/* FILE: pdb2cif.C */ /* 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. This indemnification shall include, but is not limited to, any and all claims alleging products liability. */ /* PDB SOFTWARE LICENSE AGREEMENT BY CLICKING THE ACCEPTANCE BUTTON OR INSTALLING OR USING THIS "SOFTWARE, THE INDIVIDUAL OR ENTITY LICENSING THE SOFTWARE ("LICENSEE") IS CONSENTING TO BE BOUND BY AND IS BECOMING A PARTY TO THIS AGREEMENT. IF LICENSEE DOES NOT AGREE TO ALL OF THE TERMS OF THIS AGREEMENT THE LICENSEE MUST NOT INSTALL OR USE THE SOFTWARE. 1. LICENSE AGREEMENT This is a license between you ("Licensee") and the Protein Data Bank (PDB) at Rutgers, The State University of New Jersey (hereafter referred to as "RUTGERS"). The software is owned by RUTGERS and protected by copyright laws, and some elements are protected by laws governing trademarks, trade dress and trade secrets, and may be protected by patent laws. 2. LICENSE GRANT RUTGERS grants you, and you hereby accept, non-exclusive, royalty-free perpetual license to install, use, modify, prepare derivative works, incorporate into other computer software, and distribute in binary and source code format, or any derivative work thereof, together with any associated media, printed materials, and on-line or electronic documentation (if any) provided by RUTGERS (collectively, the "SOFTWARE"), subject to the following terms and conditions: (i) any distribution of the SOFTWARE shall bind the receiver to the terms and conditions of this Agreement; (ii) any distribution of the SOFTWARE in modified form shall clearly state that the SOFTWARE has been modified from the version originally obtained from RUTGERS. 2. COPYRIGHT; RETENTION OF RIGHTS. The above license grant is conditioned on the following: (i) you must reproduce all copyright notices and other proprietary notices on any copies of the SOFTWARE and you must not remove such notices; (ii) in the event you compile the SOFTWARE, you will include the copyright notice with the binary in such a manner as to allow it to be easily viewable; (iii) if you incorporate the SOFTWARE into other code, you must provide notice that the code contains the SOFTWARE and include a copy of the copyright notices and other proprietary notices. All copies of the SOFTWARE shall be subject to the terms of this Agreement. 3. NO MAINTENANCE OR SUPPORT; TREATMENT OF ENHANCEMENTS RUTGERS is under no obligation whatsoever to: (i) provide maintenance or support for the SOFTWARE; or (ii) to notify you of bug fixes, patches, or upgrades to the features, functionality or performance of the SOFTWARE ("Enhancements") (if any), whether developed by RUTGERS or third parties. If, in its sole discretion, RUTGERS makes an Enhancement available to you and RUTGERS does not separately enter into a written license agreement with you relating to such bug fix, patch or upgrade, then it shall be deemed incorporated into the SOFTWARE and subject to this Agreement. You are under no obligation whatsoever to provide any Enhancements to RUTGERS or the public that you may develop over time; however, if you choose to provide your Enhancements to RUTGERS, or if you choose to otherwise publish or distribute your Enhancements, in source code form without contemporaneously requiring end users or RUTGERS to enter into a separate written license agreement for such Enhancements, then you hereby grant RUTGERS a non-exclusive, royalty-free perpetual license to install, use, modify, prepare derivative works, incorporate into the SOFTWARE or other computer software, distribute, and sublicense your Enhancements or derivative works thereof, in binary and source code form. 4. FEES. 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Title and related rights in the content accessed through the SOFTWARE is the property of the applicable content owner and is protected by applicable law. The license granted under this Agreement gives Licensee no rights to such content. 7. DISCLAIMER OF WARRANTY. THE SOFTWARE IS PROVIDED FREE OF CHARGE, AND, THEREFORE, ON AN "AS IS" BASIS, WITHOUT WARRANTY OF ANY KIND, INCLUDING WITHOUT LIMITATION THE WARRANTIES THAT IT IS FREE OF DEFECTS, MERCHANTABLE, FIT FOR A PARTICULAR PURPOSE OR NON-INFRINGING. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE SOFTWARE IS BORNE BY LICENSEE. SHOULD THE SOFTWARE PROVE DEFECTIVE IN ANY RESPECT, THE LICENSEE AND NOT LICENSOR ASSUMES THE ENTIRE COST OF ANY SERVICE AND REPAIR. THIS DISCLAIMER OF WARRANTY CONSTITUTES AN ESSENTIAL PART OF THIS AGREEMENT. NO USE OF THE PRODUCT IS AUTHORIZED HEREUNDER EXCEPT UNDER THIS DISCLAIMER. 8. LIMITATION OF LIABILITY. 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. */ /* program to extract informat from crystallographic softwares */ #include #include #include #include #include "structure.h" #include "harv.h" #include "util.h" extern CELL cell; extern REFINE refine; extern PDBX_REFINE pdbx_refine; extern SYMMETRY symmetry ; extern REFINE_HIST refine_hist; extern REFINE_ANALYZE refine_analyze; extern STRUCT_CONN struct_conn; extern DATABASE_PDB_MATRIX database_PDB_matrix; extern ATOM_SITES atom_sites; extern PDBX_REFINE_TLS pdbx_refine_tls_single; PDBX_REFINE_TLS pdbx_refine_tls_single; extern PDBX_REFINE_TLS_GROUP pdbx_refine_tls_group_single; PDBX_REFINE_TLS_GROUP pdbx_refine_tls_group_single; extern REFLNS reflns; extern DIFFRN_DETECTOR diffrn_detector; extern DIFFRN_SOURCE diffrn_source; extern COMPUTING computing; REFINE_LS_SHELL refine_ls_shell; REFLNS_SHELL reflns_shell; PDBX_REFINE_TLS_GROUP pdbx_refine_tls_group[50]; PDBX_REFINE_TLS pdbx_refine_tls[50]; STRUCT_NCS_DOM struct_ncs_dom[20]; STRUCT_NCS_DOM_LIM struct_ncs_dom_lim[20]; REFINE_LS_RESTR refine_ls_restr[100]; REFINE_LS_RESTR_NCS refine_ls_restr_ncs[20]; PDBX_XPLOR_FILE pdbx_xplor_file[80]; void write_remark_text(FILE *fout, char **line, int nline); void write_non_standard_remark(FILE *fout, char **line, int nline); void write_remark_200(FILE *fout, char **line, int n); void write_ls_restr_type(FILE *fout, char * , int i); void convert_restr_2_standard(FILE *fout, char *type, int i, const char **pair, int npair); void pdb2cif_coord(FILE *fout, char *inpfile); void write_PDB_item(FILE *fout, char *str, long len, int format, int digit); void write_PDB_resid(FILE *fout, char *str, long len); void write_PDB_30_70(FILE *fout, char *str, int n) ; //column 30_70 void write_PDB_6_27(FILE *fout, char *str); void extract_PDB_tls_weird(char *infile); void extract_PDB_tls_weird_refmac(char *infile); void extract_PDB_head(char *infile); void extract_PDB_tls(char *infile); void extract_PDB_ncs(char *infile); void extract_PDB_refine_ls_restr(char *infile, char *prog); void extract_PDB_conn(FILE *fout,char *infile); void write_refine_hist(FILE *fout); void write_refine_analyze(FILE *fout); void write_refine_ls_restr(FILE *fout); void write_tls(FILE *fout); void write_ncs(FILE *fout); void write_conn(FILE *fout, char *line, int atom1, int atom2, int alt1, int comp1, int comp2, int asym1, int seq1, int seq2, int ins1, int sym1, int sym2); void write_database_PDB_matrix(FILE *fout); void write_atom_sites(FILE *fout); void write_pdbx_xplor_file(FILE *fout); int NR=0, NTLS=0, NCS=0, NLIM=0, NNCS=0; char PROG[40]; void pdb_2_cif(FILE *fout, char *infile) { refine_ls_restr[0].number = INI; refine_ls_restr[0].dev_ideal =INI ; refine_ls_restr[0].dev_ideal_target = INI; refine_ls_restr[0].weight = INI; extract_PDB_head(infile); extract_PDB_refine_ls_restr(infile, PROG); write_pdbx_xplor_file(fout); write_refine_hist(fout); write_refine_analyze(fout); write_refine_ls_restr(fout); extract_PDB_tls(infile); // extract_PDB_tls_weird(infile); // extract_PDB_tls_weird_refmac(infile); if(NTLS>0) write_tls(fout); extract_PDB_ncs(infile); write_ncs(fout); write_database_PDB_matrix(fout); write_atom_sites(fout); extract_PDB_conn (fout, infile); pdb2cif_coord(fout, infile); strcpy(computing.structure_refinement , PROG); } void write_pdbx_xplor_file(FILE *fout) { int i; for(i=0;i<80;i++){ if(pdbx_xplor_file[i].param_file || pdbx_xplor_file[i].topol_file){ if(i==0){ fprintf(fout,"%s %s %s %s" ,"\nloop_\n", "_ndb_xplor_file.serial_no\n", "_ndb_xplor_file.param_file\n", "_ndb_xplor_file.topol_file\n" ); } fprintf(fout,"%d\n", i+1); (pdbx_xplor_file[i].param_file)?fprintf(fout,"'%s'\n", pdbx_xplor_file[i].param_file):fprintf(fout," ? \n"); (pdbx_xplor_file[i].topol_file)?fprintf(fout,"'%s'\n", pdbx_xplor_file[i].topol_file):fprintf(fout," ? \n"); } } }; void write_database_PDB_matrix(FILE *fout) { if(database_PDB_matrix.origx11>-9998 && database_PDB_matrix.origx22>-9998 && database_PDB_matrix.origx33>-9998){ fprintf(fout,"#\n"); fprintf(fout,"_database_PDB_matrix.origx[1][1] %.5f\n", database_PDB_matrix.origx11); fprintf(fout,"_database_PDB_matrix.origx[1][2] %.5f\n", database_PDB_matrix.origx12); fprintf(fout,"_database_PDB_matrix.origx[1][3] %.5f\n", database_PDB_matrix.origx13); fprintf(fout,"_database_PDB_matrix.origx[2][1] %.5f\n", database_PDB_matrix.origx21); fprintf(fout,"_database_PDB_matrix.origx[2][2] %.5f\n", database_PDB_matrix.origx22); fprintf(fout,"_database_PDB_matrix.origx[2][3] %.5f\n", database_PDB_matrix.origx23); fprintf(fout,"_database_PDB_matrix.origx[3][1] %.5f\n", database_PDB_matrix.origx31); fprintf(fout,"_database_PDB_matrix.origx[3][2] %.5f\n", database_PDB_matrix.origx32); fprintf(fout,"_database_PDB_matrix.origx[3][3] %.5f\n", database_PDB_matrix.origx33); } if(database_PDB_matrix.origx_vector1>-9998 && database_PDB_matrix.origx_vector2>-9998){ fprintf(fout,"_database_PDB_matrix.origx_vector[1] %.5f\n", database_PDB_matrix.origx_vector1); fprintf(fout,"_database_PDB_matrix.origx_vector[2] %.5f\n", database_PDB_matrix.origx_vector2); fprintf(fout,"_database_PDB_matrix.origx_vector[3] %.5f\n", database_PDB_matrix.origx_vector3); } } void write_atom_sites(FILE *fout) { if(atom_sites.fract_transf_matrix11>-9998 && atom_sites.fract_transf_matrix22>-9998 && atom_sites.fract_transf_matrix33>-9998){ fprintf(fout,"#\n"); fprintf(fout,"_atom_sites.fract_transf_matrix[1][1] %.5f\n", atom_sites.fract_transf_matrix11); fprintf(fout,"_atom_sites.fract_transf_matrix[1][2] %.5f\n", atom_sites.fract_transf_matrix12); fprintf(fout,"_atom_sites.fract_transf_matrix[1][3] %.5f\n", atom_sites.fract_transf_matrix13); fprintf(fout,"_atom_sites.fract_transf_matrix[2][1] %.5f\n", atom_sites.fract_transf_matrix21); fprintf(fout,"_atom_sites.fract_transf_matrix[2][2] %.5f\n", atom_sites.fract_transf_matrix22); fprintf(fout,"_atom_sites.fract_transf_matrix[2][3] %.5f\n", atom_sites.fract_transf_matrix23); fprintf(fout,"_atom_sites.fract_transf_matrix[3][1] %.5f\n", atom_sites.fract_transf_matrix31); fprintf(fout,"_atom_sites.fract_transf_matrix[3][2] %.5f\n", atom_sites.fract_transf_matrix32); fprintf(fout,"_atom_sites.fract_transf_matrix[3][3] %.5f\n", atom_sites.fract_transf_matrix33); } if(atom_sites.fract_transf_vector1>-9998 && atom_sites.fract_transf_vector2>-9998){ fprintf(fout,"_atom_sites.fract_transf_vector[1] %.5f\n", atom_sites.fract_transf_vector1); fprintf(fout,"_atom_sites.fract_transf_vector[2] %.5f\n", atom_sites.fract_transf_vector2); fprintf(fout,"_atom_sites.fract_transf_vector[3] %.5f\n", atom_sites.fract_transf_vector3); } } void write_refine_hist(FILE *fout) { fprintf(fout,"#\n"); if(refine_hist.pdbx_number_atoms_protein >-9998) fprintf(fout,"_refine_hist.pdbx_number_atoms_protein %d\n", refine_hist.pdbx_number_atoms_protein); if(refine_hist.pdbx_number_atoms_nucleic_acid >-9998) fprintf(fout,"_refine_hist.pdbx_number_atoms_nucleic_acid %d\n", refine_hist.pdbx_number_atoms_nucleic_acid); if(refine_hist.pdbx_number_atoms_ligand >-9998) fprintf(fout,"_refine_hist.pdbx_number_atoms_ligand %d\n", refine_hist.pdbx_number_atoms_ligand); if(refine_hist.number_atoms_solvent >-9998) fprintf(fout,"_refine_hist.number_atoms_solvent %d\n", refine_hist.number_atoms_solvent); if(refine_hist.number_atoms_total >-9998) fprintf(fout,"_refine_hist.number_atoms_total %d\n", refine_hist.number_atoms_total); if(refine_hist.d_res_high >-9998) fprintf(fout,"_refine_hist.d_res_high %.3f\n", refine_hist.d_res_high); if(refine_hist.d_res_low >-9998) fprintf(fout,"_refine_hist.d_res_low %.3f\n", refine_hist.d_res_low); fprintf(fout,"_refine_hist.cycle_id LAST\n"); } void write_tls(FILE *fout) { int i; if(NTLS>0 && pdbx_refine_tls_group[0].beg_label_asym_id[0] != '?' && pdbx_refine_tls_group[0].end_label_asym_id[0] != '?'){ fprintf(fout,"#\n"); fprintf(fout,"loop_\n"); fprintf(fout,"_pdbx_refine_tls_group.id\n"); fprintf(fout,"_pdbx_refine_tls_group.refine_tls_id\n"); fprintf(fout,"_pdbx_refine_tls_group.beg_label_asym_id\n"); fprintf(fout,"_pdbx_refine_tls_group.beg_label_seq_id\n"); fprintf(fout,"_pdbx_refine_tls_group.end_label_asym_id\n"); fprintf(fout,"_pdbx_refine_tls_group.end_label_seq_id\n"); fprintf(fout,"_pdbx_refine_tls_group.selection\n"); for(i=0; i-9998)? fprintf(fout, " %.4f ", pdbx_refine_tls[i].origin_x ) : fprintf(fout,"? "); (pdbx_refine_tls[i].origin_y >-9998)? fprintf(fout, " %.4f ", pdbx_refine_tls[i].origin_y ) : fprintf(fout,"? "); (pdbx_refine_tls[i].origin_z >-9998)? fprintf(fout, " %.4f ", pdbx_refine_tls[i].origin_z ) : fprintf(fout,"? "); (pdbx_refine_tls[i].T11 >-9998)? fprintf(fout, " %.4f ", pdbx_refine_tls[i].T11 ) : fprintf(fout,"? "); (pdbx_refine_tls[i].T22 >-9998)? fprintf(fout, " %.4f ", pdbx_refine_tls[i].T22 ) : fprintf(fout,"? "); (pdbx_refine_tls[i].T33 >-9998)? fprintf(fout, " %.4f ", pdbx_refine_tls[i].T33 ) : fprintf(fout,"? "); (pdbx_refine_tls[i].T12 >-9998)? fprintf(fout, " %.4f ", pdbx_refine_tls[i].T12 ) : fprintf(fout,"? "); (pdbx_refine_tls[i].T13 >-9998)? fprintf(fout, " %.4f ", pdbx_refine_tls[i].T13 ) : fprintf(fout,"? "); (pdbx_refine_tls[i].T23 >-9998)? fprintf(fout, " %.4f ", pdbx_refine_tls[i].T23 ) : fprintf(fout,"? "); (pdbx_refine_tls[i].L11 >-9998)? fprintf(fout, " %.4f ", pdbx_refine_tls[i].L11 ) : fprintf(fout,"? "); (pdbx_refine_tls[i].L22 >-9998)? fprintf(fout, " %.4f ", pdbx_refine_tls[i].L22 ) : fprintf(fout,"? "); (pdbx_refine_tls[i].L33 >-9998)? fprintf(fout, " %.4f ", pdbx_refine_tls[i].L33 ) : fprintf(fout,"? "); (pdbx_refine_tls[i].L12 >-9998)? fprintf(fout, " %.4f ", pdbx_refine_tls[i].L12 ) : fprintf(fout,"? "); (pdbx_refine_tls[i].L13 >-9998)? fprintf(fout, " %.4f ", pdbx_refine_tls[i].L13 ) : fprintf(fout,"? "); (pdbx_refine_tls[i].L23 >-9998)? fprintf(fout, " %.4f ", pdbx_refine_tls[i].L23 ) : fprintf(fout,"? "); (pdbx_refine_tls[i].S11 >-9998)? fprintf(fout, " %.4f ", pdbx_refine_tls[i].S11 ) : fprintf(fout,"? "); (pdbx_refine_tls[i].S22 >-9998)? fprintf(fout, " %.4f ", pdbx_refine_tls[i].S22 ) : fprintf(fout,"? "); (pdbx_refine_tls[i].S33 >-9998)? fprintf(fout, " %.4f ", pdbx_refine_tls[i].S33 ) : fprintf(fout,"? "); (pdbx_refine_tls[i].S12 >-9998)? fprintf(fout, " %.4f ", pdbx_refine_tls[i].S12 ) : fprintf(fout,"? "); (pdbx_refine_tls[i].S13 >-9998)? fprintf(fout, " %.4f ", pdbx_refine_tls[i].S13 ) : fprintf(fout,"? "); (pdbx_refine_tls[i].S23 >-9998)? fprintf(fout, " %.4f ", pdbx_refine_tls[i].S23 ) : fprintf(fout,"? "); (pdbx_refine_tls[i].S21 >-9998)? fprintf(fout, " %.4f ", pdbx_refine_tls[i].S21 ) : fprintf(fout,"? "); (pdbx_refine_tls[i].S31 >-9998)? fprintf(fout, " %.4f ", pdbx_refine_tls[i].S31 ) : fprintf(fout,"? "); (pdbx_refine_tls[i].S32 >-9998)? fprintf(fout, " %.4f ", pdbx_refine_tls[i].S32 ) : fprintf(fout,"? "); (pdbx_refine_tls[i].S22_S11 >-9998)? fprintf(fout, " %.4f ", pdbx_refine_tls[i].S22_S11 ) : fprintf(fout,"? "); (pdbx_refine_tls[i].S11_S33 >-9998)? fprintf(fout, " %.4f ", pdbx_refine_tls[i].S11_S33 ) : fprintf(fout,"? "); fprintf(fout,"\n"); } } void write_ncs(FILE *fout) { int i; if(NCS>0 && (struct_ncs_dom[0].details[0] != '?' || struct_ncs_dom[0].id[0] != '?')){ fprintf(fout,"#\n"); fprintf(fout,"loop_\n"); fprintf(fout,"_struct_ncs_dom.id\n"); fprintf(fout,"_struct_ncs_dom.details\n"); // printf("%d '%s' '%s'\n", NCS, struct_ncs_dom[0].id, struct_ncs_dom[0].details); for(i=0; i 0 && struct_ncs_dom_lim[0].dom_id[0] != '?' && struct_ncs_dom_lim[0].beg_label_asym_id[0] != '?' && struct_ncs_dom_lim[0].end_label_asym_id[0] != '?'){ fprintf(fout,"#\n"); fprintf(fout,"loop_\n"); fprintf(fout,"_struct_ncs_dom_lim.dom_id\n"); fprintf(fout,"_struct_ncs_dom_lim.pdbx_component\n"); fprintf(fout,"_struct_ncs_dom_lim.beg_label_asym_id\n"); fprintf(fout,"_struct_ncs_dom_lim.beg_label_seq_id\n"); fprintf(fout,"_struct_ncs_dom_lim.end_label_asym_id\n"); fprintf(fout,"_struct_ncs_dom_lim.end_label_seq_id\n"); for(i=0; i 0 && refine_ls_restr_ncs[0].rms_dev_position>-9998 && refine_ls_restr_ncs[0].pdbx_type[0] !='?'){ fprintf(fout,"#\n"); fprintf(fout,"loop_\n"); fprintf(fout,"_refine_ls_restr_ncs.dom_id\n"); fprintf(fout,"_refine_ls_restr_ncs.pdbx_type\n"); fprintf(fout,"_refine_ls_restr_ncs.pdbx_asym_id\n"); fprintf(fout,"_refine_ls_restr_ncs.pdbx_number\n"); fprintf(fout,"_refine_ls_restr_ncs.rms_dev_position\n"); fprintf(fout,"_refine_ls_restr_ncs.weight_position\n"); for(i=0; i-9998)? fprintf(fout, " %d ", refine_ls_restr_ncs[i].pdbx_number ) : fprintf(fout,"? "); (refine_ls_restr_ncs[i].rms_dev_position)? fprintf(fout," %.3f ",refine_ls_restr_ncs[i].rms_dev_position) : fprintf(fout,"? "); (refine_ls_restr_ncs[i].weight_position >-9998)? fprintf(fout, " %.3f ", refine_ls_restr_ncs[i].weight_position) : fprintf(fout,"? "); fprintf(fout,"\n"); } } } void extract_PDB_tls(char *infile) { char str[100], tls_detail[80]; int ntls=0, ng=0; FILE *finp; if((finp=fopen(infile, "r"))==NULL) open_file_error (infile, "extract_PDB_tls"); strcpy(tls_detail, "?"); pdbx_refine_tls_group[0] = pdbx_refine_tls_group_single; pdbx_refine_tls[0] = pdbx_refine_tls_single; while (fgets(str, sizeof str, finp) != NULL) { if(!strncmp_case(str, "ATOM ", 6) || !strncmp_case(str, "HETATM", 6))break; if(!strncmp_case(str, "REMARK", 6) && strstr_space(str, "REMARK 3")){ if(strstr_space(str,"REMARK 3 TLS DETAILS")){ strcpy(tls_detail, get_substr(str,"DETAILS", "\n")); if (is_space_line(tls_detail)<=1) strcpy( tls_detail,"?"); }else if(strstr_space(str," NUMBER OF TLS GROUPS :")){ // tls=get_int(str," :", "\n"); }else if(strstr_space(str,"REMARK 3 TLS GROUP :")){ ng = get_int(str," :", "\n"); if(ng>0){ sprintf(pdbx_refine_tls_group_single.id, "%d", ng); sprintf(pdbx_refine_tls_single.id, "%d", ng); while (fgets(str, sizeof str, finp) != NULL) { if(strstr_space(str, "RESIDUE RANGE :")){ if(sscanf(get_substr(str," :", "\n"), "%s%s%s%s", pdbx_refine_tls_group_single.beg_label_asym_id, pdbx_refine_tls_group_single.beg_label_seq_id, pdbx_refine_tls_group_single.end_label_asym_id, pdbx_refine_tls_group_single.end_label_seq_id) != 4) continue; }else if(strstr_space(str, " ORIGIN FOR THE GROUP (A):")){ if(sscanf(get_substr(str,":", "\n"), "%f%f%f", &pdbx_refine_tls_single.origin_x, &pdbx_refine_tls_single.origin_y, &pdbx_refine_tls_single.origin_z) !