/* FILE: _maxit.h */ /* VERSION: 1.600 */ /* DATE: 2/3/2005 */ /* Comments and Questions to: sw-help@rcsb.rutgers.edu */ /* COPYRIGHT 1999-2005 Rutgers - The State University of New Jersey This software is provided WITHOUT WARRANTY OF MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE OR ANY OTHER WARRANTY, EXPRESS OR IMPLIED. RUTGERS MAKE NO REPRESENTATION OR WARRANTY THAT THE SOFTWARE WILL NOT INFRINGE ANY PATENT, COPYRIGHT OR OTHER PROPRIETARY RIGHT. The user of this software shall indemnify, hold harmless and defend Rutgers, its governors, trustees, officers, employees, students, agents and the authors against any and all claims, suits, losses, liabilities, damages, costs, fees, and expenses including reasonable attorneys' fees resulting from or arising out of the use of this software. 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TO THE MAXIMUM EXTENT PERMITTED BY APPLICABLE LAW, IN NO EVENT WILL LICENSOR BE LIABLE FOR ANY INDIRECT, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OF OR INABILITY TO USE THE SOFTWARE, INCLUDING, WITHOUT LIMITATION, DAMAGES FOR LOSS OF GOODWILL, WORK STOPPAGE, COMPUTER FAILURE OR MALFUNCTION, OR ANY AND ALL OTHER COMMERCIAL DAMAGES OR LOSSES, EVEN IF ADVISED OF THE POSSIBILITY THEREOF. */ #ifndef _MAXIT_H_ #define _MAXIT_H_ #include #include "_validation.h" #include "remark.h" #define NDB_POLYMER_TEXT "polymer" #define NDB_NON_POLYMER_TEXT "non-polymer" #define NDB_WATER_TEXT "water" #define NDB_DNA_TEXT "DNA" #define NDB_RNA_TEXT "RNA" #define NDB_PR_TEXT "PROTEIN" #define NDB_T_RNA_TEXT "T-RNA" #define NDB_HYBRID_TEXT "DNA/RNA" typedef struct { char sheetID[4]; int numStrands; int initIndex; int initRes; int endIndex; int endRes; int sense; char curAtom[5]; int curIndex; int curRes; char prevAtom[5]; int prevIndex; int prevRes; } _SHEET; typedef struct { int FstIndex; int FstRes; int SndIndex; int SndRes; char SymOP_1[7]; char SymOP_2[7]; } _SSBOND; typedef struct { char FstAtom[5]; char altLoc1[3]; int FstIndex; int FstRes; char H_Atom[5]; char altLocH[3]; int H_Index; int H_Res; char SndAtom[5]; char altLoc2[3]; int SndIndex; int SndRes; char SymOP_1[7]; char SymOP_2[7]; } _HYDBND; typedef _LINK _SLTBRG; typedef struct { char SiteID[4]; int numRes; int alloc_numRes; int *initIndex; int *initRes; } _SITE; typedef struct { char Name[20]; char FstAtom[5]; int FstIndex; int FstRes; char SndAtom[5]; int SndIndex; int SndRes; char Replaced_Atom[5]; } _MODIFB; typedef _MODIFB _MODIFP; typedef struct { char Name[20]; char FstAtom[5]; int FstIndex; int FstRes; char SndAtom[5]; int SndIndex; int SndRes; char Replaced_Atom[5]; char Sugar_Name[26]; } _MODIFS; typedef struct { char PDB_ID[5]; int FstIndex; int FstRes; char Standard_Name[50]; char *details; } _MODRES; typedef struct { int initIndex; int initRes; int numAtoms; } _HET; typedef struct { int Entity_ID; int Old_Entity_ID; int Number; char *Type; char *Source; char *Description; } _ENTITY; typedef struct { int num; char date[20]; char replaces[10]; int mod_type; char *record; } PDB_REV; typedef struct { _RESIDUE *res; _CHAIN *chn; COORD coord[4]; int exist[4]; int chnbreak; double energy[4]; int hbond[4]; char ssbond[12]; int bridpt[2]; int ssbond1; } _NRESIDUE; typedef struct { CifString Asym_ID; char PDB_Strand_ID[3]; int chain_type; char First_Residue_Name[5]; int First_Residue_Number; int n_stbiol; _STBIOL **stbiol; } _BIOL_UNIT_INFO; class _MAXIT: public _VALIDATION { public: _MAXIT(const int, const int); ~_MAXIT(); void Insert_a_Sheet(const char*, const int, const int, const int, const int, const int, const int, const char*, const int, const int, const char*, const int, const int); void Insert_a_SSbond(const int, const int, const int, const int, const char*, const char*); void Insert_a_Hydbnd(const