R/19_output_for_other_database.R

In tidymass/metid: Metabolite identification based on MS1 and MS2 spectra

################################################################################
############################    MONA   ########################################
################################################################################

##------------------------------------------------------------------------------
#' Write MoNA Spectra to MSP Format
#'
#' This function writes positive and negative mode MS2 spectra from a given `databaseClass` object to MSP format files. The spectra are written separately for positive and negative ionization modes.
#'
#' @param database An object of class `databaseClass` containing spectral data and metadata.
#' @param path A character string specifying the directory where the MSP files will be written. Defaults to the current directory (`"."`).
#'
#' @return This function does not return any value. It writes MSP files for positive and negative mode spectra in the specified directory.
#'
#' @details
#' This function extracts the spectra from a `databaseClass` object and writes them into MSP files. The positive mode spectra are written to `spectra_pos.msp` and the negative mode spectra are written to `spectra_neg.msp`. Each entry in the MSP file includes information such as the compound name, precursor type, ion mode, collision energy, and the corresponding MS2 spectrum.
#'
#' @examples
#' \dontrun{
#' # Write MSP data from a databaseClass object
#' write_msp_mona(database = my_database, path = "output_directory")
#' }
#'
#' @author Xiaotao Shen
#' \email{xiaotao.shen@@outlook.com}
#' @export

# setwd(masstools::get_project_wd())
# load("other_files/all_ms2_database/mike_in_house/msDatabase_hilic0.0.2")
# database = msDatabase_hilic0.0.2
# setwd("other_files/all_ms2_database/mike_in_house")
# write_msp_mona(database = database)
# x = read_msp_mona(file = "spectra_pos.msp")

write_msp_mona <-
  function(database, path = ".") {
    options(warn = -1)
    spectra.info = database@spectra.info
    spectra_pos = database@spectra.data$Spectra.positive
    spectra_neg = database@spectra.data$Spectra.negative
    
    if (length(spectra_pos) == 0 &
        length(spectra_neg) == 0) {
      message("No MS2 spectra.")
    }
    
    # temp = read_lines("2021_6_10/MoNA-export-LC-MS-MS_Spectra.msp")
    
    ####positive mode
    if (length(spectra_pos) > 0) {
      message(crayon::yellow("Write positive mode..."))
      unlink(
        x = file.path(path, "spectra_pos.msp"),
        recursive = TRUE,
        force = TRUE
      )
      sink(file = file.path(path, "spectra_pos.msp"),
           append = TRUE)
      purrr::walk2(
        .x = names(spectra_pos),
        .y = spectra_pos,
        .f = function(compound_id, spectra) {
          message(compound_id)
          purrr::walk2(
            .x = names(spectra),
            .y = spectra,
            .f = function(ce, single_spectra) {
              temp_spectra_info =
                spectra.info %>%
                dplyr::filter(Lab.ID == compound_id)
              result =
                c(
                  paste("Name:", temp_spectra_info$Compound.name),
                  paste("Synon:", temp_spectra_info$Synon),
                  paste("DB#:", temp_spectra_info$mona.ID),
                  paste("InChIKey:", temp_spectra_info$InChIKey),
                  paste("InChI:", temp_spectra_info$InChI),
                  paste("SMILES:", temp_spectra_info$SMILES),
                  paste("Precursor_type:", temp_spectra_info$Precursor_type),
                  paste("Spectrum_type:", "MS2"),
                  paste("PrecursorMZ:", temp_spectra_info$PrecursorMZ),
                  paste(
                    "Instrument_type:",
                    temp_spectra_info$Instrument.type
                  ),
                  paste("Instrument:", temp_spectra_info$Instrument),
                  paste("Ion_mode:", "P"),
                  paste("Collision_energy:", ce),
                  paste("Formula:", temp_spectra_info$Formula),
                  paste("MW:", temp_spectra_info$MW),
                  paste("ExactMass:", temp_spectra_info$mz),
                  paste("Comments:", temp_spectra_info$Comments),
                  paste("Num Peaks:", nrow(single_spectra))
                )
              single_spectra2 =
                single_spectra %>%
                apply(1, function(x) {
                  paste(x, collapse = " ")
                })
              result =
                c(result, single_spectra2, "")
              cat(
                result,
                file = file.path(path, "spectra_pos.msp"),
                append = TRUE,
                sep = "\n"
              )
              # writeLines(text = result, con = fileConn)
            }
          )
        }
      )
      sink()
      sink(NULL)
      message(crayon::green("Done."))
    }
    
