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#include <iostream.h>
#include <qstring.h>
#include <qlist.h>
#include <qtextstream.h>
#include <qfile.h>
#include "chemdata.h"
#include "dpoint.h"
#include "text.h"
#include "defs.h"
bool ChemData::load_mdl(QString fn) {
QFile f(fn);
if (!f.open(IO_ReadOnly)) {
return false;
}
// molfiles are formatted text
QTextStream t(&f);
QString wholefile = t.read();
f.close();
return ProcessMDL(wholefile);
}
bool ChemData::ProcessMDL(QString wf) {
QTextStream t(&wf, IO_ReadOnly);
QList<DPoint> atoms;
QList<Text> labels;
Text *nt;
QString tmpline, tfont;
DPoint *newpt, *s1, *e1;
int atomcount, bondcount;
int d1, d2, d3, d4, n, o1;
double left = 999.0, top = 999.0;
int bi1 = 0;
double bd1 = 0.0;
// first line contains molecule name. If it starts with $, that probably
// indicates an MDL file format other than molfile.
QString line = t.readLine();
if (line.left(1) == QString("$")) {
cout << "Can't read this type of MDL file!" << endl;
return false;
}
// Second and third lines contain optional info. Discard for now
line = t.readLine();
line = t.readLine();
// Fourth line contains counts -- how many atoms, bonds, etc. Parse values
line = t.readLine();
atomcount = line.mid(1, 3).toShort();
bondcount = line.mid(4, 3).toShort();
// read in atom lines
for (n = 0; n < atomcount; n++) {
line = t.readLine();
newpt = new DPoint;
newpt->x = line.mid( 1, 10).toDouble();
newpt->y = -line.mid(11, 10).toDouble();
if (newpt->x < left) left = newpt->x;
if (newpt->y < top) top = newpt->y;
tmpline = line.mid(31,3);
tmpline = tmpline.stripWhiteSpace();
if (tmpline != QString("C")) {
nt = new Text(r);
nt->setPoint(newpt);
nt->setJustify(JUSTIFY_CENTER);
nt->Highlight(true);
nt->setText(tmpline);
tmpline.fill(' ');
nt->setTextMask(tmpline);
labels.append(nt);
}
atoms.append(newpt);
}
// now read in bonds - link to atoms read above
for (n = 0; n < bondcount; n++) {
line = t.readLine();
d1 = line.mid(1,3).toShort();
d2 = line.mid(4,3).toShort();
d3 = line.mid(7,3).toShort();
d4 = line.mid(10,3).toShort();
// remember, QList starts at 0, but atom list in molfile assumed to start
// at 1, so offset accordingly!
s1 = atoms.at(d1 - 1);
e1 = atoms.at(d2 - 1);
o1 = d3; // set order
if (d4 == 1) o1 = 5; // stereo up
if (d4 == 6) o1 = 7; // stereo down
addBond( s1, e1, 1, o1, QColor(0,0,0), true );
bd1 += s1->distanceTo(e1);
bi1++;
}
// Add labels after adding bonds
for (nt = labels.first(); nt != NULL; nt = labels.next() )
addText(nt);
double avglen = bd1 / (double)bi1;
double sf = r->getFixedLength_bond() / avglen;
// scale to match current fixed length
left *= sf;
top *= sf;
for (tmp_pt = atoms.first(); tmp_pt != NULL; tmp_pt = atoms.next() ) {
tmp_pt->x *= sf;
tmp_pt->y *= sf;
}
// move to fit on page
cout << left << endl;
cout << top << endl;
if ( left < 0.0 )
Move(-left + 5, 0);
if ( top < 0.0 )
Move(0, -top + 5);
return true;
}
bool ChemData::save_mdl(QString fn) {
QList<DPoint> up;
QList<Drawable> uo;
Text *tmp_text;
Bond *tmp_bond;
QString tmpline;
int acount = 0, bcount = 0;
// get all unique points and objects
up = UniquePoints();
uo = UniqueObjects();
if (up.count() == 0) return false; // don't write an empty file
// open file and text stream
QFile f(fn);
if (!f.open(IO_WriteOnly)) {
return false;
}
QTextStream t(&f);
// Copy text from Text objects to element field in DPoint
for (tmp_draw = uo.first(); tmp_draw != NULL; tmp_draw = uo.next() ) {
if (tmp_draw->Type() == TYPE_TEXT) {
tmp_text = (Text *)tmp_draw; // is this cheating?
tmp_text->Start()->element = tmp_text->getText();
}
}
// write first three lines -- blank, unless we want to add comments etc.
t << endl;
t << endl;
t << endl;
// find counts...
for (tmp_pt = up.first(); tmp_pt != 0; tmp_pt = up.next() ) {
acount++;
}
for (tmp_draw = uo.first(); tmp_draw != 0; tmp_draw = uo.next() ) {
if (tmp_draw->Type() == TYPE_BOND) bcount++;
}
// write counts line
t.width(3);
t << acount;
t.width(3);
t << bcount << " 0 0 0 0 0 0 0 0 1" << endl;
// Write atom list
for (tmp_pt = up.first(); tmp_pt != NULL; tmp_pt = up.next() ) {
tmpline = tmp_pt->element;
if (tmpline.length() < 3) tmpline.append(' ');
if (tmpline.length() < 3) tmpline.append(' ');
t.width(10);
t << tmp_pt->x;
t.width(10);
t << -tmp_pt->y << " 0.0000 " << tmpline;
t << " 0 0 0 0 0 0 0 0 0 0 0 0" << endl;
}
// write bond list
for (tmp_draw = uo.first(); tmp_draw != NULL; tmp_draw = uo.next() ) {
if (tmp_draw->Type() == TYPE_BOND) {
tmp_bond = (Bond *)tmp_draw; // I ask again, is this cheating?
t.width(3);
t << up.find( tmp_bond->Start() ) + 1;
t.width(3);
t << up.find( tmp_bond->End() ) + 1;
t.width(3);
t << tmp_bond->Order();
if (tmp_bond->Order() < 4)
t << " 0 0 0 0" << endl;
if (tmp_bond->Order() == 5)
t << " 1 0 0 0" << endl;
if (tmp_bond->Order() == 7)
t << " 6 0 0 0" << endl;
}
}
f.close();
return true;
}
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