/* FILE: ccp4.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. */ /* a program to extract information form the CCP4 program */ #include #include #include #include #include "structure.h" #include "harv.h" #include "nrutil.h" #include "util.h" #define LEN 256 #define NBIN 100 void mlphare_log(FILE *fout, char *inpfile, char *method); //PHASING_MIR phasing_mir ; extern CELL cell ; extern SYMMETRY symmetry; extern PDBX_PHASING_DM pdbx_phasing_dm; PDBX_PHASING_DM_SHELL pdbx_phasing_dm_shell; extern PDBX_PHASING_MR pdbx_phasing_MR; extern REFINE refine; PHASING_MAD phasing_mad; PDBX_PHASING_MAD_SET pdbx_phasing_mad_set; PDBX_PHASING_MAD_SET_SHELL pdbx_phasing_mad_set_shell[NBIN]; PDBX_PHASING_MAD_SET_SITE pdbx_phasing_mad_set_site; PDBX_PHASING_MAD_SHELL pdbx_phasing_mad_shell[NBIN]; PHASING_MAD_SET phasing_mad_set; PHASING_MIR phasing_mir; PHASING_MIR_DER phasing_mir_der; PHASING_MIR_DER_SHELL phasing_mir_der_shell; PHASING_MIR_DER_SITE phasing_mir_der_site; PHASING_MIR_SHELL phasing_mir_shell; void convert_restr_refmac5_cif(char *str); void CCP4_phase_file_assign(FILE *fout, char *inpfile, char *format, char *method) /* assign the files (from phasing) to different subroutines */ { FILE *fp; if((fp = fopen(inpfile, "r"))==NULL) { printf("Can not open the file %s (routine:CCP4_phase_file_assign)\n", inpfile); return; } if(!strcmp_case(format, "PDB")) { /*take as heavy atom XYZ */ heavy_coord_pdb(fout, inpfile, method); return; } /* must be prephadata log file and mlphare log file*/ if(!strcmp_case(format, "LOG")) { CCP4_MAD_wave(fout, inpfile, method); mlphare_log(fout, inpfile,method); return; } if(!strcmp_case(format, "CIF")) { CCP4_mlphare_cif(fout, inpfile, method); return; } fclose(fp); } void mlphare_log(FILE *fout, char *inpfile, char *method) { char tmp[80], **str=NULL, **line=NULL, **atom=NULL, **deriv=NULL, bfact[30]; int n,m,i,k, j,nline, ntoken=0, nbin=0, na, nd, nr; int refl_sh[NBIN],refl_a_sh[NBIN], refl_c_sh[NBIN], refl=0,refl_a=0, refl_c=0; float fom_sh[NBIN],fom_a_sh[NBIN], fom_c_sh[NBIN],resL_sh[NBIN],resH_sh[NBIN]; int ref_a_sh[500][NBIN], ref_c_sh[500][NBIN], ref_a[500], ref_c[500]; float loc_a_sh[500][NBIN], php_a_sh[500][NBIN], rc_a_sh[500][NBIN]; float loc_c_sh[500][NBIN], php_c_sh[500][NBIN], rc_c_sh[500][NBIN]; float loc_a[500], php_a[500], rc_a[500], loc_c[500], php_c[500], rc_c[500]; float fom=0, fom_a=0, fom_c=0, *resL_set,*resH_set ; int n1, n2,n3, n4,n5,n6; float a1, a2, a3, a4, a5, a6; FILE *fp; // 500 max derivatives const char *phasing_shell[8] = { "d_res_high", "d_res_low", "reflns", "fom", "reflns_centric", "FOM_centric", "reflns_acentric", "FOM_acentric" }; const char *items_site[7] = { "id", "atom_type_symbol", "fract_x", "fract_y", "fract_z", "B_iso", "Occupancy" }; const char *item_der_shell[12] = { "der_id", "id", "d_res_high", "d_res_low", "pdbx_reflns_acentric", "pdbx_loc_acentric", "pdbx_power_acentric", "pdbx_R_cullis_acentric", "pdbx_reflns_centric", "pdbx_loc_centric", "pdbx_power_centric", "pdbx_R_cullis_centric", }; if((fp=fopen(inpfile, "r"))==NULL) open_file_error(inpfile, "mlphare_log"); str = get_lines_from_file(inpfile, &nline); // for(n=0; n0) strcpy(symmetry.space_group_name_H_M, tmp); strcpy(tmp, ""); strcpy(tmp, get_substr(str[i],"number", ")")); if(strlen(tmp)>0) symmetry.Int_Tables_number= atoi(tmp); }else if(strstr_space(str[i], "Protein Resolution Limits are from") && pattern5(str[i], "from" , "to", "Angstroms", "", "")){ phasing_mad.pdbx_d_res_low = get_float(str[i],"from","to"); phasing_mad.pdbx_d_res_high = get_float(str[i],"to", "Angstroms"); }else if(strstr_space(str[i], "Resolution of each shell in angstroms:")){ line = string_token(str[i+1]," " , &ntoken); nbin = ntoken; resL_sh[0] = phasing_mad.pdbx_d_res_low; resH_sh[0] = atof(line[0]); for(k=1; k0 && nd>0 && nr == nd){ if(!strcmp_case(method,"mir")) print_mmcif_head(fout,"_phasing_MIR_der_site", items_site, 7); else print_mmcif_head(fout,"_pdbx_phasing_MAD_set_site", items_site, 7); for(i=0; i0){ if(!strcmp_case(method,"mir")) print_mmcif_head(fout, "_phasing_MIR_der_shell", item_der_shell, 12); else print_mmcif_head(fout, "_pdbx_phasing_MAD_set_shell", item_der_shell, 12); for(j=0; j0) { fprintf(fout,"\nloop_\n" "_phasing_MAD_set.expt_id\n" "_phasing_MAD_set.clust_id\n" "_phasing_MAD_set.set_id\n" "_phasing_MAD_set.wavelength\n" "_phasing_MAD_set.f_prime\n" "_phasing_MAD_set.f_double_prime\n" ); for( i=0; i0)printf("hello item=%s %s\n", category,item); strcpy(tmp,str); if(!strcmp_case(category, "_PHASING_MIR_SHELL") && ncat>0){ replace_first_str(tmp,"_PHASING_MIR","_pdbx_phasing_MAD",str); }else if(!strcmp_case(category, "_PHASING_MIR") && ncat>0){ if(!strcmp_case(item,"entry_id") || !strcmp_case(item,"method") || !strcmp_case(item,"details")){ replace_first_str(tmp,"_PHASING_MIR","_phasing_MAD",str); }else{ replace_first_str(tmp,"_PHASING_MIR.","_phasing_MAD.pdbx_",str); } }else if(!strcmp_case(category, "_PHASING_MIR_DER_SITE")&& ncat>0){ replace_first_str(tmp,"_PHASING_MIR_DER_SITE", "_pdbx_phasing_MAD_set_site",str); if(!strcmp_case(item, "der_id")){ replace_first_str(tmp,"_PHASING_MIR_DER_SITE.der_id", "_pdbx_phasing_MAD_set_site.set_id",str); }else if(!strcmp_case(item, "Occupancy_anom")){ replace_first_str(tmp,"_phasing_MIR_der_site.Occupancy_anom", "_pdbx_phasing_MAD_set_site.Occupancy",str); }else if(!strcmp_case(item, "Occupancy_anom_esd")){ replace_first_str(tmp,"_phasing_MIR_der_site.occupancy_anom_esd", "_pdbx_phasing_MAD_set_site.occupancy_esd",str); } }else if(!strcmp_case(category,"_PHASING_MIR_DER") && ncat>0){ replace_first_str(tmp,"_PHASING_MIR_DER", "_pdbx_phasing_MAD_set",str); if(!strcmp_case(item, "Reflns_anomalous")){ replace_first_str(tmp,"_phasing_MIR_der.Reflns_anomalous", "_pdbx_phasing_MAD_set.Reflns",str); }else if(!strcmp_case(item, "R_cullis_anomalous")){ replace_first_str(tmp,"_phasing_MIR_der.R_cullis_anomalous", "_pdbx_phasing_MAD_set.R_cullis",str); } } if(strstr(str,"\n")) fprintf(fout, "%s", str); else fprintf(fout, "%s\n", str); } } fclose(fp); } void CCP4_ref_refmac5(FILE *fout, char *inpfile, char *file_format,char *method) /* assign the files (from refinement) to different subroutines */ { char str[512],tmp[512], category[100],item[100]; int k=0; FILE *fp; if((fp = fopen(inpfile, "r"))==NULL) open_file_error(inpfile,"CCP4_ref_refmac5"); if(strstr(file_format, "PDB")) pdb_2_cif(fout, inpfile); else if (strstr(file_format, "CIF")) { if( is_cif(inpfile)< 5) { printf("The input file (%s) for refmac5 is not in mmCIF format",inpfile); return; } // nline=num_of_line(inpfile); // line=new char *[nline]; k=0; while (fgets(str, sizeof str, fp) != NULL) { rid_of_front_space(str); if(str[0] !