char*, const char*, const int, const int, const char*, const char*, const int, const int, const char*, const char*, const int, const int, const char*, const char*); void Insert_a_Sltbrg(const char*, const char*, const int, const int, const char*, const char*, const int, const int, const char*, const char*); void Insert_a_Site(const char*, const int, const int); void Insert_a_Het(const int, const int, const int); void Insert_a_Modifb(const char*, const char*, const int, const int, const char*, const int, const int, const char*); void Insert_a_Modifp(const char*, const char*, const int, const int, const char*, const int, const int, const char*); void Insert_a_Modifs(const char*, const char*, const int, const int, const char*, const int, const int, const char*, const char*); void Insert_a_Modres(const char*, const int, const int, const char*, const char*); void input_structural_features(const int); void output_structural_features(const int); // void update_pdb_and_pub_numbers(); void pdb_to_ndb_general(const char*, const int); void pdb_to_ndb_proc_remarks(); void pdb_to_ndb_postprocessing(); void delete_atom_count(); void ndb_to_pdb_general(const int); void add_remark_90(); void ndb_to_cif_general(const int, const int, const int, const int, const int); void update_encapsulated_cif(); void cif_to_ndb_general(const int, const int, const int, const int, const int, const int, const int, const int, const int); void cif_to_ndb_exchange(const int, const int); void ndb_to_cif_coordinates(const int, const int, const int, const int, const int, const int, const int, const int); void open_mmcif_file(); void write_mmcif_file(const int, const int, const int); void Output_Stbiol(); void Input_Entity(); void Output_Entity(); void match_entity_with_molecules(); void get_entity_card(); void get_compnd_card(); void get_origx_card(); void get_scale_card(); void get_cryst_card(); // void get_expdta_card(); void get_title_card(); void get_dchem_and_inhibt_cards(); void get_het_card(); void ndb_add_missing_information(const char*, const int, const char*); void write_restraints_correspondences(FILE*); void ndb_write_hydrogen_index(); void generate_ncs_strands(); int get_matrix(double m[3][4], const int); void add_modification_information(); void get_create_secondary_structures_using_promotif(const char*); void delete_atoms(const char *); void insert_atoms(const char *); void delete_residues(const char *); void insert_residues(const char *); void replace_residues(const char *); void set_refine_program(_MAXIT*); void merge_remarks(_MAXIT*); void switch_residue_name_from_sequences(); void moving_waters(); void check_chnids(); void change_coordinates_symm(const char*); void change_coordinates_non_symm(const char*); void remove_secondary_structures(); void check_atom_number_count(); void get_virus_matrix_from_remark_350(const int); void switch_hydrogen_labeling(); void convert_between_fractional_and_orthogonal(const int); void classification(FILE*, FILE*, char*); void delete_na_structural_features(); void update_na_structural_features(); void cif_process_revdat(); void cif_layer1_to_layer2_revdat(); void delete_terminal_atoms(); void correct_atom_name(); void renumber_pdb_numbers(); void search_complexity(); void remove_ebi_remark_500(); void generate_symmetry_and_ncs_related_strands(const char*, const int); void generate_ncs_related_strands(const char*, const int); void generate_packing(); void write_pdb_files(const char*, const int); // void match_struct_asym(); void get_one_letter_code_from_coordinates(); void check_cryst1_card(); void get_biol_unit_formation(); void put_biol_unit_formation(); private: // pdb_to_ndb void pdb_to_ndb_proc_header(const char*); void pdb_to_ndb_proc_compnd_and_source(const int); int get_entity_index(const