    ###negative mode
    if (length(spectra_neg) > 0) {
      message(crayon::yellow("Write negative mode..."))
      unlink(
        x = file.path(path, "spectra_neg.msp"),
        recursive = TRUE,
        force = TRUE
      )
      sink(file = file.path(path, "spectra_neg.msp"),
           append = TRUE)
      purrr::walk2(
        .x = names(spectra_neg),
        .y = spectra_neg,
        .f = function(compound_id, spectra) {
          message(compound_id)
          purrr::walk2(
            .x = names(spectra),
            .y = spectra,
            .f = function(ce, single_spectra) {
              temp_spectra_info =
                spectra.info %>%
                dplyr::filter(Lab.ID == compound_id)
              result =
                c(
                  paste("Name:", temp_spectra_info$Compound.name),
                  paste("Synon:", temp_spectra_info$Synon),
                  paste("DB#:", temp_spectra_info$mona.ID),
                  paste("InChIKey:", temp_spectra_info$InChIKey),
                  paste("InChI:", temp_spectra_info$InChI),
                  paste("SMILES:", temp_spectra_info$SMILES),
                  paste("Precursor_type:", temp_spectra_info$Precursor_type),
                  paste("Spectrum_type:", "MS2"),
                  paste("PrecursorMZ:", temp_spectra_info$PrecursorMZ),
                  paste(
                    "Instrument_type:",
                    temp_spectra_info$Instrument.type
                  ),
                  paste("Instrument:", temp_spectra_info$Instrument),
                  paste("Ion_mode:", "P"),
                  paste("Collision_energy:", ce),
                  paste("Formula:", temp_spectra_info$Formula),
                  paste("MW:", temp_spectra_info$MW),
                  paste("ExactMass:", temp_spectra_info$mz),
                  paste("Comments:", temp_spectra_info$Comments),
                  paste("Num Peaks:", nrow(single_spectra))
                )
              single_spectra2 =
                single_spectra %>%
                apply(1, function(x) {
                  paste(x, collapse = " ")
                })
              result =
                c(result, single_spectra2, "")
              cat(
                result,
                file = file.path(path, "spectra_neg.msp"),
                append = TRUE,
                sep = "\n"
              )
              # writeLines(text = result, con = fileConn)
            }
          )
        }
      )
      sink()
      sink(NULL)
      message(crayon::green("Done."))
    }
  }


##------------------------------------------------------------------------------
#' Write MoNA Spectra to MGF Format
#'
#' This function writes positive and negative mode MS2 spectra from a given `databaseClass` object to MGF format files. The spectra are written separately for positive and negative ionization modes.
#'
#' @param database An object of class `databaseClass` containing spectral data and metadata.
#' @param path A character string specifying the directory where the MGF files will be written. Defaults to the current directory (`"."`).
#'
#' @return This function does not return any value. It writes MGF files for positive and negative mode spectra in the specified directory.
#'
#' @details
#' This function extracts the spectra from a `databaseClass` object and writes them into MGF files. The positive mode spectra are written to `spectra_pos.mgf` and the negative mode spectra are written to `spectra_neg.mgf`. Each entry in the MGF file includes information such as the compound name, precursor type, ion mode, collision energy, and the corresponding MS2 spectrum.
#'
#' @examples
#' \dontrun{
#' # Write MGF data from a databaseClass object
#' write_mgf_mona(database = my_database, path = "output_directory")
#' }
#'
#' @author Xiaotao Shen
#' \email{xiaotao.shen@@outlook.com}
#' @export

# setwd(masstools::get_project_wd())
# load("other_files/all_ms2_database/mike_in_house/msDatabase_hilic0.0.2")
# database = msDatabase_hilic0.0.2
# setwd("other_files/all_ms2_database/mike_in_house")
# write_mgf_mona(database = database)
# x = read_mgf_mona(file = "spectra_pos.mgf")

write_mgf_mona <-
  function(database, path = ".") {
    options(warn = -1)
    spectra.info = database@spectra.info
    spectra_pos = database@spectra.data$Spectra.positive
    spectra_neg = database@spectra.data$Spectra.negative
    
    if (length(spectra_pos) == 0 &
        length(spectra_neg) == 0) {
      message("No MS2 spectra.")
    }
    
