1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235
|
/*
Theseus - maximum likelihood superpositioning of macromolecular structures
Copyright (C) 2004-2015 Douglas L. Theobald
This file is part of THESEUS.
THESEUS is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as
published by the Free Software Foundation, either version 3 of
the License, or (at your option) any later version.
THESEUS is distributed in the hope that it will be useful, but
WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public
License along with THESEUS in the file 'COPYING'. If not, see
<http://www.gnu.org/licenses/>.
-/_|:|_|_\-
*/
#include <stdlib.h>
#include <stdio.h>
#include <string.h>
#include <unistd.h>
#include <gsl/gsl_version.h>
#include "termcol.h"
#include "Error.h"
extern void
ilaver_(int *vers_major, int *vers_minor, int *vers_patch);
static void
Expert1(void)
{
printf("\n");
printf(" Expert options:\n");
printf(" {%s2%s} = Maximum Likelihood \n", tc_GREEN, tc_NC);
printf(" -g hierarchical model for variances \n");
printf(" 0 = none (may not converge) \n");
printf(" {%s1%s} = inverse gamma distribution \n", tc_GREEN, tc_NC);
printf(" -J print very expert options \n");
printf(" -o reference file to superimpose on, \n");
printf(" all rotations are relative to the first model in this file \n");
printf(" -p requested relative precision for convergence {%s1e-7%s} \n", tc_GREEN, tc_NC);
printf(" -t ndf, degrees of freedom for scaled inverse chi2 \n");
printf(" -Z don't orient final superposition along principal axes \n");
printf(" -z n fixed shape parameter for inverse gamma distribution \n");
}
static void
Expert2(void)
{
fputc('\n', stdout);
printf(" Very expert options (i.e. unsupported, caveat emptor):\n");
printf(" -0 don't calculate translations \n");
printf(" -1 don't calculate rotations \n");
printf(" -2 convert Lele file to PDB format \n");
printf(" -3 n:n scale and shape params for inverse gamma for random variances \n");
printf(" -4 n:n:n radius of gyration for Gaussian generated atoms \n");
printf(" -5 TenBerge algorithm for mean \n");
printf(" -6 write Bob Edgar's SSM (structure similarity matrix) \n");
printf(" -B read and write binary coordinate files \n");
printf(" 1 = read a PDB file, write a binary of it and quit \n");
printf(" 2 = read a binary, superimpose, and write a PDB \n");
printf(" 3 = read a PDB file, superimpose, and write a binary \n");
printf(" 4 = read a binary, superimpose, and write a binary \n");
printf(" -c use ML atomic covariance weighting (fit correlations, slower) \n");
printf(" -e embedding algorithm for initializing the average structure \n");
printf(" 0 = none; use randomly chosen model \n");
printf(" -G full 3D coordinate PCA (vector PCA is default) \n");
printf(" -H write 3D coordinate PCA morph files (for use with CNS/XPLOR) \n");
printf(" -j # of landmarks for random coords generation \n");
printf(" -K n number of mixtures for mixture Gaussian \n");
printf(" -N do a \"null run\" -- no superposition \n");
printf(" -O Olve's segID file \n");
printf(" -Q n scale all coordinates by this factor \n");
printf(" -R0 randomly translate and rotate before superpositioning \n");
printf(" -T n number of threads \n");
printf(" -U print logL for each iteration \n");
printf(" -u calculate bias-corrected average structure \n");
printf(" -W wordy/verbose \n");
printf(" -X seed the algorithm with the superposition in the file \n");
printf(" -x no iterations in inner loop (superimposing to average) \n");
printf(" -y don't calculate the average structure \n");
printf(" -Y print extra stats, gyration radii, Durbin-Watson autocorrelation \n");
}
void
Usage(int expert)
{
// int vers_major, vers_minor, vers_patch;
// ilaver_(&vers_major, &vers_minor, &vers_patch);
PrintTheseusPre();
printf(" Usage: \n");
printf(" theseus [options] <pdb files> \n\n");
printf(" Algorithm options: \n");
printf(" -a atoms to include in superposition \n");
printf(" %s0%s = alpha carbons and phosphorous atoms \n", tc_GREEN, tc_NC);
printf(" 1 = backbone \n");
printf(" 2 = all \n");
printf(" 3 = alpha and beta carbons \n");
printf(" 4 = all heavy atoms (all but hydrogens) \n");
printf(" or \n");
printf(" a colon-delimited string specifying the atom-types PDB-style \n");
printf(" e.g., -a ' CA : N ' \n");
printf(" selects the alpha carbons and backone nitrogens \n");
printf(" -f only read the first model of a multi-model PDB file \n");