char*, const int); int is_entity_a_protein(const int); void insert_a_card(const int, const int, const int, char*); One_Card_Info_Format** get_remarks(const int, int&); int* get_blocks_of_remarks(const int, int&, One_Card_Info_Format**); int pdb_to_ndb_proc_remark(const int, One_Card_Info_Format**, const int, REMARKS*, const int); int pdb_to_ndb_proc_remark_special(One_Card_Info_Format*, const int, REMARKS*); void pdb_to_ndb_postprocessing_remarks(); // ndb_to_pdb void ndb_to_pdb_processing_authors(); void ndb_to_pdb_processing_shelx_and_tnt(); void ndb_to_pdb_processing_synchrotron(); void ndb_to_pdb_proc_header(); void replace_pdb_compnd_source_card(); void add_compnd_card(const char*, const int); void ndb_to_pdb_get_source_card(const int, const int, const int, int*, const int, PDB_Source_Format*); void ndb_to_pdb_get_remarks(const int); int find_user_defined_remark(const int); void ndb_to_pdb_get_group_remarks(); void ndb_to_pdb_get_general_remark(const int, REMARKS*, const int, const int, const int, const int); void ndb_to_pdb_get_general_remark(REMARKS*); void ndb_to_pdb_get_general_remark(REMARKS*, One_Card_Info_Format*); void ndb_to_pdb_print_remark_value(char*, One_Card_Info_Format*, REMARKS*, const int, const int); int ndb_to_pdb_get_remark_from_premark(const int); int ndb_to_pdb_get_remark_103_104(); void ndb_to_pdb_get_remark_280_crystal(); void ndb_to_pdb_get_remark_290(); int ndb_to_pdb_get_remark_300(); int ndb_to_pdb_get_remark_350(); void ndb_to_pdb_get_remark_375(); void ndb_to_pdb_get_remark_465(); void ndb_to_pdb_get_remark_470(); void ndb_to_pdb_get_remark_500(const int); void output_close_contact(ISTable*, BTreeObj<_DIndex>&, const int); void ndb_to_pdb_get_remark_525(); void ndb_to_pdb_processing_nmr_remarks(); int check_virus_ncs_remark_300(); int check_virus_ncs_remark_350(); void rms_deviation_of_bonds(); void rms_deviation_of_angles(); void outside_torsions(); void non_cis_trans_torsions(); void get_cispep_cards(); void construct_remark_900(); // ndb_to_cif void ndbcif_process_general(const int); void ndbcif_process_site_gen(const int); void ndbcif_process_rcsb_link(const int); void ndbcif_process_struct_sheet(const int); void ndbcif_process_struct_conn(const int); void ndbcif_process_nonstandard_list(const int); void ndbcif_process_struct_conf(const int); void ndbcif_process_stasym(const int); void ndbcif_process_entity_poly_seq(const int, const int); void ndbcif_process_asym_poly_seq_ndb(const int); void processing_r_factor(const double); void ndbcif_postprocessing_molecule_weight(); void ndbcif_postprocessing_exptl_crystal(); void ndbcif_postprocessing_wavelength_id(); void ndbcif_postprocessing_ncs_oper(); void ndbcif_postprocessing_cif_standard(const int, const int); void ndbcif_process_general_category(const int, const int); void ndbcif_process_remark(const int, const int); void ndbcif_process_matrix(const int); void ndbcif_process_name(const int); void ndbcif_process_refine_ls_restr(const int); void ndbcif_process_database_pdb_rev(const int); void get_ebi_validate_contact(); void get_ebi_validate_bond(); void get_ebi_validate_angle(); void get_ebi_validate_torsion(); void get_ebi_validate_peptide_omega(); int get_pdb_ndb_ids(const int id_option, CifString ids[3]); // cif_to_ndb void ndb_processing_categories_mapping(const int); void cifndb_process_category(ISTable*, const int, const int); void cifndb_process_general(const int, const int, const int, int *, char SerialNo[10][82], char*, const int); void cifndb_process_special(const int, const int, const int, int *, char SerialNo[10][82], const char*); void cifndb_process_general_category(ISTable*, const int, const int); void cifndb_process_remark(ISTable*, const int, const int); void cifndb_process_refine_ls_restr(ISTable*); void