str()[0]);
00348         insertion_code = residue.getInsertionCode();
00349       }
00350     };
00351 
00352 
00355     struct BALL_EXPORT RecordUNKNOWN
00356     {
00357       Real max_record_size[SIZE_OF_PDB_RECORD_LINE];
00358     };
00359     
00362     struct BALL_EXPORT RecordANISOU
00363     {
00364       RecordType  record_type;
00365       RecordName  record_name;
00366       Integer     serial_number;
00367       Atom        atom_name;
00368       Character   alternate_location_indicator;
00369       Residue     residue;
00370       Integer     u11;
00371       Integer     u22;
00372       Integer     u33;
00373       Integer     u12;
00374       Integer     u13;
00375       Integer     u23;
00376       LString4    segment_ID;
00377       LString2    element_symbol;
00378       LString2    charge; 
00379     };
00380 
00383     struct BALL_EXPORT RecordATOM
00384     {
00385       RecordType  record_type;
00386       RecordName  record_name;
00387       Integer     serial_number;
00388       Atom        atom_name;
00389       Character   alternate_location_indicator;
00390       Residue     residue;
00391       Real        orthogonal_vector[3];
00392       Real        occupancy;
00393       Real        temperature_factor;
00394       LString4    segment_ID;
00395       LString2    element_symbol;
00396       LString2    charge; 
00397       LString4    partial_charge; // not standard! Read if option PARSE_PARTIAL_CHARGES is set!
00398     };
00399 
00402     struct BALL_EXPORT RecordAUTHOR
00403     {
00404       RecordType   record_type;
00405       RecordName   record_name;
00406       Continuation continuation;
00407       PDBList      authors;
00408     };
00409 
00412     struct BALL_EXPORT RecordCAVEAT
00413     {
00414       RecordType   record_type;
00415       RecordName   record_name;
00416       Continuation continuation;
00417       IDcode       entry_code;
00418       PDBString    comment;
00419     };
00420 
00423     struct BALL_EXPORT RecordCISPEP
00424     {
00426       RecordType     record_type;
00427       RecordName     record_name;
00428       Integer        record_serial_number;
00429       Residue        residue[2];
00430       Integer        specific_model_ID;
00431       Real           angle_measure;
00432     };
00433 
00436     struct BALL_EXPORT RecordCOMPND
00437     {
00438       RecordType        record_type;
00439       RecordName        record_name;
00440       Continuation      continuation;
00441       SpecificationList component_description;
00442     };
00443     
00446     struct BALL_EXPORT RecordCONECT
00447     {
00448       RecordType record_type;
00449       RecordName record_name;
00450       Integer    atom_serial_number;
00451       Integer    bond_atom[4];
00452       Integer    hbond_atom[4];
00453       Integer    salt_bridge_atom[2];
00454       
00455       void clear()
00456       {
00457         record_type = PDB::RECORD_TYPE__CONECT;
00458         record_name[0] = '\0';
00459         atom_serial_number = 0;
00460         bond_atom[0] = bond_atom[1] = bond_atom[2] = bond_atom[3] = 0;
00461         hbond_atom[0] = hbond_atom[1] = hbond_atom[2] = hbond_atom[3] = 0;
00462         salt_bridge_atom[0] = salt_bridge_atom[1] = 0;
00463       }
00464     };
00465 
00468     struct BALL_EXPORT RecordCRYST1
00469     {
00470       RecordType record_type;
00471       RecordName record_name;
00473       struct UnitCell
00474       {
00475         Real     a;
00476         Real     b;
00477         Real     c;
00478         Real     alpha;
00479         Real     beta;
00480         Real     gamma;
00481         LString  space_group;
00482         Integer  z_value;
00483       } unit_cell;
00484     };
00485 
00488     struct BALL_EXPORT RecordDBREF
00489     {
00490       RecordType record_type;
00491       RecordName record_name;
00492       IDcode     entry_code;
00493       Character  chain_ID;
00495       struct InitialSequence
00496       {
00497         Integer  number;
00498         AChar    insertion_code;
00499       } initial_sequence;
00501       struct EndingSequence
00502       {
00503         Integer  number;
00504         AChar    insertion_code;
00505       } ending_sequence;
00506       LString6   sequence_database_name;
00507       LString8   sequence_database_accession_code;
00508       LString12  sequence_database_ID_code;
00510       struct InitialDatabaseSegment
00511       {
00512         Integer  number;
