A reader for SHELX files. It currently supports SHELXL. * *
The SHELX format is described on the net: * * http://www.msg.ucsf.edu/local/programs/shelxl/ch_07.html. * * modified by Bob Hanson 2006/04 to allow * variant CrystalMaker .cmdf file reading * -- but by 2/2010 looks like these ASCII CrystalMaker files aren't used * anymore by CrystalMaker, and instead it uses a binary format. * CrystalMaker2.2.3 seems to attempt to read the files, but actually cannot. * At least not for the file given at http://www.ch.ic.ac.uk/chemime/ * */ public class ShelxReader extends AtomSetCollectionReader { private String[] sfacElementSymbols; private boolean isCmdf; private String[] tokens; private char altloc = '\0'; private int part; @Override public void initializeReader() { setFractionalCoordinates(true); } @Override protected boolean checkLine() throws Exception { int lineLength ; if (line.length() == 0 || line.startsWith(" ")) return true; // '=' as last char of line means continue on next line while ((lineLength = line.length()) > 0 && line.charAt(lineLength - 1) == '=') line = line.substring(0, lineLength - 1) + rd(); tokens = getTokens(); String command = tokens[0].toUpperCase(); if (command.equals("TITL")) { if (!doGetModel(++modelNumber, null)) return checkLastModel(); sfacElementSymbols = null; applySymmetryAndSetTrajectory(); setFractionalCoordinates(true); asc.newAtomSet(); asc.setAtomSetName(line.substring(4).trim()); return true; } if (command.equals("NOTE")) { isCmdf = true; return true; } if (!doProcessLines || lineLength < 3) return true; if (unsupportedRecordTypes.indexOf(";" + command + ";") >= 0) return true; for (int i = supportedRecordTypes.length; --i >= 0;) if (command.equals(supportedRecordTypes[i])) { processSupportedRecord(i); return true; } if (!isCmdf) assumeAtomRecord(); return true; } private final static String unsupportedRecordTypes = ";ZERR;DISP;UNIT;LAUE;REM;MORE;TIME;" + "HKLF;OMIT;SHEL;BASF;TWIN;EXTI;SWAT;HOPE;MERG;" + "SPEC;RESI;MOVE;ANIS;AFIX;HFIX;FRAG;FEND;EXYZ;" + "EXTI;EADP;EQIV;" + "CONN;BIND;FREE;" + "DFIX;DANG;BUMP;SAME;SADI;CHIV;FLAT;DELU;SIMU;" + "DEFS;ISOR;NCSY;SUMP;" + "L.S.;CGLS;BLOC;DAMP;STIR;WGHT;FVAR;" + "BOND;CONF;MPLA;RTAB;HTAB;LIST;ACTA;SIZE;TEMP;" + "WPDB;" + "FMAP;GRID;PLAN;MOLE;"; /** * Supported records -- remove from unsupportedRecordTypes if added here */ final private static String[] supportedRecordTypes = { "TITL", "CELL", "SPGR", "SFAC", "LATT", "SYMM", "NOTE", "ATOM", "PART", "END" }; private void processSupportedRecord(int recordIndex) throws Exception { //System.out.println(recordIndex+" "+line); switch (recordIndex) { case 0: // TITL case 9: // END break; case 1: // CELL cell(); break; case 2: // SPGR setSpaceGroupName(PT.parseTrimmedAt(line, 4)); break; case 3: // SFAC parseSfacRecord(); break; case 4: // LATT parseLattRecord(); break; case 5: // SYMM parseSymmRecord(); break; case 6: // NOTE isCmdf = true; break; case 7: // ATOM isCmdf = true; processCmdfAtoms(); break; case 8: // PART processPartRecord(); break; } } private void processPartRecord() { // email exchange with Brian McMahon 22.10.11 // see // https://journals.iucr.org/c/issues/2015/01/00/fa3356/ (in the below I // take PART to be the same as // _atom_site_disorder_group): // // "The use of PART numbers, introduced in SHELXL93, has proved invaluable // in the refinement of disordered structures. Two atoms are considered to // be bonded if they have the same PART number or if one of them is in // PART 0. The resulting connectivity table is used for the generation of // H atoms (HFIX and AFIX), for setting up restraints such as DELU, SIMU, // RIGU, CHIV, BUMP and SAME, and for generating tables of geometric // parameters (BOND, CONF, HTAB). Usually, most of the atoms are in // PART 0, but, for example, a molecule or side chain disordered over // three positions could use PART 1, PART 2 and PART 3. If the PART // number is negative, bonds are not generated to symmetry-equivalent // atoms. It should be noted that positive PART numbers 1, 2, 3 etc. // correspond to the alternative location indicators A, B, C etc. in // PDB format. However, this notation is difficult to use when there // is a disorder within a disorder." // atom.basLoc provides the base altloc "n" of "-n" // as symmetry is applied, if basLoc is found, then // the cloned atom is given an incremented altloc // this only works with C2 and m; with higher-order symmetry, this // will dump all the symmetry-related groups into the same configuration=2 // PART 1 become altloc '1' part = parseIntStr(tokens[1]); altloc = (char) (part == 0 ? 