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();
404 Real orthogonal_vector[3];
464 Integer bond_atom[4];
465 Integer hbond_atom[4];
466 Integer salt_bridge_atom[2];
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;
486 Integer bond_atom[4];
491 record_name[0] =
'\0';
492 atom_serial_number = 0;
493 bond_atom[0] = bond_atom[1] = bond_atom[2] = bond_atom[3] = 0;
502 Integer bond_atom[4];
507 record_name[0] =
'\0';
508 atom_serial_number = 0;
509 bond_atom[0] = bond_atom[1] = bond_atom[2] = bond_atom[3] = 0;
518 Integer bond_atom[1];
523 record_name[0] =
'\0';
524 atom_serial_number = 0;
534 Integer bond_atom[2];
539 record_name[0] =
'\0';
540 atom_serial_number = 0;
541 bond_atom[0] = bond_atom[1] = 0;
550 Integer bond_atom[3];
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;
690 strncpy(record_name, RECORD_TAG_HELIX, 6);
693 initial_residue.
clear();
694 terminal_residue.
clear();
720 Real orthogonal_vector[3];
827 strcpy(record_name, RECORD_TAG_MASTER);
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;
858 Real transformation_matrix[4];
867 Real transformation_matrix[4];
876 Real transformation_matrix[4];
887 IDcode replacing_entry_code[8];
894 Real transformation_matrix[4];
901 Real transformation_matrix[4];
908 Real transformation_matrix[4];
928 LString6 name_of_modified_record[4];
936 Real transformation_matrix[4];
944 Real transformation_matrix[4];
952 Real transformation_matrix[4];
977 ResidueName residue_name[13];
987 strncpy(record_name, RECORD_TAG_SEQRES, 6);
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';
1027 strncpy(record_name, RECORD_TAG_SHEET, 6);
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();
1050 Real standard_vector_deviation[3];
1124 IDcode old_codes[8];
1134 SymmetryOperator symmetry_operator[2];
1140 strncpy(record_name, RECORD_TAG_SSBOND, 6);
1142 partner_residue[0].
clear();
1143 partner_residue[1].
clear();
1144 symmetry_operator[0] = 0;
1145 symmetry_operator[1] = 0;
1185 strncpy(record_name, RECORD_TAG_TURN, 6);
1186 sequence_number = 0;
1188 initial_residue.
clear();
1189 terminal_residue.
clear();
1201 Real translation_vector[3];
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
std::vector< AtomEntry > atoms
BALL_EXPORT const char * RECORD_TAG_SITE
Continuation continuation
BALL_EXPORT const char * FORMAT_SHEET
BALL_EXPORT const char * FORMAT_ENDMDL
BALL_EXPORT const char * RECORD_TAG_MTRIX2
BALL_EXPORT const char * FORMAT_CON06_1
BALL_EXPORT const char * FORMAT_CON06
BALL_EXPORT const char * FORMAT_SCALE1
BALL_EXPORT const char * RECORD_TAG_ORIGX1
BALL_EXPORT const char * RECORD_TAG_SEQADV
BALL_EXPORT const char * RECORD_TAG_CON062
BALL_EXPORT const char * RECORD_TAG_FTNOTE
BALL_EXPORT const char * RECORD_TAG_HET
Residue residue_in_previous_strand
BALL_EXPORT const char * FORMAT_CON06_2
std::vector< NCSMatrix > ncs_matrices
BALL_EXPORT const char * RECORD_TAG_REVDAT
BALL_EXPORT const char * RECORD_TAG_MODRES
const SecondaryStructure * getSecondaryStructure() const
Character alternate_location_indicator
BALL_EXPORT const char * FORMAT_SIGUIJ
BALL_EXPORT const RecordTypeFormat RECORD_TYPE_FORMAT[]
BALL_EXPORT const char * RECORD_TAG_MODEL
BALL_EXPORT const char * RECORD_TAG_MTRIX1
const Chain * getChain() const
BALL_EXPORT const char * FORMAT_CRYST1
BALL_EXPORT const char * FORMAT_CAVEAT
BALL_EXPORT const char * FORMAT_CON06_3
BALL_EXPORT const char * RECORD_TAG_CISPEP
Integer number_of_residues
BALL_EXPORT const char * RECORD_TAG_SCALE1
