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/* name: autobondrot.c */
/* author: J. Michael Word */
/* date written: 7/ 9/99 */
/* purpose: manipulations of moving atoms */
/*****************************************************************/
/* NOTICE: This is free software and the source code is freely */
/* available. You are free to redistribute or modify under the */
/* conditions that (1) this notice is not removed or modified */
/* in any way and (2) any modified versions of the program are */
/* also available for free. */
/* ** Absolutely no Warranty ** */
/* Copyright (C) 1999 J. Michael Word */
/*****************************************************************/
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include "utility.h"
#include "autobondrot.h"
#include "readPDBrecs.h"
/*describeXformDB() writes header-comments to the .map file! */
void describeXformDB(FILE *outf, xformDatabase* xdb, char *cch);
void fillinTransformationRec(transformData* xform, char* rec);
xformDatabase* initXformDB();
transformData* newTransformation(char* rec);
transformData* deleteTransformation(transformData* xform,
abrAtomListProc delAtomProc, void *otherstuff);
void appendTransformation(xformDatabase* xdb, transformData* xform);
void appendAtomRec(transformData* xform, char* rec, abrMkAtomProc mkAtom, void *atomstuff);
xformAtomRecords * newXformAtomRecord(char *rec, abrMkAtomProc mkAtom, void *otherstuff);
xformAtomRecords* deleteXformAtomRecord(xformAtomRecords *xr,
abrAtomListProc delAtomProc, void *deletestuff);
void indexLevels(xformDatabase* xdb);
void buildXDBsortedAtomRecs(xformDatabase* xdb);
void rebuildTmat(transformData* xform);
atom* orientedAtoms(xformDatabase* xdb);
void setOrientation(xformDatabase* xdb, goToRec* g);
void cleanupListExtras(atom *alst, xformDatabase* xdb,
abrAtomListProc delAtomProc, void *deletestuff);
void initializeXFStack(xformDatabase* xdb);
int pushXFStack(xformDatabase* xdb, matrix4* ctm);
void popXFStack(xformDatabase* xdb);
matrix4* topXFStack(xformDatabase* xdb);
double runnameAndTorsion(xformDatabase* xdb, char* buf, int max);
void addGoToRecord(xformDatabase* xdb, char *rec);
void XFdescribeAtomList(FILE *outf, atom* a);
void appendBiasFunction(transformData* xform, char *rec);
int compareXDBAtomRecs(const void *a, const void *b);
void scanXDBinputText(xformDatabase* xdb, FILE *inf, FILE *outf,
abrMkAtomProc mkAtom, void *atomstuff, char *cch);
void doListCleanupProcessing(xformDatabase* xdb, abrAtomListProc inputListProc, void *liststuff);
#define MAX_XF_REC_LEN 300
static char XFworkBuf[MAX_XF_REC_LEN + 1];
/*e.g. angle values held in XFworkBuf for output to .map file*/
/* read in records and interpret them to fillout a database */
xformDatabase* readTransformationDatabase(FILE *inf, FILE *outf,
abrMkAtomProc mkAtom, void *atomstuff,
abrAtomListProc inputListProc, void *liststuff,
char *cch)
{
/*
mabis.inf == FILE *inf
outf == FILE *outf
newMovingAtom == abrMkAtomProc mkAtom
&mabis == void *atomstuff
movingAtomListProcessing == abrAtomListProc inputListProc
NULL == void *liststuff
RAW_HEADER_COMMENT == char *cch
*/
xformDatabase* xdb = NULL;
xdb = initXformDB();
if (xdb)
{
scanXDBinputText(xdb, inf, outf, mkAtom, atomstuff, cch);
indexLevels(xdb);
buildXDBsortedAtomRecs(xdb);
doListCleanupProcessing(xdb, inputListProc, liststuff);
/*describeXformDB() writes header-comments to the .map file! */
describeXformDB(outf, xdb, cch);
}
return xdb;
}
void scanXDBinputText(xformDatabase* xdb, FILE *inf, FILE *outf,