00513         AChar    insertion_code;
00514       } initial_database_segment;
00516       struct EndingDatabaseSegment
00517       {
00518         Integer  number;
00519         AChar    insertion_code;
00520       } ending_database_segment;
00521     };
00522 
00524     struct BALL_EXPORT RecordEND
00525     {
00526       RecordType record_type;
00527       RecordName record_name;
00528     };
00529 
00531     struct BALL_EXPORT RecordENDMDL
00532     {
00533       RecordType record_type;
00534       RecordName record_name;
00535     };
00536     
00538     struct BALL_EXPORT RecordEXPDTA
00539     {
00540       RecordType   record_type;
00541       RecordName   record_name;
00542       Continuation continuation;
00543       SList        technique;
00544     };
00545     
00547     struct BALL_EXPORT RecordFORMUL
00548     {
00549       RecordType record_type;
00550       RecordName record_name;
00551       Integer    component_number;
00552       LString3   het_ID;
00553       Integer    continuation_number;
00554       Character  is_water;
00555       PDBString  chemical_formula;
00556     };
00557     
00559     struct BALL_EXPORT RecordFTNOTE
00560     {
00561       RecordType record_type;
00562       RecordName record_name;
00563       Integer    number;
00564       PDBString  text;
00565     };
00566     
00568     struct BALL_EXPORT RecordHEADER
00569     {
00570       RecordType record_type;
00571       RecordName record_name;
00572       String40   classification;
00573       Date       deposition_date;
00574       IDcode     ID_code;
00575     };
00576     
00578     struct BALL_EXPORT RecordHELIX
00579     {
00580       RecordType    record_type;
00581       RecordName    record_name;
00582       Integer       serial_number;
00583       LString3      helix_ID;
00584       Residue       initial_residue;
00585       Residue       terminal_residue;
00586       Integer       helix_class;
00587       PDBString     comment;
00588       Integer       length;
00589 
00590       RecordHELIX() { clear(); }
00591       void clear()
00592       {
00593         record_type = RECORD_TYPE__HELIX;
00594         strncpy(record_name, RECORD_TAG_HELIX, 6);
00595         serial_number = 0;
00596         helix_ID[0] = '\0';
00597         initial_residue.clear();
00598         terminal_residue.clear();
00599         helix_class = 0;
00600         comment[0] = '\0';
00601         length = 0;
00602       }
00603     };
00604     
00606     struct BALL_EXPORT RecordHET
00607     {
00608       RecordType record_type;
00609       RecordName record_name;
00610       Residue    residue;
00611       Integer    number_of_HETATM_records;
00612       PDBString  text;
00613     };
00614     
00616     struct BALL_EXPORT RecordHETATM
00617     {
00618       RecordType  record_type;
00619       RecordName  record_name;
00620       Integer     serial_number;
00621       Atom        atom_name;
00622       Character   alternate_location_indicator;
00623       Residue     residue;
00624       Real        orthogonal_vector[3];
00625       Real        occupancy;
00626       Real        temperature_factor;
00627       LString4    segment_ID;
00628       LString2    element_symbol;
00629       LString2    charge; 
00630     };
00631     
00633     struct BALL_EXPORT RecordHETNAM
00634     {
00635       RecordType   record_type;
00636       RecordName   record_name;
00637       Continuation continuation;
00638       LString3     het_ID;
00639       PDBString    chemical_name;
00640     };
00641     
00643     struct BALL_EXPORT RecordHETSYN
00644     {
00645       RecordType   record_type;
00646       RecordName   record_name;
00647       Continuation continuation;
00648       LString3     het_ID;
00649       SList        het_synonyms;
00650     };
00651     
00653     struct BALL_EXPORT RecordHYDBND
00654     {
00655       RecordType       record_type;
00656       RecordName       record_name;
00658       struct BALL_EXPORT HydrogenPartnerAtom
00659       {
00660         Atom           atom_name;
00661         Character      alternate_location_indicator;
00662         Residue        residue;
00663       };
00664 
00665       HydrogenPartnerAtom hydrogen_partner_atom[2];
00667       struct BALL_EXPORT HydrogenAtom
00668       {
00669         Atom           atom_name;
00670         Character      alternate_location_indicator;
00671         Residue        residue;
00672       };
00673       HydrogenAtom hydrogen_atom;
