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5 #ifndef BALL_FORMAT_PDBDEFS_H
6 #define BALL_FORMAT_PDBDEFS_H
12 #ifndef BALL_KERNEL_ATOM_H
16 #ifndef BALL_KERNEL_SECONDARYSTRUCTURE_H
20 #ifndef BALL_KERNEL_CHAIN_H
24 #ifndef BALL_KERNEL_RESIDUE_H
28 #ifndef BALL_DATATYPES_HASHSET_H
32 #ifndef BALL_MATHS_MATRIX44_H
353 insertion_code =
' ';
355 void set(const ::BALL::Residue& residue)
357 strncpy(name, residue.getName().c_str(), 3);
358 sequence_number = residue.getID().toInt();
359 const Chain* chain = residue.getChain();
360 chain_ID = (chain == 0 ?
' ' : chain->
getName().
c_str()[0]);
361 insertion_code = residue.getInsertionCode();
471 record_name[0] =
'\0';
472 atom_serial_number = 0;
473 bond_atom[0] = bond_atom[1] = bond_atom[2] = bond_atom[3] = 0;
474 hbond_atom[0] = hbond_atom[1] = hbond_atom[2] = hbond_atom[3] = 0;
475 salt_bridge_atom[0] = salt_bridge_atom[1] = 0;
491 record_name[0] =
'\0';
492 atom_serial_number = 0;
493 bond_atom[0] = bond_atom[1] = bond_atom[2] = bond_atom[3] = 0;
507 record_name[0] =
'\0';
508 atom_serial_number = 0;
509 bond_atom[0] = bond_atom[1] = bond_atom[2] = bond_atom[3] = 0;
523 record_name[0] =
'\0';
524 atom_serial_number = 0;
539 record_name[0] =
'\0';
540 atom_serial_number = 0;
541 bond_atom[0] = bond_atom[1] = 0;
555 record_name[0] =
'\0';
556 atom_serial_number = 0;
557 bond_atom[0] = bond_atom[1] = bond_atom[2] = 0;
610 } initial_database_segment;
616 } ending_database_segment;
693 initial_residue.
clear();
694 terminal_residue.
clear();
828 zero = number_of_HET_records = number_of_HELIX_records
829 = number_of_SHEET_records = number_of_TURN_records
830 = number_of_SITE_records = number_of_ORIGX_SCALE_MTRIX_records
831 = number_of_ATOM_HETATM_records = number_of_TER_records
832 = number_of_CONECT_records = number_of_SEQRES_records = 0;
990 number_of_residues_in_chain = 0L;
991 residue_name[0][0] =
'\0';
992 residue_name[1][0] =
'\0';
993 residue_name[2][0] =
'\0';
994 residue_name[3][0] =
'\0';
995 residue_name[4][0] =
'\0';
996 residue_name[5][0] =
'\0';
997 residue_name[6][0] =
'\0';
998 residue_name[7][0] =
'\0';
999 residue_name[8][0] =
'\0';
1000 residue_name[9][0] =
'\0';
1001 residue_name[10][0] =
'\0';
1002 residue_name[11][0] =
'\0';
1003 residue_name[12][0] =
'\0';
1029 sheet_ID[0] =
'\0';;
1030 number_of_strands = 0;
1031 initial_residue.
clear();
1032 terminal_residue.
clear();
1033 sense_of_strand = 0;
1034 atom_name_in_current_strand[0] =
'\0';
1035 residue_in_current_strand.
clear();
1036 atom_name_in_previous_strand[0] =
'\0';
1037 residue_in_previous_strand.
clear();
1142 partner_residue[0].
clear();
1143 partner_residue[1].
clear();
1144 symmetry_operator[0] = 0;
1145 symmetry_operator[1] = 0;
1186 sequence_number = 0;
1188 initial_residue.
clear();
1189 terminal_residue.
