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misc/extra/src/main/java/org/openscience/cdk/io/INChIContentProcessorTool.java
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| Original file line number | Diff line number | Diff line change |
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| /* | ||
| * Copyright (c) 2017 John Mayfield <jwmay@users.sf.net> | ||
| * | ||
| * Contact: cdk-devel@lists.sourceforge.net | ||
| * | ||
| * 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 | ||
| */ | ||
|
|
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| package org.openscience.cdk.io; | ||
|
|
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| import org.openscience.cdk.interfaces.IAtom; | ||
| import org.openscience.cdk.interfaces.IAtomContainer; | ||
| import org.openscience.cdk.interfaces.IBond; | ||
| import org.openscience.cdk.tools.ILoggingTool; | ||
| import org.openscience.cdk.tools.LoggingToolFactory; | ||
|
|
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| import java.util.regex.Matcher; | ||
| import java.util.regex.Pattern; | ||
|
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| final class INChIContentProcessorTool { | ||
|
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| private static ILoggingTool logger = LoggingToolFactory.createLoggingTool(INChIContentProcessorTool.class); ; | ||
|
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| public INChIContentProcessorTool() {} | ||
|
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| /** | ||
| * Processes the content from the formula field of the INChI. | ||
| * Typical values look like C6H6, from INChI=1.12Beta/C6H6/c1-2-4-6-5-3-1/h1-6H. | ||
| */ | ||
| public IAtomContainer processFormula(IAtomContainer parsedContent, String atomsEncoding) { | ||
| logger.debug("Parsing atom data: ", atomsEncoding); | ||
|
|
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| Pattern pattern = Pattern.compile("([A-Z][a-z]?)(\\d+)?(.*)"); | ||
| String remainder = atomsEncoding; | ||
| while (remainder.length() > 0) { | ||
| logger.debug("Remaining: ", remainder); | ||
| Matcher matcher = pattern.matcher(remainder); | ||
| if (matcher.matches()) { | ||
| String symbol = matcher.group(1); | ||
| logger.debug("Atom symbol: ", symbol); | ||
| if (symbol.equals("H")) { | ||
| // don't add explicit hydrogens | ||
| } else { | ||
| String occurenceStr = matcher.group(2); | ||
| int occurence = 1; | ||
| if (occurenceStr != null) { | ||
| occurence = Integer.parseInt(occurenceStr); | ||
| } | ||
| logger.debug(" occurence: ", occurence); | ||
| for (int i = 1; i <= occurence; i++) { | ||
| parsedContent.addAtom(parsedContent.getBuilder().newInstance(IAtom.class, symbol)); | ||
| } | ||
| } | ||
| remainder = matcher.group(3); | ||
| if (remainder == null) remainder = ""; | ||
| logger.debug(" Remaining: ", remainder); | ||
| } else { | ||
| logger.error("No match found!"); | ||
| remainder = ""; | ||
| } | ||
| logger.debug("NO atoms: ", parsedContent.getAtomCount()); | ||
| } | ||
| return parsedContent; | ||
| } | ||
|
|
||
| /** | ||
| * Processes the content from the connections field of the INChI. | ||
| * Typical values look like 1-2-4-6-5-3-1, from INChI=1.12Beta/C6H6/c1-2-4-6-5-3-1/h1-6H. | ||
| * | ||
| * @param bondsEncoding the content of the INChI connections field | ||
| * @param container the atomContainer parsed from the formula field | ||
| * @param source the atom to build the path upon. If -1, then start new path | ||
| * | ||
| * @see #processFormula | ||
| */ | ||
| public void processConnections(String bondsEncoding, IAtomContainer container, int source) { | ||
| logger.debug("Parsing bond data: ", bondsEncoding); | ||
|
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| IBond bondToAdd = null; | ||
| /* Fixme: treatment of branching is too limited! */ | ||
| String remainder = bondsEncoding; | ||
| while (remainder.length() > 0) { | ||
| logger.debug("Bond part: ", remainder); | ||
| if (remainder.charAt(0) == '(') { | ||
| String branch = chopBranch(remainder); | ||
| processConnections(branch, container, source); | ||
| if (branch.length() + 2 <= remainder.length()) { | ||
| remainder = remainder.substring(branch.length() + 2); | ||
| } else { | ||
| remainder = ""; | ||
| } | ||
| } else { | ||
| Pattern pattern = Pattern.compile("^(\\d+)-?(.*)"); | ||
| Matcher matcher = pattern.matcher(remainder); | ||
| if (matcher.matches()) { | ||
| String targetStr = matcher.group(1); | ||
| int target = Integer.parseInt(targetStr); | ||
| logger.debug("Source atom: ", source); | ||
| logger.debug("Target atom: ", targetStr); | ||
| IAtom targetAtom = container.getAtom(target - 1); | ||
| if (source != -1) { | ||
| IAtom sourceAtom = container.getAtom(source - 1); | ||
| bondToAdd = container.getBuilder().newInstance(IBond.class, sourceAtom, targetAtom, | ||
| IBond.Order.SINGLE); | ||
| container.addBond(bondToAdd); | ||
| } | ||
| remainder = matcher.group(2); | ||
| source = target; | ||
| logger.debug(" remainder: ", remainder); | ||
| } else { | ||
| logger.error("Could not get next bond info part"); | ||
| return; | ||
| } | ||
| } | ||
| } | ||
| } | ||
|
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| /** | ||
| * Extracts the first full branch. It extracts everything between the first | ||
| * '(' and the corresponding ')' char. | ||
| */ | ||
| private String chopBranch(String remainder) { | ||
| boolean doChop = false; | ||
| int branchLevel = 0; | ||
| StringBuffer choppedString = new StringBuffer(); | ||
| for (int i = 0; i < remainder.length(); i++) { | ||
| char currentChar = remainder.charAt(i); | ||
| if (currentChar == '(') { | ||
| if (doChop) choppedString.append(currentChar); | ||
| doChop = true; | ||
| branchLevel++; | ||
| } else if (currentChar == ')') { | ||
| branchLevel--; | ||
| if (branchLevel == 0) { | ||
| doChop = false; | ||
| break; | ||
| } | ||
| if (doChop) choppedString.append(currentChar); | ||
| } else if (doChop) { | ||
| choppedString.append(currentChar); | ||
| } | ||
| } | ||
| return choppedString.toString(); | ||
| } | ||
|
|
||
| } |
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