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@kimisyo(晶 公畑)

原子の特徴を計算するプログラムを作成してみた

Last updated at Posted at 2021-02-07

#はじめに
分子の記述子計算ソフトウェアについては様々な情報があるが、原子の記述子計算についてはあまりないため自力で実装し、githubに登録してみた。

#環境

  • JDK 11
  • CDK 2.2

#対象記述子

CDKに搭載されている以下のもの

  • EffectiveAtomPolarizability
  • StabilizationPlusCharge
  • SigmaElectronegativity
  • PiElectronegativity
  • PartialSigmaCharge
  • PartialTChargeMMFF94
  • AtomDegree
  • AtomValance
  • AtomHybridizationVSEPR
  • AtomHybridization

その他

論文等から独自に実装してみたもの

  • longestMaxTopInMolecule
    • 分子内の2つの原子間の結合の最大数(分子全体で同じ値)
  • highestMaxTopInMolecule
    • その原子から見て分子内の他の原子との結合の最大数
  • diffSPAN
  • longestMaxTopDistInMolecule - highestMaxTopDistInMatrixRow
  • relSPAN
  • highestMaxTopDistInMatrixRow / longestMaxTopDistInMolecule

#使い方

ビルド方法

CDKなのでJavaのインストールをした後、CDK2.2.jarを指定してjavacでコンパイルする必要がある。

使い方

以下の通り。SDFとCSVの両方に出力するようにしてみた。

java -cp <ClassPathの指定> AtomicCircleDescriptorCalculator <input mol or sdf> <output mol or sdf> <output csv>

SDFの場合、プロパティに全原子分の値が原子順に半角空白区切りでで並ぶように出力している。

例

> <PartialTChargeMMFF94>
NaN -0.9 0.1382 0.0 0.0 -0.1382 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.8

ソース

こちらに全体はあるが、CDKでSDFの読み書きをしたり、SDFにプロパティを追加したりする参考にもなると思うため、以下に張り付けておく。

AtmicDescriptorCalculator.java
public class AtomicDescriptorCalculator {

    /* AtomicDescriptor 種別の定義 */
    public static HashMap<String, AbstractAtomicDescriptor> atomicDescriptorMap = new HashMap<String, AbstractAtomicDescriptor>();

    static {
        atomicDescriptorMap.put("EffectiveAtomPolarizability",
                new org.openscience.cdk.qsar.descriptors.atomic.EffectiveAtomPolarizabilityDescriptor());
        atomicDescriptorMap.put("StabilizationPlusCharge",
                new org.openscience.cdk.qsar.descriptors.atomic.StabilizationPlusChargeDescriptor());
        atomicDescriptorMap.put("SigmaElectronegativity",
                new org.openscience.cdk.qsar.descriptors.atomic.SigmaElectronegativityDescriptor());
        atomicDescriptorMap.put("PiElectronegativity",
                new org.openscience.cdk.qsar.descriptors.atomic.PiElectronegativityDescriptor());
        atomicDescriptorMap.put("PartialSigmaCharge",
                new org.openscience.cdk.qsar.descriptors.atomic.PartialSigmaChargeDescriptor());
        atomicDescriptorMap.put("PartialTChargeMMFF94",
                new org.openscience.cdk.qsar.descriptors.atomic.PartialTChargeMMFF94Descriptor());
        atomicDescriptorMap.put("AtomDegree", new org.openscience.cdk.qsar.descriptors.atomic.AtomDegreeDescriptor());
        atomicDescriptorMap.put("AtomValance", new org.openscience.cdk.qsar.descriptors.atomic.AtomValenceDescriptor());
        atomicDescriptorMap.put("AtomHybridizationVSEPR",
                new org.openscience.cdk.qsar.descriptors.atomic.AtomHybridizationVSEPRDescriptor());
        atomicDescriptorMap.put("AtomHybridization",
                new org.openscience.cdk.qsar.descriptors.atomic.AtomHybridizationDescriptor());
    }

    public static void main(String args[]) throws IOException{

        // 引数のチェック
        if (args.length != 3) {
            System.err.println("AtomicCircleDescriptorCalculator <input mol or sdf> <output mol or sdf> <output csv>");
            System.exit(1);
        }

