pl.poznan.put.pdb.PdbRemark465Line Maven / Gradle / Ivy

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package pl.poznan.put.pdb;

import org.apache.commons.lang3.StringUtils;
import org.immutables.value.Value;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import pl.poznan.put.pdb.analysis.DefaultPdbResidue;
import pl.poznan.put.pdb.analysis.ImmutableDefaultPdbResidue;
import pl.poznan.put.pdb.analysis.PdbResidue;

import java.util.Arrays;
import java.util.Collections;
import java.util.Locale;
import java.util.Objects;

/** A representation of REMARK 465 in PDB format which describes missing residues. */
@Value.Immutable
public abstract class PdbRemark465Line implements ChainNumberICode {
  // @formatter:off
  /*
     REMARK 465
     REMARK 465 MISSING  RESIDUES
     REMARK 465 THE FOLLOWING  RESIDUES WERE NOT LOCATED IN THE
     REMARK 465 EXPERIMENT.  (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
     REMARK 465 IDENTIFIER;  SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.)
     REMARK 465
     REMARK 465   M RES C SSSEQI
     REMARK 465     ARG A    46
     REMARK 465     GLY A    47
     REMARK 465     ALA A    48
     REMARK 465     ARG A    49
     REMARK 465     MET A    50

     REMARK 465
     REMARK 465 MISSING RESIDUES
     REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE
     REMARK 465 EXPERIMENT. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
     REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.)
     REMARK 465   MODELS 1-20
     REMARK 465     RES C SSSEQI
     REMARK 465     MET A     1
     REMARK 465     GLY A     2
  */
  // @formatter:on

  public static final String PROLOGUE =
      "REMARK 465                                                                      \n"
          + "REMARK 465 MISSING RESIDUES                                                     \n"
          + "REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE                       \n"
          + "REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN               \n"
          + "REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.)                \n"
          + "REMARK 465                                                                      \n"
          + "REMARK 465   M RES C SSSEQI                                                     ";
  private static final String[] COMMENT_LINES = {
    "REMARK 465",
    "REMARK 465 MISSING RESIDUES",
    "REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE",
    "REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN",
    "REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.)",
    "REMARK 465 M RES C SSSEQI",
    "REMARK 465 EXPERIMENT. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER;",
    "REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.)",
    "REMARK 465 RES C SSSEQI"
  };
  private static final String REMARK_FORMAT =
      "  %1s %3s %c %5d%c                                                     ";
  private static final String FORMAT = "REMARK 465 " + PdbRemark465Line.REMARK_FORMAT;
  private static final Logger LOGGER = LoggerFactory.getLogger(PdbRemark465Line.class);

  /**
   * Checks if {@code line} is just a comment or a line with actual information.
   *
   * @param line A line of text.
   * @return True if {@code line} contains a comment only.
   */
  public static boolean isCommentLine(final String line) {
    final String lineTrimmed = StringUtils.normalizeSpace(line);

    return Arrays.stream(PdbRemark465Line.COMMENT_LINES)
            .anyMatch(comment -> Objects.equals(lineTrimmed, StringUtils.normalizeSpace(comment)))
        || lineTrimmed.startsWith("REMARK 465   MODELS");
  }

  /**
   * Parses a line of text to create an instance of this class.
   *
   * @param line A line of text starting with REMARK 465.
   * @return An instance of this class
   */
  public static PdbRemark465Line parse(final String line) {
    if (line.length() < 79) {
      throw new PdbParsingException("PDB REMARK line is not at least 79 character long");
    }

    try {
      final String recordName = line.substring(0, 6).trim();

      if (!Objects.equals("REMARK", recordName)) {
        throw new PdbParsingException("PDB line does not start with REMARK");
      }
      final int remarkNumber = Integer.parseInt(line.substring(7, 10).trim());
      if (remarkNumber != 465) {
        throw new PdbParsingException("Unsupported REMARK line occurred");
      }

      final String remarkContent = StringUtils.stripEnd(line.substring(11, 79), null);
      final int modelNumber =
          (remarkContent.charAt(2) == ' ') ? 0 : Integer.parseInt(remarkContent.substring(2, 3));
      final String residueName = remarkContent.substring(4, 7).trim();
      final String chainIdentifier = Character.toString(remarkContent.charAt(8));
      final int residueNumber = Integer.parseInt(remarkContent.substring(10, 15).trim());
      final String insertionCode =
          (remarkContent.length() == 15) ? " " : Character.toString(remarkContent.charAt(15));
      return ImmutablePdbRemark465Line.of(
          modelNumber, residueName, chainIdentifier, residueNumber, insertionCode);
    } catch (final NumberFormatException e) {
      throw new PdbParsingException("Failed to parse PDB REMARK 465 line", e);
    }
  }

  /** @return The value of the {@code modelNumber} attribute */
  @Value.Parameter(order = 1)
  public abstract int modelNumber();

  /** @return The value of the {@code residueName} attribute */
  @Value.Parameter(order = 2)
  public abstract String residueName();

  /** @return The value of the {@code chainIdentifier} attribute */
  @Override
  @Value.Parameter(order = 3)
  public abstract String chainIdentifier();

  /** @return The value of the {@code residueNumber} attribute */
  @Override
  @Value.Parameter(order = 4)
  public abstract int residueNumber();

  /** @return The value of the {@code insertionCode} attribute */
  @Override
  @Value.Parameter(order = 5)
  public abstract String insertionCode();

  @Override
  public final String toString() {
    return toPdb();
  }

  /** @return A line in PDB format. */
  public final String toPdb() {
    if (chainIdentifier().length() != 1) {
      PdbRemark465Line.LOGGER.error(
          "Field 'chainIdentifier' is longer than 1 char. Only first letter will be taken");
    }
    if (insertionCode().length() != 1) {
      PdbRemark465Line.LOGGER.error(
          "Field 'insertionCode' is longer than 1 char. Only first letter will be taken");
    }

    final String modelNumberString = (modelNumber() == 0) ? " " : String.valueOf(modelNumber());
    final char chain = chainIdentifier().charAt(0);
    final char icode = insertionCode().charAt(0);

    return String.format(
        Locale.US,
        PdbRemark465Line.FORMAT,
        modelNumberString,
        residueName(),
        chain,
        residueNumber(),
        icode);
  }

  /**
   * Creates an instance of {@link DefaultPdbResidue} marked as missing and without atoms.
   *
   * @return An instance of a missing residue.
   */
  public final PdbResidue toResidue() {
    return ImmutableDefaultPdbResidue.of(
        PdbResidueIdentifier.from(this), residueName(), residueName(), Collections.emptyList());
  }
}