00674       SymmetryOperator first_non_hydrogen_atom;
00675       SymmetryOperator second_non_hydrogen_atom;
00676     };
00677     
00679     struct BALL_EXPORT RecordJRNL
00680     {
00681       RecordType record_type;
00682       RecordName record_name;
00683       LString    text;
00684     };
00686     struct BALL_EXPORT RecordKEYWDS
00687     {
00688       RecordType   record_type;
00689       RecordName   record_name;
00690       Continuation continuation;
00691       PDBList      keywords;
00692     };
00694     struct BALL_EXPORT RecordLINK
00695     {
00696       RecordType      record_type;
00697       RecordName      record_name;
00699       struct BALL_EXPORT LinkPartner
00700       {
00701         Atom          atom_name;
00702         Character     alternate_location_indicator;
00703         Residue       residue;
00704       };
00705       LinkPartner link_partner[2];
00706       SymmetryOperator first_atom;
00707       SymmetryOperator second_atom;
00708     };
00710     struct BALL_EXPORT RecordMASTER
00711     {
00712       RecordType record_type;
00713       RecordName record_name;
00714       Integer    number_of_REMARK_records;
00715       Integer    zero;
00716       Integer    number_of_HET_records;
00717       Integer    number_of_HELIX_records;
00718       Integer    number_of_SHEET_records;
00719       Integer    number_of_TURN_records;
00720       Integer    number_of_SITE_records;
00721       Integer    number_of_ORIGX_SCALE_MTRIX_records;
00722       Integer    number_of_ATOM_HETATM_records;
00723       Integer    number_of_TER_records;
00724       Integer    number_of_CONECT_records;
00725       Integer    number_of_SEQRES_records;
00726 
00727       RecordMASTER() { clear(); }
00728       void clear()
00729       {
00730         record_type = RECORD_TYPE__MASTER;
00731         strcpy(record_name, RECORD_TAG_MASTER);
00732         zero = number_of_HET_records = number_of_HELIX_records
00733              = number_of_SHEET_records = number_of_TURN_records
00734              = number_of_SITE_records = number_of_ORIGX_SCALE_MTRIX_records
00735              = number_of_ATOM_HETATM_records = number_of_TER_records
00736              = number_of_CONECT_records = number_of_SEQRES_records = 0;
00737       }
00738     };
00740     struct BALL_EXPORT RecordMODEL
00741     {
00742       RecordType record_type;
00743       RecordName record_name;
00744       Integer    model_serial_number;
00745     };
00747     struct BALL_EXPORT RecordMODRES
00748     {
00749       RecordType  record_type;
00750       RecordName  record_name;
00751       IDcode      entry_code;
00752       Residue     residue;
00753       ResidueName standard_residue_name;
00754       PDBString   comment;
00755     };
00757     struct BALL_EXPORT RecordMTRIX1
00758     {
00759       RecordType record_type;
00760       RecordName record_name;
00761       Integer    serial_number;
00762       Real       transformation_matrix[4];
00763       Integer    is_given;
00764     };
00766     struct BALL_EXPORT RecordMTRIX2
00767     {
00768       RecordType record_type;
00769       RecordName record_name;
00770       Integer    serial_number;
00771       Real       transformation_matrix[4];
00772       Integer    is_given;
00773     };
00775     struct BALL_EXPORT RecordMTRIX3
00776     {
00777       RecordType record_type;
00778       RecordName record_name;
00779       Integer    serial_number;
00780       Real       transformation_matrix[4];
00781       Integer    is_given;
00782     };
00784     struct BALL_EXPORT RecordOBSLTE
00785     {
00786       RecordType   record_type;
00787       RecordName   record_name;
00788       Continuation continuation;
00789       Date         entry_replaced_date;
00790       IDcode       entry_code;
00791       IDcode       replacing_entry_code[8];
00792     };
00794     struct BALL_EXPORT RecordORIGX1
00795     {
00796       RecordType record_type;
00797       RecordName record_name;
00798       Real       transformation_matrix[4];
00799     };
00801     struct BALL_EXPORT RecordORIGX2
00802     {
00803       RecordType record_type;
00804       RecordName record_name;
00805       Real       transformation_matrix[4];
00806     };
00808     struct BALL_EXPORT RecordORIGX3
00809     {
00810       RecordType record_type;
00811       RecordName record_name;
00812       Real       transformation_matrix[4];
00813     };
00815     struct BALL_EXPORT RecordREMARK
00816     {
