XEvent Clipboard::checkEvent()
{
XEvent e;
XIfEvent(resourceManager->dpy, &e, &clipboardPredicate, reinterpret_cast<XPointer>(window.get()));
DEBUG_CLIP("A selection notify has arrived!");
DEBUG_CLIP("Requester = 0x" << hex << e.xselectionrequest.requestor << dec);
DEBUG_CLIP("Target atom = " << getAtomName(resourceManager->dpy, e.xselection.target));
DEBUG_CLIP("Property atom = " << getAtomName(resourceManager->dpy, e.xselection.property));
DEBUG_CLIP("Selection atom = " << getAtomName(resourceManager->dpy, e.xselection.selection));
return e;
}
// Print out the details of an atom, taking the form:
// Atom Type Atomic Number Atomic Mass(amu) #CGBFS x y z
void Logger::print(const Atom& a) const
{
int q = a.getCharge();
Vector c(3);
c = a.getCoords();
outfile << std::fixed << std::setprecision(6);
outfile << std::setw(10) << getAtomName(q);
outfile << std::setw(10) << q;
outfile << std::setw(10) << a.getMass();
outfile << std::setw(10) << a.getNbfs();
outfile << std::setw(4) << "(" << std::setw(8) << c(0);
outfile << ", " << std::setw(8) << c(1);
outfile << ", " << std::setw(8) << c(2) << ")\n";
}
// Return the atomic number of an atom with text n
// the reverse of getAtomName
int getAtomCharge(const std::string& n)
{
// Make it upper case
std::string name = n;
std::transform(name.begin(), name.end(), name.begin(), ::toupper);
int q = 1;
bool found = false;
while (!found && q < 109 ){
if(getAtomName(q) == name){
found = true;
}
q++;
}
return q-1;
}
// Print out the basis set specification in the format:
// (example is C atom in 3-21G basis set)
// BASIS: 6-31G
// Total no. of cgbfs: 9
// Total no. of primitives: 9
// ===============
// Specification
// ===============
// Atom Shell #CGBFs #Prims
// ......................................
// C s 3 6
// p 6 3
// (if full = true, then continue with this)
// ===============
// Basis Functions
// ===============
// Atom Shell BF Coeff Exponent
// .................................................
// C s 1 0.0617669 172.2560
// 0.358794 25.91090
// 0.700713 5.533350
// etc...
void Logger::print(Basis& b, bool full) const
{
// Collect the data needed for printing
int nbfs = b.getNBFs(); // Store number of cgbfs and prims
int nprims = 0;
Vector qs = b.getCharges();
// Sort the qs and get rid of duplicates
qs.sort();
Vector qtemp(qs.size());
qtemp[0] = qs(0);
int k = 1;
for (int i = 1; i < qs.size(); i++){
if (qs(i) != qtemp[k-1]){
qtemp[k] = qs(i);
k++;
}
}
qs = qtemp;
qs.resizeCopy(k);
// Now sum over all basis functions to get the number of prims
Vector c(3); c[0] = 0.0; c[1] = 0.0; c[2] = 0.0;
BF bftemp(c, 0, 0, 0, c, c);
for (int i = 0; i < nbfs; i++){
bftemp = b.getBF(i);
nprims += bftemp.getNPrims();
}
// Start printing
title("Basis Set");
outfile << "BASIS: " << b.getName() << "\n";
outfile << "Total no. of cgbfs: " << nbfs << "\n";
outfile << "Total no. of prims: " << nprims << "\n";
title("Specification");
outfile << std::setw(8) << "Atom";
outfile << std::setw(8) << "Shell";
outfile << std::setw(8) << "#CGBFs";
outfile << std::setw(8) << "#Prims\n";
outfile << std::string(35, '.') << "\n";
// loop over the atom types
outfile << std::setprecision(2);
Vector subshells; Vector sublnums;
for (int i = 0; i < k; i++){
int nc = 0; int np = 0;
outfile << std::setw(8) << getAtomName(qs(i));
subshells = b.getShells(qs[i]);
sublnums = b.getLnums(qs[i]);
outfile << std::setw(8) << getShellName(sublnums[0]);
outfile << std::setw(8) << subshells[0];
for (int j = 0; j < subshells[0]; j++){
np += b.getBF(qs[i], j).getNPrims();
}
nc += subshells[0];
outfile << std::setw(8) << np << "\n";