='#') k++; if(k==1 && !strncmp_case(str,"data_",5)) continue; check_category(str, category, item); if(strlen(category)>0 && strlen(item)>0 ){ if(!strcmp_case(category, "_refine")) continue; if((!strcmp_case(category, "_entry") || !strcmp_case(category, "_diffrn")) && !strcmp_case(item, "id")) continue; if(!strcmp_case(category, "_audit") && !strcmp_case(item, "creation_date")) continue; if(strstr(category,"_ccp4_refine_tls")){ strcpy(tmp, strstr(str, "tls")+3 ); strcpy(str, "_pdbx_refine_tls"); strcat(str, tmp); }else if(!strcmp_case(category,"_refine_ls_restr_ncs")&& !strncmp_case(item,"ccp4",4)){ strcpy(tmp, strstr(str, "ccp4")+4 ); strcpy(str, "_refine_ls_restr_ncs.pdbx"); strcat(str, tmp); }else if(!strcmp_case(category,"_struct_ncs_dom_lim")&& !strncmp_case(item,"ccp4",4)){ strcpy(tmp, strstr(str, "ccp4")+4 ); strcpy(str, "_struct_ncs_dom_lim.pdbx"); strcat(str, tmp); }else if(!strcmp_case(category,"_refine_ls_shell")&& !strcmp_case(item,"R_factor_R_all")){ strcpy(str,"_refine_ls_shell.R_factor_all\n"); } } convert_restr_refmac5_cif(str); strstr(str,"\n") ? fprintf(fout,"%s", str ) : fprintf(fout,"%s\n", str ); } fprintf(fout,"\n#\n"); rewind(fp); while (fgets(str, sizeof str, fp) != NULL) { //only _refine. check_category(str, category, item); if(strlen(category)>0 && strlen(item)>0 && !strcmp_case(category,"_refine") ){ strcpy(tmp,str); if (!strcmp_case(item,"B_iso_mean")){ refine.B_iso_mean = get_float(tmp, "B_iso_mean","\n"); /* }else if(!strcmp_case(item,"ls_matrix_type") && strchr(str, "\"")){ refine.ls_matrix_type = get_substr(str, "\"","\""); }else if (!strcmp_case(item,"ls_matrix_type") && strchr(tmp, "'")){ refine.ls_matrix_type = get_substr(str, "'","'"); }else if (!strcmp_case(item,"solvent_model_details")){ refine.solvent_model_details = get_substr(tmp, "'","'"); */ }else if (!strcmp_case(item,"aniso_B[1][1]")){ refine.aniso_B11 = get_float(tmp, "aniso_B[1][1]","\n"); }else if (!strcmp_case(item,"aniso_B[2][2]")){ refine.aniso_B22 = get_float(tmp, "aniso_B[2][2]","\n"); }else if (!strcmp_case(item,"aniso_B[3][3]")){ refine.aniso_B33 = get_float(tmp, "aniso_B[3][3]","\n"); }else if (!strcmp_case(item,"aniso_B[1][2]")){ refine.aniso_B12 = get_float(tmp, "aniso_B[1][2]","\n"); }else if (!strcmp_case(item,"aniso_B[1][3]")){ refine.aniso_B13 = get_float(tmp, "aniso_B[1][3]","\n"); }else if (!strcmp_case(item,"aniso_B[2][3]")){ refine.aniso_B23 = get_float(tmp, "aniso_B[2][3]","\n"); }else if (!strcmp_case(item,"solvent_vdw_probe_radii")){ refine.pdbx_solvent_vdw_probe_radii = get_float(tmp, "solvent_vdw_probe_radii","\n"); }else if (!strcmp_case(item,"solvent_ion_probe_radii")){ refine.pdbx_solvent_ion_probe_radii = get_float(tmp, "solvent_ion_probe_radii","\n"); }else if (!strcmp_case(item,"solvent_shrinkage_radii")){ refine.pdbx_solvent_shrinkage_radii = get_float(tmp, "solvent_shrinkage_radii","\n"); }else if (!strcmp_case(item,"ls_d_res_high")){ refine.ls_d_res_high = get_float(tmp, "ls_d_res_high","\n"); }else if (!strcmp_case(item,"ls_d_res_low")){ refine.ls_d_res_low = get_float(tmp, "ls_d_res_low","\n"); }else if (!strcmp_case(item,"ls_R_factor_R_work")){ refine.ls_R_factor_R_work = get_float(tmp, "ls_R_factor_R_work","\n"); }else if (!strcmp_case(item,"")){ refine.ls_R_factor_R_free = get_float(tmp, "ls_R_factor_R_free","\n"); }else if (!strcmp_case(item,"ls_R_factor_R_all")){ refine.ls_R_factor_all = get_float(tmp, "ls_R_factor_R_all","\n"); }else if (!strcmp_case(item,"ls_wR_factor_R_work")){ refine.ls_wR_factor_R_work = get_float(tmp, "ls_wR_factor_R_work","\n"); }else if (!strcmp_case(item,"ls_wR_factor_R_free")){ refine.ls_wR_factor_R_free = get_float(tmp, "ls_wR_factor_R_free","\n"); }else if (!strcmp_case(item,"ls_percent_reflns_obs")){ refine.ls_percent_reflns_obs = get_float(tmp, "ls_percent_reflns_obs","\n"); }else if (!strcmp_case(item,"ls_percent_reflns_R_free")){ refine.ls_percent_reflns_R_free = get_float(tmp, "ls_percent_reflns_R_free","\n"); }else if (!strcmp_case(item,"correlation_coeff_Fo_to_Fc")){ refine.correlation_coeff_Fo_to_Fc = get_float(tmp, "correlation_coeff_Fo_to_Fc","\n"); }else if(!strcmp_case(item,"ls_Correlation_coeff_Fo_to_Fc")){ refine.correlation_coeff_Fo_to_Fc = get_float(tmp,"ls_Correlation_coeff_Fo_to_Fc", "\n"); }else if (!strcmp_case(item,"correlation_coeff_Fo_to_Fc_free")){ refine.correlation_coeff_Fo_to_Fc_free = get_float(tmp, "correlation_coeff_Fo_to_Fc_free","\n"); }else if (!strcmp_case(item,"ls_Correlation_coeff_Fo_to_Fc_free")){ refine.correlation_coeff_Fo_to_Fc_free = get_float(tmp, "ls_Correlation_coeff_Fo_to_Fc_free","\n"); }else if (!strcmp_case(item,"pdbx_overall_ESU_R")){ refine.pdbx_overall_ESU_R = get_float(tmp, "pdbx_overall_ESU_R","\n"); }else if (!strcmp_case(item,"pdbx_overall_ESU_R_Free")){ refine.pdbx_overall_ESU_R_Free = get_float(tmp, "pdbx_overall_ESU_R_Free","\n"); }else if (!strcmp_case(item,"pdbx_overall_ESU_ML")){ refine.overall_SU_ML = get_float(tmp, "pdbx_overall_ESU_ML","\n"); }else if (!strcmp_case(item,"ls_Overall_ESU_ML")){ refine.overall_SU_ML = get_float(tmp, "ls_Overall_ESU_ML","\n"); }else if (!strcmp_case(item,"pdbx_overall_ESU_B")){ refine.overall_SU_B = get_float(tmp, "pdbx_overall_ESU_B","\n"); }else if (!strcmp_case(item,"ls_Overall_ESU_B")){ refine.overall_SU_B = get_float(tmp, "ls_Overall_ESU_B","\n"); }else if (!strcmp_case(item,"ls_number_reflns_R_work")){ refine.ls_number_reflns_R_work = get_int(tmp, "ls_number_reflns_R_work","\n"); }else if (!strcmp_case(item,"ls_number_reflns_R_free")){ refine.ls_number_reflns_R_free = get_int(tmp, "ls_number_reflns_R_free","\n"); }else if (!strcmp_case(item,"ls_number_reflns_obs")){ refine.ls_number_reflns_obs = get_int(tmp, "ls_number_reflns_obs","\n"); }else if(!strcmp_case(item,"ls_Overall_ESU_Rfree")){ refine.pdbx_overall_ESU_R_Free = get_float(tmp,"ls_Overall_ESU_Rfree", "\n"); } } } }else if(strstr(file_format, "LOG")) { printf("REFMAC5 produce a CIF file containing statistics. Please give\n"); printf("the file name (use option -iCIF file_name).