cifreader.java

化学图形处理软件

            String value = line.substring(14).trim();
            a = parseIntoDouble(value);
            possiblySetCellParams(a,b,c,alpha,beta,gamma);
        } else if (command.equals("length_b")) {
            String value = line.substring(14).trim();
            b = parseIntoDouble(value);
            possiblySetCellParams(a,b,c,alpha,beta,gamma);
        } else if (command.equals("length_c")) {
            String value = line.substring(14).trim();
            c = parseIntoDouble(value);
            possiblySetCellParams(a,b,c,alpha,beta,gamma);
        } else if (command.equals("angle_alpha")) {
            String value = line.substring(17).trim();
            alpha = parseIntoDouble(value);
            possiblySetCellParams(a,b,c,alpha,beta,gamma);
        } else if (command.equals("angle_beta")) {
            String value = line.substring(16).trim();
            beta = parseIntoDouble(value);
            possiblySetCellParams(a,b,c,alpha,beta,gamma);
        } else if (command.equals("angle_gamma")) {
            String value = line.substring(17).trim();
            gamma = parseIntoDouble(value);
            possiblySetCellParams(a,b,c,alpha,beta,gamma);
        }        
    }
    
    private void possiblySetCellParams(double a,double b,double c,double alpha,double beta,double gamma) {
        if (a != 0.0 && b != 0.0 && c != 0.0 &&
            alpha != 0.0 && beta != 0.0 && gamma != 0.0) {
            logger.info("Found and set crystal cell parameters");
            Vector3d[] axes = CrystalGeometryTools.notionalToCartesian(a,b,c, alpha, beta, gamma);
            
            crystal.setA(axes[0]);
            crystal.setB(axes[1]);
            crystal.setC(axes[2]);
        }
    }
    
    private void processLoopBlock() throws IOException {
        String line = input.readLine().trim();
        if (line.startsWith("_atom")) {
            logger.info("Found atom loop block");
            processAtomLoopBlock(line);
        } else {
            logger.warn("Skipping loop block");
            skipUntilEmptyOrCommentLine(line);
        }
    }

    private void skipUntilEmptyOrCommentLine(String line) throws IOException {
        // skip everything until empty line, or comment line
        while (line != null && line.length() > 0 && line.charAt(0) != '#') {
            line = input.readLine().trim();
        }
    }
    
