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 Displaylist::ProbeSurface(Residue *reslist, MIAtomList a)
{
vector<SURFDOT>::iterator p;
MIAtom_iter pa;
Residue *res = reslist;
float r1, dx, dy, dz, dr;
int i;
MIAtomList b;
MIAtom *atom;
while (res != NULL)
{
for (i = 0; i < res->atomCount(); i++)
{
atom = res->atom(i);
for (pa = a.begin(); pa != a.end(); pa++)
{
if (atom == *pa)
{
continue;
}
}
r1 = atom->getRadius();
for (pa = a.begin(); pa != a.end(); pa++)
{
if (AtomDist(**pa, *atom) < (r1 + (*pa)->getRadius()))
{
b.push_back(atom);
break;
}
}
}
res = res->next();
}
for (p = CurrentDots.begin(); p != CurrentDots.end(); p++)
{
dr = 0.0;
for (pa = b.begin(); pa != b.end(); pa++)
{
r1 = (*pa)->getRadius();
r1 = r1*r1;
dx = (*pa)->x() - (*p).x;
dx = dx*dx;
if (dx < r1)
{
dy = (*pa)->y() - (*p).y;
dy = dy*dy;
if (dx+dy < r1)
{
dz = (*pa)->z() - (*p).z;
dz = dz*dz;
dr = (dx+dy+dz*dz)-r1;
}
}
}
if (dr < -0.4)
{
(*p).color = Colors::WHITE;
if (dr < -1.2)
{
(*p).color = Colors::PINK;
if (dr < -2.4)
{
(*p).color = Colors::RED;
}
}
}
else
{
(*p).color = -abs((*p).color);
}
}
}
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);
}
static void AddAnnotations(Molecule *model)
{
if (model == NULL)
{
return;
}
std::map<Residue*, std::string> annotations;
std::string err_type;
std::vector<std::string> headers = *model->GetFileHead();
for (size_t i = 0; i < headers.size(); ++i)
{
// get class of error
if (strncmp("REMARK 500 SUBTOPIC:", headers[i].c_str(), 20)==0
|| strncmp("REMARK 501 SUBTOPIC:", headers[i].c_str(), 20)==0)
{
err_type = ""; // clear type on new subtopic
if (headers[i].size() > 22)
{
if (headers[i].find("BOND LENGTHS", 21)!=std::string::npos)
{
err_type = std::string("Geometry (bond length)");
}
else if (headers[i].find("BOND ANGLES", 21)!=std::string::npos)
{
err_type = std::string("Geometry (bond angle)");
}
else if (headers[i].find("CHIRAL", 21)!=std::string::npos)
{
err_type = std::string("Geometry (chiral)");
}
else if (headers[i].find("NON-CIS", 21)!=std::string::npos)
{
err_type = std::string("Omega");
}
else if (headers[i].find("CLOSE CONTACTS", 21)!=std::string::npos)
{
err_type = std::string("Van der Waals");
}
else if (headers[i].find("TORSION ANGLES", 21)!=std::string::npos)
{
err_type = std::string("Phi-psi");
}
else if (headers[i].find("ELECTRON DENSITY", 21)!=std::string::npos)
{
err_type = std::string("Density");
}
else if (headers[i].find("ELECTRON DENSITY", 21)!=std::string::npos)
{
err_type = std::string("Density");
}
else if (headers[i].find("ROTAMER", 21)!=std::string::npos)
{
err_type = std::string("Rotamer chi-1");
}
else if (headers[i].find("CIS PEPTIDE", 21)!=std::string::npos)
{
err_type = std::string("Cis peptide");
}
}
}
int dum;
char rname[4], rnum[6];
char chain;
if (err_type != ""
&& (strncmp("REMARK 500 ", headers[i].c_str(), 13)==0
|| strncmp("REMARK 501 ", headers[i].c_str(), 13)==0))
{
if ((sscanf(headers[i].c_str(),
"REMARK 500 %d %s %c %s", &dum, rname, &chain, rnum)==4)
|| (sscanf(headers[i].c_str(),
"REMARK 501 %d %s %c %s", &dum, rname, &chain, rnum)==4))
{
Residue *res = residue_from_name(model->residuesBegin(), rnum, chain);
if (res != NULL)
{
std::string tmp = annotations[res];
if (tmp.size()==0)
tmp = ::format("Error in %c %s %s: %s", chain, rnum, rname, err_type.c_str());
else
tmp = ::format("%s, %s", tmp.c_str(), err_type.c_str());
annotations[res] = tmp;
}
}
}
}
bool hidden = !QSettings().value("DisplayView/autoShowError", true).toBool();
for (std::map<Residue*, std::string>::iterator i = annotations.begin(); i!=annotations.end(); ++i)
{
Residue *res = i->first;
std::string &text = i->second;
MIAtom *atom = atom_from_name("CA", *res);
if (atom == NULL && res->atomCount() > 0)
{
atom = res->atom(0);
}
if (atom != NULL)
{
Annotation *annotation = new Annotation(text.c_str(), atom->x(), atom->y(), atom->z());
annotation->setHidden(hidden);
model->addAnnotation(annotation);
}
}
}
