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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
-/_|:|_|_\-
*/
#ifndef COORDS_SEEN
#define COORDS_SEEN
#include <stdio.h>
#include "DLTmath.h"
#include "PDBCds.h"
typedef struct Algorithm Algorithm;
typedef struct Statistics Statistics;
typedef struct StCds StCds;
typedef struct StCdsArray StCdsArray;
typedef struct CdsParams CdsParams;
typedef struct Params Params;
typedef struct Priors Priors;
typedef struct Cds Cds;
typedef struct CdsArray CdsArray;
struct Algorithm
{
char cmdline[1024]; /* copy of the command line */
int argc;
char **argv;
char **infiles; /* an array of the input files listed on the command line */
int filenum; /* number of input files */
char rootname[FILENAME_MAX];
int weight; /* weighting method */
int verbose; /* lots of output */
double precision; /* requested relative precision to converge to */
int iterations; /* max # of iterations allowed for outer loop of MultiPose() */
int rounds; /* running counter of rounds of the outer loop of MultiPose() */
int innerrounds; /* running counter of rounds of the inner loop of MultiPose() */
double milliseconds; /* how long the calculation took */
int write_file; /* flag to write output pdb file, default = 1 = yes */
int atoms; /* flag for atom types to include in superposition, CA, CB, backbone, P, etc. */
char *selection; /* character array holding user input for residues/alignment columns to include */
char *atomslxn; /* character array holding user input for atom types to include */
int revsel; /* reverse the sense of the residues to select in selection above (i.e. exclude them) */
int embedave; /* flag to initialize the algorithm with an embedded average (distance geometry) */
int landmarks; /* # of landmarks (Dryden files) */
int writestats; /* flag to write out stat files */
int FragDist;
int random;
int pca; /* flag to do Principal Components Analysis on covariance matrix */
int fullpca;
int cormat; /* flag to do PCA with correlation matrix instead of covariance matrix */
int tenberge;
int morph;
int stats; /* calculate moment stats */
double constant; /* minimum variance allowed */
int info; /* just calculate stats for given pdb file and quit */
int princaxes; /* flag to align final superposition with principle axes of mean structure */
int nullrun;
int binary; /* flag to read and write binary structure files */
int mbias; /* flag to calculate bias-corrected mean */
int domp; /* don't initialize Bayes w/MultiPose ML */
int doave; /* don't calculate an average structure */
int dotrans;
int dorot;
int dohierarch;
int docovars;
int alignment; /* flag for superimposing based on a sequence alignment */
int covweight; /* flag to do atomic, row-wise covariance matrix weighting */
int varweight; /* flag to do variance weighing (i.e., a diagonal covariance matrix) */
int leastsquares; /* flag to do classical least squares, all variances equal, no covars */
int hierarch; /* flag to use hierarchical variances, e.g. inverse gamma distributed vars */
int fmodel; /* read only first or all models in a pdb file */
int noinnerloop; /* don't iterate the inner loop */
int fasta; /* flag to write out FASTA sequence files for each PDB model read in */
int olve; /* Olve Peersen's pet requests */
int abort;
int seed; /* random number seed, can be specified by user */
int mixture;
int threads; /* flag to run with pthreads */
double minc;
int printlogL;
int bfact;
int convlele; /* flag to convert Lele's formatted files */
double param[2]; /* Random generation of structures, params for inverse gamma */
double radii[3]; /* Random generation of structures, radii of gyration for generating mean forms */
int ssm;
int bayes;
int ipmat;
int missing;
int scale; /* calculate scale factors for each structure */
int instfile; /* print out PDB files in each internal round of the MultiPose algorithm */
int pu; /* for testing Pu's QCP rotation method */
int amber; /* switch for special treatment of AMBER8 PDB formatted files */
int atom_names;
double scalefactor; /* value to scale all structures by */
int morphfile; /* flag to read and write morphometric .tps files */