clear();
1236 coordinate_transformation_records = 0;
1237 atomic_coordinate_records = 0;
1291 strcpy(space_group,
"");
1301 matrix[0] = m(0,0); matrix[1] = m(0,1); matrix[2] = m(0,2); matrix[3] = m(0,3);
1302 matrix[4] = m(1,0); matrix[5] = m(1,1); matrix[6] = m(1,2); matrix[7] = m(1,3);
1303 matrix[8] = m(2,0); matrix[9] = m(2,1); matrix[10] = m(2,2); matrix[11] = m(2,3);
1322 conect_atoms.
clear();
1323 hydrogen_bonds.clear();
1324 saltbridges.clear();
1345 : current_chain(0x0),
1346 current_residue(0x0),
1348 residue_insertion_code(
' '),
1352 strncpy(residue_name,
"UNK", 4);
1353 strncpy(pdb_id,
" ", 5);
1365 #endif // BALL_FORMAT_PDBDEFS_H
Residue residue_in_previous_strand
const BALL_EXPORT char * RECORD_TAG_SIGUIJ
const BALL_EXPORT char * FORMAT_SCALE3
Real standard_occupancy_deviation
const BALL_EXPORT char * RECORD_TAG_CON063
std::vector< std::pair< AChar, String > > chain_residue_names
const BALL_EXPORT char * RECORD_TAG_CON06
const BALL_EXPORT char * FORMAT_UNKNOWN
Character alternate_location_indicator
const BALL_EXPORT char * RECORD_TAG_HETATM
BALL_EXPORT AtomList atoms(const AtomContainer &fragment, const String &expression=String())
const BALL_EXPORT char * RECORD_TAG_CAVEAT
const BALL_EXPORT char * RECORD_TAG_SSBOND
const BALL_EXPORT char * RECORD_TAG_ORIGX2
const SecondaryStructure * getSecondaryStructure() const
const BALL_EXPORT char * FORMAT_AUTHOR
const BALL::Chain * chain
Atom atom_name_in_previous_strand
const BALL_EXPORT char * RECORD_TAG_MODEL
const BALL_EXPORT char * RECORD_TAG_SPRSDE
const BALL_EXPORT char * RECORD_TAG_HET
const Chain * current_chain
const BALL_EXPORT char * RECORD_TAG_CON061
Integer number_of_TER_records
const BALL_EXPORT char * RECORD_TAG_FORMUL
const BALL_EXPORT char * FORMAT_JRNL
Continuation continuation
const BALL_EXPORT char * RECORD_TAG_KEYWDS
Atom atom_name_in_current_strand
const BALL_EXPORT char * FORMAT_SLTBRG
Integer number_of_TURN_records
const BALL_EXPORT char * FORMAT_MODRES
const BALL_EXPORT char * RECORD_TAG_SLTBRG
Integer number_of_REMARK_records
const Residue * getResidue() const
const BALL_EXPORT char * FORMAT_MTRIX1
Continuation continuation
Integer atom_serial_number
const BALL_EXPORT char * RECORD_TAG_SCALE1
HydrogenAtom hydrogen_atom
Integer number_of_ORIGX_SCALE_MTRIX_records
Continuation continuation
const BALL_EXPORT char * RECORD_TAG_TER
Integer atom_serial_number
const String & getName() const
const BALL_EXPORT char * RECORD_TAG_TVECT
const BALL_EXPORT char * FORMAT_HYDBND
const BALL_EXPORT char * RECORD_TAG_JRNL
const BALL_EXPORT char * FORMAT_MASTER
const BALL_EXPORT char * FORMAT_SIGUIJ
const BALL_EXPORT char * RECORD_TAG_SEQRES
SymmetryOperator second_non_hydrogen_atom
const BALL_EXPORT char * RECORD_TAG_HETSYN
const BALL_EXPORT char * FORMAT_OBSLTE
const BALL_EXPORT char * FORMAT_CON06_3
const BALL_EXPORT char * FORMAT_MODEL
Integer number_of_SITE_records
const BALL_EXPORT char * FORMAT_SEQADV
Continuation continuation
const BALL_EXPORT char * FORMAT_SHEET
SymmetryOperator second_atom