00817       RecordType record_type;
00818       RecordName record_name;
00819       Integer    remark_number;
00820       LString    text;
00821     };
00823     struct BALL_EXPORT RecordREVDAT
00824     {
00825       RecordType   record_type;
00826       RecordName   record_name;
00827       Integer      modification_number;
00828       Continuation continuation;
00829       Date         modification_date;
00830       String5      modification_ID;
00831       Integer      modification_type;
00832       LString6     name_of_modified_record[4];
00833     };
00834 
00836     struct BALL_EXPORT RecordSCALE1
00837     {
00838       RecordType record_type;
00839       RecordName record_name;
00840       Real       transformation_matrix[4];
00841     };
00842 
00844     struct BALL_EXPORT RecordSCALE2
00845     {
00846       RecordType record_type;
00847       RecordName record_name;
00848       Real       transformation_matrix[4];
00849     };
00850 
00852     struct BALL_EXPORT RecordSCALE3
00853     {
00854       RecordType record_type;
00855       RecordName record_name;
00856       Real       transformation_matrix[4];
00857     };
00858 
00860     struct BALL_EXPORT RecordSEQADV
00861     {
00862       RecordType  record_type;
00863       RecordName  record_name;
00864       IDcode      id_code;
00865       Residue     residue;
00866       LString4    database;
00867       LString9    db_id_code;
00868       LString3    db_res;
00869       Integer     db_seq;
00870       LString21   comment;
00871     };
00872 
00874     struct BALL_EXPORT RecordSEQRES
00875     {
00876       RecordType  record_type;
00877       RecordName  record_name;
00878       Integer     serial_number;
00879       Character   chain_ID;
00880       Integer     number_of_residues_in_chain;
00881       ResidueName residue_name[13];
00882 
00883       RecordSEQRES()
00884       {
00885         clear();
00886       }
00887 
00888       void clear()
00889       {
00890         record_type = RECORD_TYPE__SEQRES;
00891         strncpy(record_name, RECORD_TAG_SEQRES, 6);
00892         serial_number = 0;
00893         chain_ID = ' ';
00894         number_of_residues_in_chain = 0L;
00895         residue_name[0][0] = '\0';
00896         residue_name[1][0] = '\0';
00897         residue_name[2][0] = '\0';
00898         residue_name[3][0] = '\0';
00899         residue_name[4][0] = '\0';
00900         residue_name[5][0] = '\0';
00901         residue_name[6][0] = '\0';
00902         residue_name[7][0] = '\0';
00903         residue_name[8][0] = '\0';
00904         residue_name[9][0] = '\0';
00905         residue_name[10][0] = '\0';
00906         residue_name[11][0] = '\0';
00907         residue_name[12][0] = '\0';
00908       }
00909     };
00910 
00912     struct BALL_EXPORT RecordSHEET
00913     {
00914       RecordType    record_type;
00915       RecordName    record_name;
00916       Integer       strand_number;
00917       LString3      sheet_ID;
00918       Integer       number_of_strands;
00919       Residue       initial_residue;
00920       Residue       terminal_residue;
00921       Integer       sense_of_strand;
00922       Atom          atom_name_in_current_strand;
00923       Residue       residue_in_current_strand;
00924       Atom          atom_name_in_previous_strand;
00925       Residue       residue_in_previous_strand;
00926 
00927       RecordSHEET() { clear(); }
00928       void clear()
00929       {
00930         record_type = RECORD_TYPE__SHEET;
00931         strncpy(record_name, RECORD_TAG_SHEET, 6);
00932         strand_number = 0;
00933         sheet_ID[0] = '\0';;
00934         number_of_strands = 0; 
00935         initial_residue.clear();
00936         terminal_residue.clear();
00937         sense_of_strand = 0;
00938         atom_name_in_current_strand[0] = '\0';
00939         residue_in_current_strand.clear();
00940         atom_name_in_previous_strand[0] = '\0';
00941         residue_in_previous_strand.clear();
00942       }
00943     };
00944 
00946     struct BALL_EXPORT RecordSIGATM
00947     {
00948       RecordType  record_type;
00949       RecordName  record_name;
00950       Integer     serial_number;
00951       Atom        atom_name;
00952       Character   alternate_location_indicator;
00953       Residue     residue;
00954       Real        standard_vector_deviation[3];
00955       Real        standard_occupancy_deviation;
00956       Real        standard_temperature_deviation;