abrMkAtomProc mkAtom, void *atomstuff, char *cch) {
transformData* xform = NULL;
char *s = NULL;
char saynull[] = "NULL:identity transformation:";
while(readRecord(inf, XFworkBuf, MAX_XF_REC_LEN) >= 0) {
if (isAtom(XFworkBuf) || isHet(XFworkBuf)) {
if (! xform) { /* make someplace to hang these atoms */
xform = newTransformation(saynull);
appendTransformation(xdb, xform);
}
if (! xform) {
errmsg("could not create Identity transformation - Atom skipped");
}
else if (isPseudoAtom(XFworkBuf)) { /* ignore pseudo atoms */ }
else {
appendAtomRec(xform, XFworkBuf, mkAtom, atomstuff);
}
}
else {
s = XFworkBuf + strspn(XFworkBuf, " \t\n\r");
if (!strncasecmp(s, "BONDROT",7)
|| !strncasecmp(s, "ROT", 3)
|| !strncasecmp(s, "TRANS",5)
|| !strncasecmp(s, "SAVE", 4) || (s[0] == '(')
|| !strncasecmp(s, "RESTORE",7) || (s[0] == ')') ) {
xform = newTransformation(s);
appendTransformation(xdb, xform);
}
else if (!strncasecmp(s, "GO", 2)) {
addGoToRecord(xdb, s);
}
else if (!strncasecmp(s, "COS", 3)
|| !strncasecmp(s, "POLY", 4)
|| !strncasecmp(s, "CONST", 5) ) {
if (xform) {
appendBiasFunction(xform, s);
}
else {
warn("no transformation to attach bias function:");
warn(s);
}
}
else if (s[0] == '#' || s[0] == '\0') {
/* comments are ok - we do nothing */
}
else if (s[0] == '@') { /* include file */
FILE *if2 = NULL;
if2 = fopen(s+1, "r");
if (if2) { /* recursive call */
fprintf(outf, "%s%s\n", cch, s);
scanXDBinputText(xdb, if2, outf, mkAtom, atomstuff, cch);
fclose(if2);
}
else {
warn("could not open include file:");
warn(s+1);
}
}
else {
warn("unknown record type:");
warn(s);
}
}
}
}
void discardXformDB(xformDatabase* xdb,
abrAtomListProc delAtomProc, void *deletestuff) {
int i = 0;
transformData *p = NULL, *next = NULL;
goToRec *g = NULL, *nextg = NULL;
if (xdb) {
for(p = xdb->xforms; p; p = next) {
next = p->next;
deleteTransformation(p, delAtomProc, deletestuff);
}
xdb->xforms = NULL;
xdb->last = NULL;
for(i = 0; i < MAX_XFORM_LEVELS; i++) {
xdb->level[i] = NULL;
}
xdb->nlevs = 0;
xdb->nstack = 0;
free(xdb->ctmstack[0]); /* all stack elements allocated in a block */
for(g = xdb->golist; g; g = nextg) {
nextg = g->next;
free(g);
}
if (xdb->sortedByRes) { free(xdb->sortedByRes); }
xdb->sortedByRes = NULL;
free(xdb);
}
}
void autobondrot(FILE *outf, xformDatabase* xdb,
abrProbeProc probeProc, void *probestuff,
abrAtomListProc delAtomProc, void *deletestuff,
int dumpGoToAtoms)
{/*autobondrot()*/
/*where: (see probe/autobondrot(...); )
outf == stderr
xdb == xdb
probeProc == movingDoCommand
probestuff == mcis
delAtomProc == deleteMovingAtom
deletestuff == mabis
dumpGoToAtoms == Verbose
*/
int overflow = FALSE, cursor = 0;
transformData* xform = NULL;
goToRec* g = NULL;
atom* alst = NULL;
double torsionScore = 0.0;
if (xdb)
{
if (xdb->golist) /*working from a list of GO statements */
{/*if using GO statements: specific orientations requested */
for(g = xdb->golist; g; g = g->next)
{
setOrientation(xdb, g);
alst = orientedAtoms(xdb); /* atom* alst == atom *allMovingAtoms */
torsionScore = runnameAndTorsion(xdb, XFworkBuf, MAX_XF_REC_LEN);
/*torsionScore is NOT a score, holds angle-bias to modify score*/
if (dumpGoToAtoms)
{
fprintf(outf, "REMARK Atoms Rotated To %s\n", XFworkBuf);
XFdescribeAtomList(outf, alst);
}
probeProc(XFworkBuf, torsionScore, alst, probestuff);
/* process the oriented atoms */
/*probeProc == movingDoCommand() which calls doCommand()*/
/*where: (see probe.c/movingDoCommand() )
XFworkBuf == char* orientationName holds angle values