BALL_EXPORT const char * RECORD_TAG_REMARK
BALL_EXPORT const char * FORMAT_MTRIX2
BALL_EXPORT const char * RECORD_TAG_SPRSDE
SymmetryOperator second_atom
Real standard_occupancy_deviation
BALL_EXPORT const char * RECORD_TAG_SOURCE
char Specification[SIZE_OF_PDB_RECORD_LINE+1]
BALL_EXPORT const char * FORMAT_CONECT
std::vector< const Bond * > ssbonds
BALL_EXPORT const char * RECORD_TAG_HETNAM
BALL_EXPORT const char * FORMAT_SPRSDE
BALL_EXPORT const char * FORMAT_ATOM_PARTIAL_CRG
Integer number_of_SEQRES_records
BALL_EXPORT const char * FORMAT_HETNAM
BALL_EXPORT const char * FORMAT_TER
Integer number_of_CONECT_records
BALL_EXPORT const char * FORMAT_HYDBND
SymmetryOperator first_atom
AtomEntry(const BALL::Atom &a)
BALL_EXPORT const char * RECORD_TAG_MASTER
BALL_EXPORT const char * RECORD_TAG_LINK
const ::BALL::Residue * current_residue
HashSet< const ::BALL::Atom * > conect_atoms
BALL_EXPORT const char * FORMAT_END
BALL_EXPORT const char * RECORD_TAG_CRYST1
Integer number_of_TURN_records
char SpecificationList[SIZE_OF_PDB_RECORD_LINE+1]
Integer number_of_strands
const BALL::Chain * chain
SymmetryOperator first_atom
Character alternate_location_indicator
BALL_EXPORT const char * FORMAT_MODEL
BALL_EXPORT const char * RECORD_TAG_CON06
Character alternate_location_indicator
BALL_EXPORT const char * FORMAT_MODRES
std::vector< const SecondaryStructure * > sec_structs
const Residue * getResidue() const
BALL_EXPORT const char * FORMAT_HET
BALL_EXPORT const char * RECORD_TAG_CAVEAT
BALL_EXPORT const char * RECORD_TAG_CON064
char LString[SIZE_OF_PDB_RECORD_LINE+1]
BALL_EXPORT const char * FORMAT_COMPND
BALL_EXPORT const char * FORMAT_TITLE
Integer number_of_HELIX_records
BALL_EXPORT const char * FORMAT_FTNOTE
BALL_EXPORT const char * FORMAT_HEADER
NCSMatrix(const BALL::Matrix4x4 &m, bool is_given)
BALL_EXPORT const char * RECORD_TAG_HEADER
const BALL::SecondaryStructure * sec_struct
BALL_EXPORT const char * FORMAT_CON06_4
BALL_EXPORT const char * RECORD_TAG_HETATM
Integer record_serial_number
BALL_EXPORT const char * FORMAT_ORIGX3
Integer number_of_ATOM_HETATM_records
Integer number_of_ORIGX_SCALE_MTRIX_records
Integer model_serial_number
BALL_EXPORT const char * RECORD_TAG_AUTHOR
std::vector< const Bond * > hydrogen_bonds
BALL_EXPORT const char * RECORD_TAG_HYDBND
BALL_EXPORT const char * RECORD_TAG_CON061
Integer number_of_HETATM_records
BALL_EXPORT const char * FORMAT_SOURCE
Integer atom_serial_number
BALL_EXPORT const char * FORMAT_MTRIX1
BALL_EXPORT const char * FORMAT_TVECT
BALL_EXPORT const char * FORMAT_REMARK
SpecificationList component_description
Integer atom_serial_number
BALL_EXPORT const char * FORMAT_AUTHOR
BALL_EXPORT const char * FORMAT_EXPDTA
BALL_EXPORT const char * FORMAT_DBREF
Integer modification_type
BALL_EXPORT const char * RECORD_TAG_HETSYN
std::list< Position > bonds
Real standard_temperature_deviation
BALL_EXPORT const char * FORMAT_HETSYN
BALL_EXPORT const char * RECORD_TAG_ORIGX3
Continuation continuation
BALL_EXPORT const char * RECORD_TAG_JRNL
Continuation continuation
Integer number_of_TER_records
std::vector< const Bond * > saltbridges
BALL_EXPORT const char * RECORD_TAG_TURN
BALL_EXPORT const char * RECORD_TAG_TVECT
BALL_EXPORT const char * FORMAT_OBSLTE
BALL_EXPORT const char * RECORD_TAG_ANISOU
Atom atom_name_in_current_strand
BALL_EXPORT const char * FORMAT_SIGATM
Integer number_of_SHEET_records
Continuation continuation
Character alternate_location_indicator
Integer atom_serial_number