        FileInputStream fis = null;
        IteratingSDFReader isr = null;
        FileWriter sdfFr = new FileWriter(args[1]);
        SDFWriter sdfWriter = new SDFWriter(sdfFr);
        ArrayList<AtomInfo> atomInfoList = new ArrayList<AtomInfo>();

        try {
            fis = new FileInputStream(new File(args[0]));
            isr = new IteratingSDFReader(fis, DefaultChemObjectBuilder.getInstance());

            // Syby AtomTypeMatcher の定義
            SybylAtomTypeMatcher typeMatcher = SybylAtomTypeMatcher.getInstance(DefaultChemObjectBuilder.getInstance());

            int cnt = 1;
            // 各分子の読み込み
            while (isr.hasNext()) {

                IAtomContainer mol = (IAtomContainer) isr.next();

                System.out.println("*** " + (cnt++) + " ***" + mol.getProperty("cdk:Title"));

                // 原子タイプの取得
                IAtomType[] atomTypes = typeMatcher.findMatchingAtomTypes(mol);

                // ShortestPaths格納用マトリクス
                int[][] shortestPaths = new int[mol.getAtomCount()][mol.getAtomCount()];

                // 最大パスの保持
                int longestMaxTopDistInMolecule = Integer.MIN_VALUE;

                // 分子毎のAtom情報
                AtomInfo[] atomInfoArrayByMolecule = new AtomInfo[mol.getAtomCount()];

                // 各原子の読み込みと原子記述子の計算、格納
                for (IAtom atom : mol.atoms()) {
                    // AtomInfoの生成
                    AtomInfo atomInfo = new AtomInfo();
                    atomInfoArrayByMolecule[atom.getIndex()] = atomInfo;
                    atomInfo.setTitle(mol.getProperty("cdk:Title"));
                    // atomInfo.setIndex(atom.getIndex()+1);
                    atomInfo.setIndex(atom.getIndex());
                    atomInfo.setSymbol(atom.getSymbol());
                    if (atomTypes[atom.getIndex()] != null) {
                        atomInfo.setAtomType(atomTypes[atom.getIndex()].getAtomTypeName());
                    }

                    // 原子記述子計算
                    for (String descriptorName : atomicDescriptorMap.keySet()) {
                        AbstractAtomicDescriptor aad = atomicDescriptorMap.get(descriptorName);
                        DescriptorValue dv = aad.calculate(atom, mol);
                        String aadValue = dv.getValue().toString();
                        atomInfo.setDescriptor(descriptorName, aadValue);
                    }

                    // パスに関する記述子の計算
                    ShortestPaths sp = new ShortestPaths(mol, atom);
                    atomInfo.setHighestMaxTopDistInMatrixRow(Integer.MIN_VALUE);
                    for (IAtom atom_target : mol.atoms()) {
                        shortestPaths[atom.getIndex()][atom_target.getIndex()] = sp.distanceTo(atom_target);
                        // 水素は無視する
                        if (!atom.getSymbol().equals("H") && !atom_target.getSymbol().equals("H")) {
                            if (sp.distanceTo(atom_target) > atomInfo.getHighestMaxTopDistInMatrixRow()) {
                                atomInfo.setHighestMaxTopDistInMatrixRow(sp.distanceTo(atom_target));
                            }
                            if (sp.distanceTo(atom_target) > longestMaxTopDistInMolecule) {
                                longestMaxTopDistInMolecule = sp.distanceTo(atom_target);
                            }
                        }
                    }
                }

                // 分子中の最大パスの設定
                for (int i = 0; i < shortestPaths.length; i++) {
                    atomInfoArrayByMolecule[i].setLongestMaxTopDistInMolecule(longestMaxTopDistInMolecule);
                }

                // 各原子の登録
                for (int i = 0; i < atomInfoArrayByMolecule.length; i++) {
                    if (!atomInfoArrayByMolecule[i].getSymbol().equals("H")) {
                        atomInfoList.add(atomInfoArrayByMolecule[i]);
                    }
                }