char LString[SIZE_OF_PDB_RECORD_LINE+1]
char PDBString[SIZE_OF_PDB_RECORD_LINE+1]
const BALL_EXPORT char * FORMAT_MTRIX3
Continuation continuation
const BALL_EXPORT char * RECORD_TAG_FTNOTE
Integer record_serial_number
const BALL_EXPORT char * RECORD_TAG_MTRIX2
const BALL::SecondaryStructure * sec_struct
std::vector< const Bond * > ssbonds
Size atomic_coordinate_records
NCSMatrix(const BALL::Matrix4x4 &m, bool is_given)
const BALL_EXPORT char * RECORD_TAG_MTRIX1
const BALL_EXPORT char * RECORD_TAG_CON064
const BALL_EXPORT char * RECORD_TAG_ENDMDL
char PDBList[SIZE_OF_PDB_RECORD_LINE+1]
Integer continuation_number
std::list< Position > bonds
SymmetryOperator second_atom
const BALL_EXPORT char * RECORD_TAG_SCALE2
const BALL_EXPORT char * FORMAT_TVECT
const BALL_EXPORT char * RECORD_TAG_MODRES
const BALL_EXPORT char * FORMAT_EXPDTA
const BALL_EXPORT char * RECORD_TAG_SCALE3
const BALL_EXPORT char * FORMAT_SCALE2
Integer atom_serial_number
Residue residue_in_current_strand
const BALL_EXPORT char * RECORD_TAG_OBSLTE
const BALL_EXPORT char * RECORD_TAG_SHEET
LString8 sequence_database_accession_code
const BALL_EXPORT char * FORMAT_TER
const BALL_EXPORT char * FORMAT_ENDMDL
const BALL_EXPORT char * FORMAT_HETATM
Integer modification_type
std::vector< NCSMatrix > ncs_matrices
const ::BALL::Residue * current_residue
const BALL_EXPORT char * RECORD_TAG_TURN
const BALL_EXPORT char * FORMAT_MTRIX2
const BALL_EXPORT char * FORMAT_CON06_4
Character alternate_location_indicator
const BALL_EXPORT char * RECORD_TAG_TITLE
Integer number_of_HETATM_records
const BALL_EXPORT char * RECORD_TAG_ORIGX1
Continuation continuation
LString6 sequence_database_name
Integer number_of_residues
Character alternate_location_indicator
const BALL_EXPORT char * FORMAT_COMPND
const BALL_EXPORT char * RECORD_TAG_CRYST1
const BALL_EXPORT char * RECORD_TAG_EXPDTA
LString12 sequence_database_ID_code
std::vector< const Bond * > hydrogen_bonds
const BALL_EXPORT char * FORMAT_ATOM_PARTIAL_CRG
const BALL_EXPORT char * FORMAT_SIGATM
const BALL_EXPORT char * FORMAT_CON06_1
const BALL_EXPORT char * FORMAT_SCALE1
Integer modification_number
const BALL_EXPORT char * RECORD_TAG_SITE
Integer number_of_SHEET_records
const BALL_EXPORT char * RECORD_TAG_SIGATM
const BALL_EXPORT char * FORMAT_SSBOND
const BALL_EXPORT char * FORMAT_ANISOU
char SList[SIZE_OF_PDB_RECORD_LINE+1]
const BALL_EXPORT char * RECORD_TAG_AUTHOR
const BALL_EXPORT char * FORMAT_ORIGX2
AChar residue_insertion_code
std::list< Position > saltbridges
const BALL_EXPORT char * RECORD_TAG_SEQADV
const BALL_EXPORT char * FORMAT_TITLE
SymmetryOperator first_atom
Character alternate_location_indicator
const BALL_EXPORT char * FORMAT_HETNAM
const BALL_EXTERN_VARIABLE double c
Integer model_serial_number
HashSet< const ::BALL::Atom * > conect_atoms
const BALL_EXPORT char * RECORD_TAG_ORIGX3
const BALL_EXPORT char * RECORD_TAG_REMARK
const BALL_EXPORT char * RECORD_TAG_MASTER
const BALL_EXPORT char * RECORD_TAG_LINK
const BALL_EXPORT RecordTypeFormat RECORD_TYPE_FORMAT[]
