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/*
Theseus - maximum likelihood superpositioning of macromolecular structures
Copyright (C) 2004-2014 Douglas L. Theobald
This program 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 2 of the License, or
(at your option) any later version.
This program 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 this program; if not, write to the:
Free Software Foundation, Inc.,
59 Temple Place, Suite 330,
Boston, MA 02111-1307 USA
-/_|:|_|_\-
*/
#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(" Default usage is equivalent to: \n");
printf(" theseus %s-a0 -e2 -g1 -i200 -p1e-7 -v -P0%s your.pdb \n", tc_GREEN, tc_NC);
printf("\n");
printf(" Expert options:\n");
printf(" -e embedding algorithm for initializing the average structure \n");
printf(" 0 = none; use randomly chosen model \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(" -n don't write transformed pdb file \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(" -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(" -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(" For more help see the man page: type 'man theseus' \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(" -c use ML atomic covariance weighting (fit correlations, slower) \n");
printf(" -d calculate scale factors (for morphometrics) \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(" -q read and write Rohlf TPS morphometric landmark 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);
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);
}
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);
}
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