    private void processAtomLoopBlock(String firstLine) throws IOException {
        int atomLabel = -1; // -1 means not found in this block
        int atomSymbol = -1;
        int atomFractX = -1;
        int atomFractY = -1;
        int atomFractZ = -1;
        int atomRealX = -1;
        int atomRealY = -1;
        int atomRealZ = -1;
        String line = firstLine.trim();
        int headerCount = 0;
        boolean hasParsableInformation = false;
        while (line != null && line.charAt(0) == '_') {
            headerCount++;
            if (line.equals("_atom_site_label") ||
                line.equals("_atom_site_label_atom_id")) {
                atomLabel = headerCount;
                hasParsableInformation = true;
                logger.info("label found in col: " + atomLabel);
            } else if (line.startsWith("_atom_site_fract_x")) {
                atomFractX = headerCount;
                hasParsableInformation = true;
                logger.info("frac x found in col: " + atomFractX);
            } else if (line.startsWith("_atom_site_fract_y")) {
                atomFractY = headerCount;
                hasParsableInformation = true;
                logger.info("frac y found in col: " + atomFractY);
            } else if (line.startsWith("_atom_site_fract_z")) {
                atomFractZ = headerCount;
                hasParsableInformation = true;
                logger.info("frac z found in col: " + atomFractZ);
            } else if (line.equals("_atom_site.Cartn_x")) {
                atomRealX = headerCount;
                hasParsableInformation = true;
                logger.info("cart x found in col: " + atomRealX);
            } else if (line.equals("_atom_site.Cartn_y")) {
                atomRealY = headerCount;
                hasParsableInformation = true;
                logger.info("cart y found in col: " + atomRealY);
            } else if (line.equals("_atom_site.Cartn_z")) {
                atomRealZ = headerCount;
                hasParsableInformation = true;
                logger.info("cart z found in col: " + atomRealZ);
            } else if (line.equals("_atom_site.type_symbol")) {
                atomSymbol = headerCount;
                hasParsableInformation = true;
                logger.info("type_symbol found in col: " + atomSymbol);
            } else {
                logger.warn("Ignoring atom loop block field: " + line);
            }
            line = input.readLine().trim();
        }
        if (hasParsableInformation == false ) {
            logger.info("No parsable info found");
            skipUntilEmptyOrCommentLine(line);
        } else {
            // now that headers are parsed, read the data
            while(line != null && line.length() > 0 && line.charAt(0) != '#') {
                logger.debug("new row");
                StringTokenizer tokenizer = new StringTokenizer(line);
                if (tokenizer.countTokens() < headerCount) {
                    logger.warn("Column count mismatch; assuming continued on next line");
                    logger.debug("Found #expected, #found: " + headerCount + ", " + tokenizer.countTokens());
                    tokenizer = new StringTokenizer(line + input.readLine());
                }
                int colIndex = 0;
                // process one row
                IAtom atom = crystal.getBuilder().newAtom("C");
                Point3d frac = new Point3d();
                Point3d real = new Point3d();
                boolean hasFractional = false;
                boolean hasCartesian = false;
                while (tokenizer.hasMoreTokens()) {
                    colIndex++;
                    String field = tokenizer.nextToken();
                    logger.debug("Parsing col,token: " + colIndex + "=" + field);
                    if (colIndex == atomLabel) {
                        if (atomSymbol == -1) {
                            // no atom symbol found, use label
                            String element = extractFirstLetters(field);
                            atom.setSymbol(element);
                        }
                        atom.setID(field);
                    } else if (colIndex == atomFractX) {
                        hasFractional = true;
                        frac.x = parseIntoDouble(field);
                    } else if (colIndex == atomFractY) {
                        hasFractional = true;
                        frac.y = parseIntoDouble(field);
                    } else if (colIndex == atomFractZ) {
                        hasFractional = true;
                        frac.z = parseIntoDouble(field);
                    } else if (colIndex == atomSymbol) {
                        atom.setSymbol(field);
                    } else if (colIndex == atomRealX) {
                        hasCartesian = true;
                        logger.debug("Adding x3: " + parseIntoDouble(field));
                        real.x = parseIntoDouble(field);
                    } else if (colIndex == atomRealY) {
                        hasCartesian = true;
                        logger.debug("Adding y3: " + parseIntoDouble(field));
                        real.y = parseIntoDouble(field);
                    } else if (colIndex == atomRealZ) {
                        hasCartesian = true;
                        logger.debug("Adding x3: " + parseIntoDouble(field));
                        real.z = parseIntoDouble(field);
                    }
                }
                if (hasCartesian) {
                    Vector3d a = crystal.getA();
                    Vector3d b = crystal.getB();
                    Vector3d c = crystal.getC();
                    frac = CrystalGeometryTools.cartesianToFractional(a, b, c, real);
                    atom.setFractionalPoint3d(frac);
                }
                if (hasFractional) {
                    atom.setFractionalPoint3d(frac);
                }
                logger.debug("Adding atom: " + atom);
                crystal.addAtom(atom);
                
                // look up next row
                line = input.readLine().trim();
            }
        }
    }
    
    /**
     * Process double in the format: '.071(1)'.
     */
    private double parseIntoDouble(String value) {
        double returnVal = 0.0;
        if (value.charAt(0) == '.') value = "0" + value;
        int bracketIndex = value.indexOf("(");
        if (bracketIndex != -1) {
            value = value.substring(0, bracketIndex);
        }
        try {
            returnVal = Double.parseDouble(value);
        } catch (Exception exception) {
            logger.error("Could not parse double string: " + value);
        }
        return returnVal;
    }
    
    private String extractFirstLetters(String value) {
        StringBuffer result = new StringBuffer();
        for (int i=0; i<value.length(); i++) {
            if (Character.isDigit(value.charAt(i))) {
                break;
            } else {
                result.append(value.charAt(i));
            }
        }
        return result.toString();
    }
    
    public void close() throws IOException {
        input.close();
    }
}