=3 ) continue; }else if(pattern5(str, " T11:", "T22", "", "","")){ pdbx_refine_tls_single.T11=get_float(str, " T11:", "T22"); pdbx_refine_tls_single.T22=get_float(str, " T22:", "\n"); }else if(pattern5(str, " T33:", "T12", "", "","")){ pdbx_refine_tls_single.T33=get_float(str, " T33:", "T12"); pdbx_refine_tls_single.T12=get_float(str, " T12:", "\n"); }else if(pattern5(str, " T13:", "T23", "", "","")){ pdbx_refine_tls_single.T13=get_float(str, " T13:", "T23"); pdbx_refine_tls_single.T23=get_float(str, " T23:", "\n"); }else if(pattern5(str, " L11:", "L22", "", "","")){ pdbx_refine_tls_single.L11=get_float(str, " L11:", "L22"); pdbx_refine_tls_single.L22=get_float(str, " L22:", "\n"); }else if(pattern5(str, " L33:", "L12", "", "","")){ pdbx_refine_tls_single.L33=get_float(str, " L33:", "L12"); pdbx_refine_tls_single.L12=get_float(str, " L12:", "\n"); }else if(pattern5(str, " L13:", "L23", "", "","")){ pdbx_refine_tls_single.L13=get_float(str, " L13:", "L23"); pdbx_refine_tls_single.L23=get_float(str, " L23:", "\n"); }else if(pattern5(str, " S11:", "S12:", "S13:", "","")){ pdbx_refine_tls_single.S11=get_float(str, " S11:", "S12"); pdbx_refine_tls_single.S12=get_float(str, " S12:", "S13"); pdbx_refine_tls_single.S13=get_float(str, " S13:", "\n"); }else if(pattern5(str, " S21:", "S22:", "S23:", "","")){ pdbx_refine_tls_single.S21=get_float(str, " S21:", "S22"); pdbx_refine_tls_single.S22=get_float(str, " S22:", "S23"); pdbx_refine_tls_single.S23=get_float(str, " S23:", "\n"); }else if(pattern5(str, " S31:", "S32:", "S33:", "","")){ pdbx_refine_tls_single.S31=get_float(str, " S31:", "S32"); pdbx_refine_tls_single.S32=get_float(str, " S32:", "S33"); pdbx_refine_tls_single.S33=get_float(str, " S33:", "\n"); break; } } strcpy(pdbx_refine_tls_single.details, tls_detail); strcpy(pdbx_refine_tls_single.method, "refined"); pdbx_refine_tls_single.S22_S11 = pdbx_refine_tls_single.S22 - pdbx_refine_tls_single.S11; pdbx_refine_tls_single.S11_S33 = pdbx_refine_tls_single.S11 - pdbx_refine_tls_single.S33; pdbx_refine_tls_group[ntls] = pdbx_refine_tls_group_single; pdbx_refine_tls[ntls] = pdbx_refine_tls_single; ntls++; NTLS=ntls; } } } } fclose(finp); } void extract_PDB_tls_weird(char *infile) { char str[100], tls_detail[80], tmp[20]; int ntls=0; FILE *finp; if((finp=fopen(infile, "r"))==NULL) open_file_error (infile, "extract_PDB_tls_weird"); strcpy(tls_detail, "?"); while (fgets(str, sizeof str, finp) != NULL) { if(!strncmp_case(str, "ATOM ", 6) || !strncmp_case(str, "HETATM", 6))break; if(strstr_space(str,"REMARK 3 TLS DETAILS")){ strcpy(tls_detail, get_substr(str,"DETAILS", "\n")); if (is_space_line(tls_detail)<=1) strcpy( tls_detail,"?"); }else if(strstr_space(str,"REMARK 3 NUMBER OF TLS GROUPS :")){ // ng=get_int(str," :", "\n"); }else if(strstr_space(str,"REMARK 3 Number of pieces in the TLS group")){ sprintf(pdbx_refine_tls_group_single.id, "%d", ntls+1); sprintf(pdbx_refine_tls_single.id, "%d", ntls+1); while (fgets(str, sizeof str, finp) != NULL) { if(pattern5(str, "REMARK 3 From", " to ", "", "", "")){ get_string(str, 16,17, tmp); strcpy(pdbx_refine_tls_group_single.beg_label_asym_id,tmp); get_string(str, 18,21,pdbx_refine_tls_group_single.beg_label_seq_id); get_string(str, 25,26,pdbx_refine_tls_group_single.end_label_asym_id ); get_string(str, 27,30,pdbx_refine_tls_group_single.end_label_seq_id); }else if(strstr_space(str, "REMARK 3 Origin for the group :")){ fgets(str, sizeof str, finp); pdbx_refine_tls_single.origin_x = get_float_by_length(str, 12,19); pdbx_refine_tls_single.origin_y = get_float_by_length(str, 20,28); pdbx_refine_tls_single.origin_z = get_float_by_length(str, 29,38); }else if(strstr_space(str,"REMARK 3 T tensor (T11, T22, T33, T12, T13, T23)")){ fgets(str, sizeof str, finp); pdbx_refine_tls_single.T11=get_float_by_length(str, 11,18); pdbx_refine_tls_single.T22=get_float_by_length(str, 19,26); pdbx_refine_tls_single.T33=get_float_by_length(str, 27,34); pdbx_refine_tls_single.T12=get_float_by_length(str, 35,42); pdbx_refine_tls_single.T13=get_float_by_length(str, 43,50); pdbx_refine_tls_single.T23=get_float_by_length(str, 51,58); }else if(strstr_space(str,"REMARK 3 L tensor (L11, L22, L33, L12, L13, L23)")){ fgets(str, sizeof str, finp); pdbx_refine_tls_single.L11=get_float_by_length(str, 11,18); pdbx_refine_tls_single.L22=get_float_by_length(str, 19,26); pdbx_refine_tls_single.L33=get_float_by_length(str, 27,34); pdbx_refine_tls_single.L12=get_float_by_length(str, 35,42); pdbx_refine_tls_single.L13=get_float_by_length(str, 43,50); pdbx_refine_tls_single.L23=get_float_by_length(str, 51,58); }else if(strstr_space(str,"REMARK 3 S tensor (S22-S11, S11-S33, S12, S13, S23, S21, S31)")){ fgets(str, sizeof str, finp); pdbx_refine_tls_single.S22_S11=get_float_by_length(str, 11,18); pdbx_refine_tls_single.S11_S33=get_float_by_length(str, 19,26); pdbx_refine_tls_single.S12=get_float_by_length(str, 27,34); pdbx_refine_tls_single.S13=get_float_by_length(str, 35,42); pdbx_refine_tls_single.S23=get_float_by_length(str, 43,50); pdbx_refine_tls_single.S21=get_float_by_length(str, 51,58); pdbx_refine_tls_single.S31=get_float_by_length(str, 59,66); pdbx_refine_tls_single.S32=get_float_by_length(str, 67,74); pdbx_refine_tls_single.S11=INI; pdbx_refine_tls_single.S22=INI; pdbx_refine_tls_single.S33=INI; strcpy(pdbx_refine_tls_single.details, tls_detail); strcpy(pdbx_refine_tls_single.method, "refine"); pdbx_refine_tls_group[ntls] = pdbx_refine_tls_group_single; pdbx_refine_tls[ntls] = pdbx_refine_tls_single; ntls++; NTLS=ntls; break; } } } } fclose(finp); } void extract_PDB_tls_weird_refmac(char *infile) { char str[256], tls_detail[80], tmp1[20], tmp2[20] ; int ntls=0; FILE *finp; if((finp=fopen(infile, "r"))==NULL) open_file_error (infile, "extract_PDB_head"); strcpy(tls_detail, "?"); while (fgets(str, sizeof str, finp) != NULL) { sscanf(str, "%s %*s %s ", tmp1, tmp2); if(!strcmp_case(tmp1, "TLS") && !strcmp_case(tmp2, "domain")){ strcpy(tls_detail, str+3); rid_of_end_space(tls_detail); if (is_space_line(tls_detail)<=1) strcpy( tls_detail,"?"); }else if(!strcmp_case(tmp1, "RANGE")){ get_string(str, 8,9, pdbx_refine_tls_group_single.beg_label_asym_id); get_string(str, 9,12,pdbx_refine_tls_group_single.beg_label_seq_id); get_string(str, 17,18,pdbx_refine_tls_group_single.end_label_asym_id); get_string(str, 18,21,pdbx_refine_tls_group_single.end_label_seq_id); }else if(!strcmp_case(tmp1, "ORIGIN")){ pdbx_refine_tls_single.origin_x = get_float_by_length(str, 8,14); pdbx_refine_tls_single.origin_y = get_float_by_length(str, 15,22); pdbx_refine_tls_single.origin_z = get_float_by_length(str, 23,26); }else if(!strcmp_case(tmp1, "T")&& !strncmp_case(str, "T ", 4) ){ pdbx_refine_tls_single.T11=get_float_by_length(str, 5,11); pdbx_refine_tls_single.T22=get_float_by_length(str, 12,19); pdbx_refine_tls_single.T33=get_float_by_length(str, 20,27); pdbx_refine_tls_single.T12=get_float_by_length(str, 28,35); pdbx_refine_tls_single.T13=get_float_by_length(str, 36,43); pdbx_refine_tls_single.T23=get_float_by_length(str, 44,51); }else if(!strcmp_case(tmp1, "L")&& !strncmp_case(str, "L ", 4) ){ pdbx_refine_tls_single.L11=get_float_by_length(str, 5,11); pdbx_refine_tls_single.L22=get_float_by_length(str, 12,19); pdbx_refine_tls_single.L33=get_float_by_length(str, 20,27); pdbx_refine_tls_single.L12=get_float_by_length(str, 28,35); pdbx_refine_tls_single.L13=get_float_by_length(str, 36,43); pdbx_refine_tls_single.L23=get_float_by_length(str, 44,51); }else if(!strcmp_case(tmp1, "S") && !strncmp_case(str, "S ", 4) ){ pdbx_refine_tls_single.S22_S11=get_float_by_length(str, 5,11); pdbx_refine_tls_single.S11_S33=get_float_by_length(str, 12,19); pdbx_refine_tls_single.S12=get_float_by_length(str, 20,27); pdbx_refine_tls_single.S13=get_float_by_length(str, 28,35); pdbx_refine_tls_single.S23=get_float_by_length(str, 36,43); pdbx_refine_tls_single.S21=get_float_by_length(str, 44,51); pdbx_refine_tls_single.S31=get_float_by_length(str, 52,59); pdbx_refine_tls_single.S32=get_float_by_length(str, 60,67); pdbx_refine_tls_single.S11=INI; pdbx_refine_tls_single.S22=INI; pdbx_refine_tls_single.S33=INI; strcpy(pdbx_refine_tls_single.details, tls_detail); strcpy(pdbx_refine_tls_single.method, "refine"); sprintf(pdbx_refine_tls_group_single.id, "%d", ntls+1); sprintf(pdbx_refine_tls_single.id, "%d", ntls+1); pdbx_refine_tls_group[ntls] = pdbx_refine_tls_group_single; pdbx_refine_tls[ntls] = pdbx_refine_tls_single; ntls++; } } NTLS=ntls; fclose(finp); } void write_non_standard_remark(FILE *fout, char **line, int nline) { int i; fprintf(fout,"# \n"); fprintf(fout,"_database_PDB_remark.id ?