torsionScore == double scoreBias
alst == atom *allMovingAtoms existance implies autobondrot
probestuff == void *userdata == mcis
*/
cleanupListExtras(alst, xdb, delAtomProc, deletestuff);
}
return; /* can quit when we are done with the 'go to's */
}/*if using GO statements: specific orientations requested */
/*else: working from intermixed atoms and transformations */
/* initialize transformation values */
for(cursor=0; cursor < xdb->nlevs; cursor++) {
xform = xdb->level[cursor];
xform->currVal = xform->startVal;
rebuildTmat(xform);
}
#define ABR_COMP_EPSILON 0.00001
overflow = FALSE;
cursor = xdb->nlevs - 1;
while(cursor >= 0)
{
while(! overflow)
{
alst = orientedAtoms(xdb); /* atom* alst == atom *allMovingAtoms */
torsionScore = runnameAndTorsion(xdb, XFworkBuf, MAX_XF_REC_LEN);
/*torsionScore is NOT a score, holds angle-bias to modify score*/
probeProc(XFworkBuf, torsionScore, alst, probestuff);
/* process the oriented atoms */
/*probeProc == movingDoCommand() which calls doCommand()*/
/*where: (see probe.c/movingDoCommand() )
XFworkBuf == char* orientationName holds angle values
torsionScore == double scoreBias
alst == atom *allMovingAtoms existance implies autobondrot
probestuff == void *userdata == mcis
*/
cleanupListExtras(alst, xdb, delAtomProc, deletestuff);
cursor = xdb->nlevs - 1;
xform = xdb->level[cursor];
xform->currVal += xform->stepVal;
rebuildTmat(xform);
overflow = (xform->stepVal > 0)
? (xform->currVal > (xform->endVal + ABR_COMP_EPSILON))
: (xform->currVal < (xform->endVal - ABR_COMP_EPSILON));
}
xform = xdb->level[cursor];
xform->currVal = xform->startVal;
rebuildTmat(xform);
overflow = FALSE;
if (--cursor >= 0)
{
xform = xdb->level[cursor];
xform->currVal += xform->stepVal;
rebuildTmat(xform);
overflow = (xform->stepVal > 0)
? (xform->currVal > (xform->endVal + ABR_COMP_EPSILON))
: (xform->currVal < (xform->endVal - ABR_COMP_EPSILON));
}
}
}
}/*autobondrot()*/
/*describeXformDB() writes header-comments to the .map file! */
void describeXformDB(FILE *outf, xformDatabase* xdb, char *cch)
{
int n = 0, slev = 0;
transformData *p = NULL;
xformAtomRecords *xa = NULL;
biasFunction *f = NULL;
goToRec *g = NULL;
if (cch == NULL) { cch = "#"; }
if (xdb)
{/*xdb exists, write comments to .map file*/
slev = 0;
fprintf(outf, "%sAUTOBONDROT with %d variables\n", cch, xdb->nlevs);
for(p = xdb->xforms; p; p = p->next) {
if (p->type == NULLxform) {
#ifdef DUMP_EXTRA_XDB_DESCR
fprintf(outf, "%sNULL transformation\n", cch);
#else
fprintf(outf, "%s\n", cch);
#endif
}
else if (p->type == ROTxform || p->type == TRANSxform) {
if (p->type == ROTxform) {
fprintf(outf, "%sROT ", cch);
}
else if (p->type == TRANSxform) {
fprintf(outf, "%sTRANS ", cch);
}
fprintf(outf, "%s ", ((p->name)?(p->name):""));
#ifdef DUMP_EXTRA_XDB_DESCR
fprintf(outf, "orig %g scan from %g to %g by %g (curr %g)\n",
p->phase, p->startVal, p->endVal,
p->stepVal, p->currVal);
#else
fprintf(outf, "orig %g scan from %g to %g by %g\n",
p->phase, p->startVal, p->endVal,
p->stepVal);
#endif
fprintf(outf, "%s AXIS(%g, %g, %g -> %g, %g, %g)\n", cch,
p->a1.x, p->a1.y, p->a1.z,
p->a2.x, p->a2.y, p->a2.z);
#ifdef DUMP_EXTRA_XDB_DESCR
fprintf(outf, "%s %12g %12g %12g %12g\n", cch,
p->tmat.element[0][0],
p->tmat.element[0][1],
p->tmat.element[0][2],
p->tmat.element[0][3]);
fprintf(outf, "%s %12g %12g %12g %12g\n", cch,
p->tmat.element[1][0],
p->tmat.element[1][1],
p->tmat.element[1][2],
p->tmat.element[1][3]);
fprintf(outf, "%s %12g %12g %12g %12g\n", cch,