    
    ####positive mode
    if (length(spectra_pos) > 0) {
      message(crayon::yellow("Write positive mode..."))
      unlink(
        x = file.path(path, "spectra_pos.mgf"),
        recursive = TRUE,
        force = TRUE
      )
      sink(file = file.path(path, "spectra_pos.mgf"),
           append = TRUE)
      purrr::walk2(
        .x = names(spectra_pos),
        .y = spectra_pos,
        .f = function(compound_id, spectra) {
          message(compound_id)
          purrr::walk2(
            .x = names(spectra),
            .y = spectra,
            .f = function(ce, single_spectra) {
              temp_spectra_info =
                spectra.info %>%
                dplyr::filter(Lab.ID == compound_id)
              result =
                c(
                  paste("Name:", temp_spectra_info$Compound.name),
                  paste("Synon:", temp_spectra_info$Synon),
                  paste("DB#:", temp_spectra_info$mona.ID),
                  paste("InChIKey:", temp_spectra_info$InChIKey),
                  paste("InChI:", temp_spectra_info$InChI),
                  paste("SMILES:", temp_spectra_info$SMILES),
                  paste("Precursor_type:", temp_spectra_info$Precursor_type),
                  paste("Spectrum_type:", "MS2"),
                  paste("PrecursorMZ:", temp_spectra_info$PrecursorMZ),
                  paste(
                    "Instrument_type:",
                    temp_spectra_info$Instrument.type
                  ),
                  paste("Instrument:", temp_spectra_info$Instrument),
                  paste("Ion_mode:", "P"),
                  paste("Collision_energy:", ce),
                  paste("Formula:", temp_spectra_info$Formula),
                  paste("MW:", temp_spectra_info$MW),
                  paste("ExactMass:", temp_spectra_info$mz),
                  paste("Comments:", temp_spectra_info$Comments),
                  paste("Num Peaks:", nrow(single_spectra))
                )
              single_spectra2 =
                single_spectra %>%
                apply(1, function(x) {
                  paste(x, collapse = " ")
                })
              result =
                c("BEGIN IONS", result, single_spectra2, "END IONS")
              cat(
                result,
                file = file.path(path, "spectra_pos.mgf"),
                append = TRUE,
                sep = "\n"
              )
              # writeLines(text = result, con = fileConn)
            }
          )
        }
      )
      sink()
      sink(NULL)
      message(crayon::green("Done."))
    }
    
    ###negative mode
    if (length(spectra_neg) > 0) {
      message(crayon::yellow("Write negative mode..."))
      unlink(
        x = file.path(path, "spectra_neg.mgf"),
        recursive = TRUE,
        force = TRUE
      )
      sink(file = file.path(path, "spectra_neg.mgf"),
           append = TRUE)
      purrr::walk2(
        .x = names(spectra_neg),
        .y = spectra_neg,
        .f = function(compound_id, spectra) {
          message(compound_id)
          purrr::walk2(
            .x = names(spectra),
            .y = spectra,
            .f = function(ce, single_spectra) {
              temp_spectra_info =
                spectra.info %>%
                dplyr::filter(Lab.ID == compound_id)
              result =
                c(
                  paste("Name:", temp_spectra_info$Compound.name),
                  paste("Synon:", temp_spectra_info$Synon),
                  paste("DB#:", temp_spectra_info$mona.ID),
                  paste("InChIKey:", temp_spectra_info$InChIKey),
                  paste("InChI:", temp_spectra_info$InChI),
                  paste("SMILES:", temp_spectra_info$SMILES),
                  paste("Precursor_type:", temp_spectra_info$Precursor_type),
                  paste("Spectrum_type:", "MS2"),
                  paste("PrecursorMZ:", temp_spectra_info$PrecursorMZ),
                  paste(
                    "Instrument_type:",
                    temp_spectra_info$Instrument.type
                  ),
                  paste("Instrument:", temp_spectra_info$Instrument),
                  paste("Ion_mode:", "P"),
                  paste("Collision_energy:", ce),
                  paste("Formula:", temp_spectra_info$Formula),
                  paste("MW:", temp_spectra_info$MW),
                  paste("ExactMass:", temp_spectra_info$mz),
                  paste("Comments:", temp_spectra_info$Comments),
                  paste("Num Peaks:", nrow(single_spectra))
                )
              single_spectra2 =
                single_spectra %>%
                apply(1, function(x) {
                  paste(x, collapse = " ")
                })
              result =
                c("BEGIN IONS", result, single_spectra2, "END IONS")
              cat(
                result,
                file = file.path(path, "spectra_neg.mgf"),
                append = TRUE,
                sep = "\n"
              )
              # writeLines(text = result, con = fileConn)
            }
          )
        }
      )
      sink()
      sink(NULL)
      message(crayon::green("Done."))
    }
  }



################################################################################
############################    MassBank   #####################################
################################################################################


