* * http://www.mdli.com/downloads/public/ctfile/ctfile.jsp *
*
* also: http://www.mdl.com/downloads/public/ctfile/ctfile.pdf
*
* simple symmetry extension via load command: 9/2006 hansonr@stolaf.edu
*
* setAtomCoord(atom, x, y, z) applySymmetryAndSetTrajectory()
*
* simple 2D-->3D conversion using
*
* load "xxx.mol" FILTER "2D"
*
*
* Jmol 14.8.2 adds bond type 15 (quintuple) and 16 (sextuple)
*
*/
public class MolReader extends AtomSetCollectionReader {
/*
* from ctfile.pdf:
*
* $MDL REV 1 date/time
* $MOL
* $HDR
* [Molfile Header Block (see Chapter 4) = name, pgm info, comment]
* $END HDR
* $CTAB
* [Ctab Block (see Chapter 2) = count + atoms + bonds + lists + props]
* $END CTAB
* $RGP
* rrr [where rrr = Rgroup number]
* $CTAB
* [Ctab Block]
* $END CTAB
* $END RGP
* $END MOL
*/
private boolean haveAtomSerials;
protected boolean allow2D = true;
private int iatom0;
private V3000Rdr vr;
private int atomCount;
private String[] atomData;
public BS bsDeleted;
private boolean haveNonzeroZ;
/**
* fix charges for RN(=O)(O), =N(O)*, =N
*/
private boolean fixN;
private boolean is3D;
private int nDouble;
private int nH, nC;
@Override
public void initializeReader() throws Exception {
fixN = checkFilterKey("FIXN");
}
@Override
protected boolean checkLine() throws Exception {
boolean isMDL = (line.startsWith("$MDL"));
if (isMDL) {
discardLinesUntilStartsWith("$HDR");
rd();
if (line == null) {
Logger.warn("$HDR not found in MDL RG file");
continuing = false;
return false;
}
} else if (line.equals("M END")) {
return true;
}
if (doGetModel(++modelNumber, null)) {
iatom0 = asc.ac;
processMolSdHeader();
processCtab(isMDL);
vr = null;
if (isLastModel(modelNumber)) {
continuing = false;
return false;
}
}
if (line != null && line.indexOf("$$$$") < 0)
discardLinesUntilStartsWith("$$$$");
return true;
}
@Override
public void finalizeSubclassReader() throws Exception {
finalizeReaderMR();
}
protected void finalizeReaderMR() throws Exception {
if (fixN) {
addJmolScript("{search('[Nv4+0,nv4+0]')}.formalCharge=1;{search('{[Ov1-0]}[Nv4+1,nv4+1]')}.formalCharge=-1;");
}
check2D3D();
if (bsDeleted != null) {
asc.getBSAtoms(-1).andNot(bsDeleted);
}
isTrajectory = false;
finalizeReaderASCR();
}
/**
* Make some attempt to account for missing 2D/3D information or wrong information
* @throws Exception
*/
private void check2D3D() throws Exception {
if (haveNonzeroZ) {
if (is2D) {
is2D = optimize2D = false;
}
} else if (!is2D && !is3D) {
// all z values zero and no 2D or 3D flag
if (nC > 0 && nH == 0 && nDouble != 0) {
// JME does not write the 2D/3D line correctly
// double bonds with carbons and no hydrogens
// assume is 2D
is2D = true;
}
}
if (is2D) {
if (!allow2D) {
throw new Exception("File is 2D, not 3D");
}
set2D();
}
}
private void processMolSdHeader() throws Exception {
// We aren't being this strict. Line definitions are from ctfile.pdf (October 2003)
String header = "";
// Line 1: Molecule name. This line is unformatted, but like all
// other lines in a molfile may not extend beyond column 80.
// If no name is available, a blank line must be present.
// Caution: This line must not contain any of the reserved
// tags that identify any of the other CTAB file types
// such as $MDL (RGfile), $$$$ (SDfile record separator),
// $RXN (rxnfile), or $RDFILE (RDfile headers).