p->tmat.element[2][0],
p->tmat.element[2][1],
p->tmat.element[2][2],
p->tmat.element[2][3]);
fprintf(outf, "%s %12g %12g %12g %12g\n", cch,
p->tmat.element[3][0],
p->tmat.element[3][1],
p->tmat.element[3][2],
p->tmat.element[3][3]);
#endif
}
else if (p->type == SAVExform) {
fprintf(outf, "%sSAVE transformation (level %d)\n", cch, ++slev);
}
else if (p->type == RESTORExform) {
fprintf(outf, "%sRESTORE transformation (level %d)\n", cch, slev);
if (slev > 0) { slev--; }
}
else {
fprintf(outf, "%sUNKNOWN transformation (type %d)\n", cch, p->type);
}
for(f = p->funcs; f; f = f->next) {
if (f->type == CONSTbiasfunc) {
fprintf(outf, "%s CONST bias function %g\n", cch, f->v);
}
else if (f->type == POLYbiasfunc) {
fprintf(outf, "%s POLYNOMIAL bias function %g*(x - %g)^%g\n", cch,
f->v, f->ph, f->freq);
}
else if (f->type == COSbiasfunc) {
fprintf(outf, "%s COSINE bias function %g*(%g - cos(%g*(x - %g)))/2\n", cch,
f->v, f->shift, f->freq, f->ph);
}
else {
fprintf(outf, "%s UNKNOWN bias function type: %d\n", cch, f->type);
}
}
for(xa = p->recs; xa; xa = xa->next) {
fprintf(outf, "%s %4.4s%c%3.3s%2s%4d%c %8.3f%8.3f%8.3f%6.2f%6.2f %s\n", cch,
xa->a->atomname, xa->a->altConf,
xa->a->r->resname, xa->a->r->chain,
xa->a->r->resid, xa->a->r->resInsCode,
xa->loc.x, xa->loc.y, xa->loc.z,
xa->a->occ, xa->a->bval, xa->a->r->segid);
}
}
#ifdef DUMP_EXTRA_XDB_DESCR
for(i = 0; i < MAX_XFORM_LEVELS; i++) {
if (xdb->level[i]) {
fprintf(outf, "%sLevel%d (%s %d)\n", cch, i,
((xdb->level[i]->name)?(xdb->level[i]->name):""),
xdb->level[i]->num);
}
}
#endif
n = 0;
for(g = xdb->golist; g; g = g->next) {
++n;
#ifdef DUMP_EXTRA_XDB_DESCR
fprintf(outf, "%sGO %d", cch, n);
for(i = 0; i < xdb->nlevs; i++) {
fprintf(outf, ": %g ", g->level[i]);
}
fprintf(outf, "\n");
#endif
}
fprintf(outf, "%sread %d GO statements\n", cch, n);
}/*xdb exists, write comments to .map file*/
else
{
fprintf(outf, "NULL xformDatabase\n");
}
}
void XFdescribeAtomList(FILE *outf, atom* a) {
int i = 0;
for(; a; a = a->next) {
fprintf(outf, "ATOM %4d %4.4s%c%3.3s%2s%4d%c %8.3f%8.3f%8.3f%6.2f%6.2f auto\n",
++i, a->atomname, a->altConf,
a->r->resname, a->r->chain,
a->r->resid, a->r->resInsCode,
a->loc.x, a->loc.y, a->loc.z,
a->occ, a->bval);
}
}
xformDatabase* initXformDB() {
xformDatabase *xdb = NULL;
matrix4 *mp = NULL;
int i = 0;
xdb = (xformDatabase *)malloc(sizeof(xformDatabase));
if (!xdb) {
warn("could not create transformation database");
return NULL;
}
mp = (matrix4*)malloc(sizeof(matrix4)*MAX_XFORM_STACK_DEPTH);
if (!mp) {
warn("could not create transformation stack");
if (xdb) { free(xdb); }
return NULL;
}
xdb->xforms = xdb->last = NULL;
xdb->nlevs = 0;
for(i = 0; i < MAX_XFORM_LEVELS; i++) {
xdb->level[i] = NULL;
}
xdb->nstack = 0;
for(i = 0; i < MAX_XFORM_STACK_DEPTH; i++) {
xdb->ctmstack[i] = &(mp[i]);
}
initializeXFStack(xdb);
xdb->golist = xdb->glast = NULL;
xdb->sortedByRes = NULL;
return xdb;
}
transformData* newTransformation(char* rec) {
transformData* xform = NULL;
if (rec) {
xform = (transformData *)malloc(sizeof(transformData));
if (!xform) {
warn("could not create transformation");
return NULL;
}
xform->next = NULL;
xform->recs = NULL;
xform->lastrec = NULL;
xform->funcs = NULL;
fillinTransformationRec(xform, rec);
}
return xform;
}
void fillinTransformationRec(transformData* xform, char* rec) {
char *p = NULL, *s = NULL;
xform->name = NULL;
xform->num = -1; /* filled in during indexing */
xform->type = 0;
xform->phase = 0.0;
xform->startVal= 0.0;
xform->endVal = 0.0;
xform->stepVal = 0.0;