int scaleanchor; /* model index for relative scaling -- scale of this model = 1 */
int randgibbs; /* Randomly initialize GibbsMet */
double covnu;
};
struct Statistics
{
double stddev; /* combined standard deviation of all atomic positions */
double var;
double phi;
double alpha;
double starting_paRMSD, starting_pawRMSD; /* stats for initial superposition */
double starting_mlRMSD;
double starting_stddev, starting_logL;
double ave_paRMSD; /* average pairwise RMSD */
double ave_pawRMSD; /* average weighted pairwise RMSD */
double RMSD_from_mean; /* average RMSD from the mean structure */
double mlRMSD; /* max lik RMSD, actually a sigma */
double logL, mlogL, AIC, BIC, nparams, ndata, chi2; /* likelihood stats */
double skewness[4]; /* for x, y, z residuals and total */
double kurtosis[4];
double SES, SEK;
int median; /* index of structure closest to mean */
double wtnorm; /* normalization factor for atomic row-wise weight matrix */
double hierarch_p1, hierarch_p2; /* parameters of the hierarchical variance PDF */
double hierarch_chi2;/* chi^2 value for fit of hierarchical variances */
double hierarch_chi2_P; /* P-value */
double omnibus_chi2; /* overall chi^2, including hierarchical and overall fit */
double omnibus_chi2_P; /* P-value */
double precision; /* actual precision to which the algorithm converged */
};
/* StCds is for holding static working sets of coordinates */
struct StCds
{
int model; /* model number, not really used */
int vlen; /* number of coordinates */
int aalen; /* number of real residues, no gaps, used for CA alignments */
double *x, *y, *z; /* x,y,z atomic coordinates */
double *o; /* occupancy */
double *b; /* B-factor */
/* not to be accessed - for space only */
char *resName_space;
};
struct StCdsArray
{
int vlen; /* number of coordinates */
int cnum; /* number of Cds in array */
Cds **cds; /* pointer to an array of pointers to Cds */
Cds *avecds; /* average Cds of all in CdsArray */
double *evals;
double *samplevar3N; /* atomic sample variances */
double **CovMat; /* the atomic, row-wise covariance matrix */
};
struct CdsParams
{
int vlen; /* number of coordinates */
double *prvar; /* prior variances */
double *residual_x, *residual_y, *residual_z;
double *covx, *covy, *covz; /* covariance matrix weighted x,y,z cds */
double **matrix; /* 3x3 rotation matrix */
double **last_matrix; /* temp 3x3 rotation matrix */
double **last_outer_matrix; /* temp 3x3 rotation matrix */
double radgyr; /* radius of gyration */
double **innerprod; /* vlen x vlen inner product matrix */
double **innerprod2; /* 3 x 3 inner product matrix */
double center[3]; /* weighted centroid of coordinates */
double last_center[3]; /* temp centroid of coordinates */
double translation[3]; /* translation vector, based on weighted center */
double RMSD_from_mean; /* rmsd from the mean structure */
double wRMSD_from_mean; /* weighted rmsd from mean structure */
double ref_wRMSD_from_mean;
double evals[4]; /* quaternion evals (residual sums) */
double **evecs; /* 4x4 quaternion evecs (rotation vectors) */
};
struct Params
{
int vlen; /* number of coordinates */
int cnum; /* number of Cds in array */
CdsParams **cdsp; /* array of coords parameters */
Cds *avecds; /* average Cds of all in CdsArray */
Cds *tcds; /* target Cds */
double *w; /* diagonal atomic weights */
double *var; /* atomic variance estimates */
double *evals;
double *samplevar3N; /* atomic sample variances */
int *df; /* degrees of freedom for variances, for incomplete data alignments */
double *S2; /* theoretical NMR order parameters */
double *residuals; /* 3 x vlen x cnum vector of normalized residuals */
double **Var_matrix; /* the variances of the distances in distmat */
double **Dij_matrix; /* average distance distance matrix for the CdsArray */
Matrix3D *distmat;
double **CovMat; /* the atomic, row-wise covariance matrix */
double **WtMat; /* inverse of the CovMat */
double **FullCovMat;
double **pcamat; /* vlen x vlen sized matrix for PC eigenvectors */
double *pcavals; /* PCA eigenvalues */
};
struct Priors
{
int vlen; /* number of coordinates */
