Java tutorial
/************************************************************************* * * * This file is part of the 20n/act project. * * 20n/act enables DNA prediction for synthetic biology/bioengineering. * * Copyright (C) 2017 20n Labs, Inc. * * * * Please direct all queries to act@20n.com. * * * * This program is free software: you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation, either version 3 of the License, or * * (at your option) any later version. * * * * 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 General Public License for more details. * * * * You should have received a copy of the GNU General Public License * * along with this program. If not, see <http://www.gnu.org/licenses/>. * * * *************************************************************************/ package com.act.biointerpretation.mechanisminspection; import act.server.MongoDB; import act.server.NoSQLAPI; import act.shared.Chemical; import act.shared.Reaction; import chemaxon.calculations.clean.Cleaner; import chemaxon.formats.MolExporter; import chemaxon.formats.MolFormatException; import chemaxon.formats.MolImporter; import chemaxon.struc.Molecule; import chemaxon.struc.RxnMolecule; import org.apache.commons.cli.CommandLine; import org.apache.commons.cli.CommandLineParser; import org.apache.commons.cli.DefaultParser; import org.apache.commons.cli.HelpFormatter; import org.apache.commons.cli.Option; import org.apache.commons.cli.Options; import org.apache.commons.cli.ParseException; import org.apache.commons.lang3.StringUtils; import org.apache.logging.log4j.LogManager; import org.apache.logging.log4j.Logger; import java.io.File; import java.io.FileOutputStream; import java.io.IOException; import java.util.ArrayList; import java.util.List; public class ReactionRenderer { private static final Logger LOGGER = LogManager.getFormatterLogger(ReactionRenderer.class); public static final String OPTION_READ_DB = "d"; public static final String OPTION_RXN_IDS = "r"; public static final String OPTION_DIR_PATH = "f"; public static final String OPTION_FILE_FORMAT = "e"; public static final String OPTION_HEIGHT = "y"; public static final String OPTION_WIDTH = "x"; public static final String OPTION_COFACTOR = "c"; public static final String HELP_MESSAGE = StringUtils .join(new String[] { "This class renders representations of a reaction." }, ""); public static final List<Option.Builder> OPTION_BUILDERS = new ArrayList<Option.Builder>() { { add(Option.builder(OPTION_READ_DB).argName("read db name").desc("The name of the read DB to use") .hasArg().required().longOpt("db")); add(Option.builder(OPTION_RXN_IDS).argName("id").desc("The id of the reaction to validate").hasArgs() .valueSeparator(',').required().longOpt("id")); add(Option.builder(OPTION_DIR_PATH).argName("dir path") .desc("The dir path where the image will be rendered").hasArg().required().longOpt("dir path")); // The list of file formats supported are here: https://marvin-demo.chemaxon.com/marvin/help/formats/formats.html add(Option.builder(OPTION_FILE_FORMAT).argName("file format").desc("The file format for the image") .hasArg().required().longOpt("file format")); add(Option.builder(OPTION_HEIGHT).argName("height").desc("height of image").hasArg().longOpt("height")); add(Option.builder(OPTION_WIDTH).argName("width").desc("width of image").hasArg().longOpt("width")); add(Option.builder(OPTION_COFACTOR).argName("cofactor") .desc("true if cofactors need to be rendered, false otherwise").hasArg().longOpt("cofactor")); add(Option.builder("h").argName("help").desc("Prints this help message").longOpt("help")); } }; public static final HelpFormatter HELP_FORMATTER = new HelpFormatter(); static { HELP_FORMATTER.setWidth(100); } private static final String DEFAULT_FORMAT = "png"; private static final Integer DEFAULT_WIDTH = 1000; private static final Integer DEFAULT_HEIGHT = 1000; private static final String XENON_INCHI = "InChI=1S/Xe"; private static final String SMARTS_FORMAT = "smarts"; String format; Integer width; Integer height; public ReactionRenderer() { this.format = DEFAULT_FORMAT; this.width = DEFAULT_WIDTH; this.height = DEFAULT_HEIGHT; } public ReactionRenderer(String format, Integer width, Integer height) { this.format = format; this.width = width; this.height = height; } public void drawReaction(MongoDB db, Long reactionId, String dirPath, boolean includeCofactors) throws IOException { RxnMolecule renderedReactionMolecule = getRxnMolecule(db, reactionId, includeCofactors); String fileName = StringUtils.join(new String[] { reactionId.toString(), ".", format }); drawRxnMolecule(renderedReactionMolecule, new File(dirPath, fileName)); } public String getSmartsForReaction(MongoDB