xform->currVal = 0.0; /* varied during processing */
xform->a1.x = 0.0;
xform->a1.y = 0.0;
xform->a1.z = 0.0;
xform->a2.x = 0.0;
xform->a2.y = 0.0;
xform->a2.z = 0.0;
v3identityMat(&(xform->tmat)); /* varied during processing */
p = strtok(rec, XFORMREC_DELIM);
if (p) {
s = p + strspn(rec, " \t");
if (!strncasecmp(s, "NULL", 4)) {
xform->type = NULLxform;
}
else if (!strncasecmp(s, "BONDROT", 7) || !strncasecmp(s, "ROT", 3)) {
xform->type = ROTxform;
}
else if (!strncasecmp(s, "TRANS", 5)) {
xform->type = TRANSxform;
}
else if (!strncasecmp(s, "SAVE", 4) || (s[0] == '(')) {
xform->type = SAVExform;
}
else if (!strncasecmp(s, "RESTORE", 7) || (s[0] == ')')) {
xform->type = RESTORExform;
}
if (xform->type == ROTxform || xform->type == TRANSxform) {
p = strtok(NULL, XFORMREC_DELIM);
xform->name = strdup(p?p:"/NULL/");
if (p) {
p = strtok(NULL, XFORMREC_DELIM);
if (p) {
xform->phase = atof(p);
p = strtok(NULL, XFORMREC_DELIM);
if (p) {
xform->startVal = atof(p);
p = strtok(NULL, XFORMREC_DELIM);
if (p) {
xform->endVal = atof(p);
p = strtok(NULL, XFORMREC_DELIM);
if (p) {
xform->stepVal = atof(p);
p = strtok(NULL, XFORMREC_DELIM);
if (p) {
xform->a1.x = atof(p);
p = strtok(NULL, XFORMREC_DELIM);
if (p) {
xform->a1.y = atof(p);
p = strtok(NULL, XFORMREC_DELIM);
if (p) {
xform->a1.z = atof(p);
p = strtok(NULL, XFORMREC_DELIM);
if (p) {
xform->a2.x = atof(p);
p = strtok(NULL, XFORMREC_DELIM);
if (p) {
xform->a2.y = atof(p);
p = strtok(NULL, XFORMREC_DELIM);
if (p) {
xform->a2.z = atof(p);
} /* a2z */
} /* a2y */
} /* a2x */
} /* a1z */
} /* a1y */
} /* a1x */
} /* stepVal */
} /* endVal */
} /* startVal */
} /* phase */
} /* name */
/* insure agreement between range and step direction */
if (xform->startVal < xform->endVal) {
xform->stepVal = fabs(xform->stepVal);
}
else if (xform->startVal > xform->endVal) {
xform->stepVal = -fabs(xform->stepVal);
}
else { /* must be equal */
warn("TRANSFORMATION where start == end (step reset)");
xform->stepVal = 9999; /* error */
}
} /* ROT || TRANS */
} /* type */
if (xform->name == NULL) { xform->name = strdup(""); }
}
transformData* deleteTransformation(transformData* xform,
abrAtomListProc delAtomProc, void *deletestuff) {
transformData* following = NULL;
xformAtomRecords *p = NULL, *next = NULL;
biasFunction *f = NULL, *nextf = NULL;
if (xform) {
for (p = xform->recs; p; p = next) {
next = p->next;
deleteXformAtomRecord(p, delAtomProc, deletestuff);
}
xform->recs = xform->lastrec = NULL;
if (xform->name != NULL) {
free(xform->name);
xform->name = NULL;
}
for (f = xform->funcs; f; f = nextf) {
nextf = f->next;
f->next = NULL;
free(f);
}
xform->funcs = NULL;
following = xform->next;
xform->next = NULL;
free(xform);
}
return following;
}
void appendTransformation(xformDatabase* xdb, transformData* xform) {
if (xdb && xform) {
if (xdb->xforms == NULL) {
xdb->xforms = xform;
xdb->last = NULL;
}
if (xdb->last != NULL) {
xdb->last->next = xform;
}
xdb->last = xform;
}
}
void appendAtomRec(transformData* xform, char* rec, abrMkAtomProc mkAtom, void *atomstuff) {
xformAtomRecords * xr = NULL;
if (xform && rec) {
xr = newXformAtomRecord(rec, mkAtom, atomstuff);
if (xr) {
if (xform->recs == NULL) {
xform->recs = xr;
xform->lastrec = NULL;
}
if (xform->lastrec != NULL) {
xform->lastrec->next = xr;
}
xform->lastrec = xr;
}
}
}
xformAtomRecords * newXformAtomRecord(char *rec, abrMkAtomProc mkAtom, void *atomstuff) {
xformAtomRecords *xr = NULL;
int getAtno(int);
if (rec) {
xr = (xformAtomRecords *)malloc(sizeof(xformAtomRecords));