cifndb_process_matrix(ISTable*, const int); void cifndb_process_struct_site_gen(ISTable*); void cifndb_process_rcsb_link(ISTable*); void cifndb_process_struct_conf(ISTable*); void cifndb_process_sheet(); void cifndb_process_struct_conn(ISTable*); void cifndb_process_database_pdb_rev(ISTable*); void put_into_card(const char*, const int, const int); void ndb_processing_requests(); void ndb_processing_em_software(); void ndb_processing_struct_category(); void ndb_processing_struct_sheet_hbond(); void ndb_processing_ndb_database_PDB_obs_spr_category(); void ndb_processing_struct_ref_seq_and_diff(); void post_processing_from_cif_to_ndb(); // promotif void find_helices(const int, _NRESIDUE**); void find_sheets(const int, _NRESIDUE**, const char*); void find_ssbonds(const int, _NRESIDUE**); void get_refn_card(); int find_entity_index(const int); char *get_protein_descriptor(_CHAIN *chain); void ndb_get_protein_name(char*, const int); void get_descriptor_ligand(char*); void insert_formul_card(const char*, const int, const int); void insert_het_card(_CHAIN*, const char*, const int, const char*, const int); void get_bspair_second_chain(const char*, const char*, const char*, char*, int&, char*); void Clear_Structural_Feature(); void get_derived_features(CifFileObj*); void get_na_derived_features(CifFileObj*); int _alloc_sheet, _n_sheet; _SHEET** _sheet; int _alloc_ssbond, _n_ssbond; _SSBOND **_ssbond; int _alloc_hydbnd, _n_hydbnd; _HYDBND **_hydbnd; int _alloc_sltbrg, _n_sltbrg; _SLTBRG **_sltbrg; int _alloc_site, _n_site; _SITE** _site; int _alloc_het, _n_het; _HET** _het; int _alloc_modifb, _n_modifb; _MODIFB **_modifb; int _alloc_modifp, _n_modifp; _MODIFP **_modifp; int _alloc_modifs, _n_modifs; _MODIFS **_modifs; int _alloc_modres, _n_modres; _MODRES **_modres; int _n_entity; _ENTITY* _entity; int _exist_helix; int _exist_sheet; int _exist_ssbond; int _create_final_file; int _n_biol_unit_info; _BIOL_UNIT_INFO **_biol_unit_info; }; extern void pdb_to_ndb(const char*, const char*, const char*, const int, const int, const int, const char*, const int); extern void pdb_to_cif(const char*, const char*, const char*, const int, const int, const int, const int, const int, const int, const int, const int, const char*, const int, const int, const int); extern void ndb_to_pdb(const char*, const char*, const char*, const int, const int); extern void ndb_to_ndb(const char*, const char*, const char*, const int); extern void ndb_to_cif(const char*, const char*, const char*, const int, const int, const int, const int, const int, const int, const int, const int, const int); extern void cif_to_ndb(const char*, const char*, const char*, const int, const int, const int, const int, const int, const int, const char*, const int); extern void cif_to_pdb(const char*, const char*, const char*, const int, const int, const int, const int, const int, const int, const char*, const int); extern void cif_to_cif(const char*, const char*, const char*, const int, const int, const int, const int, const int, const int, const int, const int, const int, const int, const int, const int, const int, const char*, const int, const int, const int); extern void pdb_to_encapsulated_cif(const char*, const char*, const char*, const int, const int, const int); extern void fractional_to_orthogonal(const char*, const char*, const char*); extern void fractional_to_orthogonal(const char*, const char*, const char*, const int); extern void orthogonal_to_fractional(const char*, const char*, const char*, const int); extern void generate_sym_strands_NDB(const char*, const char*, const char*, const int); extern void generate_sym_strands_CIF(const char*, const char*, const char*, const int); extern void generate_ncs_strands_NDB(const char*, const char*, const char*, const