void XMLArchive::WriteField(const Residue &res)
{
/* write a RESIDUE field */
tags.push_back("Residue");
calc_indent();
char secstr = res.secstr();
// this fixes a wierd bug - if these happen to be 0 - disaster!
if (!isalpha(secstr))
{
secstr = 'U';
}
if (!isalpha(res.name1()))
{
secstr = 'X';
}
f = format("%s<Residue name=\"%s\" type=\"%s\" chain=\"%d\" secstr=\"%c\" confomer=\"%d\" flags=\"%d\" linkage_type=\"%d\" name1=\"%c\" seqpos=\"%d\" >\n",
indent, res.name().c_str(), res.type().c_str(), (int)res.chain_id(), secstr, (int)res.confomer(), (int)res.flags(), (int)res.linkage_type(), res.name1(), res.seqpos());
Write(f);
inTag++;
for (int i = 0; i < res.atomCount(); i++)
{
WriteField(res.atom(i));
}
EndTag();
}
void RibbonEngine::updateChains(PainterDevice *pd)
{
if (!isEnabled())
return;
m_chains.clear();
QList<Primitive *> list;
list = primitives().subList(Primitive::ResidueType);
unsigned int currentChain = 0;
QVector<Vector3d> pts;
// Get a list of residues for the molecule
const Molecule *molecule = pd->molecule();
foreach(Primitive *p, list) {
Residue *r = static_cast<Residue *>(p);
if(r->name() =="HOH") {
continue;
}
if(r->chainNumber() != currentChain) {
// this residue is on a new chain
if(pts.size() > 0)
m_chains.push_back(pts);
currentChain = r->chainNumber();
pts.clear();
}
foreach (unsigned long atom, r->atoms()) {
// should be CA
QString atomId = r->atomId(atom);
atomId = atomId.trimmed();
if (atomId == "CA") {
pts.push_back(*molecule->atomById(atom)->pos());
}
else if (atomId == "N" && m_useNitrogens == 2) {
pts.push_back(*molecule->atomById(atom)->pos());
}
} // end atoms in residue
} // end primitive list (i.e., all residues)
Residue *SymmResidue(const Residue *Model, CMapHeaderBase *mh, float center[3], float r, int color)
{
/* set unity to true if operator = x,y,z to avoid looking at 0,0,0 position */
const Residue *model;
Residue *res = NULL, *newres, *Res = NULL;
char label[MAXNAME];
int nlabel;
int nadd = 0;
int i, j, k, n = 0;
float minxyz[3], maxxyz[3];
float sminxyz[3], smaxxyz[3];
float fx, fy, fz;
int ix, iy, iz;
float x1, y1, z1;
float cx1, cy1, cz1, cx2, cy2, cz2;
float pos[3];
float cx, cy, cz, dx, dy, dz;
float symmat[3][4];
float ctof[3][3];
float ftoc[3][3];
for (j = 0; j < 3; j++)
{
for (k = 0; k < 3; k++)
{
ctof[j][k] = mh->ctof[j][k];
ftoc[j][k] = mh->ftoc[j][k];
}
}
minxyz[0] = 9999.0;
minxyz[1] = 9999.0;
minxyz[2] = 9999.0;
maxxyz[0] = -9999.0;
maxxyz[1] = -9999.0;
maxxyz[2] = -9999.0;
cx = center[X];
cy = center[Y];
cz = center[Z];
cx1 = center[X]-r;
cy1 = center[Y]-r;
cz1 = center[Z]-r;
cx2 = center[X]+r;
cy2 = center[Y]+r;
cz2 = center[Z]+r;
transform(ctof, &cx, &cy, &cz);
transform(ctof, &cx1, &cy1, &cz1);
transform(ctof, &cx2, &cy2, &cz2);
for (int symmop = 0; symmop < mh->nsym; symmop++)
{
/* put res at end of list */
sprintf(label, "#%d", symmop);
nlabel = strlen(label);
for (j = 0; j < 3; j++)
{
for (k = 0; k < 4; k++)
{
symmat[j][k] = mh->symops[j][k][symmop];
}
}
/* find min max of model in fractional */
