/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *\ * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * ** ** ** ** ** ** ** ** ** ** ** ********* ** ** ** ********** ********** *** *** ** ** ** ********** ** **** **** ** ********** ** ** ** ** ** ** ** ** ** ********** ** ** ** ******** ** ** ** ** ** ** ** ** ****** ******** ** ** ** ** ** ** ** ****** *** ** ** ** ************** ** ** ** *** ** ********** ** ************** ** ** ** *** ***************** ******** ** ** ** *********** ********* ** ********* ** ** ** *********** ** ** ** *** ** ********** ** ** ** ** ** ****** ** ** ********** ** ** ** ** ** ****** ******** ** ** ** * ** ** ********* ** ** ** * ** ** ** ** ** ** ** *** ********** ** ** ** ** ** *** ********** ********** ** ** ********* ** ** ** ** ** ** E N S E M B L E T O O L S ** ** ** ** Version 2.1 ** ** ** ** ** ** Principal Investigator: Julie D. Forman-Kay ** ** ** ** Author: Mickaël Krzeminski ** ** ** ** Date: November 2012 ** ** ** ** ** ************************************************************************************* ** ** ** ** ** Copyright (C) The Hospital for Sick Children, 2001 ** ** ** ** Distribution of substantively modified versions of this module is prohibited ** ** without the explicit permission of the copyright holder. ** ** ** ** Any use of this work or derivative works in whole or in part for any ** ** commercial purpose or for monetary gain is prohibited. ** ** ** ** ** ** NO WARRANTY ** ** This software package is provided 'as is' without warranty of any kind, ** ** expressed or implied. ** ** ** ** ** * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * \* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ #ifndef __USAGE_HEADER__ #define __USAGE_HEADER__ enum toolsPrograms { __GET_INFO__, __MAKE_CSP__, __EXTRACT_CSP__, __COMBINE_CSP__, __COMBINE_CDP__, __PDB2SEQ__, __RG__, __SS_DISTR__, __CONTACT_MAP__, __CACA_VSIJ__, __SURFACE__, __R2__, __READ_ENS__, __READ_BEST__, __PDB2TRADES__, __ANALYZE__ }; void Usage(enum toolsPrograms TP, char *prog) { char usage[1000] = "\nUsage:\n\t"; strcpy(&usage[9], prog); counter seek = strlen(usage); switch (TP) { case __GET_INFO__: strcpy(&usage[seek], " ENSEMBLE_FILE [ENSEMBLE_FILE...]\n\n\ The program provides information about files that have been generated by ENSEMBLE.\n\ ENSEMBLE_FILE corresponds to one of these files. You can specify as many files as you want."); break; //=================================================================================================================== case __MAKE_CSP__: strcpy(&usage[seek], " -f list_file [-o output.csp] [-h]\n\n\ Where: * list_file is the file that contains the list of all structural files,\n\ * output.csp is the concatenated structural file.\n\n\ The list_file file can be made of the absolute or relative pathway of the structural file, one per line, as following:\n\ /home/user_x/Project_Y/Structures_A/conf_18.pdb\n\ /home/user_x/Project_Y/Structures_B/conf_2.ent\n\ ...\n\n\ * The -h flag displays this help."); break; //=================================================================================================================== case __EXTRACT_CSP__: strcpy(&usage[seek], " -f CSP_file [-p pathway] [-x prefix] [-s start] [-l 1 [2 3 8-10]]\n\n\ Where: -f specifies the input CSP file,\n\ -p specifies the pathway where the files will be extracted. If not specified, files are extracted in the current directory,\n\ -x specifies the prefix used before the conformer number of the filename (Default is conf_),\n\ -s specifies the starting conformer number (Default is 1),\n\ -l specifies the list of conformers to extract. Of note: a CSP file does ALWAYS start from conformer 1."); break; //=================================================================================================================== case __COMBINE_CSP__: strcpy(&usage[seek], " -o CSP_file CSP_file_1 [CSP_file_2] [CSP_file_3] [...]\n\n\ Where: -o specifies the output CSP file name,\n\ CSP_file_1, CSP_FILE_2... are the absolute or relative pathways of CSP files to combine.\n\ Note that the order CSP files are specified is important."); break; //=================================================================================================================== case __COMBINE_CDP__: strcpy(&usage[seek], " -o CDP_file CDP_file_1 [CDP_file_2] [CDP_file_3] [...]\n\n\ Where: -o specifies the output CDP file name,\n\ CDP_file_1, CDP_FILE_2... are the absolute or relative pathways of CDP files to combine.\n\ Note that the order CDP files are specified is important."); break; //=================================================================================================================== case __PDB2SEQ__: strcpy(&usage[seek], " PDB_file\n\n\ The program displays the one-letter sequence and puts X when the amino acid does not belong to the twenty common ones."); break; //=================================================================================================================== case __PDB2TRADES__: strcpy(&usage[seek], "-o output_file [-t] PDB_file1 [PDB_file2][PDB_file3]\n\n\ The program reorganized the atoms of a PDB file so that it foolows the output of a structure generated by TraDES.\n\ The PDB_files can be PDB or CSP files.