db, Long reactionId, boolean includeCofactors) throws IOException { RxnMolecule rxnMolecule = getRxnMolecule(db, reactionId, includeCofactors); return getSmartsNotation(rxnMolecule); } public RxnMolecule getRxnMolecule(MongoDB db, Long reactionId, boolean includeCofactors) { RxnMolecule renderedReactionMolecule = new RxnMolecule(); List<Long> substrateIds = getSubstrates(db, reactionId, includeCofactors); List<Long> productIds = getProducts(db, reactionId, includeCofactors); for (Long sub : substrateIds) { Chemical chemical = db.getChemicalFromChemicalUUID(sub); Molecule mol = importMoleculeOrXenon(chemical); renderedReactionMolecule.addComponent(mol, RxnMolecule.REACTANTS); } for (Long prod : productIds) { Chemical chemical = db.getChemicalFromChemicalUUID(prod); Molecule mol = importMoleculeOrXenon(chemical); renderedReactionMolecule.addComponent(mol, RxnMolecule.PRODUCTS); } return renderedReactionMolecule; } private List<Long> getSubstrates(MongoDB db, Long reactionId, boolean includeCofactors) { Reaction r = db.getReactionFromUUID(reactionId); List<Long> substrates = new ArrayList<>(); for (Long id : r.getSubstrates()) { substrates.add(id); } if (includeCofactors) { for (Long id : r.getSubstrateCofactors()) { substrates.add(id); } } return substrates; } private List<Long> getProducts(MongoDB db, Long reactionId, boolean includeCofactors) { Reaction r = db.getReactionFromUUID(reactionId); List<Long> products = new ArrayList<>(); for (Long id : r.getProducts()) { products.add(id); } if (includeCofactors) { for (Long id : r.getProductCofactors()) { products.add(id); } } return products; } public void drawRxnMolecule(RxnMolecule molecule, File imageFile) throws IOException { // Change the reaction arrow type. molecule.setReactionArrowType(RxnMolecule.REGULAR_SINGLE); drawMolecule(molecule, imageFile); } public void drawMolecule(Molecule molecule, File imageFile) throws IOException { // Calculate coordinates with a 2D coordinate system. Cleaner.clean(molecule, 2, null); byte[] graphics = MolExporter.exportToBinFormat(molecule, getFormatAndSizeString()); try (FileOutputStream fos = new FileOutputStream(imageFile)) { fos.write(graphics); } } public String getSmartsNotation(Molecule mol) throws IOException { return MolExporter.exportToFormat(mol, SMARTS_FORMAT); } /** * Imports the molecule if possible, or else returns a Xenon atom as a placeholder for rendering. * * @throws MolFormatException */ private Molecule importMoleculeOrXenon(Chemical chemical) { try { return chemical.importAsMolecule(); } catch (MolFormatException e) { LOGGER.warn("No molecule returned for chemical %d. Replacing with Xenon.", chemical.getUuid()); try { return MolImporter.importMol(XENON_INCHI); } catch (MolFormatException f) { LOGGER.error("Could not import xenon inchi; something is very wrong."); throw new RuntimeException(f); } } } public String getFormat() { return format; } public void setFormat(String format) { this.format = format; } public Integer getWidth() { return width; } public void setWidth(Integer width) { this.width = width; } public Integer getHeight() { return height; } public void setHeight(Integer height) { this.height = height; } private String getFormatAndSizeString() { return format + StringUtils.join(":w", width.toString(), ",", "h", height.toString()); } public static void main(String[] args) throws IOException { Options opts = new Options(); for (Option.Builder b : OPTION_BUILDERS) { opts.addOption(b.build()); } CommandLine cl = null; try { CommandLineParser parser = new DefaultParser(); cl = parser.parse(opts, args); } catch (ParseException e) { System.err.format("Argument parsing failed: %s\n", e.getMessage()); HELP_FORMATTER.printHelp(ReactionRenderer.class.getCanonicalName(), HELP_MESSAGE, opts, null, true); System.exit(1); } if (cl.hasOption("help")) { HELP_FORMATTER.printHelp(ReactionRenderer.class.getCanonicalName(), HELP_MESSAGE, opts, null, true); return; } Integer height = Integer.parseInt(cl.getOptionValue(OPTION_HEIGHT, "1000")); Integer width = Integer.parseInt(cl.getOptionValue(OPTION_WIDTH, "1000")); Boolean representCofactors = cl.hasOption(OPTION_COFACTOR) && Boolean.parseBoolean(cl.getOptionValue(OPTION_COFACTOR)); NoSQLAPI api = new NoSQLAPI(cl.getOptionValue(OPTION_READ_DB), cl.getOptionValue(OPTION_READ_DB)); for (String val : cl.getOptionValues(OPTION_RXN_IDS)) { Long reactionId = Long.parseLong(val); ReactionRenderer renderer = new ReactionRenderer(cl.getOptionValue(OPTION_FILE_FORMAT), width, height); renderer.drawReaction(api.getReadDB(), reactionId, cl.getOptionValue(OPTION_DIR_PATH), representCofactors); LOGGER.info(renderer.getSmartsForReaction(api.getReadDB(), reactionId, representCofactors)); } } }