for (int j = 1; j < subshells.size(); j++){
outfile << std::setw(8) << "";
outfile << std::setw(8) << getShellName(sublnums[j]);
outfile << std::setw(8) << subshells[j];
np = 0;
for (int l = 0; l < subshells[j]; l++){
np += b.getBF(qs[i], nc + l).getNPrims();
}
nc += subshells[j];
outfile << std::setw(8) << np << "\n";
}
}
outfile << std::setprecision(8);
// Now print out basis functions if required
if (full) {
title("Basis Functions");
outfile << std::setw(8) << "Atom";
outfile << std::setw(8) << "Shell";
outfile << std::setw(5) << "BF";
outfile << std::setw(18) << "Coeff";
outfile << std::setw(18) << "Exponent\n";
outfile << std::string(58, '.') << "\n";
// Loop over all the basis functions
Vector subshell; Vector sublnums;
Vector coeffs; Vector exps;
std::string filler = "";
for (int i = 0; i < k; i++){
subshell = b.getShells(qs(i));
sublnums = b.getLnums(qs(i));
// Loop over shells
int sum = 0;
for (int r = 0; r < subshell.size(); r++){
// Loop over bfs
for (int s = 0; s < subshell[r]; s++){
bftemp = b.getBF(qs(i), s+sum);
coeffs = bftemp.getCoeffs();
exps = bftemp.getExps();
// Loop over coeffs/exps
for (int t = 0; t < coeffs.size(); t++){
filler = ((r == 0 && s==0 && t==0) ? getAtomName(qs[i]) : "");
outfile << std::setw(8) << filler;
filler = ((s == 0 && t == 0) ? getShellName(sublnums[r]) : "");
outfile << std::setw(8) << filler;
filler = (t == 0 ? std::to_string(s+1) : "");
outfile << std::setw(5) << filler;
outfile << std::setw(18) << std::setprecision(8) << coeffs(t);
outfile << std::setw(18) << std::setprecision(8) << exps(t) << "\n";
}
}
sum += subshell[r];
}
}
}
}
int identifyAtom(char* name, char resname[], int Verbose) { /*dcr041007 allow warning choice*/
int n = -1, emitWarning = 0;
switch(name[0]) {
case '*': case '\'': case '"': case '`': case '_':
case '+': case '-': case ' ':
case '0': case '1': case '2': case '3': case '4':
case '5': case '6': case '7': case '8': case '9':
switch(name[1]) {
case 'A':
switch(name[3]) {
case '1': n = atomO; emitWarning = 1; break;
case '2': n = atomN; emitWarning = 1; break;
} break;
case 'B': n = atomB; break;
case 'C': n = atomC; break;
case 'D': n = atomH; break;
case 'F': n = atomF; break;
case 'H':
switch(name[2]) {
case 'E': n = fixAtomName(name,resname,2) ? atomHe : atomH; break;
case 'F': n = fixAtomName(name,resname,2) ? atomHf : atomH; break;
case 'G': n = fixAtomName(name,resname,2) ? atomHg : atomH; break;
case 'O': n = fixAtomName(name,resname,2) ? atomHo : atomH; break;
/* case 'S': n = fixAtomName(name,resname,2) ? atomHs : atomH; break; */
default : n = atomH; break;
} break;
case 'I': n = atomI; break;
case 'K': n = atomK; break;
case 'N': n = atomN; break;
case 'O': n = atomO; break;
case 'P': n = atomP; break;
/*case 'S': n = atomS; break;*/
case 'S':
if(name[0] == ' ' && name[2] == 'E')
{/*_SE likely refmac,cns missplaced Selenium atom name dcr041007*/
n = atomSe; emitWarning = 1; break;
}
else {n = atomS; break;} /*050121 NO warning for other S*/
case 'U': n = atomU; break;
case 'V': n = atomV; break;
case 'W': n = atomW; break;
case 'Y': n = atomY; break;
} break;
case 'A':
switch(name[1]) {
case 'C': n = atomC; emitWarning = 1;break;/*nonstd!*/
case 'G': n = atomAg; break;
case 'H': n = atomH; emitWarning = 1;break;
case 'L': n = atomAl; break;
case 'M': n = atomAm; break;
case 'N': n = atomN; emitWarning = 1;break;
case 'O': n = atomO; emitWarning = 1;break;
case 'P': n = atomP; emitWarning = 1;break;
case 'R': n = atomAr; break;
case 'S': n = atomAs; break;
case 'T': n = atomAt; break;
case 'U': n = atomAu; break;
} break;
case 'B':
switch(name[1]) {