if (!xr) {
warn("could not create Xform atom record");
return NULL;
}
xr->next = NULL;
xr->a = mkAtom(rec, atomstuff);
if (xr->a) {
/* record the original position on the atom */
xr->loc = xr->a->loc; /* so that we can continually return to it */
}
else {
free(xr); /* may be an H when implicitH processing is being used */
xr = NULL;
}
}
return xr;
}
void doListCleanupProcessing(xformDatabase* xdb, abrAtomListProc inputListProc, void *liststuff) {
atom* alst = NULL, *a = NULL;
int i = 0;
if (xdb) {
alst = NULL;
if (xdb->sortedByRes) { /* (re-)compose the atom list from the sort index */
for(i=0; xdb->sortedByRes[i]; i++) {
a = xdb->sortedByRes[i]->a;
a->next = alst;
alst = a;
}
}
if (alst && inputListProc) {
inputListProc(alst, liststuff);
}
}
}
xformAtomRecords* deleteXformAtomRecord(xformAtomRecords *xr,
abrAtomListProc delAtomProc, void *deletestuff) {
xformAtomRecords* following = NULL;
if (xr) {
if (xr->a != NULL) {
delAtomProc(xr->a, deletestuff);
xr->a = NULL;
}
following = xr->next;
xr->next = NULL;
free(xr);
}
return following;
}
void indexLevels(xformDatabase* xdb) {
transformData* xform = NULL;
int n = 0;
if (xdb) {
n = 0;
for(xform = xdb->xforms; xform; xform = xform->next) {
if (xform->type == ROTxform || xform->type == TRANSxform) {
/* the NULL transformation does not get indexed (it is not a scan dimension) */
xform->num = n;
xdb->level[n++] = xform;
}
}
xdb->nlevs = n;
}
}
void buildXDBsortedAtomRecs(xformDatabase* xdb) {
transformData *xform = NULL;
xformAtomRecords *xa = NULL;
xformAtomRecords **srtvec = NULL;
int n = 0;
if (xdb) {
n = 0; /* first count the number of atoms */
for (xform = xdb->xforms; xform; xform = xform->next) {
for(xa = xform->recs; xa; xa = xa->next) {
n++;
}
}
/* build an array with extra room for a terminating null pointer */
srtvec = (xformAtomRecords**)malloc((n + 1)*sizeof(xformAtomRecords*));
if (!srtvec) {
errmsg("could not create atom sorted-order array");
xdb->sortedByRes = NULL;
return;
}
n = 0; /* now we store pointers to the AtomRecs in the array */
for (xform = xdb->xforms; xform; xform = xform->next) {
for(xa = xform->recs; xa; xa = xa->next) {
srtvec[n] = xa;
n++;
}
}
srtvec[n] = NULL; /* array ends with a NULL */
qsort(&(srtvec[0]), n, sizeof(xformAtomRecords*), compareXDBAtomRecs);
xdb->sortedByRes = srtvec; /* stash away the sorted array */
}
}
/* compare function used in sorting the transformation atom records */
int compareXDBAtomRecs(const void *avptr, const void* bvptr) {
xformAtomRecords **ar = (xformAtomRecords **)avptr;
xformAtomRecords **br = (xformAtomRecords **)bvptr;
atom *a = NULL, *b = NULL;
int cmpval = 0, t = 0;
a = ar[0]->a;
b = br[0]->a;
/* Divide into separate residues. Atom sorting within a residue is less important. */
if (strcmp(a->r->chain, b->r->chain) > 0) { cmpval = 1; }
else if (strcmp(a->r->chain, b->r->chain) < 0) { cmpval = -1; }
else {
if (a->r->resid > b->r->resid) { cmpval = 1; }
else if (a->r->resid < b->r->resid) { cmpval = -1; }
else {
if (a->r->resInsCode > b->r->resInsCode) { cmpval = 1; }
else if (a->r->resInsCode < b->r->resInsCode) { cmpval = -1; }
else {
if (a->atomname[2] > b->atomname[2]) { cmpval = 1; }
else if (a->atomname[2] < b->atomname[2]) { cmpval = -1; }
else {
t = strcmp(a->atomname, b->atomname);
if (t != 0) { cmpval = t; }
else {
if (a->altConf > b->altConf) { cmpval = 1; }
else if (a->altConf < b->altConf) { cmpval = -1; }
else {
if (a->loc.x - 0.001 > b->loc.x) { cmpval = 1; }
else if (a->loc.x + 0.001 < b->loc.x) { cmpval = -1; }