\n"); fprintf(fout,"_database_PDB_remark.text \n;\n"); for(i=0; i0)fprintf(fout,";\n"); fprintf(fout,"\n%s\n;\n", rnum); } n++; fprintf(fout,"%s", line[i]); strcpy(rnum_old, rnum); } } fprintf(fout,";\n"); } void write_remark_200(FILE *fout, char **line, int nline) { char *exptl_method=(char *) "?"; int i, exptl_crystals_number=INI; float a1; for(i=0;i-998){ fprintf(fout, "#\n _diffrn.ambient_temp %f\n", a1); } }else if(strstr_space(line[i], "REMARK 200 PH :")){ //exptl_crystal_grow.ph if((a1 = get_float(line[i],":", "\n"))>-998){ fprintf(fout, "#\n _exptl_crystal_grow.ph %f\n", a1); } }else if(strstr_space(line[i], "REMARK 200 RADIATION SOURCE :")){ //diffrn_source. diffrn_source.source = get_substr(line[i],":", "\n"); }else if(strstr_space(line[i], "REMARK 200 BEAMLINE :")){ diffrn_source.pdbx_synchrotron_beamline= get_substr(line[i],":", "\n"); }else if(strstr_space(line[i], "REMARK 200 X-RAY GENERATOR MODEL :")){ diffrn_source.type=get_substr(line[i],":", "\n"); /* }else if(strstr_space(line[i], "REMARK 200 WAVELENGTH OR RANGE (A) :")){ //diffrn_radiation. diffrn_radiation.pdbx_wavelength_list = get_substr(line[i],":", "\n"); }else if(strstr_space(line[i], "REMARK 200 MONOCHROMATOR :")){ diffrn_radiation.monochromator = get_substr(line[i],":", "\n"); }else if(strstr_space(line[i], "REMARK 200 DIFFRACTION PROTOCOL:")){ diffrn_radiation.pdbx_diffrn_protocol = get_substr(line[i],":", "\n"); }else if(strstr_space(line[i], " INTENSITY-INTEGRATION SOFTWARE : ")){ strcpy(computing.data_collection, get_substr(line[i],":", "\n")); }else if(strstr_space(line[i], " DATA SCALING SOFTWARE : ")){ strcpy(computing.data_reduction, get_substr(line[i],":", "\n")); */ }else if(strstr_space(line[i], "REMARK 200 NUMBER OF UNIQUE REFLECTIONS :")){ //reflns. reflns.number_obs= get_int(line[i],":", "\n"); }else if(strstr_space(line[i], "REMARK 200 RESOLUTION RANGE HIGH (A) :")){ reflns.d_resolution_high= get_float(line[i],":", "\n"); }else if(strstr_space(line[i], "REMARK 200 RESOLUTION RANGE LOW (A) :")){ reflns.d_resolution_low= get_float(line[i],":", "\n"); }else if(strstr_space(line[i], "REMARK 200 REJECTION CRITERIA (SIGMA(I)) :")){ reflns.percent_possible_obs = get_float(line[i],":", "\n"); }else if(strstr_space(line[i], "REMARK 200 COMPLETENESS FOR RANGE (%) : ")){ reflns.percent_possible_obs = get_float(line[i],":", "\n"); }else if(strstr_space(line[i], "REMARK 200 DATA REDUNDANCY : ")){ reflns.pdbx_redundancy = get_float(line[i],":", "\n"); }else if(strstr_space(line[i], "REMARK 200 R MERGE (I) :")){ reflns.pdbx_Rmerge_I_obs = get_float(line[i],":", "\n"); }else if(strstr_space(line[i], "REMARK 200 R SYM (I) :")){ reflns.pdbx_Rsym_value= get_float(line[i],":", "\n"); }else if(strstr_space(line[i], "REMARK 200 FOR THE DATA SET :")){ reflns.pdbx_netI_over_av_sigmaI = get_float(line[i],":", "\n"); }else if(strstr_space(line[i], "REMARK 200 FOR THE DATA SET :")){ reflns.pdbx_netI_over_av_sigmaI = get_float(line[i],":", "\n"); //reflns_shell. }else if(strstr_space(line[i], "REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) :")){ reflns_shell.nbin = 1; reflns_shell.d_res_high[0]= get_float(line[i],":", "\n"); }else if(strstr_space(line[i], "REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) :")){ reflns_shell.d_res_low[0]= get_float(line[i],":", "\n"); }else if(strstr_space(line[i], "REMARK 200 COMPLETENESS FOR SHELL (%) :")){ reflns_shell.percent_possible_all[0]= get_float(line[i],":", "\n"); }else if(strstr_space(line[i], "REMARK 200 DATA REDUNDANCY IN SHELL :")){ reflns_shell.pdbx_redundancy[0]= get_float(line[i],":", "\n"); }else if(strstr_space(line[i], "REMARK 200 R MERGE FOR SHELL (I) :")){ reflns_shell.Rmerge_I_obs[0]= get_float(line[i],":", "\n"); }else if(strstr_space(line[i], "REMARK 200 R SYM FOR SHELL (I) :")){ reflns_shell.pdbx_Rsym_value[0] = get_float(line[i],":", "\n"); }else if(strstr_space(line[i], "REMARK 200 FOR SHELL : ")){ reflns_shell.meanI_over_sigI_obs[0] = get_float(line[i],":", "\n"); } } //exptl. if(exptl_method[0]!='?')fprintf(fout, "#\n_exptl.method '%s'\n", exptl_method); if(exptl_crystals_number >-9998) fprintf(fout, "_exptl.crystals_number %d\n", exptl_crystals_number); //_diffrn_detector. if(diffrn_detector.detector[0] !='?') fprintf(fout, "_diffrn_detector.detector '%s'\n", diffrn_detector.detector); if(diffrn_detector.type[0] !='?') fprintf(fout, "_diffrn_detector.type '%s'\n", diffrn_detector.type); if(diffrn_detector.details[0] !='?') fprintf(fout, "_diffrn_detector.details '%s'\n", diffrn_detector.details); if(diffrn_detector.pdbx_collection_date[0] !='?' ) fprintf(fout, "_diffrn_detector.pdbx_collection_date '%s'\n", diffrn_detector.pdbx_collection_date); //diffrn_source. if(diffrn_source.source[0] !='?') fprintf(fout, "_diffrn_source.source '%s'\n",diffrn_source.source); if(diffrn_source.pdbx_synchrotron_beamline[0] !='?') fprintf(fout, "_diffrn_source.pdbx_synchrotron_beamline '%s'\n", diffrn_source.pdbx_synchrotron_beamline); if(diffrn_source.type[0] !='?') fprintf(fout, "_diffrn_source.type '%s'\n",diffrn_source.type); //_reflns if (reflns.d_resolution_low>-9998) fprintf(fout,"_reflns.d_resolution_low %.2f\n",reflns.d_resolution_low); if (reflns.d_resolution_high>-9998) fprintf(fout,"_reflns.d_resolution_high %.2f\n", reflns.d_resolution_high); if (reflns.number_obs>-9998) fprintf(fout,"_reflns.number_obs %d\n", reflns.number_obs); if (reflns.percent_possible_obs>-9998) fprintf(fout,"_reflns.percent_possible_obs %.3f\n", reflns.percent_possible_obs); if (reflns.pdbx_Rmerge_I_obs>-9998) fprintf(fout,"_reflns.pdbx_Rmerge_I_obs %.3f\n",reflns.pdbx_Rmerge_I_obs); if (reflns.B_iso_Wilson_estimate>-9998) fprintf(fout,"_reflns.B_iso_Wilson_estimate %.3f\n",reflns.B_iso_Wilson_estimate); if (reflns.pdbx_chi_squared>-9998) fprintf(fout,"_reflns.pdbx_chi_squared %.3f\n", reflns.pdbx_chi_squared); if (reflns.pdbx_redundancy>-9998) fprintf(fout,"_reflns.pdbx_redundancy %.3f\n",reflns.pdbx_redundancy ); if (reflns.pdbx_scaling_rejects>-9998) fprintf(fout,"_reflns.pdbx_scaling_rejects %d\n", reflns.pdbx_scaling_rejects); if (reflns.pdbx_netI_over_av_sigmaI>-9998) fprintf(fout,"_reflns.pdbx_netI_over_av_sigmaI %.3f\n", reflns.pdbx_netI_over_av_sigmaI); if (reflns.pdbx_Rsym_value>-9998) fprintf(fout,"_reflns.pdbx_Rsym_value %.3f\n",reflns.pdbx_Rsym_value); } void extract_PDB_conn(FILE *fout, char *infile) // for the connectivity { char str[100], **line=NULL, id[50], item[20]; char atom[6], comp[6], sn[6], asym, seq[6], ins, alt; int n0=0,n1=0,n2=0, n=0, i, nremark=0, nline=0; FILE *finp; if((finp=fopen(infile, "r"))==NULL) open_file_error (infile, "extract_PDB_ncs"); strcpy(id, "SSBOND SLTBRG HYDBND LINK "); n=0; while (fgets(str, sizeof str, finp) != NULL) { if(!strncmp_case(str, "ATOM ", 6) || !strncmp_case(str, "HETATM", 6) ) break; n++; } rewind(finp); line = new char *[n+1]; n=0; while (fgets(str, sizeof str, finp) != NULL) { if(!strncmp_case(str, "ATOM ", 6) || !strncmp_case(str, "HETATM", 6) ) break; if(!strncmp_case(str, "REMARK ", 7)) { n1=get_int_by_length(str, 6, 9); nremark++; if(n1>0 && n1<999) n0++; else n2++; } line[n]=new char[90]; strcpy(line[n],str); n++; } nline=n; write_remark_200(fout, line, n); if(nremark>0){ if(n2>5)// standard remarks write_non_standard_remark(fout, line, n); else write_remark_text(fout, line, n); } for(i=0;i0){ sprintf(struct_ncs_dom[ncs].id, "%d", ng); while (fgets(str, sizeof str, finp) != NULL) { if(strstr_space(str,"REMARK 3 CHAIN NAMES :")) strcpy(struct_ncs_dom[ncs].details, get_substr(str," :", "\n")); else if(strstr_space(str," COMPONENT C SSSEQI TO C SSSEQI CODE")){ while (fgets(str, sizeof str, finp) != NULL) { n=sscanf(str+11, "%d %s %d %s %d %d", &n0, c1, &n1, c2, &n2, &n3); if(n==6){ struct_ncs_dom_lim[nlim].pdbx_component=n0; strcpy(struct_ncs_dom_lim[nlim].dom_id, struct_ncs_dom[ncs].id); strcpy(struct_ncs_dom_lim[nlim].beg_label_asym_id, c1); struct_ncs_dom_lim[nlim].beg_label_seq_id = n1; strcpy(struct_ncs_dom_lim[nlim].end_label_asym_id, c2); struct_ncs_dom_lim[nlim].end_label_seq_id = n2; nlim++; }else if(strstr_space(str,"GROUP CHAIN COUNT RMS WEIGHT")){ while (fgets(str, sizeof str, finp) != NULL) { if(pattern5(str,":", " ; ", " ; ", "", "")){ strcpy(refine_ls_restr_ncs[nncs].dom_id,struct_ncs_dom[ncs].id); get_string(str, 10, 31,refine_ls_restr_ncs[nncs].pdbx_type); get_string(str, 35, 38,refine_ls_restr_ncs[nncs].pdbx_asym_id); refine_ls_restr_ncs[nncs].pdbx_number = get_int(str,":"," ;"); refine_ls_restr_ncs[nncs].rms_dev_position = get_float(str,"; "," ;"); refine_ls_restr_ncs[nncs].weight_position = get_float(strstr(str, ";")+1 ,"; ","\n"); nncs++; }else break; } }else break; } } } ncs++; } }else if(strstr_space(str,"REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT")){ //CNS while (fgets(str, sizeof str, finp) != NULL) { if(pattern5(str,"REMARK 3", " :", ";", "", "")){ strcpy(refine_ls_restr_ncs[nncs].dom_id, "?"); strcpy(refine_ls_restr_ncs[nncs].pdbx_type, get_substr(str, "REMARK 3 ", ":")); strcpy(refine_ls_restr_ncs[nncs].pdbx_asym_id, "?"); refine_ls_restr_ncs[nncs].pdbx_number = INI; refine_ls_restr_ncs[nncs].rms_dev_position = get_float(str,":"," ;"); refine_ls_restr_ncs[nncs].weight_position = get_float(str,";","\n"); nncs++; }else break; } } } } NNCS=nncs; NLIM=nlim; NCS=ncs; } void extract_PDB_refine_ls_restr(char *infile, char *prog) //RMS DEVIATIONS FROM IDEAL VALUES (refine_ls_restr) { char str[100], tmp[100]; int nr=0; FILE *finp; if((finp=fopen(infile, "r"))==NULL) open_file_error (infile, "extract_PDB_refine_ls_restr"); while (fgets(str, sizeof str, finp) != NULL) { if(strstr_space(str, "REMARK 3")<=0)continue; if(!strncmp_case(str, "ATOM ", 6) || !strncmp_case(str, "HETATM", 6) ) break; if(strstr_case(prog, "refmac") || strstr_case(prog, "restrain")){ //refmac5 if(strstr_space(str, "RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT")|| strstr_space(str, "ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT")|| strstr_space(str, "ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT")){ while (fgets(str, sizeof str, finp) != NULL) { if(pattern5(str,"REMARK 3", "):", ";", ";","")){ strcpy(refine_ls_restr[nr].type, get_substr(str,"REMARK 3", ":")); strcpy(tmp, strstr(str,"):")); refine_ls_restr[nr].number = get_int(tmp, "):", ";"); refine_ls_restr[nr].dev_ideal = get_float(tmp, ";", ";"); refine_ls_restr[nr].dev_ideal_target = get_float(strstr(tmp,";")+1, ";", "\n"); refine_ls_restr[nr].weight = -9998; nr++; NR=nr; // printf("hello %d %s", NR, str); }else{ break; } } }else if(strstr_space(str, "DISTANCE RESTRAINTS. RMS SIGMA")|| //rare case strstr_space(str, "ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA" )){ while (fgets(str, sizeof str, finp) != NULL) { if(pattern5(str, "REMARK 3","(", ")", ":", ";")){ strcpy(refine_ls_restr[nr].type, get_substr(str,"REMARK 3", " :")); refine_ls_restr[nr].number = INI; refine_ls_restr[nr].dev_ideal = get_float(str, ":", ";"); refine_ls_restr[nr].dev_ideal_target = -9998; refine_ls_restr[nr].weight = get_float(str, ";", "\n"); nr++; NR=nr; }else{ break; } } } }else if(strstr_case(prog, "shelx")){ //shelx if(strstr_space(str, " RMS DEVIATIONS FROM RESTRAINT TARGET VALUES.")){ while (fgets(str, sizeof str, finp) != NULL) {//shelx if(pattern5(str, "REMARK ", " 3 ", " (", ") ",":")){ strcpy(refine_ls_restr[nr].type, get_substr(str,"REMARK 3", ":")); refine_ls_restr[nr].number = INI; refine_ls_restr[nr].dev_ideal = get_float(str, ":", "\n"); refine_ls_restr[nr].weight = INI; nr++; NR=nr; }else{ break; } } } }else if(strstr_case(prog, "cns") || strstr_case(prog, "xplor")|| strstr_case(prog, "cnx")){ //CNS/XPLOR/CNX if(strstr_space(str, "ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA")){ while (fgets(str, sizeof str, finp) != NULL) { if(pattern5(str, "(", ") ", ":", ";", "\n")){ strcpy(refine_ls_restr[nr].type, "?"); strcpy(refine_ls_restr[nr].type, get_substr(str,"REMARK 3", ":")); refine_ls_restr[nr].number = INI; refine_ls_restr[nr].dev_ideal = get_float(str, ":", ";"); refine_ls_restr[nr].weight =get_float(str, ";", "\n") ; nr++; NR=nr; }else{ break; } } }else if(strstr_space(str, "REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES.")){ while (fgets(str, sizeof str, finp) != NULL) { if(pattern5(str, "(", ") ", ":", "", "")){ strcpy(refine_ls_restr[nr].type, "?"); strcpy(refine_ls_restr[nr].type, get_substr(str,"REMARK 3", ":")); refine_ls_restr[nr].number = INI; refine_ls_restr[nr].dev_ideal = get_float(str, ":", "\n"); refine_ls_restr[nr].weight =INI ; nr++; NR=nr; }else{ break; } } } }else if(strstr_case(prog, "tnt")){ //TNT if(strstr_space(str, "REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. RMS WEIGHT COUNT")){ while (fgets(str, sizeof str, finp) != NULL) { if(pattern5(str, "REMARK", ":", ";", ";", "\n")){ strcpy(refine_ls_restr[nr].type, "?"); strcpy(refine_ls_restr[nr].type, get_substr(str," 3 ", ":")); refine_ls_restr[nr].dev_ideal = get_float(str, ":", ";"); refine_ls_restr[nr].weight = get_float(str, ";", ";") ; refine_ls_restr[nr].number = get_int(strstr_case(str,";")+1, ";", "\n"); nr++; NR=nr; }else{ break; } } } } else if(strstr_case(prog, "NUCLSQ")|| strstr_case(prog, "PROLSQ")){ //NUCLSQ if(strstr_space(str, " DISTANCE RESTRAINTS. RMS SIGMA")|| strstr_space(str, " NON-BONDED CONTACT RESTRAINTS.") || strstr_space(str, "ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA")){ while (fgets(str, sizeof str, finp) != NULL) { if(pattern5(str, "REMARK", ") ", ":", ";", "\n")){ strcpy(refine_ls_restr[nr].type, "?"); strcpy(refine_ls_restr[nr].type, get_substr(str," 3 ", ":")); refine_ls_restr[nr].dev_ideal = get_float(str, ":", ";"); refine_ls_restr[nr].weight = get_float(str, ";", "\n") ; refine_ls_restr[nr].number = INI; nr++; NR=nr; }else{ break; } } } else if(strstr_space(str, "REMARK 3 PLANE RESTRAINT (A) :")|| strstr_space(str, "REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) :")){ strcpy(refine_ls_restr[nr].type, "?"); strcpy(refine_ls_restr[nr].type, get_substr(str," 3 ", ":")); refine_ls_restr[nr].dev_ideal = get_float(str, ":", ";"); refine_ls_restr[nr].weight = get_float(str, ";", "\n") ; refine_ls_restr[nr].number = INI; nr++; NR=nr; } } } fclose(finp); } void extract_PDB_head(char *infile) { char str[100], *details=NULL, tmp[80]; int nr=0, ntop=0, nparam=0; FILE *finp; if((finp=fopen(infile, "r"))==NULL) open_file_error (infile, "extract_PDB_head"); strcpy(PROG, "?"); while (fgets(str, sizeof str, finp) != NULL) { if( !strncmp_case(str, "ATOM", 4) || !strncmp_case(str, "HETATM", 6)) break; //DATA USED IN REFINEMENT. (refine.) if(strstr_space(str, "REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) :")){ refine.ls_d_res_high = get_float(str, ":", "\n"); refine_hist.d_res_high = refine.ls_d_res_high; }else if (strstr_space(str, "REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) :")){ refine.ls_d_res_low = get_float(str, ":", "\n"); refine_hist.d_res_low = get_float(str, ":", "\n"); }else if (strstr_space(str, "REMARK 3 DATA CUTOFF (SIGMA(F)) :")){ refine.pdbx_ls_sigma_F = get_float(str, ":", "\n"); }else if (strstr_space(str, "REMARK 3 DATA CUTOFF HIGH (ABS(F)) :")){ refine.pdbx_data_cutoff_high_absF = get_float(str, ":", "\n"); }else if (strstr_space(str, "REMARK 3 DATA CUTOFF LOW (ABS(F)) :")){ refine.pdbx_data_cutoff_low_absF = get_float(str, ":", "\n"); }else if (strstr_space(str, "REMARK 3 COMPLETENESS FOR RANGE (%) :") || strstr_space(str, "REMARK 3 COMPLETENESS (WORKING+TEST) (%) :")){ refine.ls_percent_reflns_obs = get_float(str, ":", "\n"); }else if (strstr_space(str, "REMARK 3 NUMBER OF REFLECTIONS :")){ refine.ls_number_reflns_obs= get_int(str, ":", "\n"); }else if (strstr_space(str, "REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) :")){ refine.ls_number_reflns_all = get_int(str, ":", "\n"); //FIT TO DATA USED IN REFINEMENT. (refine.) }else if (strstr_space(str, "REMARK 3 CROSS-VALIDATION METHOD :") ){ refine.pdbx_ls_cross_valid_method = get_substr(str, ":", "\n"); }else if (strstr_space(str, "REMARK 3 FREE R VALUE TEST SET SELECTION :")){ refine.pdbx_R_Free_selection_details =get_substr(str, ":", "\n"); }else if (strstr_space(str, "REMARK 3 R VALUE (WORKING + TEST SET) :")){ refine.ls_R_factor_all = get_float(str, ":", "\n"); }else if (strstr_space(str, "REMARK 3 R VALUE (WORKING SET) :") ){ refine.ls_R_factor_R_work = get_float(str, ":", "\n"); }else if (strstr_space(str, "REMARK 3 FREE R VALUE :")){ refine.ls_R_factor_R_free = get_float(str, ":", "\n"); }else if (strstr_space(str, "REMARK 3 FREE R VALUE TEST SET SIZE (%) :")){ refine.ls_percent_reflns_R_free = get_float(str, ":", "\n"); }else if (strstr_space(str, "REMARK 3 FREE R VALUE TEST SET COUNT :")){ refine.ls_number_reflns_R_free = get_int(str, ":", "\n"); }else if (strstr_space(str, "REMARK 3 ESTIMATED ERROR OF FREE R VALUE :")){ refine.ls_R_factor_R_free_error = get_float(str, ":", "\n"); // FIT TO DATA USED IN REFINEMENT (NO CUTOFF)._pdbx_refine. }else if (strstr_space(str, "REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) :")){ pdbx_refine.R_factor_all_no_cutoff = get_float(str, ":", "\n"); if(strstr_case(PROG, "SHELX")) refine.ls_R_factor_all = pdbx_refine.R_factor_all_no_cutoff; }else if (strstr_space(str, "REMARK 3 R VALUE (WORKING SET, NO CUTOFF) :")){ pdbx_refine.R_factor_obs_no_cutoff = get_float(str, ":", "\n"); if(strstr_case(PROG, "SHELX")) refine.ls_R_factor_obs = pdbx_refine.R_factor_obs_no_cutoff; }else if (strstr_space(str, "REMARK 3 FREE R VALUE (NO CUTOFF) :")){ pdbx_refine.free_R_factor_no_cutoff = get_float(str, ":", "\n"); if(strstr_case(PROG, "SHELX")) refine.ls_R_factor_R_free = pdbx_refine.free_R_factor_no_cutoff; }else if ( strstr_space(str, "REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) :")){ pdbx_refine.free_R_val_test_set_size_perc_no_cutoff = get_float(str, ":", "\n"); if(strstr_case(PROG, "SHELX")) refine.ls_percent_reflns_R_free =pdbx_refine.free_R_val_test_set_size_perc_no_cutoff; }else if (strstr_space(str, "REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) :")){ pdbx_refine.free_R_val_test_set_ct_no_cutoff = get_int(str, ":", "\n"); if(strstr_case(PROG, "SHELX")) refine.ls_number_reflns_R_free=pdbx_refine.free_R_val_test_set_ct_no_cutoff; }else if (strstr_space(str, "REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) :")){ pdbx_refine.number_reflns_obs_no_cutoff = get_int(str, ":", "\n"); if(strstr_case(PROG, "SHELX")) refine.ls_number_reflns_all = pdbx_refine.number_reflns_obs_no_cutoff; // FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). }else if (strstr_space(str, "REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) :")){ pdbx_refine.R_factor_all_4sig_cutoff = get_float(str, ":", "\n"); }else if (strstr_space(str, "REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) :")){ pdbx_refine.R_factor_obs_4sig_cutoff = get_float(str, ":", "\n"); }else if (strstr_space(str, "REMARK 3 FREE R VALUE (F>4SIG(F)) :")){ pdbx_refine.free_R_factor_4sig_cutoff = get_float(str, ":", "\n"); }else if (strstr_space(str, "REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) :")){ pdbx_refine.free_R_val_test_set_size_perc_4sig_cutoff = get_float(str, ":", "\n"); }else if (strstr_space(str, "REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) :")){ pdbx_refine.free_R_val_test_set_ct_4sig_cutoff = get_int(str, ":", "\n"); }else if (strstr_space(str, "REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) :")){ pdbx_refine.number_reflns_obs_4sig_cutoff = get_int(str, ":", "\n"); // B VALUES.