\n"); fclose(fp); return; } fclose(fp); } void convert_restr_refmac5_cif(char *str) { char *param, stand[40], tmp[60], *str_old=NULL; int i; static const char *refmac_cif_28[] = { "r_bond_refined_d ,\"Bond distances: refined atoms \",,", "r_bond_other_d ,\"Bond distances: others \",,", "r_angle_refined_deg ,\"Bond angles : refined atoms \",,", "r_angle_other_deg ,\"Bond angles : others \",,", "r_dihedral_angle_1_deg ,\"Torsion angles, period 1. refined \",,", "r_dihedral_angle_2_deg ,\"Torsion angles, period 2. refined \",,", "r_dihedral_angle_3_deg ,\"Torsion angles, period 3. refined \",,", "r_dihedral_angle_4_deg ,\"Torsion angles, period 4. refined \",,", "r_chiral_restr ,\"Chiral centres: refined atoms \",,", "r_gen_planes_refined ,\"Planar groups: refined atoms \",,", "r_gen_planes_other ,\"Planar groups: others \",,", "r_nbd_refined ,\"VDW repulsions: refined atoms \",,", "r_nbd_other ,\"VDW repulsions: others \",,", "r_nbtor_refined ,\"VDW; torsion: refined atoms \",,", "r_nbtor_other ,\"VDW; torsion: others \",,", "r_xyhbond_nbd_refined ,\"HBOND: refined atoms \",,", "r_symmetry_vdw_refined ,\"VDW repulsions; symmetry: refined atoms \",,", "r_symmetry_vdw_other ,\"VDW repulsions; symmetry: others \",,", "r_symmetry_hbond_refined ,\"HBOND; symmetry: refined atoms \",,", "r_symmetry_hbond_other ,\"HBOND; symmetry: others \",,", "r_mcbond_it ,\"M. chain bond B values: refined atoms \",,", "r_mcbond_other ,\"M. chain bond B values: others \",,", "r_mcangle_it ,\"M. chain angle B values: refined atoms \",,", "r_mcangle_other ,\"M. chain angle B values: others \",,", "r_scbond_it ,\"S. chain bond B values: refined atoms \",,", "r_scbond_other ,\"S. chain bond B values: others \",,", "r_scangle_it ,\"S. chain angle B values: refined atoms \",,", "r_scangle_other ,\"S. chain angle B values: others \",," }; str_old=str; for(i=0;i<28;i++){ if(sscanf(refmac_cif_28[i], "%s", stand) != 1 ) continue; strcpy(tmp , refmac_cif_28[i] + strlen(stand)+1); param = get_substr(tmp, ",", ",,"); if(strstr_case(str, param)){ replace_first_str(str_old, param, stand, str); break; } } } void CCP4_ref_restrain(FILE *fout, char inpfile[], char *file_format, char method[]) /* assign the files (from refinement) to different subroutines */ { char str[512], tmp[512]; int k; FILE *fp; if((fp = fopen(inpfile, "r"))==NULL) { printf("Can not open the file %s (routine:CCP4_ref_restrain)\n",inpfile); return; } if(strstr(file_format, "PDB")){ pdb_2_cif(fout, inpfile); }else if (strstr(file_format, "CIF")) { if( is_cif(inpfile)< 5) { printf("The input file (%s) for restrain is not in mmCIF format",inpfile); return; } k=0; while (fgets(str, sizeof str, fp) != NULL) { strcpy(tmp, str); rid_of_front_space(tmp); if(tmp[0] !='#') k++; if(k==1 && !strncmp_case(tmp,"data_",5)) continue; fprintf(fout,"%s", str ); } }else if(strstr(file_format, "LOG")) { printf("RESTRAIN produce a CIF file containing statistics. Please\n"); printf("give the file name (use option -iCIF file_name).\n"); return; } fclose(fp); } /* void CCP4_ref_restrain_log(FILE *fout, char inpfile[], char method[]) { } */ void CCP4_phasing_DM(FILE *fout, char *inpfile,char *format,char *method) /* extract the information. FOM after density modification. */ { FILE *fp; int n=0, nref=0, m=0; char str[256], juck[80]; float resol_L, resol_H, fm, phi; char *method1=NULL, *method2=NULL,meth[256], *tmp=NULL; float nf, a1,a2,a3,a4,a5; if((fp = fopen(inpfile, "r"))==NULL) { printf("Can not open the file %s(routine:CCP4_phasing_DM)\n",inpfile); return; } if(!strcmp_case(format, "CIF") || !strcmp_case(format, "PDB")){ write_cif_or_pdb(fout, inpfile, format,method); return; } while (fgets(str, sizeof str, fp) != NULL) { upperstr(str); if(strstr_case(str, "