case 'A': n = atomBa; break;
case 'E': n = atomBe; break;
case 'I': n = atomBi; break;
case 'K': n = atomBk; break;
case 'R': n = atomBr; break;
} break;
case 'C':
switch(name[1]) {
case 'A': n = atomCa; break;
case 'C': n = atomC; emitWarning = 1;break;
case 'D': n = atomCd; break;
case 'E': n = atomCe; break;
case 'F': n = atomCf; break;
case 'H': n = atomH; emitWarning = 1;break;
case 'L': n = atomCl; break;
case 'M': n = atomCm; break;
case 'N': n = atomN; emitWarning = 1;break;
case 'O': n = atomCo; emitWarning = 1;break;
case 'P': n = atomP; emitWarning = 1;break;
case 'R': n = atomCr; break;
case 'S': n = atomCs; break;
case 'U': n = atomCu; break;
default: n = atomC; emitWarning = 1;break;
} break;
case 'D':
switch(name[1]) {
case 'Y': n = atomDy; break;
case 'C': n = atomC; emitWarning = 1;break;
case 'H': n = atomH; emitWarning = 1;break;
case 'N': n = atomN; emitWarning = 1;break;
case 'O': n = atomO; emitWarning = 1;break;
case 'P': n = atomP; emitWarning = 1;break;
default: n = atomH; emitWarning = 1;break;
} break;
case 'E':
switch(name[1]) {
case 'R': n = atomEr; break;
case 'S': n = atomEs; break;
case 'U': n = atomEu; break;
case 'C': n = atomC; emitWarning = 1;break;
case 'H': n = atomH; emitWarning = 1;break;
case 'N': n = atomN; emitWarning = 1;break;
case 'O': n = atomO; emitWarning = 1;break;
case 'P': n = atomP; emitWarning = 1;break;
} break;
case 'F':
switch(name[1]) {
case 'E': n = atomFe; break;
case 'M': n = atomFm; break;
case 'R': n = atomFr; break;
case 'C': n = atomC; emitWarning = 1;break;
case 'H': n = atomH; emitWarning = 1;break;
case 'N': n = atomN; emitWarning = 1;break;
case 'O': n = atomO; emitWarning = 1;break;
case 'P': n = atomP; emitWarning = 1;break;
} break;
case 'G':
switch(name[1]) {
case 'A': n = atomGa; break;
case 'D': n = atomGd; break;
case 'E': n = atomGe; break;
case 'C': n = atomC; emitWarning = 1;break;
case 'H': n = atomH; emitWarning = 1;break;
case 'N': n = atomN; emitWarning = 1;break;
case 'O': n = atomO; emitWarning = 1;break;
case 'P': n = atomP; emitWarning = 1;break;
} break;
case 'H':
switch(name[1]) {
case 'E': n = fixAtomName(name,resname,1) ? atomHe : atomH; break;
case 'F': n = fixAtomName(name,resname,1) ? atomHf : atomH; break;
case 'G': n = fixAtomName(name,resname,1) ? atomHg : atomH; break;
case 'O': n = fixAtomName(name,resname,1) ? atomHo : atomH; break;
/* case 'S': n = fixAtomName(name,resname,1) ? atomHs : atomH; break; */
default : n = atomH; break;
} break;
/* case 'E': */
/* if (isdigit(name[2])) { n = atomH; emitWarning = 1;} */ /* Hepsilon?? */
/* else {n = atomHe; emitWarning = 1;} */
/* break; */
/* case 'F': n = atomHf; emitWarning = 1;break; */
/* case 'G': */
/* if (isdigit(name[2])) { n = atomH; emitWarning = 1;} */ /* Hgamma?? */
/* else {n = atomHg; emitWarning = 1;} */
/* break; */
/* case 'O': n = atomHo; emitWarning = 1;break; */
/* default: n = atomH; emitWarning = 1;break; */
/* } break; */
case 'I':
switch(name[1]) {
case 'N': n = atomIn; break;
case 'R': n = atomIr; break;
} break;
case 'K':
if (name[1] == 'R') n = atomKr; break;
case 'L':
switch(name[1]) {
case 'A': n = atomLa; break;
case 'I': n = atomLi; break;
case 'U': n = atomLu; break;
} break;
case 'M':
switch(name[1]) {
case 'D': n = atomMd; break;
case 'G': n = atomMg; break;
case 'N': n = atomMn; break;
case 'O': n = atomMo; break;
} break;
case 'N':
switch(name[1]) {
case 'A': n = atomNa; emitWarning = 1;break;
case 'B': n = atomNb; emitWarning = 1;break;
case 'C': n = atomC; emitWarning = 1;break;
case 'D': n = atomNd; emitWarning = 1;break;
case 'E': n = atomNe; emitWarning = 1;break;
