org.openscience.cdk.io.CIFReader Maven / Gradle / Ivy
/* Copyright (C) 2003-2007 The Chemistry Development Kit (CDK) project
*
* Contact: [email protected]
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU Lesser General Public License
* as published by the Free Software Foundation; either version 2.1
* of the License, or (at your option) any later version.
* All we ask is that proper credit is given for our work, which includes
* - but is not limited to - adding the above copyright notice to the beginning
* of your source code files, and to any copyright notice that you may distribute
* with programs based on this work.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU Lesser General Public License for more details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA.
*
*/
package org.openscience.cdk.io;
import java.io.BufferedReader;
import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.io.Reader;
import java.io.StringReader;
import java.util.StringTokenizer;
import javax.vecmath.Point3d;
import javax.vecmath.Vector3d;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.geometry.CrystalGeometryTools;
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IChemFile;
import org.openscience.cdk.interfaces.IChemModel;
import org.openscience.cdk.interfaces.IChemObject;
import org.openscience.cdk.interfaces.IChemSequence;
import org.openscience.cdk.interfaces.ICrystal;
import org.openscience.cdk.io.formats.CIFFormat;
import org.openscience.cdk.io.formats.IResourceFormat;
import org.openscience.cdk.tools.ILoggingTool;
import org.openscience.cdk.tools.LoggingToolFactory;
/**
* This is not a reader for the CIF and mmCIF crystallographic formats.
* It is able, however, to extract some content from such files.
* It's very ad hoc, not written
* using any dictionary. So please complain if something is not working.
* In addition, the things it does read are considered experimental.
*
* The CIF example on the IUCR website has been tested, as well as Crambin (1CRN)
* in the PDB database.
*
* @cdk.module io
* @cdk.githash
*
* @cdk.keyword file format, CIF
* @cdk.keyword file format, mmCIF
*
* @author E.L. Willighagen
* @cdk.created 2003-10-12
* @cdk.iooptions
*/
public class CIFReader extends DefaultChemObjectReader {
private BufferedReader input;
private static ILoggingTool logger = LoggingToolFactory.createLoggingTool(CIFReader.class);
private ICrystal crystal = null;
// cell parameters
private double a = 0.0;
private double b = 0.0;
private double c = 0.0;
private double alpha = 0.0;
private double beta = 0.0;
private double gamma = 0.0;
/**
* Create an CIF like file reader.
*
* @param input source of CIF data
*/
public CIFReader(Reader input) {
this.input = new BufferedReader(input);
}
public CIFReader(InputStream input) {
this(new InputStreamReader(input));
}
public CIFReader() {
this(new StringReader(""));
}
@Override
public IResourceFormat getFormat() {
return CIFFormat.getInstance();
}
@Override
public void setReader(Reader reader) throws CDKException {
this.input = new BufferedReader(input);
}
@Override
public void setReader(InputStream input) throws CDKException {
setReader(new InputStreamReader(input));
}
@Override
public boolean accepts(Class testClass) {
if (IChemFile.class.equals(testClass)) return true;
Class[] interfaces = testClass.getInterfaces();
for (int i = 0; i < interfaces.length; i++) {
if (IChemFile.class.equals(interfaces[i])) return true;
}
Class superClass = testClass.getSuperclass();
if (superClass != null) return this.accepts(superClass);
return false;
}
/**
* Read a ChemFile from input.
*
* @return the content in a ChemFile object
*/
@Override
public T read(T object) throws CDKException {
if (object instanceof IChemFile) {
IChemFile cf = (IChemFile) object;
try {
cf = readChemFile(cf);
} catch (IOException e) {
logger.error("Input/Output error while reading from input.");
}
return (T) cf;
} else {
throw new CDKException("Only supported is reading of ChemFile.");
}
}
/**
* Read the ShelX from input. Each ShelX document is expected to contain
* one crystal structure.
*
* @return a ChemFile with the coordinates, charges, vectors, etc.
*/
private IChemFile readChemFile(IChemFile file) throws IOException {
IChemSequence seq = file.getBuilder().newInstance(IChemSequence.class);
IChemModel model = file.getBuilder().newInstance(IChemModel.class);
crystal = file.getBuilder().newInstance(ICrystal.class);
String line = input.readLine();
boolean end_found = false;
while (input.ready() && line != null && !end_found) {
if (line.length() == 0) {
logger.debug("Skipping empty line");
// skip empty lines
} else if (line.charAt(0) == '#') {
logger.warn("Skipping comment: ", line);
// skip comment lines
} else if (!(line.charAt(0) == '_' || line.startsWith("loop_"))) {
logger.warn("Skipping unrecognized line: ", line);
// skip line
} else {
/* determine CIF command */
String command = "";
int spaceIndex = line.indexOf(' ');
if (spaceIndex != -1) {
// everything upto space is command
try {
command = line.substring(0, spaceIndex);
} catch (StringIndexOutOfBoundsException sioobe) {
// disregard this line
break;
}
} else {
// complete line is command
command = line;
}
logger.debug("command: ", command);
if (command.startsWith("_cell")) {
processCellParameter(command, line);
} else if (command.equals("loop_")) {
processLoopBlock();
} else if (command.equals("_symmetry_space_group_name_H-M")) {
String value = line.substring(29).trim();
crystal.setSpaceGroup(value);
} else {
// skip command
logger.warn("Skipping command: ", command);
line = input.readLine();
if (line.startsWith(";")) {
logger.debug("Skipping block content");
line = input.readLine();
if (line != null) line = line.trim();
while (!line.equals(";")) {
line = input.readLine();
if (line != null) line = line.trim();
logger.debug("Skipping block line: ", line);
}
line = input.readLine();
}
}
}
line = input.readLine();
}
logger.info("Adding crystal to file with #atoms: ", crystal.getAtomCount());
model.setCrystal(crystal);
seq.addChemModel(model);
file.addChemSequence(seq);
return file;
}
private void processCellParameter(String command, String line) {
command = command.substring(6); // skip the "_cell." part
if (command.equals("length_a")) {
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();
if (line != null) line = line.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().newInstance(IAtom.class, "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();
if (line != null) line = line.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();
}
@Override
public void close() throws IOException {
input.close();
}
}