int cnum; /* number of Cds in array */
double alpha;
Cds *meancds; /* mean Cds of all in CdsArray */
double *prvar;
double *prevals;
double **PrCovMat; /* the atomic, row-wise covariance matrix */
double **PrInvCovMat; /* inverse of the PrCovMat */
};
/* Cds is for holding working sets of coordinates */
struct Cds
{
char filename[FILENAME_MAX];
int model; /* model number, not really used */
int vlen; /* number of coordinates */
int aalen; /* number of real residues, no gaps, used for CA alignments */
char **resName; /* residue name */
char *chainID; /* chain ID */
int *resSeq; /* residue number */
double **wc; /* 3 x K matrix matrix of working coordinates, aliased to x,y,z below */
double *x, *y, *z; /* x,y,z atomic coordinates */
double *o; /* occupancy */
double *b; /* B-factor */
int *nu, *mu; /* binary flag vectors for present and missing data, respectively */
double **sc; /* 3 x K matrix matrix of static coordinates, aliased to sx,sy,sz below */
double *sx, *sy, *sz; /* x,y,z atomic coordinates */
double *so; /* occupancy */
double *sb; /* B-factor */
double **cc; /* inv covariance weighted coordinates */
double *covx, *covy, *covz; /* inv covariance matrix weighted x,y,z cds */
double *prvar; /* prior variances */
double *residual_x, *residual_y, *residual_z;
double **matrix; /* 3x3 rotation matrix */
double **last_matrix; /* temp 3x3 rotation matrix */
double **last_outer_matrix; /* temp 3x3 rotation matrix */
double radgyr; /* radius of gyration */
double **outerprod; /* vlen x vlen outer product matrix */
double **innerprod; /* 3 x 3 inner product matrix */
double center[3]; /* weighted centroid of coordinates */
double last_center[3]; /* temp centroid of coordinates */
double translation[3]; /* translation vector, based on weighted center */
double RMSD_from_mean; /* rmsd from the mean structure */
double wRMSD_from_mean; /* weighted rmsd from mean structure */
double evals[4]; /* quaternion evals (residual sums) */
double **evecs; /* 4x4 quaternion evecs (rotation vectors) */
double bfact_c;
double scale;
/* not to be accessed - for space only */
char *resName_space;
};
/* CdsArray is an array of Cds, plus a bunch of stuff necessary to
do the ML superposition for this family of Cds.
*/
struct CdsArray
{
struct PDBCdsArray *pdbA; /* associated PDBCdsArray */
struct CdsArray *scratchA; /* associated scratch array of Cds */
char outfile_name[FILENAME_MAX];
int vlen; /* number of coordinates */
int cnum; /* number of Cds in array */
char *anchorf_name;
char *mapfile_name;
char *msafile_name;
Cds **cds; /* pointer to an array of pointers to Cds */
Cds *avecds; /* average Cds of all in CdsArray */
double **ac; /* average coords matrix */
Cds *tcds; /* target Cds */
double **tc;
double *w; /* diagonal atomic weights */
double *var; /* atomic variance estimates */
double *evals;
double *samplevar3N; /* atomic sample variances */
int *df; /* degrees of freedom for variances, used for incomplete data alignments */
double *S2; /* theoretical NMR order parameters */
double *residuals; /* 3 x vlen x cnum vector of normalized residuals */
double **Var_matrix; /* the variances of the distances in distmat */
double **Dij_matrix; /* average distance distance matrix for the CdsArray */
Matrix3D *distmat;
double **CovMat; /* the atomic, row-wise covariance matrix */
double **WtMat; /* normalized inverse of the CovMat */
double **FullCovMat;
double **pcamat; /* vlen x vlen sized matrix for principle component eigenvectors */
double *pcavals; /* PCA eigenvalues */
double **tmpmatKK1; /* must be careful that these aren't accesses by subroutines */
double **tmpmatKK2;
double **tmpmat3a, **tmpmat3b, **tmpmat3c, **tmpmat3d; /* 3x3 scratch matrices */
double *tmpvecK;
double *tmpvec3a;
};
/* global declarations (necessary for leave(), I think) */
extern CdsArray *baseA; /* main array of selected pdb cds, never modified */
extern PDBCdsArray *pdbA; /* array holding all of the pdb file coordinate info,
much of it unused in the actual calculations */
extern Algorithm *algo;
extern Statistics *stats;
#endif
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