  • Solvent flattening")){ method1 = (char *)"Solvent flattening "; }else if(strstr_case(str, "
  • Histogram matching")){ method2 = (char *)"Histogram matching"; }else if(strstr_case(str, "Number of reflections included in phase recombination =")){ pdbx_phasing_dm.reflns = get_int(str,"= ", "\n"); }else if(strstr_case(str, "Auto Wang-radius")){ pdbx_phasing_dm.mask_radius = get_int(str,"Wang-radius", "\n"); }else if(pattern5(str, "Effective resolution:"," A", "","","")){ pdbx_phasing_dm.d_res_high = get_float(str,":", "A"); }else if(strstr_case(str, "% of cell Min Rho Max Rho Mean Rho Std.Dev.")){ while (fgets(str, sizeof str, fp) != NULL){ if(strstr_case(str,"Protein:")){ tmp= strstr(str,":")+1; m=sscanf(tmp, "%f%f%f%f%f\n", &a1, &a2, &a3, &a4, &a5); if(m==5){ pdbx_phasing_dm.protein_percent_sol = a1; pdbx_phasing_dm.protein_min_density = a2; pdbx_phasing_dm.protein_max_density = a3; pdbx_phasing_dm.protein_mean_density = a4; pdbx_phasing_dm.protein_mean_density_esd = a5; } } else if(strstr_case(str,"Solvent:")){ tmp= strstr(str,":")+1; m=sscanf(tmp, "%f%f%f%f%f\n", &a1, &a2, &a3, &a4, &a5); if(m==5){ pdbx_phasing_dm.solvent_percent_sol = a1; pdbx_phasing_dm.solvent_min_density = a2; pdbx_phasing_dm.solvent_max_density = a3; pdbx_phasing_dm.solvent_mean_density = a4; pdbx_phasing_dm.solvent_mean_density_esd = a5; } }else break; } }else if (strstr_space(str,"RMIN - RMAX S^2 NREFLS SIGMAA MEAN FOM")>0){ n=0; while (fgets(str, sizeof str, fp) != NULL){ upperstr(str); if(!is_space_line(str))continue; if(strstr(str, "------") || strstr(str, "CYCLE") || strlen(str)<20 )break; if(strstr_space(str, "(calc) (comb)") >0 ) continue; if(sscanf(str, "%f %f %s %f %s %s %s %f %f %s %s", &resol_L, &resol_H, juck, &nf , juck, juck,juck, &fm,&phi, juck,juck)==11){ nref=(int) nf; pdbx_phasing_dm_shell.d_res_low[n] = resol_L; pdbx_phasing_dm_shell.d_res_high[n] = resol_H; pdbx_phasing_dm_shell.reflns[n] = nref; pdbx_phasing_dm_shell.fom[n] = fm; pdbx_phasing_dm_shell.delta_phi_final[n] = phi; n++; if(n>=NBIN-1){ printf("Warning! No DM statistics will be written\n"); n=0; break; } } } } } pdbx_phasing_dm_shell.number_bin = n; if(method1 && method2){ strcpy(meth,method1); strcat(meth, " and "); strcat(meth, method2); strcpy(pdbx_phasing_dm.method , meth); }else if(method1 && !method2){ strcpy(pdbx_phasing_dm.method , method1); }else if(!method1 && method2){ strcpy(pdbx_phasing_dm.method , method2); } fclose(fp); } void CCP4_phasing_SOLOMON(FILE *fout, char *inpfile, char *format,char *method) /* extract the information. FOM after density modification. */ { FILE *fp; int i, j=0, nc=0, nline=0, nb1,nb2,refl_c[NBIN], refl_a[NBIN], nref, m, n, ncol=0; char str[512],charact, **fomlines, tmp[80]; float resL_c[NBIN],resH_c[NBIN],fom_c[NBIN],resL_a[NBIN],resH_a[NBIN],fom_a[NBIN]; float