const BALL_EXPORT char * FORMAT_REMARK
SymmetryOperator first_atom
const BALL_EXPORT char * RECORD_TAG_REVDAT
const BALL_EXPORT char * RECORD_TAG_HEADER
Integer number_of_SEQRES_records
const BALL_EXPORT char * RECORD_TAG_DBREF
const BALL_EXPORT char * RECORD_TAG_SOURCE
Continuation continuation
Integer specific_model_ID
const BALL_EXPORT char * RECORD_TAG_END
const BALL_EXPORT char * RECORD_TAG_CONECT
Integer atom_serial_number
char SpecificationList[SIZE_OF_PDB_RECORD_LINE+1]
Integer number_of_strands
const BALL_EXPORT char * RECORD_TAG_MTRIX3
Continuation continuation
const BALL_EXPORT char * FORMAT_HELIX
Character alternate_location_indicator
const BALL_EXPORT char * RECORD_TAG_HELIX
const BALL_EXPORT char * RECORD_TAG_HETNAM
const BALL_EXPORT char * FORMAT_KEYWDS
SymmetryOperator first_non_hydrogen_atom
const BALL_EXPORT char * FORMAT_TURN
const BALL_EXPORT char * FORMAT_CRYST1
const BALL_EXPORT char * FORMAT_SPRSDE
Integer number_of_HET_records
const BALL_EXPORT char * RECORD_TAG_ATOM
const BALL_EXPORT char * FORMAT_HETSYN
Integer number_of_ATOM_HETATM_records
AtomEntry(const BALL::Atom &a)
const BALL_EXPORT char * FORMAT_HEADER
const BALL::Residue * residue
const BALL_EXPORT char * FORMAT_CONECT
const BALL_EXPORT char * FORMAT_SEQRES
ResidueName standard_residue_name
Continuation continuation
const BALL_EXPORT char * FORMAT_ORIGX3
Character alternate_location_indicator
const BALL_EXPORT char * FORMAT_FTNOTE
Real standard_temperature_deviation
SpecificationList sources
const BALL_EXPORT char * RECORD_TAG_HYDBND
Integer number_of_residues_in_chain
const char * c_str() const BALL_NOEXCEPT
const BALL_EXPORT char * FORMAT_SOURCE
std::vector< const SecondaryStructure * > sec_structs
Integer number_of_CONECT_records
const BALL_EXPORT char * FORMAT_HET
const BALL_EXPORT char * FORMAT_LINK
Continuation continuation
const BALL_EXPORT char * FORMAT_CON06
const BALL_EXPORT char * RECORD_TAG_ANISOU
Integer atom_serial_number
const BALL_EXPORT char * RECORD_TAG_CON062
const BALL_EXPORT char * FORMAT_CAVEAT
std::list< Position > hbonds
const BALL_EXPORT char * RECORD_TAG_CISPEP
Character alternate_location_indicator
Continuation continuation
void set(const ::BALL::Residue &residue)
const BALL_EXPORT char * FORMAT_CISPEP
std::vector< AtomEntry > atoms
Continuation continuation
Integer atom_serial_number
Size coordinate_transformation_records
PDBString chemical_formula
const BALL_EXPORT char * FORMAT_SITE
const BALL_EXPORT char * FORMAT_ATOM
char Specification[SIZE_OF_PDB_RECORD_LINE+1]
const BALL_EXPORT char * RECORD_TAG_COMPND
const BALL_EXPORT char * FORMAT_END
const BALL_EXPORT char * FORMAT_REVDAT
Character alternate_location_indicator
const char * format_string
const BALL_EXPORT char * FORMAT_DBREF
std::vector< const Bond * > saltbridges
SpecificationList component_description
const Chain * getChain() const
Integer number_of_HELIX_records
const BALL_EXPORT char * FORMAT_ORIGX1
Character alternate_location_indicator
const BALL_EXPORT char * FORMAT_FORMUL
const BALL_EXPORT char * FORMAT_CON06_2