std::list< Position > hbonds
BALL_EXPORT const char * RECORD_TAG_SSBOND
Character alternate_location_indicator
BALL_EXPORT const char * RECORD_TAG_HELIX
const BALL::Residue * residue
BALL_EXPORT const char * RECORD_TAG_ORIGX2
BALL_EXPORT const char * RECORD_TAG_OBSLTE
Continuation continuation
BALL_EXPORT const char * FORMAT_ORIGX2
BALL_EXPORT const char * FORMAT_SITE
BALL_EXPORT const char * RECORD_TAG_CON063
BALL_EXPORT const char * RECORD_TAG_TITLE
LString8 sequence_database_accession_code
BALL_EXPORT const char * RECORD_TAG_SCALE3
const Chain * current_chain
BALL_EXPORT const char * RECORD_TAG_EXPDTA
BALL_EXPORT const char * FORMAT_SCALE2
BALL_EXPORT const char * RECORD_TAG_ENDMDL
BALL_EXPORT const char * FORMAT_MASTER
BALL_EXPORT const char * FORMAT_FORMUL
Integer number_of_HET_records
LString12 sequence_database_ID_code
Integer specific_model_ID
BALL_EXPORT const char * FORMAT_ATOM
BALL_EXPORT const char * RECORD_TAG_SHEET
Integer number_of_SITE_records
Character alternate_location_indicator
HydrogenAtom hydrogen_atom
BALL_EXPORT const char * FORMAT_SSBOND
Continuation continuation
char PDBList[SIZE_OF_PDB_RECORD_LINE+1]
Integer modification_number
BALL_EXPORT const char * FORMAT_MTRIX3
Atom atom_name_in_previous_strand
BALL_EXPORT const char * RECORD_TAG_SIGATM
Integer atom_serial_number
Character alternate_location_indicator
Integer number_of_residues_in_chain
BALL_EXPORT const char * FORMAT_LINK
Character alternate_location_indicator
-*- Mode: C++; tab-width: 2; -*-
Continuation continuation
SpecificationList sources
Integer atom_serial_number
BALL_EXPORT const char * RECORD_TAG_DBREF
char PDBString[SIZE_OF_PDB_RECORD_LINE+1]
BALL_EXPORT const char * RECORD_TAG_SCALE2
Character alternate_location_indicator
SymmetryOperator second_non_hydrogen_atom
Continuation continuation
BALL_EXPORT const char * RECORD_TAG_ATOM
const String & getName() const
BALL_EXPORT const char * RECORD_TAG_COMPND
void set(const ::BALL::Residue &residue)
BALL_EXPORT const char * RECORD_TAG_SEQRES
std::vector< std::pair< AChar, String > > chain_residue_names
Residue residue_in_current_strand
BALL_EXPORT const char * FORMAT_SEQADV
BALL_EXPORT const char * FORMAT_CISPEP
Integer number_of_REMARK_records
std::list< Position > saltbridges
BALL_EXPORT const char * FORMAT_KEYWDS
BALL_EXPORT const char * FORMAT_SEQRES
BALL_EXPORT const char * RECORD_TAG_SLTBRG
BALL_EXPORT const char * RECORD_TAG_SIGUIJ
Continuation continuation
Continuation continuation
BALL_EXPORT const char * FORMAT_HETATM
LString6 sequence_database_name
BALL_EXPORT const char * FORMAT_SLTBRG
Size atomic_coordinate_records
BALL_EXPORT const char * RECORD_TAG_KEYWDS
BALL_EXPORT const char * FORMAT_HELIX
BALL_EXPORT const char * RECORD_TAG_CONECT
BALL_EXPORT const char * FORMAT_JRNL
ResidueName standard_residue_name
Continuation continuation
Continuation continuation
BALL_EXPORT const char * RECORD_TAG_TER
BALL_EXPORT const char * FORMAT_ANISOU
Size coordinate_transformation_records
BALL_EXPORT const char * RECORD_TAG_MTRIX3
BALL_EXPORT const char * FORMAT_REVDAT
BALL_EXPORT const char * RECORD_TAG_END
AChar residue_insertion_code
SymmetryOperator first_non_hydrogen_atom
BALL_EXPORT const char * RECORD_TAG_FORMUL
BALL_EXPORT const char * FORMAT_SCALE3
Integer atom_serial_number
BALL_EXPORT const char * FORMAT_TURN
BALL_EXPORT const char * FORMAT_ORIGX1
char SList[SIZE_OF_PDB_RECORD_LINE+1]
BALL_EXPORT const char * FORMAT_UNKNOWN
SymmetryOperator second_atom