00957       LString4    segment_ID;
00958       LString2    element_symbol;
00959       LString2    charge; 
00960     };
00961 
00963     struct BALL_EXPORT RecordSIGUIJ
00964     {
00965       RecordType  record_type;
00966       RecordName  record_name;
00967       Integer     serial_number;
00968       Atom        atom_name;
00969       Character   alternate_location_indicator; 
00970       Residue     residue;
00971       Integer     sig11;
00972       Integer     sig22;
00973       Integer     sig33;
00974       Integer     sig12;
00975       Integer     sig13;
00976       Integer     sig23;
00977       LString4    segment_ID;
00978       LString2    element_symbol;
00979       LString2    charge; 
00980     };
00981 
00983     struct BALL_EXPORT RecordSITE
00984     {
00985       RecordType    record_type;
00986       RecordName    record_name;
00987       Integer       sequence_number;
00988       LString3      name;
00989       Integer       number_of_residues;
00990       Residue       residue[4];
00991     };
00992 
00994     struct BALL_EXPORT RecordSLTBRG
00995     {
00996       RecordType      record_type;
00997       RecordName      record_name;
00999       struct BALL_EXPORT PartnerAtom
01000       {
01001         Atom          atom_name;
01002         Character     alternate_location_indicator;
01003         Residue       residue;
01004       };
01005       
01006       PartnerAtom partner_atom[2];
01007       SymmetryOperator first_atom;
01008       SymmetryOperator second_atom;
01009     };
01010 
01012     struct BALL_EXPORT RecordSOURCE
01013     {
01014       RecordType        record_type;
01015       RecordName        record_name;
01016       Continuation      continuation;
01017       SpecificationList sources;
01018     };
01019 
01021     struct BALL_EXPORT RecordSPRSDE
01022     {
01023       RecordType        record_type;
01024       RecordName        record_name;
01025       Continuation      continuation;
01026       Date              date;
01027       IDcode            id_code;
01028       IDcode            old_codes[8];
01029     };
01030 
01032     struct BALL_EXPORT RecordSSBOND
01033     {
01034       RecordType    record_type;
01035       RecordName    record_name;
01036       Integer       serial_number;
01037       Residue       partner_residue[2];
01038       SymmetryOperator symmetry_operator[2];
01039       
01040       RecordSSBOND() { clear(); }
01041       void clear()
01042       {
01043         record_type = RECORD_TYPE__SSBOND;
01044         strncpy(record_name, RECORD_TAG_SSBOND, 6);
01045         serial_number = 0;
01046         partner_residue[0].clear();
01047         partner_residue[1].clear();
01048         symmetry_operator[0] = 0;
01049         symmetry_operator[1] = 0;
01050       }
01051     };
01052 
01055     struct BALL_EXPORT RecordTER
01056     {
01057       RecordType  record_type;
01058       RecordName  record_name;
01059       Integer     serial_number;
01060       Residue     residue;
01061     };
01062 
01065     struct BALL_EXPORT RecordTITLE
01066     {
01067       RecordType   record_type;
01068       RecordName   record_name;
01069       Continuation continuation;
01070       PDBString    title;
01071     };
01072 
01075     struct BALL_EXPORT RecordTURN
01076     {
01077       RecordType    record_type;
01078       RecordName    record_name;
01079       Integer       sequence_number;
01080       LString3      turn_ID;
01081       Residue       initial_residue;
01082       Residue       terminal_residue;
01083       PDBString     comment;
01084       
01085       RecordTURN() { clear(); }
01086       void clear()
01087       {
01088         record_type = RECORD_TYPE__TURN;
01089         strncpy(record_name, RECORD_TAG_TURN, 6);
01090         sequence_number = 0;
01091         turn_ID[0] = '\0';;
01092         initial_residue.clear();
01093         terminal_residue.clear();
01094         comment[0] = '\0';
01095       }
01096     };
01097 
01100     struct BALL_EXPORT RecordTVECT
01101     {
01102       RecordType record_type;
01103       RecordName record_name;
01104       Integer    serial_number;
01105       Real       translation_vector[3];
01106       PDBString  comment;
01107     };
01109 
01113     struct BALL_EXPORT BookKeeping
01114     {
01115       Size remark_records;
01116       Size het_records;
01117       Size helix_records;
01118       Size sheet_records;
01119       Size turn_records;
01120       Size site_records;