0 : '0' + Math.abs(part)); } private boolean isCentroSymmetric; private void parseLattRecord() throws Exception { int latt = parseIntStr(tokens[1]); isCentroSymmetric = (latt > 0); if (latt ==1 || latt == -1) return; asc.getXSymmetry().setLatticeParameter(latt); } boolean haveXYZ; private void parseSymmRecord() throws Exception { if (!haveXYZ) { setSymmetryOperator("x,y,z"); haveXYZ = true; } setSymmetryOperator(line.substring(4).trim()); } private void cell() throws Exception { /* example: * CELL wavelngth a b c alpha beta gamma * CELL 1.54184 7.11174 21.71704 30.95857 90.000 90.000 90.000 * * or CrystalMaker file: * * CELL a b c alpha beta gamma * CELL 7.11174 21.71704 30.95857 90.000 90.000 90.000 */ int ioff = tokens.length - 6; if (ioff == 2) asc.setInfo("wavelength", Float.valueOf(parseFloatStr(tokens[1]))); for (int ipt = 0; ipt < 6; ipt++) setUnitCellItem(ipt, parseFloatStr(tokens[ipt + ioff])); } private void parseSfacRecord() { // an SFAC record is one of two cases // a simple SFAC record contains element names // a general SFAC record contains coefficients for a single element boolean allElementSymbols = true; for (int i = tokens.length; allElementSymbols && --i >= 1;) { String token = tokens[i]; allElementSymbols = isValidElementSymbolNoCaseSecondChar(token); } String[] sfacTokens = PT.getTokens(line.substring(4)); if (allElementSymbols) parseSfacElementSymbols(sfacTokens); else parseSfacCoefficients(sfacTokens); } private void parseSfacElementSymbols(String[] sfacTokens) { if (sfacElementSymbols == null) { sfacElementSymbols = sfacTokens; } else { int oldCount = sfacElementSymbols.length; int tokenCount = sfacTokens.length; sfacElementSymbols = AU.arrayCopyS(sfacElementSymbols, oldCount + tokenCount); for (int i = tokenCount; --i >= 0;) sfacElementSymbols[oldCount + i] = sfacTokens[i]; } } private void parseSfacCoefficients(String[] sfacTokens) { float a1 = parseFloatStr(sfacTokens[1]); float a2 = parseFloatStr(sfacTokens[3]); float a3 = parseFloatStr(sfacTokens[5]); float a4 = parseFloatStr(sfacTokens[7]); float c = parseFloatStr(sfacTokens[9]); // element # is these floats rounded to nearest int int z = Math.round(a1 + a2 + a3 + a4 + c); String elementSymbol = getElementSymbol(z); int oldCount = 0; if (sfacElementSymbols == null) { sfacElementSymbols = new String[1]; } else { oldCount = sfacElementSymbols.length; sfacElementSymbols = AU.arrayCopyS(sfacElementSymbols, oldCount + 1); sfacElementSymbols[oldCount] = elementSymbol; } sfacElementSymbols[oldCount] = elementSymbol; } private void assumeAtomRecord() throws Exception { // this line gives an atom, because any line not starting with // a SHELX command is an atom float x = Float.NaN, y = Float.NaN, z = Float.NaN; float occ = 1; int elementIndex = -1; String atomName = null; try { atomName = tokens[0]; elementIndex = parseIntStr(tokens[1]) - 1; x = parsePrecision(tokens[2])%10; y = parsePrecision(tokens[3])%10; z = parsePrecision(tokens[4])%10; occ = parseFloatStr(tokens[5])%10; } catch (Exception e) { // must have a NaN } if (Float.isNaN(x) || Float.isNaN(y) || Float.isNaN(z)) { Logger.error("skipping line " + line); return; } Atom atom = asc.addNewAtom(); atom.atomName = atomName; atom.foccupancy = occ; boolean isQPeak = atomName.startsWith("Q"); if (isQPeak) { atom.elementSymbol = "Xx"; } else if (sfacElementSymbols != null && elementIndex >= 0 && elementIndex < sfacElementSymbols.length) { atom.elementSymbol = sfacElementSymbols[elementIndex]; } setAtomCoordXYZ(atom, x, y, z); atom.altLoc = altloc; atom.part = part; if (tokens.length == 12) { float[] data = new float[8]; data[0] = parseFloatStr(tokens[6]); //U11 data[1] = parseFloatStr(tokens[7]); //U22 data[2] = parseFloatStr(tokens[8]); //U33 data[3] = parseFloatStr(tokens[11]); //U12 data[4] = parseFloatStr(tokens[10]); //U13 data[5] = parseFloatStr(tokens[9]); //U23 for (int i = 0; i < 6; i++) if (Float.isNaN(data[i])) { Logger.error("Bad anisotropic Uij data: " + line); return; } asc.setAnisoBorU(atom, data, 8); // Ortep Type 8: D = 2pi^2, C = 2, a*b* } } private void processCmdfAtoms() throws Exception { while (rd() != null && line.length() > 10) { tokens = getTokens(); addAtomXYZSymName(tokens, 2, getSymbol(tokens[0]), tokens[1]); } } private String getSymbol(String sym) { if (sym == null) return "Xx"; int len = sym.length(); if (len < 2) return sym; char ch1 = sym.charAt(1); if (ch1 >= 'a' && ch1 <= 'z') return sym.substring(0, 2); return "" + sym.charAt(0); } public static boolean isValidElementSymbolNoCaseSecondChar(String str) { if (str == null) return false; int length = str.length(); if (length == 0) return false; char chFirst = str.charAt(0); if (length == 1) return Atom.isValidSym1(chFirst); if (length > 2) return false; char chSecond = str.charAt(1); return Atom.isValidSymNoCase(chFirst, chSecond); } @Override public void applySymmetryAndSetTrajectory() throws Exception { if (isCentroSymmetric && !ignoreFileSymmetryOperators) { if (!haveXYZ) { setSymmetryOperator("x,y,z"); } asc.getXSymmetry().getSymmetry().addInversion(); isCentroSymmetric = false; haveXYZ = false; } applySymTrajASCR(); } @Override public void finalizeSubclassReader() throws Exception { super.finalizeReaderASCR(); asc.xtalSymmetry.setPartProperty(); } }