fom, a; fomlines = set_memory_2d(500,300); if((fp = fopen(inpfile, "r"))==NULL) { printf("Can not open the file %s(routine:CCP4_phasing_SOLOMON)\n",inpfile); return; } if(!strcmp_case(format, "CIF") || !strcmp_case(format, "PDB")){ write_cif_or_pdb(fout, inpfile, format,method); return; } while (fgets(str, sizeof str, fp) != NULL) { upperstr(str); nc=0; if (strstr_space(str, "Reflections with Combined Phase Information")>0){ while (fgets(str, sizeof str, fp) != NULL){ upperstr(str); strcpy(fomlines[nc], str); nc++; ncol = nc; if(nc>=500){ printf("Warning! The log file for SOLOMON may be wrong!!\n"); return; } if(strstr_space(str, "Mean Variation of Information")>0){ nline=nc; break; } } }else if(strstr_space(str,"Overall Figures of Merit")){ n=0; while (fgets(str, sizeof str, fp) != NULL){ if(n++>10 || strstr_case(str, "HEADER INFORMATION") || strstr_case(str,"Title") )break; m=sscanf(str, "%s%d%f",tmp, &nref, &fom); if(m==3){ if(!strcmp_case(tmp, "CENTRIC")){ pdbx_phasing_dm.reflns_centric = nref; pdbx_phasing_dm.fom_centric = fom; }else if(!strcmp_case(tmp, "NON-CENTRIC")){ pdbx_phasing_dm.reflns_acentric = nref; pdbx_phasing_dm.fom_acentric = fom; }else if(!strcmp_case(tmp, "TOTAL")){ pdbx_phasing_dm.reflns = nref; pdbx_phasing_dm.fom = fom; break; } } } }else if(strstr_space(str,"new solvdens:")){ n=sscanf(strstr_case(str, ":") +1 ,"%f", &a); if(n==1)pdbx_phasing_dm.solvent_mean_density = a; }else if(strstr_space(str,"mean density of protein:")){ n=sscanf(strstr_case(str, ":") +1 ,"%f", &a); if(n==1)pdbx_phasing_dm.protein_mean_density = a; }else if(strstr_space(str,"sd of protein:")){ n=sscanf(strstr_case(str, ":") +1 ,"%f", &a); if(n==1)pdbx_phasing_dm.protein_mean_density_esd = a; } } charact='-'; nb1=0; for(i=0; i=NBIN-1){ printf("Warning! The log file for SOLOMON may be wrong!!\n"); return; } } if(strstr(str, "NON-CENTRIC")){ j=i; break; } } nb2=0; for(i=j; i=NBIN-1){ printf("Warning! The log file for SOLOMON may be wrong!!\n"); return; } } } if(fomlines) free_memory_2d(fomlines, ncol); if(nb1==nb2 && nb1>0){ pdbx_phasing_dm_shell.number_bin=nb1; for(i=0; i0){ if(cc_F_tmp>cc_F) { pdbx_phasing_MR.angle_alpha = a1; pdbx_phasing_MR.angle_beta = a2; pdbx_phasing_MR.angle_gamma = a3; pdbx_phasing_MR.fract_x = a4; pdbx_phasing_MR.fract_y = a5; pdbx_phasing_MR.fract_z = a6; cc_I = cc_I_tmp; cc_F = cc_F_tmp; r_fact = r_fact_tmp; if(cc_F>0)pdbx_phasing_MR.correlation_coeff_Fo_to_Fc = cc_F; if(cc_I>0)pdbx_phasing_MR.correlation_coeff_Io_to_Ic = cc_I; if(r_fact>0)pdbx_phasing_MR.R_factor = r_fact; } } break; } } } } }else if(strstr_space(str, "** RIGID BODY FITTING FUNCTION REQUESTED **")){ cc_F=0; r_fact=0; cc_I=0; while (fgets(str, sizeof str, fp) != NULL) { if(strstr_space(str,"Resolution limits are:")){ strcpy(tmp,strstr_case(str,"are:")+4); n=sscanf(tmp,"%f%f", &resL,&resH); if(n==2){ pdbx_phasing_MR.d_res_high_fit = resH; pdbx_phasing_MR.d_res_low_fit = resL; } }else if(strstr_space(str," TABLE Alpha Beta Gamma Tx Ty Tz Corr_F Rfac Corr_I Pkcount")){ while (fgets(str, sizeof str, fp) != NULL) { if (is_space_line(str) ==0) continue; if(pattern5(str, "SOLUTIONF", ".", ".", ".", ".")){ n=sscanf(str,"%*s%d %f%f%f %f%f%f %f%f%f", &m, &a1,&a2,&a3, &a4,&a5,&a6, &cc_F_tmp, &r_fact_tmp, &cc_I_tmp); if(n==10 && m>0){ if(cc_F_tmp>cc_F) { pdbx_phasing_MR.angle_alpha = a1; pdbx_phasing_MR.angle_beta = a2; pdbx_phasing_MR.angle_gamma = a3; pdbx_phasing_MR.fract_x = a4; pdbx_phasing_MR.fract_y = a5; pdbx_phasing_MR.fract_z = a6; cc_I = cc_I_tmp; cc_F = cc_F_tmp; r_fact = r_fact_tmp; if(cc_F>0)pdbx_phasing_MR.correlation_coeff_Fo_to_Fc = cc_F; if(cc_I>0)pdbx_phasing_MR.correlation_coeff_Io_to_Ic = cc_I; if(r_fact>0)pdbx_phasing_MR.R_rigid_body = r_fact; } } break; } } } } } } fclose(fp); } void CCP4_phaser(FILE *fout, char *inpfile,char *format, char *method) /* extract things from Amore */ { char str[512], tmp[512]; int n=0; float a1,a2,a3,resL,resH; FILE *fp; if((fp = fopen(inpfile, "r"))==NULL) { printf("Can not open the file %s(routine:CCP4_amore)\n",inpfile); return; } while (fgets(str, sizeof str, fp) != NULL) { if(strstr_space(str," Resolution:")){ n=sscanf(strstr(str,":")+1,"%f%f", &resH,&resL); if(n==2){ pdbx_phasing_MR.d_res_high_translation = resH; pdbx_phasing_MR.d_res_low_translation = resL; }else if(n==1){ pdbx_phasing_MR.d_res_high_translation = resH; } }else if(pattern5(str,"SOLU 6DIM ", " EULER", ".", ".", "FRAC" )){ get_data_set_id(str, "EULER", "FRAC", tmp); n=sscanf(tmp,"%f%f%f", &a1,&a2,&a3); if(n==3){ pdbx_phasing_MR.angle_alpha = a1; pdbx_phasing_MR.angle_beta = a2; pdbx_phasing_MR.angle_gamma = a3; } get_data_set_id(str, "FRAC","\n", tmp); n=sscanf(tmp,"%f%f%f", &a1,&a2,&a3); if(n==3){ pdbx_phasing_MR.fract_x = a1; pdbx_phasing_MR.fract_y = a2; pdbx_phasing_MR.fract_z = a3; } break; } } fclose(fp); } void CCP4_molrep(FILE *fout, char *inpfile,char *format, char *method) /* extract things from Amore */ { char str[512], tmp[256]; int n=0; float cc_F=0, r_fact=0,cc_F_tmp=0, r_fact_tmp=0,resL=0,resH=0; float a1,a2,a3,a4,a5,a6; FILE *fp; if((fp = fopen(inpfile, "r"))==NULL) open_file_error(inpfile, "CCP4_molrep"); while (fgets(str, sizeof str, fp) != NULL) { if(strstr_space(str,"Sol_--- Rotation function ---")){ while (fgets(str, sizeof str, fp) != NULL) { if(pattern5(str, "Sol_ Resmin,Resmax :" ,"","", "","")){ strcpy(tmp,strstr(str,":")+1); n=sscanf(tmp,"%f%f", &resL,&resH); if(n==2){ pdbx_phasing_MR.d_res_high_rotation = resH ; pdbx_phasing_MR.d_res_low_rotation = resL ; } break; } } }else if(strstr_space(str,"Sol_--- Translation function ---")){ while (fgets(str, sizeof str, fp) != NULL) { if(pattern5(str, "sol_", "Resmin", "Resmax", ":", "")){ strcpy(tmp,strstr(str,":")+1); n=sscanf(tmp,"%f%f", &resL,&resH); if(n==2){ pdbx_phasing_MR.d_res_high_translation = resH; pdbx_phasing_MR.d_res_low_translation = resL; } break; } } }else if(pattern5(str, "sol_", "_Rf_", "_Tf_", "", "") || pattern5(str, "sol_Mon_", "_Rf_", "_Tf_"," ", "") ){ n=sscanf(str,"%*s %f%f%f %f%f%f %f%f", &a1,&a2,&a3, &a4,&a5,&a6, &r_fact_tmp, &cc_F_tmp); if(n==8){ if(cc_F_tmp>cc_F) { cc_F = cc_F_tmp; r_fact = r_fact_tmp; pdbx_phasing_MR.correlation_coeff_Fo_to_Fc = cc_F; pdbx_phasing_MR.R_factor = r_fact; pdbx_phasing_MR.angle_alpha = a1; pdbx_phasing_MR.angle_beta = a2; pdbx_phasing_MR.angle_gamma = a3; pdbx_phasing_MR.fract_x = a4; pdbx_phasing_MR.fract_y = a5; pdbx_phasing_MR.fract_z = a6; } } } } fclose(fp); }