\n\ If the -t flag is omitted, then the output_file will serve as a prefix for all the PDB files. Otherwise, it is used \ as the name of the CSP that contains all specified files."); break; //=================================================================================================================== case __RG__: strcpy(&usage[seek], " list_file [-v]\n\ Where list_file contains the pathway of all PDB structural files and\n\ the -v flag corresponds to the verbose mode."); break; //=================================================================================================================== case __SS_DISTR__: strcpy(&usage[seek], " -f (list|ensemble|PDB)_file [-o output_file]\n\ Where (list|ensemble|PDB)_file is an list, ENSEMBLE or PDB file,\n\ output_file is an optional name in which results will be stored.\n\ If output_file is not specified, then results will be displayed on the screen."); break; //=================================================================================================================== case __READ_ENS__: strcpy(&usage[seek], " ens_file\n\ Where ens_file is an ENSEMBLE file type."); break; //=================================================================================================================== case __READ_BEST__: strcpy(&usage[seek], " best_file\n\ Where best_file is a Best file which has been generated by ENSEMBLE. Such a Best file contains\n\ a set of ensembles that historitically better and better fit experimental data along ENSEMBLE runs."); break; //=================================================================================================================== case __CONTACT_MAP__: strcpy(&usage[seek], " -f list_file [-h] [-o output_file] [-eps output.eps] [-ld float] [-ud float] [-colld r g b] [-colud r g b]\n\n\ Where:\n\ * -f flag specifies the list_file, which is a CSP file or a file that contains the list of all structural conformers,\n\ * -o flag specifies the output text file taht contains all Ca-Ca distances,\n\ * -eps flag specifies the EPS output file, which is the Encapsulated PostScript file displaying a 2D graphs of Ca-Ca distances,\n\ * -h flag displays this screen,\n\ * -ld flag specifies the lower distance below which the Ca-Ca distance will be displayed with the same color (default: 3.5 A),\n\ * -ud flag specifies the upper distance above which the Ca-Ca distance will be displayed with the same color (default: 10 A), \n\ * -sd flag specifies the upper standard deviation above which the Ca-Ca distance will be displayed with the same color (default: 5 A), \n\ The lowest standard deviation is always 0 A.\n\ * -colld flag specifies the RGB color of the lower distance (default: 0. 0. 0. (black)),\n\ * -colud flag specifies the color of the lower distance (default: 1. 1. 1. (white)),\n\n\ The distance between Ca-Ca atoms is displayed in the EPS file using a linear gradual color between colld and colud. Note that colld and colud flags require three values (red, green and blue intensities) which range between 0. and 1."); break; //=================================================================================================================== case __CACA_VSIJ__: strcpy(&usage[seek], " -f list_file [-h] [-o output.eps]\n\n\ Where:\n\ * -f flag specifies the list_file, which is a CSP file or a file that contains the list of all structural conformers,\n\ * -o flag specifies the EPS output file, which is the Encapsulated PostScript file displaying a 2D graphs of Ca-Ca distances,\n\ * -h flag displays this screen,\n\n\ The program computes the average Ca-Ca distance between all atom pairs versus the number of residues that separates these atoms in the sequence."); break; //=================================================================================================================== case __SURFACE__: strcpy(&usage[seek], " -f pdb_file [-h] [-o output.sfc] [-mode] [-rh2o] [-accuracy] [-radius] [-ff forcefield]\n\n\ Where:\n\ * -f flag specifies the pdb file,\n\ * -o flag specifies the output file,\n\ * -mode flag specifies the mode:\n\ |- access (default)\n\ |- contact\n\ * -rh2o flag specifies the radius of the water molecule probe in Angstroms,\n\ * -accuracy flag specifies the accuracy of calculations,\n\ * -radius flag specifies the type of radius to use for atoms:\n\ |- sigma (default)\n\ |- vdw\n\ * -ff flag specifies the forcefield used:\n\ |- Contact\n\ |- PROLSQ\n\ |- PARMALLH6\n\ |- OPLSX (Default)\n\ |- PARAM19\n\ * -h flag displays this screen,\n\n\ The program computes the accessible surface for all atoms in the pdb file."); break; //=================================================================================================================== case __R2__: strcpy(&usage[seek], " -f pdb_file [-h] [-o output.r2]\n\n\ Where:\n\ * -f flag specifies the pdb file,\n\ * -o flag specifies the output file in text format,\n\ * -h flag displays this screen,\n\n\ The program computes the number of neighbours for the provided atoms."); break; //=================================================================================================================== case __ANALYZE__: strcpy(&usage[seek], " ens_file\n\ Where ens_file is a ENSEMBLE file type."); break; } //=================================================================================================================== printf ("%s", usage); LSEP exit(0); } #endif