case 'H': n = atomH; emitWarning = 1;break;
case 'I': n = atomNi; break;
case 'N': n = atomN; emitWarning = 1;break;
case 'O': n = atomO; emitWarning = 1;break;/*nonstd!*/
case 'P': n = atomP; emitWarning = 1;break;/*nonstd!*/
case 'S': n = atomS; emitWarning = 1;break;
default: n = atomN; emitWarning = 1;break;
} break;
case 'O':
switch(name[1]) {
case 'S': n = atomOs; break;
default: n = atomO; emitWarning = 1;break;
} break;
case 'P':
switch(name[1]) {
case 'A': n = atomPa; emitWarning = 1;break;
case 'B': n = atomPb; emitWarning = 1;break;
case 'D': n = atomPd; emitWarning = 1;break;
case 'M': n = atomPm; break;
case 'O': n = atomPo; break;
case 'R': n = atomPr; break;
case 'T': n = atomPt; break;
case 'U': n = atomPu; break;
default: n = atomP; emitWarning = 1;break;
} break;
case 'R':
switch(name[1]) {
case 'A': n = atomRa; break;
case 'B': n = atomRb; break;
case 'E': n = atomRe; break;
case 'H': n = atomRh; break;
case 'N': n = atomRn; break;
case 'U': n = atomRu; break;
} break;
case 'S':
switch(name[1]) {
case 'B': n = atomSb; emitWarning = 1;break;
case 'C': n = atomSc; break;
case 'E': n = atomSe; emitWarning = 1;break;
case 'I': n = atomSi; break;
case 'M': n = atomSm; break;
case 'N': n = atomSn; break;
case 'R': n = atomSr; break;
default: n = atomS; emitWarning = 1;break;
} break;
case 'T':
switch(name[1]) {
case 'A': n = atomTa; break;
case 'B': n = atomTb; break;
case 'C': n = atomTc; break;
case 'E': n = atomTe; break;
case 'H': n = atomTh; break;
case 'I': n = atomTi; break;
case 'L': n = atomTl; break;
case 'M': n = atomTm; break;
} break;
case 'X':
if (name[1] == 'E') n = atomXe; break;
case 'Y':
if (name[1] == 'B') n = atomYb; break;
case 'Z':
switch(name[1]) {
case 'N': n = atomZn; break;
case 'R': n = atomZr; break;
} break;
default: break;
}
if (n < 0) { emitWarning = 1;
n = atomC;
switch(name[1]) {
case 'H': case 'D': n = atomH; break;
case 'C': n = atomC; break;
case 'N': n = atomN; break;
case 'O': n = atomO; break;
case 'P': n = atomP; break;
case 'S': n = atomS; break;
case 'I': n = atomI; break;
case 'K': n = atomK; break;
case 'V': n = atomV; break;
case 'W': n = atomW; break;
case 'U': n = atomU; break;
case 'A':
switch(name[2]) {
case 'G': n = atomAg; break;
case 'L': n = atomAl; break;
case 'S': n = atomAs; break;
case 'U': n = atomAu; break;
} break;
case 'F':
if (name[2] == 'E') n = atomFe; break;
case 'G':
if (name[2] == 'D') n = atomGd; break;
case 'L':
if (name[2] == 'I') n = atomLi; break;
case 'M':
switch(name[2]) {
case 'G': n = atomMg; break;
case 'N': n = atomMn; break;
case 'O': n = atomMo; break;
} break;
case 'Z':
if (name[2] == 'N') n = atomZn; break;
/* --------- default if we fall through... ---------------------*/
default: n = atomC; break;
}
}
if (emitWarning && Verbose) {/*Verbose controlled dcr041007*/
char warnstr[5]={'_','_','_','_','\0'}; /*dcr041007*/
char warnresn[5]={'_','_','_','_','\0'}; /*rmi070719*/
char* atstr;
int j=0;
while(name[j]!='\0'&&warnstr[j]!='\0')
{/*explicitly show blanks so can understand atom name problem*/
if(name[j]==' ') {warnstr[j]='_';}
else {warnstr[j]=name[j];}
j++;
}
j=0;
while(resname[j]!='\0'&&warnresn[j]!='\0')
{/*explicitly show blanks so can understand residue/atom name problem*/
if(name[j]==' ') {warnresn[j]='_';}
else {warnresn[j]=resname[j];}
j++;
}
atstr = getAtomName(n);
if(strlen(atstr)==1)
{fprintf(stderr,"WARNING: atom %s from resn %s will be treated as %s\n",warnstr,warnresn,atstr);}
else {fprintf(stderr,"WARNING: atom %s from resn %s will be treated as %s\n",warnstr,warnresn,atstr);}
/*name, getAtomName(n));*/
}
return n;
}