else {
if (a->loc.y - 0.001 > b->loc.y) { cmpval = 1; }
else if (a->loc.y + 0.001 < b->loc.y) { cmpval = -1; }
else {
if (a->loc.z - 0.001 > b->loc.z) { cmpval = 1; }
else if (a->loc.z + 0.001 < b->loc.z) { cmpval = -1; }
else {
/* records seem to have the same name and position */
note("atom duplicated in autobondrot input");
cmpval = 0;
}
}
}
}
}
}
}
}
}
return -cmpval; /* invert sort order because the list will be built "CONSed" (appended) */
}
void rebuildTmat(transformData* xform) {
vector3d v;
if (xform) {
if (xform->type == ROTxform) {
vector3d axis;
matrix4 m1, m2, m3, m4;
double twistangle = 0.0;
v = xform->a2;
v3translationMat(&v, &m1);
twistangle = xform->currVal - xform->phase;
v3makeVec(&(xform->a2), &(xform->a1), &axis);
v3rotationMat(&axis, twistangle, &m2);
v3negate(&v);
v3translationMat(&v, &m4);
v3matMul(&m2, &m1, &m3);
v3matMul(&m4, &m3, &(xform->tmat));
}
else if (xform->type == TRANSxform) {
v3sub(&(xform->a2), &(xform->a1), &v);
if (v3squaredLength(&v) > 0.000001) {
v3scale(&v, xform->currVal - xform->phase);
v3translationMat(&v, &(xform->tmat));
}
else { v3identityMat(&(xform->tmat)); }
}
}
}
atom* orientedAtoms(xformDatabase* xdb) {
transformData* xform = NULL;
xformAtomRecords* xa = NULL;
matrix4 ctm, rsltMat;
atom* alst = NULL, *a = NULL;
if (xdb) {
initializeXFStack(xdb);
v3identityMat(&ctm);
for (xform = xdb->xforms; xform; xform = xform->next) {
if (xform->type == SAVExform) {
pushXFStack(xdb, &ctm);
}
else if (xform->type == RESTORExform) {
ctm = * topXFStack(xdb);
popXFStack(xdb);
}
else if (xform != NULLxform) {
v3matMul(&(xform->tmat), &ctm, &rsltMat);
ctm = rsltMat;
}
for(xa = xform->recs; xa; xa = xa->next) {
a = xa->a;
a->loc = xa->loc; /* apply ctm to the original loc of each atom */
v3mulPointMat(&(a->loc), &ctm); /* and use to set the new position of the atom */
}
}
alst = NULL;
if (xdb->sortedByRes) { /* (re-)compose the atom list from the sort index */
int i = 0;
for(i=0; xdb->sortedByRes[i]; i++) {
a = xdb->sortedByRes[i]->a;
a->next = alst;
alst = a;
}
}
}
return alst; /* returns the list of (pre-)sorted atoms */
}
double runnameAndTorsion(xformDatabase* xdb, char* buf, int max) {
char *p = NULL;
int i = 0, n = 0;
double bias = 0.0, phi = 0.0;
biasFunction *f = NULL;
if (xdb && buf) {
bias = 0.0;
p = buf; /*dcr?: (dcr guesses) that p now points to beginning of buf */
for(i = 0; i < xdb->nlevs; i++) {
if (max > 15) { /* add value to the output buffer */
n = sprintf(p, "%g ", xdb->level[i]->currVal);
/*dcr?: that sprintf wrote n char into buf starting at p*/
p += n;
/*dcr?: p now points n nchar further along in buf*/
/*note the space after the %g conversion of double currVal*/
/*so when next char written they will have a space between*/
max -= n;
/*dcr?: max tracks available space in buf, now decremented by n */
/*buf holds the angle values in order of their use*/
/*it would be nice to reorder those values for output to .map file*/
/*e.g. so plotting of phi,tau,psi could be as phi,psi,tau ! */
/*probably this should be done at the output stage anyway*/
/*autobondrot output is from probe.c/rawEnumerate() where */
/*angle values are called char *rawname which seems to == buf */
}
/* sum up any bias functions */
for(f = xdb->level[i]->funcs; f; f = f->next) {
if (f->type == CONSTbiasfunc) {
bias += f->v;
}
else if (f->type == POLYbiasfunc) {
bias += f->v * pow(xdb->level[i]->currVal - f->ph, f->freq);
}
else if (f->type == COSbiasfunc) {
phi = f->freq * DEG2RAD * (xdb->level[i]->currVal - f->ph);