printf(" -i maximum iterations {%s200%s} \n", tc_GREEN, tc_NC);
printf(" -l superimpose with conventional least squares method \n");
printf(" -s residues to select (e.g. -s15-45:50-55) {%sall%s} \n", tc_GREEN, tc_NC);
printf(" -S residues to exclude (e.g. -S15-45:50-55) {%snone%s} \n", tc_GREEN, tc_NC);
printf(" -%sv%s use ML variance weighting (no correlations) \n", tc_GREEN, tc_NC);
printf("\n Input/output options: \n");
printf(" --amber for reading AMBER8 formatted PDB files \n");
printf(" -A sequence alignment file to use as a guide (CLUSTAL or A2M format) \n");
printf(" -E print expert options \n");
printf(" -F print FASTA files of the sequences in PDB files and quit \n");
printf(" -h help/usage \n");
printf(" -I just calculate statistics for input file (don't superposition) \n");
printf(" -M file that maps sequences in the alignment file to PDB files \n");
printf(" -r root name for output files {%stheseus%s} \n", tc_GREEN, tc_NC);
printf(" -V version \n");
printf("\n Principal components analysis: \n");
printf(" -C use covariance matrix for PCA (correlation matrix is default) \n");
printf(" -P # of principal components to calculate {%s0%s} \n", tc_GREEN, tc_NC);
printf("\n Morphometrics: \n");
printf(" -d calculate scale factors (for morphometrics) \n");
printf(" -q read and write Rohlf TPS morphometric landmark files \n");
if (expert)
Expert1();
if (expert == 2)
Expert2();
printf("\n");
printf(" Citations: \n");
printf(" Douglas L. Theobald and Phillip A. Steindel (2012) \n");
printf(" \"Optimal simultaneous superpositioning of multiple structures with missing\n");
printf(" data.\"\n");
printf(" Bioinformatics 28(15):1972-1979\n");
printf("\n");
printf(" Douglas L. Theobald and Deborah S. Wuttke (2008) \n");
printf(" \"Accurate structural correlations from maximum likelihood superpositions.\"\n");
printf(" PLOS Computational Biology, 4(2):e43\n");
printf("\n");
/* printf(" Douglas L. Theobald and Deborah S. Wuttke (2006) \n");
printf(" \"Empirical Bayes models for regularizing maximum likelihood estimation in\n");
printf(" the matrix Gaussian Procrustes problem.\"\n");
printf(" PNAS 103(49):18521-18527\n");
printf("\n");
printf(" Douglas L. Theobald and Deborah S. Wuttke (2006) \n");
printf(" \"THESEUS: Maximum likelihood superpositioning and analysis of molecular\n");
printf(" structures.\"\n");
printf(" Bioinformatics 22(17):2171-2172\n");
printf("\n"); */
printf(" http://www.theseus3d.org/\n");
printf(" Compiled with GSL version %s\n", GSL_VERSION);
//printf(" Compiled with LAPACK version %d.%d.%d\n", vers_major, vers_minor, vers_patch);
printf("I===-===-===-===-===-===-===-===-===-===-===-===-===-===-===-===-===-===-===-==I\n");
printf(" %s< END THESEUS %s >%s \n\n\n",
tc_RED, VERSION, tc_NC);
fflush(NULL);
}
void
PrintTheseusPre(void)
{
printf("\n\n");
printf(" %s< BEGIN THESEUS %s >%s \n", tc_RED, VERSION, tc_NC);
printf("I===-===-===-===-===-===-===-===-===-===-===-===-===-===-===-===-===-===-===-=I\n");
printf("I %sTHESEUS%s: Maximum likelihood multiple superpositioning I\n", tc_CYAN, tc_NC);
printf("I=-===-===-===-===-===-===-===-===-===-===-===-===-===-===-===-===-===-===-===I\n");
}
void
PrintTheseusTag(void)
{
printf(" Done. \n");
printf("I===-===-===-===-===-===-===-===-===-===-===-===-===-===-===-===-===-===-===-==I\n");
printf(" %s< END THESEUS %s >%s \n\n\n",
tc_RED, VERSION, tc_NC);
fflush(NULL);
}
#if defined(__clang__)
/* Clang/LLVM. ---------------------------------------------- */
#elif defined(__ICC) || defined(__INTEL_COMPILER)
/* Intel ICC/ICPC. ------------------------------------------ */
#elif defined(__GNUC__) || defined(__GNUG__)
/* GNU GCC/G++. --------------------------------------------- */
#elif defined(__HP_cc) || defined(__HP_aCC)
/* Hewlett-Packard C/aC++. ---------------------------------- */
#elif defined(__IBMC__) || defined(__IBMCPP__)
/* IBM XL C/C++. -------------------------------------------- */
#elif defined(_MSC_VER)
/* Microsoft Visual Studio. --------------------------------- */
#elif defined(__PGI)
/* Portland Group PGCC/PGCPP. ------------------------------- */
#elif defined(__SUNPRO_C) || defined(__SUNPRO_CC)
/* Oracle Solaris Studio. ----------------------------------- */
#endif
void
Version(void)
{
printf("\n THESEUS version %s compiled on %s %s\n by user %s with machine \"%s\" \n\n",
VERSION, __DATE__, __TIME__, getenv("USER"), getenv("HOST"));
printf(" Compiled with GSL version %s\n\n", GSL_VERSION);
fflush(NULL);
}
|