01121       Size coordinate_transformation_records;
01122       Size atomic_coordinate_records;
01123       Size ter_records;
01124       Size conect_records;
01125       Size seqres_records;
01126       
01127       BookKeeping()
01128       {
01129         clear();
01130       }
01131 
01132       void clear()
01133       {
01134         remark_records = 0;
01135         het_records = 0;
01136         helix_records = 0;
01137         sheet_records = 0;
01138         turn_records = 0;
01139         site_records = 0;
01140         coordinate_transformation_records = 0;
01141         atomic_coordinate_records = 0;
01142         ter_records = 0;
01143         conect_records = 0;
01144         seqres_records = 0;
01145       }
01146     };
01147 
01148 
01149     struct BALL_EXPORT Structure  
01150     {
01151       struct BALL_EXPORT AtomEntry
01152       {
01153         const BALL::Atom* atom;
01154         const BALL::Residue* residue;
01155         const BALL::SecondaryStructure* sec_struct;
01156         const BALL::Chain* chain;
01157         AtomEntry(const BALL::Atom& a)
01158         {
01159           atom = &a;
01160           residue = a.getResidue();
01161           sec_struct = a.getSecondaryStructure();
01162           chain = a.getChain();
01163         }
01164       };
01165       
01166 
01167       struct BALL_EXPORT ConectAtomList
01168       {
01169         Position serial_number;
01170         std::list<Position> bonds;
01171         std::list<Position> hbonds;
01172         std::list<Position> saltbridges;
01173       };
01174 
01175       struct BALL_EXPORT UnitCellInfo
01176       {
01177         Real     a;
01178         Real     b;
01179         Real     c;
01180         Real     alpha;
01181         Real     beta;
01182         Real     gamma;
01183         LString  space_group;
01184         Integer  z_value;
01185 
01186         UnitCellInfo()
01187           : a(0),
01188             b(0),
01189             c(0),
01190             alpha(0),
01191             beta(0),
01192             gamma(0),
01193             z_value(-1)
01194         {
01195           strcpy(space_group, "");  
01196         }
01197       } unitcell_info;
01198 
01199       struct BALL_EXPORT NCSMatrix
01200       {
01201         Real     matrix[12];
01202         Integer  isgiven;
01203         NCSMatrix(const BALL::Matrix4x4& m, bool is_given)
01204         {
01205           matrix[0] = m(0,0); matrix[1] = m(0,1); matrix[2] = m(0,2); matrix[3] = m(0,3);
01206           matrix[4] = m(1,0); matrix[5] = m(1,1); matrix[6] = m(1,2); matrix[7] = m(1,3);
01207           matrix[8] = m(2,0); matrix[9] = m(2,1); matrix[10] = m(2,2); matrix[11] = m(2,3);
01208           isgiven = is_given;
01209         }
01210       };
01211 
01212       std::vector<NCSMatrix> ncs_matrices;
01213       std::vector<AtomEntry> atoms;
01214 
01215       HashSet<const ::BALL::Atom*>  conect_atoms;
01216       std::vector<const Bond*>      hydrogen_bonds;
01217       std::vector<const Bond*>      saltbridges;
01218       std::vector<const Bond*>      ssbonds;
01219 
01220       std::vector<std::pair<AChar, String> >    chain_residue_names;
01221       std::vector<const SecondaryStructure*>    sec_structs;
01222 
01223       void clear()
01224       {
01225         atoms.clear();
01226         conect_atoms.clear();
01227         hydrogen_bonds.clear();
01228         saltbridges.clear();
01229         ssbonds.clear();
01230       }
01231 
01232     };
01233 
01237     struct BALL_EXPORT AdditionalAtomInfo
01238     {
01239       const Chain* current_chain;
01240       const ::BALL::Residue* current_residue;
01241       Integer residue_id;
01242       AChar residue_insertion_code;
01243       AChar chain_id;
01244       LString3 residue_name;
01245       LString4 pdb_id;
01246       Position number; // number of the ATOM/HETATM/TER record
01247       
01248       AdditionalAtomInfo()
01249         : current_chain(0x0),
01250           current_residue(0x0),
01251           residue_id(1),
01252           residue_insertion_code(' '),
01253           chain_id(' '),
01254           number(1)
01255       {
01256         strncpy(residue_name, "UNK", 4);
01257         strncpy(pdb_id, "    ", 5);
01258       }
01259     };
01260 
01263     BALL_EXPORT extern const RecordTypeFormat RECORD_TYPE_FORMAT [];
01264 
01265   } // namespace PDB
01266 
01267 } // namespace BALL
01268 
01269 #endif // BALL_FORMAT_PDBDEFS_H