int); extern void generate_ncs_strands_CIF(const char*, const char*, const char*, const int); extern void restraints_correspondences_NDB(const char*, const char*, const char*); extern void restraints_correspondences_CIF(const char*, const char*, const char*, const int); extern void remove_hydrogen_NDB(const char*, const char*, const char*, const int); extern void remove_hydrogen_CIF(const char*, const char*, const char*, const int); extern void remove_Q_atoms_CIF(const char*, const char*, const char*, const int); extern void correction_chirality_NDB(const char*, const char*, const char*, const int); extern void correction_chirality_CIF(const char*, const char*, const char*, const int); extern void renumber_pdb_number_CIF(const char*, const char*, const char*); extern void delete_atoms_NDB(const char*, const char*, const char*, const char*, const int); extern void delete_atoms_CIF(const char*, const char*, const char*, const char*, const int); extern void insert_atoms_NDB(const char*, const char*, const char*, const char*, const int); extern void insert_atoms_CIF(const char*, const char*, const char*, const char*, const int); extern void delete_residues_NDB(const char*, const char*, const char*, const char*, const int); extern void delete_residues_CIF(const char*, const char*, const char*, const char*, const int); extern void insert_residues_NDB(const char*, const char*, const char*, const char*, const int); extern void insert_residues_CIF(const char*, const char*, const char*, const char*, const int); extern void merge_remarks_NDB(const char*, const char*, const char*, const char*, const int); extern void merge_remarks_CIF(const char*, const char*, const char*, const char*, const int); extern void merge_coordinates_NDB(const char*, const char*, const char*, const char*, const int); extern void merge_coordinates_CIF(const char*, const char*, const char*, const char*, const int); extern void moving_waters_NDB(const char*, const char*, const char*, const int); extern void moving_waters_CIF(const char*, const char*, const char*, const int); extern void switch_residue_names_NDB(const char*, const char*, const char*, const int); extern void switch_residue_names_CIF(const char*, const char*, const char*, const int); extern void change_coordinates_symm_CIF(const char*, const char*, const char*, const char*); extern void change_coordinates_non_symm_CIF(const char*, const char*, const char*, const char*); extern void get_virus_matrix_from_remark_350(const char*, const char*, const char*, const int); extern void update_hydrogen_nomenclature(const char*, const char*, const char*); extern void switch_conect_from_old_to_new(); extern void switch_conect_from_new_to_old(); extern void check_file(const char*, const char*); extern void classification(const char*, const char*, FILE*, FILE*); extern void check_file(const char*, const char*, FILE*, const int); extern void cif_layer1_to_layer2(const char*, const char*, const char*); extern void merge_waters_CIF(const char*, const char*, const char*); extern void replace_residues_NDB(const char*, const char*, const char*, const char*, const int); extern void replace_residues_CIF(const char*, const char*, const char*, const char*); extern void search_complexity(const char*, const char*); extern void cif_to_biol_unit_pdb(const char*, const char*, const char*, const int, const int); extern void exchange_cif_to_internal_cif(const char*, const char*, const char*); extern void cif_to_packing_pdb(const char*, const char*, const char*, const int); extern void get_one_letter_code_from_coordinates(const char*, const char*, const char*); extern void separation_string_base_word(char *old_string, char *str1, char *str2, const char *word); extern void get_hpub_letter(const char *filename); #endif