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// moldata.h -- class MolData knows how to calculate molecular weights
// and partial charges
#ifndef MOLDATA_H
#define MOLDATA_H
#include <qstring.h>
#include <qstringlist.h>
#include <iostream>
using std::cout;
using std::endl;
class MolData {
public:
static double NameToMW(QString e) {
if (e.upper() == QString("H")) return 1.00794;
if (e.upper() == QString("HE")) return 4.0026;
if (e.upper() == QString("LI")) return 6.941;
if (e.upper() == QString("B")) return 10.811;
if (e.upper() == QString("C")) return 12.011;
if (e.upper() == QString("N")) return 14.0067;
if (e.upper() == QString("O")) return 15.9994;
if (e.upper() == QString("F")) return 18.9984;
if (e.upper() == QString("NA")) return 22.98977;
if (e.upper() == QString("MG")) return 24.305;
if (e.upper() == QString("SI")) return 28.0855;
if (e.upper() == QString("P")) return 30.97376;
if (e.upper() == QString("S")) return 32.066;
if (e.upper() == QString("CL")) return 35.4527;
if (e.upper() == QString("K")) return 39.0983;
if (e.upper() == QString("SE")) return 78.96;
if (e.upper() == QString("BR")) return 79.904;
if (e.upper() == QString("I")) return 126.9045;
return 6.0;
}
static double MW(QString x) {
cout << "Request for MW of " << x << endl;
// parse this string
QString iso; // isotope MW
QString thiselement; // current element
QString repeatnum; // number of repeats
unsigned int ptr = 0; // cursor position (pointer) in x
int isoflag = false; // isotope-override normal MW lookup if MW specified
double this_mw; // MW of this element
int repeat = 1; // number of this atom
double mw_out = 0.0; // MW returned
QStringList tokens;
do {
iso.remove(0,999);
thiselement.remove(0,999);
repeatnum.remove(0,999);
// Check if token starts with a number
if (x.at(ptr).isNumber() == true) { // read isotope value
isoflag = true;
iso.append(x.at(ptr));
ptr++;
if (x.at(ptr).isNumber() == true) {
iso.append(x.at(ptr));
ptr++;
}
if (x.at(ptr).isNumber() == true) {
iso.append(x.at(ptr));
ptr++;
}
}
// ptr now points to first letter of element
thiselement.append(x.at(ptr));
ptr++;
// if next letter is lowercase, add it too
if (x.at(ptr).category() == QChar::Letter_Lowercase) {
thiselement.append(x.at(ptr));
ptr++;
}
// if next character is number, it's the subscript
if (x.at(ptr).isNumber() == true) {
repeatnum.append(x.at(ptr));
ptr++;
if (x.at(ptr).isNumber() == true) {
repeatnum.append(x.at(ptr));
ptr++;
}
if (x.at(ptr).isNumber() == true) {
repeatnum.append(x.at(ptr));
ptr++;
}
repeat = repeatnum.toInt();
}
// Move to next letter/number
if (ptr < x.length()) {
if (x.at(ptr).isSpace() == true) ptr++;
}
if (isoflag)
this_mw = iso.toDouble();
else
this_mw = NameToMW(thiselement);
// add to molecular weight
mw_out = mw_out + (repeat * this_mw);
isoflag = false;
repeat = 1;
} while (ptr < x.length());
cout << "MW = " << mw_out << endl;
return mw_out;
}
// How many bonds (hydrogens) should this element or group have?