//
String thisDataSetName = line.trim();
asc.setCollectionName(thisDataSetName);
header += line + "\n";
// Line 2: This line has the format:
// IIPPPPPPPPMMDDYYHHmmddSSssssssssssEEEEEEEEEEEERRRRRR
// (FORTRAN: A2<--A8--><---A10-->A2I2<--F10.5-><---F12.5--><-I6-> )
// User's first and last initials (l), program name (P),
// date/time (M/D/Y,H:m), dimensional codes (d), scaling factors (S, s),
// energy (E) if modeling program input, internal
// registry number (R) if input through MDL form. A blank line can be
// substituted for line 2. If the internal registry number is more than
// 6 digits long, it is stored in an M REG line (described in Chapter 3).
rd();
if (line == null)
return;
header += line + "\n";
// default will be to have this be 3D, but we will also check
String dim = (line.length() >= 22 ? line.substring(20, 22) : null);
is3D = "3D".equals(dim);
is2D = !is3D && ("2D".equals(dim) || line.startsWith("JME "));
// Line 3: A line for comments. If no comment is entered, a blank line
// must be present.
rd();
if (line == null)
return;
line = line.trim();
header += line + "\n";
Logger.info(header);
checkCurrentLineForScript();
asc.setInfo("fileHeader", header);
newAtomSet(thisDataSetName);
}
private void processCtab(boolean isMDL) throws Exception {
if (isMDL)
discardLinesUntilStartsWith("$CTAB");
if (rd() == null)
return;
if (line.indexOf("V3000") >= 0) {
optimize2D = is2D && !noHydrogens;
vr = ((V3000Rdr) getInterface("org.jmol.adapter.readers.molxyz.V3000Rdr")).set(this);
discardLinesUntilContains("COUNTS");
vr.readAtomsAndBonds(getTokens());
} else {
readAtomsAndBonds(parseIntRange(line, 0, 3), parseIntRange(line, 3, 6));
}
applySymmetryAndSetTrajectory();
}
// 0 1 2 3 4 5 6 7
// 01234567890123456789012345678901234567890123456789012345678901234567890
// xxxxx.xxxxyyyyy.yyyyzzzzz.zzzz aaaddcccssshhhbbbvvvHHHrrriiimmmnnneee
private void readAtomsAndBonds(int ac, int bc) throws Exception {
atomCount = ac;
for (int i = 0; i < ac; ++i) {
rd();
int len = line.length();
String elementSymbol;
float x, y, z;
int charge = 0;
int isotope = 0;
int iAtom = Integer.MIN_VALUE;
x = parseFloatRange(line, 0, 10);
y = parseFloatRange(line, 10, 20);
z = parseFloatRange(line, 20, 30);
// CTFile doc for V3000:
// The “dimensional code” is maintained more explicitly.
// Thus “3D” really means 3D,
// although “2D” will be interpreted as 3D if
// any non-zero Z-coordinates are found.
if (len < 34) {
// deal with older Mol format where nothing after the symbol is used
elementSymbol = line.substring(31).trim();
} else {
elementSymbol = line.substring(31, 34).trim();
if (elementSymbol.equals("H1")) {
elementSymbol = "H";
isotope = 1;
}
if (len >= 39) {
int code = parseIntRange(line, 36, 39);
if (code >= 1 && code <= 7)
charge = 4 - code;
code = parseIntRange(line, 34, 36);
if (code != 0 && code >= -3 && code <= 4) {
isotope = JmolAdapter.getNaturalIsotope(JmolAdapter
.getElementNumber(elementSymbol)) + code;
}
//if (len >= 63) { this field is not really an atom number. It's for atom-atom mapping in reaction files
// iAtom = parseIntRange(line, 60, 63);
// if (iAtom == 0)
// iAtom = Integer.MIN_VALUE;
//}
// previous model in series may have atom numbers indicated
if (iAtom == Integer.MIN_VALUE && haveAtomSerials)
iAtom = i + 1;
}
}
addMolAtom(iAtom, isotope, elementSymbol, charge, x, y, z);
}
asc.setModelInfoForSet("dimension", (is2D ? "2D" : "3D"), asc.iSet);
rd();
if (line.startsWith("V ")) {
readAtomValues();
}
// read bonds
if (bc == 0)
asc.setNoAutoBond();
for (int i = 0; i < bc; ++i) {
if (i > 0)
rd();
String iAtom1, iAtom2;
int stereo = 0;
iAtom1 = line.substring(0, 3).trim();
iAtom2 = line.substring(3, 6).trim();
int order = parseIntRange(line, 6, 9);
if ((is2D || !is3D) && order == 1 && line.length() >= 12)
stereo = parseIntRange(line, 9, 12);
if (stereo != 0 && !is3D)
is2D = true;
order = fixOrder(order, stereo);
if (haveAtomSerials)
asc.addNewBondFromNames(iAtom1, iAtom2, order);
else
asc.addNewBondWithOrder(iatom0 + parseIntStr(iAtom1) - 1, iatom0
+ parseIntStr(iAtom2) - 1, order);
}
// read V2000 user data
Map