                // 各原子の記述子データを集めてmolオブジェクトに登録
                String longestMaxTopInMoleculeStr = "";
                String highestMaxTopInMoleculeStr = "";
                String diffSPAN3Str = "";
                String relSPAN4Str = "";
                for (int i = 0; i < atomInfoArrayByMolecule.length; i++) {
                    if(i != 0){
                        longestMaxTopInMoleculeStr += " ";
                        highestMaxTopInMoleculeStr += " ";
                        diffSPAN3Str += " ";
                        relSPAN4Str += " ";
                    }
                    longestMaxTopInMoleculeStr += atomInfoArrayByMolecule[i].getLongestMaxTopDistInMolecule();
                    highestMaxTopInMoleculeStr += atomInfoArrayByMolecule[i].getHighestMaxTopDistInMatrixRow();
                    diffSPAN3Str += atomInfoArrayByMolecule[i].getLongestMaxTopDistInMolecule() - atomInfoArrayByMolecule[i].getHighestMaxTopDistInMatrixRow();
                    relSPAN4Str += String.valueOf((double) atomInfoArrayByMolecule[i].getHighestMaxTopDistInMatrixRow() / (double) atomInfoArrayByMolecule[i].getLongestMaxTopDistInMolecule());
                }
                mol.setProperty("longestMaxTopInMolecule", longestMaxTopInMoleculeStr);
                mol.setProperty("highestMaxTopInMolecule", highestMaxTopInMoleculeStr);
                mol.setProperty("diffSPAN3", diffSPAN3Str);
                mol.setProperty("relSPAN4", relSPAN4Str);

                for (String descriptorName : atomicDescriptorMap.keySet()) {
                    String data = "";
                    for (int i = 0; i < atomInfoArrayByMolecule.length; i++) {
                        if(i != 0){
                            data += " ";
                        }
                        data += (String)atomInfoArrayByMolecule[i].getDescriptor(descriptorName);
                    }
                    mol.setProperty(descriptorName, data);
                }
                sdfWriter.write(mol);
            }

            sdfWriter.close();
            sdfFr.close();

            // 全分子/原子についてCSV出力
            FileWriter fw = new FileWriter(args[2]);

            // ヘッダ出力
            fw.write("Title,");
            fw.write("Index,");
            fw.write("Symbol,");
            fw.write("AtomType,");

            fw.write("longestMaxTopDistInMolecule,");
            fw.write("highestMaxTopDistInMatrixRow,");
            fw.write("diffSPAN3,");
            fw.write("relSPAN4");

            // 記述子計算結果の出力
            for (String descriptorName : atomicDescriptorMap.keySet()) {
                fw.write("," );
                fw.write(descriptorName);
            }
            fw.write("\n");

            // データ出力
            for (AtomInfo atomInfo : atomInfoList) {
                // 名前
                fw.write(atomInfo.getTitle() + ",");
                // ID出力
                fw.write(atomInfo.getIndex() + ",");
                // 原子
                fw.write(atomInfo.getSymbol() + ",");
                // 種別
                fw.write(atomInfo.getAtomType() + ",");

                fw.write(atomInfo.getLongestMaxTopDistInMolecule() + ",");
                fw.write(atomInfo.getHighestMaxTopDistInMatrixRow() + ",");
                fw.write(
                        (atomInfo.getLongestMaxTopDistInMolecule() - atomInfo.getHighestMaxTopDistInMatrixRow()) + ",");
                fw.write( String.valueOf((double) atomInfo.getHighestMaxTopDistInMatrixRow() / (double) atomInfo.getLongestMaxTopDistInMolecule()));

                // 記述子計算結果の出力
                for (String descriptorName : atomicDescriptorMap.keySet()) {
                    fw.write(",");
                    fw.write(atomInfo.getDescriptor(descriptorName));
                }
                fw.write("\n");
            }
            fw.close();

        } catch (Exception e) {
            e.printStackTrace();
        } finally {
            // ファイルのクローズ処理
            if (isr != null) {
                try {
                    isr.close();
                } catch (IOException e2) {
                    e2.printStackTrace();
                    ;
                }
            }
            if (fis != null) {
                try {
                    fis.close();
                } catch (IOException e2) {
                    e2.printStackTrace();
                }
            }
        }
    }
}

#おわりに
久々にJavaを使ったが、環境の準備やら、ソースの可読性がいまいちやらで非常にストレスフルであった。

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