bias += f->v * 0.5 * (f->shift - cos(phi));
}
}
}
}
return bias;
}
void addGoToRecord(xformDatabase* xdb, char *rec) {
char *p = NULL;
int i = 0;
goToRec* g = NULL;
if (xdb && rec) {
g = (goToRec *)malloc(sizeof(goToRec));
if (!g) {
warn("could not create 'go to' record");
return;
}
/* initialize */
g->next = NULL;
for(i = 0; i < MAX_XFORM_LEVELS; i++) {
g->level[i] = 0.0;
}
if (! xdb->golist) { xdb->golist = g; }
if (xdb->glast) { xdb->glast->next = g; }
xdb->glast = g;
p = strtok(rec, XFORMREC_DELIM); /* type id */
if (p) {
p = strtok(NULL, XFORMREC_DELIM);
for(i=0; p && (i < MAX_XFORM_LEVELS); i++) {
g->level[i] = atof(p);
p = strtok(NULL, XFORMREC_DELIM);
}
}
}
}
/* transformation described in the database based on the 'go to' entry */
void setOrientation(xformDatabase* xdb, goToRec* g) {
int i = 0;
if (xdb && g) {
for(i = 0; i < xdb->nlevs; i++) {
xdb->level[i]->currVal = g->level[i];
rebuildTmat(xdb->level[i]);
}
}
}
void appendBiasFunction(transformData* xform, char *rec) {
biasFunction *f = NULL;
char *p = NULL, *s = NULL;
if (xform && rec) {
f = (biasFunction *)malloc(sizeof(biasFunction));
if (!f) {
warn("could not create 'basis function' record");
return;
}
/* append to the transformation */
f->next = xform->funcs;
xform->funcs = f;
/* initialize */
f->type = CONSTbiasfunc;
f->v = 0.0;
f->ph = 0.0;
f->freq = 0;
f->shift = 0.0;
p = strtok(rec, XFORMREC_DELIM);
if (p) {
s = p + strspn(rec, " \t");
if (!strncasecmp(s, "CONST", 5)) {
f->type = CONSTbiasfunc;
}
else if (!strncasecmp(s, "POLY", 4)) {
f->type = POLYbiasfunc;
f->ph = 0.0;
f->freq = 2; /* default is a quadratic */
}
else if (!strncasecmp(s, "COS", 3)) {
f->type = COSbiasfunc;
f->ph = 60.0; /* default cos parameters (still need a scale value) */
f->freq = 3;
f->shift = 1.0;
}
p = strtok(NULL, XFORMREC_DELIM);
if (p) {
if (nonblankstr(p)) { f->v = atof(p); }
p = strtok(NULL, XFORMREC_DELIM);
if (p) {
if (nonblankstr(p)) { f->ph = atof(p); }
p = strtok(NULL, XFORMREC_DELIM);
if (p) {
if (nonblankstr(p)) { f->freq = atof(p); }
p = strtok(NULL, XFORMREC_DELIM);
if (p) {
if (nonblankstr(p)) { f->shift = atof(p); }
}
}
}
}
}
}
}
/* cull out any new atoms added in processing */
void cleanupListExtras(atom *alst, xformDatabase* xdb,
abrAtomListProc delAtomProc, void *deletestuff) {
atom *a = NULL, *prev= NULL, *next = NULL;
transformData *xform = NULL;
xformAtomRecords *xa = NULL;
if (alst && xdb) {
/* mark everything in the atom list */
for(a = alst; a; a = a->next) {
a->mark = 1;
}
/* unmark atoms reachable from the transformation database */
for(xform = xdb->xforms; xform; xform = xform->next) {
for(xa = xform->recs; xa; xa = xa->next) {
xa->a->mark = 0;
}
}
/* if still marked - must be extra - delete it */
prev = NULL;
for(a = alst; a; a = next) {
next = a->next;
if (a->mark) {
delAtomProc(a, deletestuff);
if (prev) { prev->next = next; }
}
else { prev = a; }
}
}
}
/* some stack manipulation functions */
void initializeXFStack(xformDatabase* xdb) {
xdb->nstack = 1;
v3identityMat(xdb->ctmstack[0]);
}
int pushXFStack(xformDatabase* xdb, matrix4* ctm) {
if (xdb->nstack > 0 && xdb->nstack < MAX_XFORM_STACK_DEPTH) {
xdb->nstack++;
*(xdb->ctmstack[xdb->nstack - 1]) = *ctm;
return TRUE;
}
else {
return FALSE;
}
}
void popXFStack(xformDatabase* xdb) {
if (xdb->nstack > 1) { xdb->nstack--; }
}
matrix4* topXFStack(xformDatabase* xdb) {
return (xdb->nstack > 0) ? xdb->ctmstack[xdb->nstack - 1] : NULL;
}
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