(refine.) }else if (strstr_space(str, "REMARK 3 FROM WILSON PLOT (A**2) :") || strstr_space(str, "REMARK 3 WILSON B VALUE (FROM FCALC, A**2) :" )){ reflns.B_iso_Wilson_estimate = get_float(str, ":", "\n"); }else if (strstr_space(str, "REMARK 3 MEAN B VALUE (OVERALL, A**2) :")){ refine.B_iso_mean = get_float(str, ":", "\n"); }else if (strstr_space(str, "REMARK 3 B11 (A**2) :")){ refine.aniso_B11 = get_float(str, ":", "\n"); }else if (strstr_space(str, "REMARK 3 B22 (A**2) :")){ refine.aniso_B22 = get_float(str, ":", "\n"); }else if (strstr_space(str, "REMARK 3 B33 (A**2) :")){ refine.aniso_B33 = get_float(str, ":", "\n"); }else if (strstr_space(str, "REMARK 3 B12 (A**2) :")){ refine.aniso_B12 = get_float(str, ":", "\n"); }else if (strstr_space(str, "REMARK 3 B13 (A**2) :")){ refine.aniso_B13 = get_float(str, ":", "\n"); }else if (strstr_space(str, "REMARK 3 B23 (A**2) :")){ refine.aniso_B23 = get_float(str, ":", "\n"); //CORRELATION COEFFICIENTS.(refine.) }else if (strstr_space(str, "REMARK 3 CORRELATION COEFFICIENT FO-FC :")){ refine.correlation_coeff_Fo_to_Fc = get_float(str, ":", "\n"); }else if (strstr_space(str, "REMARK 3 CORRELATION COEFFICIENT FO-FC FREE :")){ refine.correlation_coeff_Fo_to_Fc_free = get_float(str, ":", "\n"); // ESTIMATED OVERALL COORDINATE ERROR. (refine.) }else if (strstr_space(str, "REMARK 3 ESU BASED ON R VALUE (A):")){ refine.pdbx_overall_ESU_R = get_float(str, ":", "\n"); }else if (strstr_space(str, "REMARK 3 ESU BASED ON FREE R VALUE (A):")){ refine.pdbx_overall_ESU_R_Free = get_float(str, ":", "\n"); }else if (strstr_space(str, "REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): ")){ refine.overall_SU_ML = get_float(str, ":", "\n"); }else if (strstr_space(str, "REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2):")){ refine.overall_SU_B = get_float(str, ":", "\n"); // BULK SOLVENT MODELLING.(refine.) }else if (strstr_space(str, "REMARK 3 METHOD USED :")){ refine.solvent_model_details=get_substr(str, ":", "\n"); }else if (strstr_space(str, "REMARK 3 KSOL :")){ refine.solvent_model_param_ksol = get_float(str, ":", "\n"); }else if (strstr_space(str, "REMARK 3 BSOL :")){ refine.solvent_model_param_bsol = get_float(str, ":", "\n"); }else if (strstr_space(str, "REMARK 3 VDW PROBE RADIUS :")){ refine.pdbx_solvent_vdw_probe_radii = get_float(str, ":", "\n"); }else if (strstr_space(str, "REMARK 3 ION PROBE RADIUS :")){ refine.pdbx_solvent_ion_probe_radii = get_float(str, ":", "\n"); }else if (strstr_space(str, "REMARK 3 SHRINKAGE RADIUS :")){ refine.pdbx_solvent_shrinkage_radii = get_float(str, ":", "\n"); }else if (strstr_space(str, "REMARK 3 ISOTROPIC THERMAL MODEL :")){ refine.pdbx_isotropic_thermal_model= get_substr(str, ":", "\n"); }else if (strstr_space(str, "REMARK 3 STEREOCHEMISTRY TARGET VALUES : ")){ //SHELX refine.pdbx_stereochemistry_target_values= get_substr(str, ":", "\n"); }else if (strstr_space(str, "REMARK 3 REFINEMENT TARGET :")){ //CNS/REFMAC5 refine.pdbx_stereochemistry_target_values= get_substr(str, ":", "\n"); }else if (strstr_space(str, "REMARK 3 STEREOCHEMISTRY :")){ //TNT refine.pdbx_stereochemistry_target_values= get_substr(str, ":", "\n"); }else if (strstr_space(str, "REMARK 3 SPECIAL CASE:")){ refine.pdbx_stereochem_target_val_spec_case = get_substr(str, ":", "\n"); }else if (strstr_space(str, "REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: ")){ refine.pdbx_method_to_determine_struct = get_substr(str, ":", "\n"); }else if (strstr_space(str, "REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS :")){ refine.ls_number_parameters= get_int(str, ":", "\n"); }else if (strstr_space(str, "REMARK 3 NUMBER OF RESTRAINTS :")){ refine.ls_number_restraints= get_int(str, ":", "\n"); }else if (strstr_space(str, "REMARK 3 OTHER REFINEMENT REMARKS: ")){ sscanf(strstr(str, ":")+1, "%s", tmp); if(strlen(tmp)>6 && strcmp(tmp, "NULL") && strcmp(tmp, "NONE")) { details = get_substr(str, ":", "\n"); while(fgets(str, sizeof str, finp)!=NULL){ if(strncmp(str, "REMARK 3", 10)) { refine.details = details; break; } strcat(details, "\n "); strcat(details, get_substr(str, "REMARK 3 ", "\n")); } } }else if (!strncmp_case(str, "REMARK", 6) && strstr_space(str, "REMARK refinement resolution:")){ //cns_non-standard refine.ls_d_res_low = get_float(str, ":", "-"); refine.ls_d_res_high = get_float(str, "-", "\n"); }else if (!strncmp_case(str, "REMARK", 6) && strstr_space(str, "REMARK number of reflections rejected:")){//cns_non-standard refine.pdbx_ls_sigma_F = get_float(str, ":", "( "); }else if (!strncmp_case(str, "REMARK", 6) && strstr_space(str, "REMARK total number of reflections used:") ){//cns_non-standard refine.ls_percent_reflns_obs = get_float(str, " ( ", " % "); refine.ls_number_reflns_obs = get_int(str, ":", "("); }else if (!strncmp_case(str, "REMARK", 6) && strstr_space(str, "REMARK number of reflections in working set:") ){//cns_non-standard refine.ls_number_reflns_R_work = get_int(str, ":", "("); }else if (!strncmp_case(str, "REMARK", 6) && strstr_space(str, "REMARK final r= ") && pattern5(str,"r=", "free_r=", "", "", "")){//cns_non-standard refine.ls_R_factor_R_work = get_float(str, "r=", "free_r="); refine.ls_R_factor_R_free = get_float(str, "free_r=", "\n"); }else if (!strncmp_case(str, "REMARK", 6) && pattern5(str, "REMARK rmsd bonds=", "rmsd angles=", "","","") ){ strcpy(refine_ls_restr[nr].type, "?"); strcpy(refine_ls_restr[nr].type, "c_bond_d"); refine_ls_restr[nr].number = INI; refine_ls_restr[nr].dev_ideal = get_float(str, "bonds=", "rmsd angles="); refine_ls_restr[nr].weight =INI; nr++; NR=nr; strcpy(refine_ls_restr[nr].type, "?"); strcpy(refine_ls_restr[nr].type, "c_angle_d"); refine_ls_restr[nr].number = INI; refine_ls_restr[nr].dev_ideal = get_float(str, "rmsd angles=", "\n"); refine_ls_restr[nr].weight =INI; nr++; NR=nr; }else if (!strncmp_case(str, "REMARK", 6) && pattern5(str, "B rmsd for bonded mainchain", "atoms=", "target=","","")){ strcpy(refine_ls_restr[nr].type, "?"); strcpy(refine_ls_restr[nr].type, "c_mcbond_it"); refine_ls_restr[nr].number = INI; refine_ls_restr[nr].dev_ideal = get_float(str, "atoms=", "target"); refine_ls_restr[nr].weight = get_float(str, "target=", "\n"); nr++; NR=nr; }else if (!strncmp_case(str, "REMARK", 6) && pattern5(str, "B rmsd for bonded sidechain", "atoms=", "target=","","")){ strcpy(refine_ls_restr[nr].type, "?"); strcpy(refine_ls_restr[nr].type, "c_scbond_it"); refine_ls_restr[nr].number = INI; refine_ls_restr[nr].dev_ideal = get_float(str, "atoms=", "target"); refine_ls_restr[nr].weight = get_float(str, "target=", "\n"); nr++; NR=nr; }else if (!strncmp_case(str, "REMARK", 6) && pattern5(str, "B rmsd for angle mainchain", "atoms=", "target=","","")){ strcpy(refine_ls_restr[nr].type, "?"); strcpy(refine_ls_restr[nr].type, "c_mcangle_it"); refine_ls_restr[nr].number = INI; refine_ls_restr[nr].dev_ideal = get_float(str, "atoms=", "target"); refine_ls_restr[nr].weight = get_float(str, "target=", "\n"); nr++; NR=nr; }else if (!strncmp_case(str, "REMARK", 6) && pattern5(str, "B rmsd for angle sidechain", "atoms=", "target=","","")){ strcpy(refine_ls_restr[nr].type, "?"); strcpy(refine_ls_restr[nr].type, "c_scangle_it"); refine_ls_restr[nr].number = INI; refine_ls_restr[nr].dev_ideal = get_float(str, "atoms=", "target"); refine_ls_restr[nr].weight = get_float(str, "target=", "\n"); nr++; NR=nr; // printf("hello= %d, %.2f\n", NR, refine_ls_restr[NR-1].weight); }else if (!strncmp_case(str, "REMARK", 6) && (pattern5(str, "REMARK topology file", " : ", "","","") || pattern5(str,"REMARK 3 PARAMETER FILE", " : ", "","","") )){ pdbx_xplor_file[ntop].topol_file = get_substr(str," : ", "\n"); pdbx_xplor_file[ntop].ntop = ntop; ntop++; }else if (!strncmp_case(str, "REMARK", 6) && (pattern5(str, "REMARK parameter file", " : ", "","","") || pattern5(str, "REMARK 3 TOPOLOGY FILE", " : ", "","","") )){ pdbx_xplor_file[nparam].param_file = get_substr(str," : ", "\n"); pdbx_xplor_file[nparam].nparam = nparam; nparam++; }else if (strstr_space(str, "REMARK number of reflections in test set:")){//cns_non-standard refine.ls_number_reflns_R_free = get_int(str, ":", "("); refine.ls_percent_reflns_R_free = get_float(str, "( ", "%"); }else if (pattern5(str,"REMARK ", "B11=", "B22=", "B33=", "")){//cns_non-standard refine.aniso_B11 = get_float(str, "B11=", "B22="); refine.aniso_B22 = get_float(str, "B22=", "B33="); refine.aniso_B33 = get_float(str, "B33=", "\n"); }else if (pattern5(str,"REMARK ", "B12=", "B13=", "B23=", "")){//cns_non-standard refine.aniso_B12 = get_float(str, "B12=", "B13="); refine.aniso_B13 = get_float(str, "B13=", "B23="); refine.aniso_B23 = get_float(str, "B23=", "\n"); }else if (strstr_space(str,"REMARK bulk solvent: density level= ")){//cns_non-standard refine.solvent_model_param_bsol = get_float(str, "B-factor=", "A"); // FIT IN THE HIGHEST RESOLUTION BIN. (refine_ls_shell (highest) }else if (strstr_space(str, "REMARK 3 TOTAL NUMBER OF BINS USED :")){ refine_ls_shell.pdbx_total_number_of_bins_used[0] = get_int(str, ":", "\n"); refine_ls_shell.nbin = 1; }else if (strstr_space(str, "REMARK 3 BIN RESOLUTION RANGE HIGH (A) :") || strstr_space(str, "REMARK 3 BIN RESOLUTION RANGE HIGH :")){ //refmac refine_ls_shell.d_res_high[0] = get_float(str, ":", "\n"); }else if (strstr_space(str, "REMARK 3 BIN RESOLUTION RANGE LOW (A) :") || strstr_space(str, "REMARK 3 BIN RESOLUTION RANGE LOW :") ){ refine_ls_shell.d_res_low[0] = get_float(str, ":", "\n"); }else if (strstr_space(str, "REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) :")){ refine_ls_shell.percent_reflns_obs[0] = get_float(str, ":", "\n"); }else if (strstr_space(str, "REMARK 3 REFLECTIONS IN BIN (WORKING SET) :")|| strstr_space(str, "REMARK 3 REFLECTION IN BIN (WORKING SET) :")){ //refmac refine_ls_shell.number_reflns_R_work[0] = get_int(str, ":", "\n"); }else if (strstr_space(str, "REMARK 3 BIN R VALUE (WORKING SET) :")){ refine_ls_shell.R_factor_R_work[0] = get_float(str, ":", "\n"); }else if (strstr_space(str, "REMARK 3 BIN FREE R VALUE :")){ refine_ls_shell.R_factor_R_free[0] = get_float(str, ":", "\n"); }else if (strstr_space(str, "REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) :")){ refine_ls_shell.percent_reflns_R_free[0] = get_float(str, ":", "\n"); }else if (strstr_space(str, "REMARK 3 BIN FREE R VALUE SET COUNT :")|| //refmac strstr_space(str, "REMARK 3 BIN FREE R VALUE TEST SET COUNT :")){ refine_ls_shell.number_reflns_R_free[0] = get_int(str, ":", "\n"); }else if (strstr_space(str, "REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE :")){ refine_ls_shell.R_factor_R_free_error[0] = get_float(str, ":", "\n"); // NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.(refine_hist) }else if (strstr_space(str, "REMARK 3 PROTEIN ATOMS :")){ refine_hist.pdbx_number_atoms_protein = get_int(str, ":", "\n"); }else if (strstr_space(str, "REMARK 3 NUCLEIC ACID ATOMS :")){ refine_hist.pdbx_number_atoms_nucleic_acid = get_int(str, ":", "\n"); }else if (strstr_space(str, "REMARK 3 HETEROGEN ATOMS :")){ refine_hist.pdbx_number_atoms_ligand = get_int(str, ":", "\n"); }else if (strstr_space(str, "REMARK 3 SOLVENT ATOMS :")){ refine_hist.number_atoms_solvent = get_int(str, ":", "\n"); }else if (strstr_space(str, "REMARK 3 ALL ATOMS :")){ refine_hist.number_atoms_total = get_int(str, ":", "\n"); // ESTIMATED COORDINATE ERROR. (refine_analyze) }else if (strstr_space(str, "REMARK 3 ESD FROM LUZZATI PLOT (A) :")){ refine_analyze.Luzzati_coordinate_error_obs = get_float(str, ":", "\n"); }else if (strstr_space(str, "REMARK 3 ESD FROM SIGMAA (A) :")){ refine_analyze.Luzzati_sigma_a_obs = get_float(str, ":", "\n"); }else if (strstr_space(str, "REMARK 3 LOW RESOLUTION CUTOFF (A) :")){ refine_analyze.Luzzati_d_res_low_obs = get_float(str, ":", "\n"); }else if (strstr_space(str, "REMARK 3 ESD FROM C-V LUZZATI PLOT (A) :")){ refine_analyze.Luzzati_coordinate_error_free = get_float(str, ":", "\n"); }else if (strstr_space(str, "REMARK 3 ESD FROM C-V SIGMAA (A) :")){ refine_analyze.Luzzati_sigma_a_free = get_float(str, ":", "\n"); }else if (strstr_space(str, "REMARK 3 PROGRAM :")){ strcpy(PROG, get_substr(str," :", "\n")); // not remarks: } else if(!strncmp_case(str, "CRYST1 ", 7)){ cell.length_a = get_float_by_length(str,6, 14); cell.length_b = get_float_by_length(str,15, 23); cell.length_c = get_float_by_length(str,24,32) ; cell.angle_alpha = get_float_by_length(str,33,39); cell.angle_beta = get_float_by_length(str,40,46); cell.angle_gamma = get_float_by_length(str,47,53); get_string(str,55, 65, symmetry.space_group_name_H_M); rid_of_front_end_space(symmetry.space_group_name_H_M); cell.Z_PDB = get_int_by_length(str,66,69); }else if(!strncmp_case(str, "ORIGX1 ", 7)){ database_PDB_matrix.origx11 = get_float_by_length(str, 10, 19); database_PDB_matrix.origx12 = get_float_by_length(str, 20, 29); database_PDB_matrix.origx13 = get_float_by_length(str, 30, 39); database_PDB_matrix.origx_vector1 = get_float_by_length(str, 45, 54); }else if(!strncmp_case(str, "ORIGX2 ", 7)){ database_PDB_matrix.origx21 = get_float_by_length(str, 10, 19); database_PDB_matrix.origx22 = get_float_by_length(str, 20, 29); database_PDB_matrix.origx23 = get_float_by_length(str, 30, 39); database_PDB_matrix.origx_vector2 = get_float_by_length(str, 45, 54); }else if(!strncmp_case(str, "ORIGX3 ", 7)){ database_PDB_matrix.origx31 = get_float_by_length(str, 10, 19); database_PDB_matrix.origx32 = get_float_by_length(str, 20, 29); database_PDB_matrix.origx33 = get_float_by_length(str, 30, 39); database_PDB_matrix.origx_vector3 = get_float_by_length(str, 45, 54); }else if(!strncmp_case(str, "SCALE1 ", 7)){ atom_sites.fract_transf_matrix11 = get_float_by_length(str, 10, 19); atom_sites.fract_transf_matrix12 = get_float_by_length(str, 20, 29); atom_sites.fract_transf_matrix13 = get_float_by_length(str, 30, 39); atom_sites.fract_transf_vector1 = get_float_by_length(str, 45, 54); }else if(!strncmp_case(str, "SCALE2 ", 7)){ atom_sites.fract_transf_matrix21 = get_float_by_length(str, 10, 19); atom_sites.fract_transf_matrix22 = get_float_by_length(str, 20, 29); atom_sites.fract_transf_matrix23 = get_float_by_length(str, 30, 39); atom_sites.fract_transf_vector2 = get_float_by_length(str, 45, 54); }else if(!strncmp_case(str, "SCALE3 ", 7)){ atom_sites.fract_transf_matrix31 = get_float_by_length(str, 10, 19); atom_sites.fract_transf_matrix32 = get_float_by_length(str, 20, 29); atom_sites.fract_transf_matrix33 = get_float_by_length(str, 30, 39); atom_sites.fract_transf_vector3 = get_float_by_length(str, 45, 54); } } fclose(finp); } void write_PDB_resid(FILE *fout, char *str, long len) { char resname[20], resid[10]; if(len>=20){ fprintf(fout,"Please adjust the length of string!\n"); return; } strncpy(resname, str, len); resname[len] = '\0'; rid_of_front_space(resname); rid_of_end_space(resname); if(strlen(resname)<=0) { fprintf(fout,". "); return; } if(!strcmp_case(resname, "ADE")){ strcpy(resid, " A"); }else if(!strcmp_case(resname, "GUA")){ strcpy(resid, " G"); }else if(!strcmp_case(resname, "URA")){ strcpy(resid, " U"); }else if(!strcmp_case(resname, "CYT")){ strcpy(resid, " C"); }else if(!strcmp_case(resname, "THY")){ strcpy(resid, " T"); }else{ strcpy(resid, resname); } rid_of_front_end_space(resid); fprintf(fout," '%s' ", resid); } void write_PDB_item(FILE *fout, char *str, long len, int format, int digit) /*write each items for the pdb record. */ { char tmp[20]; int n; float a; if(len>=20){ fprintf(fout,"Please adjust the length of string!\n"); return; } strncpy(tmp, str, len); tmp[len] = '\0'; rid_of_front_end_space(tmp); if(strlen(tmp)<=0) { fprintf(fout,". "); return; } if(format==1){ //char fprintf(fout,"\"%s\" ", tmp); }else if(format==2){ //int if(sscanf(tmp, "%d", &n) ==1) fprintf(fout, "%d ", n); else fprintf(fout, "? "); }else if(format==3){ //float sscanf(tmp, "%f", &a); if(digit==3){ fprintf(fout,"%.3f ", a); }else if(digit==2){ fprintf(fout,"%.2f ", a); }else if(digit==1){ fprintf(fout,"%.1f ", a); }else if(digit==4){ fprintf(fout,"%.4f ", a); }else { fprintf(fout,"Please adjust the digital number (%d)\n", digit); return; } }else{ fprintf(fout,"The given format is not (int, char, float)\n"); return; } } void pdb2cif_coord(FILE *fout, char *inpfile) /* convert the coordinates and aniso. temp of a PDB file to mmcif*/ { char str[100], **atoms=NULL, **anis=NULL; int i=0, n = 0, m = 0, k=0, len; float bfactor=0; long nline=0; FILE *fp; if((fp = fopen(inpfile, "r"))==NULL) { open_file_error(inpfile, "pdb2cif_coord"); } nline=num_of_line(inpfile); atoms = new char *[nline]; anis = new char *[nline]; while (fgets(str, sizeof str, fp) != NULL) { len=strlen(str); if ((!strncmp_case(str, "ATOM ", 6) || !strncmp_case(str, "HETATM", 6) || !strncmp_case(str, "SIGATM", 6)) && len>54){ atoms[n]=new char[81]; strcpy(atoms[n], str); n++; }else if ((!strncmp_case(str, "ANISOU", 6) || !strncmp_case(str, "SIGUIJ", 6)) && len>69) { anis[m]=new char[81]; strcpy(anis[m], str); m++; } } nline = m; if(n>0){ fprintf(fout,"%s\n%s\n%s\n%s\n%s\n%s\n%s\n%s\n%s\n%s\n%s\n%s\n%s\n%s\n%s\n%s\n%s\n%s\n%s\n%s\n%s\n%s\n%s\n", "loop_", "_atom_site.group_PDB", "_atom_site.id", "_atom_site.auth_atom_id", "_atom_site.label_atom_id", "_atom_site.label_alt_id", "_atom_site.auth_comp_id", "_atom_site.label_comp_id", "_atom_site.auth_asym_id", "_atom_site.label_asym_id", "_atom_site.auth_seq_id" , "_atom_site.label_seq_id" , "_atom_site.pdbx_PDB_ins_code", "_atom_site.Cartn_x", "_atom_site.Cartn_y", "_atom_site.Cartn_z", "_atom_site.occupancy", "_atom_site.B_iso_or_equiv", "_atom_site.Cartn_x_esd", "_atom_site.Cartn_y_esd", "_atom_site.Cartn_z_esd", "_atom_site.occupancy_esd", "_atom_site.B_iso_or_equiv_esd"); for(i=0; i54 ) { strcpy(str, atoms[i]); write_PDB_item(fout, str+0, 6, 1, 0); // _atom_site.group_PDB write_PDB_6_27(fout, str); //column 6_27 write_PDB_30_70(fout, str, 1);//column 30_70 bfactor = bfactor+ get_float_by_length(str, 60, 65); } if(i0 && refine.B_iso_mean <0 && bfactor>0){ refine.B_iso_mean = bfactor/float(n); } if(m>0){ fprintf(fout,"%s\n%s\n%s\n%s\n%s\n%s\n%s\n%s\n%s\n%s\n%s\n%s\n%s\n%s\n%s\n%s\n%s\n%s\n%s\n%s\n%s\n%s\n%s\n%s\n", "loop_", "_atom_site_anisotrop.id", "_atom_site_anisotrop.pdbx_auth_atom_id", "_atom_site_anisotrop.pdbx_label_atom_id", "_atom_site_anisotrop.pdbx_label_alt_id", "_atom_site_anisotrop.pdbx_auth_comp_id", "_atom_site_anisotrop.pdbx_label_comp_id", "_atom_site_anisotrop.pdbx_auth_asym_id", "_atom_site_anisotrop.pdbx_label_asym_id", "_atom_site_anisotrop.pdbx_auth_seq_id" , "_atom_site_anisotrop.pdbx_label_seq_id" , "_atom_site_anisotrop.pdbx_PDB_ins_code", "_atom_site_anisotrop.U[1][1]", "_atom_site_anisotrop.U[1][2]", "_atom_site_anisotrop.U[1][3]", "_atom_site_anisotrop.U[2][2]", "_atom_site_anisotrop.U[2][3]", "_atom_site_anisotrop.U[3][3]", "_atom_site_anisotrop.U[1][1]_esd", "_atom_site_anisotrop.U[1][2]_esd", "_atom_site_anisotrop.U[1][3]_esd", "_atom_site_anisotrop.U[2][2]_esd", "_atom_site_anisotrop.U[2][3]_esd", "_atom_site_anisotrop.U[3][3]_esd"); for(i=0; i-9998) fprintf(fout,"_refine_analize.Luzzati_coordinate_error_obs %.3f\n", refine_analyze.Luzzati_coordinate_error_obs); if(refine_analyze.Luzzati_sigma_a_obs >-9998) fprintf(fout,"_refine_analize.Luzzati_sigma_a_obs %.3f\n", refine_analyze.Luzzati_sigma_a_obs); if(refine_analyze.Luzzati_d_res_low_obs >-9998) fprintf(fout,"_refine_analize.Luzzati_d_res_low_obs %.3f\n", refine_analyze.Luzzati_d_res_low_obs); if(refine_analyze.Luzzati_coordinate_error_free >-9998) fprintf(fout,"_refine_analize.Luzzati_coordinate_error_free %.3f\n", refine_analyze.Luzzati_coordinate_error_free); if(refine_analyze.Luzzati_sigma_a_free >-9998) fprintf(fout,"_refine_analize.Luzzati_sigma_a_free %.3f\n", refine_analyze.Luzzati_sigma_a_free); } void write_refine_ls_restr(FILE *fout) { int i; char type[80]; static const char *refmac_29[] = { "r_bond_refined_d BOND LENGTHS REFINED ATOMS (A) ", "r_bond_other_d BOND LENGTHS OTHERS (A) ", "r_angle_refined_deg BOND ANGLES REFINED ATOMS (DEGREES) ", "r_angle_other_deg BOND ANGLES OTHERS (DEGREES) ", "r_dihedral_angle_1_deg TORSION ANGLES, PERIOD 1 (DEGREES) ", "r_dihedral_angle_2_deg TORSION ANGLES, PERIOD 2 (DEGREES) ", "r_dihedral_angle_3_deg TORSION ANGLES, PERIOD 3 (DEGREES) ", "r_dihedral_angle_4_deg TORSION ANGLES, PERIOD 4 (DEGREES) ", "r_chiral_restr CHIRAL-CENTER RESTRAINTS (A**3) ", "r_gen_planes_refined GENERAL PLANES REFINED ATOMS (A) ", "r_gen_planes_other GENERAL PLANES OTHERS (A) ", "r_nbd_refined NON-BONDED CONTACTS REFINED ATOMS (A) ", "r_nbd_other NON-BONDED CONTACTS OTHERS (A) ", "r_nbtor_refined NON-BONDED TORSION REFINED ATOMS (A) ", "r_nbtor_other NON-BONDED TORSION OTHERS (A) ", "r_xyhbond_nbd_refined H-BOND (X...Y) REFINED ATOMS (A) ", "r_xyhbond_nbd_other H-BOND (X...Y) OTHERS (A) ", "r_symmetry_vdw_refined SYMMETRY VDW REFINED ATOMS (A) ", "r_symmetry_vdw_other SYMMETRY VDW OTHERS (A) ", "r_symmetry_hbond_refined SYMMETRY H-BOND REFINED ATOMS (A) ", "r_symmetry_hbond_other SYMMETRY H-BOND OTHERS (A) ", "r_mcbond_it MAIN-CHAIN BOND REFINED ATOMS (A**2) ", "r_mcangle_it MAIN-CHAIN ANGLE REFINED ATOMS (A**2) ", "r_mcbond_other MAIN-CHAIN BOND OTHER ATOMS (A**2) ", "r_scbond_it SIDE-CHAIN BOND REFINED ATOMS (A**2) ", "r_scangle_it SIDE-CHAIN ANGLE REFINED ATOMS (A**2) ", "r_rigid_bond_restr RIGID-BOND RESTRAINTS (A**2) ", "r_sphericity_free SPHERICITY; FREE ATOMS (A**2) ", "r_sphericity_bonded SPHERICITY; BONDED ATOMS (A**2) " }; static const char *cns_9[] = { "c_bond_d BOND LENGTHS (A) ", " c_angle_d ANGLE DISTANCES (A) ", " c_angle_deg BOND ANGLES (DEGREES) ", " c_dihedral_angle_d DIHEDRAL ANGLES (DEGREES) ", " c_improper_angle_d IMPROPER ANGLES (DEGREES) ", " c_mcbond_it MAIN-CHAIN BOND (A**2) ", " c_mcangle_it MAIN-CHAIN ANGLE (A**2) ", " c_scbond_it SIDE-CHAIN BOND (A**2) ", " c_scangle_it SIDE-CHAIN ANGLE (A**2) " }; static const char *xplor_9[] = { " x_bond_d BOND LENGTHS (A) ", " x_angle_d ANGLE DISTANCES (A) ", " x_angle_deg BOND ANGLES (DEGREES) ", " x_dihedral_angle_d DIHEDRAL ANGLES (DEGREES) ", " x_improper_angle_d IMPROPER ANGLES (DEGREES) ", " x_mcbond_it MAIN-CHAIN BOND (A**2) ", " x_mcangle_it MAIN-CHAIN ANGLE (A**2) ", " x_scbond_it SIDE-CHAIN BOND (A**2) ", " x_scangle_it SIDE-CHAIN ANGLE (A**2) " }; static const char *shelx_10[] = { "s_bond_d BOND LENGTHS (A) ", "s_angle_d ANGLE DISTANCES (A) ", "s_similar_dist SIMILAR DISTANCES (NO TARGET VALUES) (A) ", "s_from_restr_planes DISTANCES FROM RESTRAINT PLANES (A) ", "s_zero_chiral_vol ZERO CHIRAL VOLUMES (A**3) ", "s_non_zero_chiral_vol NON-ZERO CHIRAL VOLUMES (A**3)", "s_anti_bump_dis_restr ANTI-BUMPING DISTANCE RESTRAINTS (A) ", "s_rigid_bond_adp_cmpnt RIGID-BOND ADP COMPONENTS (A**2) ", "s_similar_adp_cmpnt SIMILAR ADP COMPONENTS (A**2) ", "s_approx_iso_adps APPROXIMATELY ISOTROPIC ADPS (A**2) " }; static const char *tnt_9[] = { "t_bond_d BOND LENGTHS (A) ", "t_angle_deg BOND ANGLES (DEGREES) ", "t_dihedral_angle_d TORSION ANGLES (DEGREES) ", "t_incorr_chiral_ct CHIRAL-CENTER RESTRAINT (A**3) ", "t_pseud_angle PSEUDOROTATION ANGLES (DEGREES) ", "t_trig_c_planes TRIGONAL CARBON PLANES (A) ", "t_gen_planes GENERAL PLANES (A) ", "t_it ISOTROPIC THERMAL FACTORS (A**2) ", "t_nbd NON-BONDED CONTACTS (A) " }; static const char *nuclsq_17[] = { " n_bond_d BOND LENGTH (A) ", " n_angle_d ANGLE DISTANCE (A)", " n_planar_d INTRAPLANAR 1-4 DISTANCE (A) ", " n_hb_or_metal_coord H-BOND OR METAL COORDINATION (A) ", " n_sugar_bond_it SUGAR-BASE BONDS (A**2)", " n_sugar_angle_it SUGAR-BASE ANGLES (A**2)", " n_phos_bond_it PHOSPHATE BONDS (A**2)", " n_phos_angle_it PHOSPHATE BOND ANGLE, H-BOND (A**2)", " n_plane_restr PLANE RESTRAINT (A)", " n_chiral_restr SINGLE TORSION CONTACT (A)", " n_sugar_bond_d SUGAR-BASE BOND DISTANCE (A)", " n_sugar_bond_angle_d SUGAR-BASE BOND ANGLE DISTANCE (A)", " n_phos_bond_d PHOSPHATE BONDS DISTANCE (A)", " n_phos_bond_angle_d PHOSPHATE BOND ANGLE, H-BOND (A)", " n_chiral_restr CHIRAL-CENTER RESTRAINT (A**3)", " n_singtor_nbd SINGLE TORSION (A)", " n_multtor_nbd MULTIPLE TORSION CONTACT (A)" }; static const char *prolsq_17[] = { " p_bond_d BOND LENGTH (A) ", " p_angle_d ANGLE DISTANCE (A)", " p_planar_d INTRAPLANAR 1-4 DISTANCE (A) ", " p_hb_or_metal_coord H-BOND OR METAL COORDINATION (A) ", " p_sugar_bond_it SUGAR-BASE BONDS (A**2)", " p_sugar_angle_it SUGAR-BASE ANGLES (A**2)", " p_phos_bond_it PHOSPHATE BONDS (A**2)", " p_phos_angle_it PHOSPHATE BOND ANGLE, H-BOND (A**2)", " p_plane_restr PLANE RESTRAINT (A)", " p_chiral_restr SINGLE TORSION CONTACT (A)", " p_sugar_bond_d SUGAR-BASE BOND DISTANCE (A)", " p_sugar_bond_angle_d SUGAR-BASE BOND ANGLE DISTANCE (A)", " p_phos_bond_d PHOSPHATE BONDS DISTANCE (A)", " p_phos_bond_angle_d PHOSPHATE BOND ANGLE, H-BOND (A)", " p_chiral_restr CHIRAL-CENTER RESTRAINT (A**3)", " p_singtor_nbd SINGLE TORSION (A)", " p_multtor_nbd MULTIPLE TORSION CONTACT (A)" }; static const char *other_17[] = { " o_bond_d BOND LENGTH (A) ", " o_angle_d ANGLE DISTANCE (A)", " o_planar_d INTRAPLANAR 1-4 DISTANCE (A) ", " o_hb_or_metal_coord H-BOND OR METAL COORDINATION (A) ", " o_sugar_bond_it SUGAR-BASE BONDS (A**2)", " o_sugar_angle_it SUGAR-BASE ANGLES (A**2)", " o_phos_bond_it PHOSPHATE BONDS (A**2)", " o_phos_angle_it PHOSPHATE BOND ANGLE, H-BOND (A**2)", " o_plane_restr PLANE RESTRAINT (A)", " o_chiral_restr SINGLE TORSION CONTACT (A)", " o_sugar_bond_d SUGAR-BASE BOND DISTANCE (A)", " o_sugar_bond_angle_d SUGAR-BASE BOND ANGLE DISTANCE (A)", " o_phos_bond_d PHOSPHATE BONDS DISTANCE (A)", " o_phos_bond_angle_d PHOSPHATE BOND ANGLE, H-BOND (A)", " o_chiral_restr CHIRAL-CENTER RESTRAINT (A**3)", " o_singtor_nbd SINGLE TORSION (A)", " o_multtor_nbd MULTIPLE TORSION CONTACT (A)" }; if(refine_ls_restr[0].dev_ideal <-9998 || NR<=0 )return; if(NR>0){ fprintf(fout,"#\n"); fprintf(fout,"loop_\n"); fprintf(fout,"_refine_ls_restr.type\n"); fprintf(fout,"_refine_ls_restr.number\n"); fprintf(fout,"_refine_ls_restr.dev_ideal\n"); fprintf(fout,"_refine_ls_restr.dev_ideal_target \n"); fprintf(fout,"_refine_ls_restr.weight \n"); } for(i=0; i-9998) ? fprintf(fout, "%d ", refine_ls_restr[i].number) : fprintf(fout,"? "); (refine_ls_restr[i].dev_ideal>-9998) ? fprintf(fout,"%.3f ", refine_ls_restr[i].dev_ideal): fprintf(fout,"? ") ; (refine_ls_restr[i].dev_ideal_target >-9998) ? fprintf(fout, "%.3f ", refine_ls_restr[i].dev_ideal_target ) : fprintf(fout,"? "); (refine_ls_restr[i].weight >-9998) ? fprintf(fout, "%.3f ", refine_ls_restr[i].weight ) : fprintf(fout,"? "); fprintf(fout,"\n"); } } void convert_restr_2_standard(FILE *fout, char *type, int k, const char **pair, int npair) { char param[80], str[80]; int id=0, i; for(i=0;i