static int Hydrogens(QString x) {
//cout << "Request for bonds/hydrogens to |" << x << "|" << endl;
// first check 'special' patterns
if (x.upper().contains("TIPS") == 1) return 1;
if (x.upper().contains("TMS") == 1) return 1;
if (x.upper().contains("MS") == 1) return 1;
if (x == "CO") return 2;
if (x == "SO") return 2;
if (x == "AcO") return 1;
if (x == "MeO") return 1;
if (x == "EtO") return 1;
if (x == "TsO") return 1;
if (x == "BnO") return 1;
if (x == "BzO") return 1;
if (x == "TBSO") return 1;
if (x == "OAc") return 1;
if (x == "OMe") return 1;
if (x == "OEt") return 1;
if (x == "OTs") return 1;
if (x == "OBn") return 1;
if (x == "OBz") return 1;
if (x == "OTBS") return 1;
if (x == "NO2") return 1;
if (x == "O2N") return 1;
if (x == "CH3") return 1;
if (x == "OH") return 1;
if (x == "HO") return 1;
if (x == "CHO") return 1;
if (x == "COOH") return 1;
if (x == "HOOC") return 1;
if (x == "CN") return 1;
if (x == "NH2") return 1;
if (x == "H2N") return 1;
if (x == "NH") return 2;
if (x == "HN") return 2;
if (x == "O-") return 1;
if (x == "-O") return 1;
int flag = false;
int ptr = 0;
QString firstelement; // element to consider
// Find first letter
do {
if (x.at(ptr).isLetter() == false)
ptr++;
else
flag = true;
} while (flag == false);
firstelement.append(x.at(ptr));
ptr++;
if (x.at(ptr).category() == QChar::Letter_Lowercase) {
firstelement.append(x.at(ptr));
ptr++;
}
if (x.at(ptr).category() == QChar::Letter_Lowercase) {
firstelement.append(x.at(ptr));
ptr++;
}
if (firstelement.upper() == QString("H")) return 1;
if (firstelement.upper() == QString("HE")) return 0;
if (firstelement.upper() == QString("LI")) return 1;
if (firstelement.upper() == QString("B")) return 3;
if (firstelement.upper() == QString("C")) return 4;
if (firstelement.upper() == QString("N")) return 3;
if (firstelement.upper() == QString("O")) return 2;
if (firstelement.upper() == QString("F")) return 1;
if (firstelement.upper() == QString("NA")) return 1;
if (firstelement.upper() == QString("MG")) return 2;
if (firstelement.upper() == QString("SI")) return 4;
if (firstelement.upper() == QString("CL")) return 1;
if (firstelement.upper() == QString("K")) return 1;
if (firstelement.upper() == QString("SE")) return 2;
if (firstelement.upper() == QString("BR")) return 1;
if (firstelement.upper() == QString("I")) return 1;
// these could cause problems
if (firstelement.upper() == QString("P")) return 3;
if (firstelement.upper() == QString("S")) return 2;
// if not known...
return 1;
}
static double partialCharge(QString ident, int method) {
double ret_pc;
ret_pc = 0.0;
return ret_pc;
}
static double bondLength(int el1, int el2, int order) {
// make el1 the smaller element (by atomic number)
int swp;
if (el1 > el2) { swp = el1; el1 = el2; el2 = swp; }
if (order == 1) {
if (el1 == 1) {
if (el2 == 6) {
return 1.09;
}
if (el2 == 7) {
return 1.01;
}
if (el2 == 8) {
return 0.96;
}
}
if (el1 == 6) {
if (el2 == 6) {
return 1.54;
}
if (el2 == 7) {
return 1.47;
}
if (el2 == 8) {
return 1.43;
}
if (el2 == 9) {
return 1.35;
}
if (el2 == 16) {
return 1.82;
}
if (el2 == 17) {
return 1.77;
}
if (el2 == 35) {
return 1.94;
}
if (el2 == 53) {
return 2.14;
}
}
if (el1 == 7) {
if (el2 == 8) {
}
}
}
if (order == 2) {
if (el1 == 6) {
if (el2 == 6) {
return 1.34;
}
if (el2 == 7) {
}
if (el2 == 8) {
}
}
}
if (order == 3) {
if (el1 == 6) {
if (el2 == 6) {
return 1.20;
}
if (el2 == 7) {
}
}
}
return 1.54;
}
static double bondAngleDegrees(int el1, int neighbors) {
if (el1 == 6) {
if (neighbors == 1) return 0.0;
if (neighbors == 2) return 180.0;
if (neighbors == 3) return 120.0;
if (neighbors == 4) return 109.47;
}
if (el1 == 7) {
if (neighbors == 1) return 180.0;
if (neighbors == 2) return 120.0;
if (neighbors == 3) return 109.47;
}
if (el1 == 8) {
if (neighbors == 1) return 180.0;
if (neighbors == 2) return 120.0;
}
if (el1 == 14) {
if (neighbors == 1) return 0.0;
if (neighbors == 2) return 180.0;
if (neighbors == 3) return 120.0;
if (neighbors == 4) return 109.47;
}
if (el1 == 15) {
if (neighbors == 1) return 180.0;
if (neighbors == 2) return 120.0;
if (neighbors == 3) return 109.47;
}
if (el1 == 16) {
if (neighbors == 1) return 180.0;
if (neighbors == 2) return 120.0;
}
return 109.47;
}
// important! maht.h expects angles in radians!
static double bondAngle(int el1, int neighbors) {
double retvald, retval;
retvald = bondAngleDegrees(el1, neighbors);
retval = retvald * 3.14159 / 180.0;
return retval;
}
};
#endif
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