model = Model;
while (model != NULL)
{
for (i = 0; i < model->atomCount(); i++)
{
if (model->atom(i)->x() < minxyz[X])
{
minxyz[X] = model->atom(i)->x();
}
if (model->atom(i)->y() < minxyz[Y])
{
minxyz[Y] = model->atom(i)->y();
}
if (model->atom(i)->z() < minxyz[Z])
{
minxyz[Z] = model->atom(i)->z();
}
if (model->atom(i)->x() > maxxyz[X])
{
maxxyz[X] = model->atom(i)->x();
}
if (model->atom(i)->y() > maxxyz[Y])
{
maxxyz[Y] = model->atom(i)->y();
}
if (model->atom(i)->z() > maxxyz[Z])
{
maxxyz[Z] = model->atom(i)->z();
}
}
model = model->next();
}
/* convert to fractional */
transform(ctof, &minxyz[X], &minxyz[Y], &minxyz[Z]);
transform(ctof, &maxxyz[X], &maxxyz[Y], &maxxyz[Z]);
/* find symmetry min max */
symm(minxyz[X], minxyz[Y], minxyz[Z],
&sminxyz[X], &sminxyz[Y], &sminxyz[Z], symmat);
symm(maxxyz[X], maxxyz[Y], maxxyz[Z],
&smaxxyz[X], &smaxxyz[Y], &smaxxyz[Z], symmat);
for (i = 0; i < 3; i++)
{
if (sminxyz[i] > smaxxyz[i])
{
float t = sminxyz[i];
sminxyz[i] = smaxxyz[i];
smaxxyz[i] = t;
}
}
/* look at unit cells -1 to +1 around minmax */
dx = cx - (sminxyz[X]+smaxxyz[X])/2.0 ;
dy = cy - (sminxyz[Y]+smaxxyz[Y])/2.0 ;
dz = cz - (sminxyz[Z]+smaxxyz[Z])/2.0 ;
for (ix = -1; ix <= 1; ix += 1)
{
for (iy = -1; iy <= 1; iy += 1)
{
for (iz = -1; iz <= 1; iz += 1)
{
/* if (symmop==0 && ix==0 && iy==0 && iz==0) continue; */
fx = ROUND(dx + ix);
fy = ROUND(dy + iy);
fz = ROUND(dz + iz);
n++;
model = Model;
while (model != NULL)
{
/* look for any atom to be within radius-
if so copy entire residue and move on */
for (i = 0; i < model->atomCount(); i++)
{
x1 = model->atom(i)->x();
y1 = model->atom(i)->y();
z1 = model->atom(i)->z();
transform(ctof, &x1, &y1, &z1);
symm(x1, y1, z1, &x1, &y1, &z1, symmat);
x1 += fx;
y1 += fy;
z1 += fz;
transform(ftoc, &x1, &y1, &z1);
pos[X] = x1;
pos[Y] = y1;
pos[Z] = z1;
if (outside_sphere(pos, r, center))
{
continue;
}
if (symmop == 0
&& x1 < model->atom(i)->x()+.1
&& x1 > model->atom(i)->x()-.1
&& y1 < model->atom(i)->y()+.1
&& y1 > model->atom(i)->y()-.1
&& z1 < model->atom(i)->z()+.1
&& z1 > model->atom(i)->z()-.1)
{
continue;
}
newres = new Residue(*model);
if (Res == NULL)
{
Res = res = newres;
}
else
{
res = res->insertResidue(newres);
}
/* now transform the atoms */
if ((int)strlen(res->name().c_str()) < MAXNAME-nlabel)
{
res->setName(res->name() + std::string(label));
}
for (j = 0; j < res->atomCount(); j++)
{
x1 = res->atom(j)->x();
y1 = res->atom(j)->y();
z1 = res->atom(j)->z();
transform(ctof, &x1, &y1, &z1);
symm(x1, y1, z1, &x1, &y1, &z1, symmat);
x1 += fx;
y1 += fy;
z1 += fz;
transform(ftoc, &x1, &y1, &z1);
res->atom(j)->setPosition(x1, y1, z1);
res->atom(j)->setColor(color);
res->atom(j)->setSymmop(symmop);
res->atom(j)->addType(AtomType::SYMMATOM);
/* save fx,fy,fz for later */
res->atom(j)->resetDelta();
res->atom(j)->addDelta(fx, fy, fz);
nadd++;
}
break;
}
model = model->next();
// if(wait.CheckForAbort()) model=NULL;
}
}
}
}
}
Logger::log("Built %d symmatoms", nadd);
return (Res);
}