##------------------------------------------------------------------------------
#' Write MassBank Spectra to MSP Format
#'
#' This function writes positive and negative mode MS2 spectra from a given `databaseClass` object to MSP format files. The spectra are written separately for positive and negative ionization modes.
#'
#' @param database An object of class `databaseClass` containing spectral data and metadata.
#' @param path A character string specifying the directory where the MSP files will be written. Defaults to the current directory (`"."`).
#'
#' @return This function does not return any value. It writes MSP files for positive and negative mode spectra in the specified directory.
#'
#' @details
#' This function extracts the spectra from a `databaseClass` object and writes them into MSP files. The positive mode spectra are written to `spectra_pos.msp` and the negative mode spectra are written to `spectra_neg.msp`. Each entry in the MSP file includes information such as the compound name, precursor type, ion mode, collision energy, and the corresponding MS2 spectrum.
#'
#' @examples
#' \dontrun{
#' # Write MSP data from a databaseClass object
#' write_msp_massbank(database = my_database, path = "output_directory")
#' }
#'
#' @author Xiaotao Shen
#' \email{xiaotao.shen@@outlook.com}
#' @export

# setwd(masstools::get_project_wd())
# load("other_files/all_ms2_database/mike_in_house/msDatabase_hilic0.0.2")
# database = msDatabase_hilic0.0.2
# setwd("other_files/all_ms2_database/mike_in_house")
# write_msp_massbank(database = database)
# x = read_msp_mona(file = "spectra_pos.msp")

write_msp_massbank <-
  function(database, path = ".") {
    options(warn = -1)
    spectra.info = database@spectra.info
    spectra_pos = database@spectra.data$Spectra.positive
    spectra_neg = database@spectra.data$Spectra.negative
    
    if (length(spectra_pos) == 0 &
        length(spectra_neg) == 0) {
      message("No MS2 spectra.")
    }
    
    
    ####positive mode
    if (length(spectra_pos) > 0) {
      message(crayon::yellow("Write positive mode..."))
      unlink(
        x = file.path(path, "spectra_pos.msp"),
        recursive = TRUE,
        force = TRUE
      )
      sink(file = file.path(path, "spectra_pos.msp"),
           append = TRUE)
      purrr::walk2(
        .x = names(spectra_pos),
        .y = spectra_pos,
        .f = function(compound_id, spectra) {
          message(compound_id)
          purrr::walk2(
            .x = names(spectra),
            .y = spectra,
            .f = function(ce, single_spectra) {
              temp_spectra_info =
                spectra.info %>%
                dplyr::filter(Lab.ID == compound_id)
              result =
                c(
                  paste("Name:", temp_spectra_info$Compound.name),
                  paste("Synon:", temp_spectra_info$Synon),
                  paste("DB#:", temp_spectra_info$massbank.ID),
                  paste("InChIKey:", temp_spectra_info$InChIKey),
                  paste("InChI:", temp_spectra_info$InChI),
                  paste("SMILES:", temp_spectra_info$SMILES),
                  paste("Precursor_type:", temp_spectra_info$Precursor_type),
                  paste("Spectrum_type:", "MS2"),
                  paste("PrecursorMZ:", temp_spectra_info$PrecursorMZ),
                  paste(
                    "Instrument_type:",
                    temp_spectra_info$Instrument.type
                  ),
                  paste("Instrument:", temp_spectra_info$Instrument),
                  paste("Ion_mode:", "POSITIVE"),
                  paste("Collision_energy:", ce),
                  paste("Formula:", temp_spectra_info$Formula),
                  paste("MW:", temp_spectra_info$MW),
                  paste("ExactMass:", temp_spectra_info$mz),
                  paste("Comments:", temp_spectra_info$Comments),
                  paste("Splash:", temp_spectra_info$Splash),
                  paste("Num Peaks:", nrow(single_spectra))
                )
              single_spectra2 =
                single_spectra %>%
                apply(1, function(x) {
                  paste(x, collapse = " ")
                })
              result =
                c(result, single_spectra2, "")
              cat(
                result,
                file = file.path(path, "spectra_pos.msp"),
                append = TRUE,
                sep = "\n"
              )
              # writeLines(text = result, con = fileConn)
            }
          )
        }
      )
      sink()
      sink(NULL)
      message(crayon::green("Done."))
    }
    
    ###negative mode
    if (length(spectra_neg) > 0) {
      message(crayon::yellow("Write negative mode..."))
      unlink(
        x = file.path(path, "spectra_neg.msp"),
        recursive = TRUE,
        force = TRUE
      )
      sink(file = file.path(path, "spectra_neg.msp"),
           append = TRUE)
      purrr::walk2(
        .x = names(spectra_neg),
        .y = spectra_neg,
        .f = function(compound_id, spectra) {
          message(compound_id)
          purrr::walk2(
            .x = names(spectra),
            .y = spectra,
            .f = function(ce, single_spectra) {
              temp_spectra_info =
                spectra.info %>%
                dplyr::filter(Lab.ID == compound_id)
              result =
                c(
                  paste("Name:", temp_spectra_info$Compound.name),
                  paste("Synon:", temp_spectra_info$Synon),
                  paste("DB#:", temp_spectra_info$massbank.ID),
                  paste("InChIKey:", temp_spectra_info$InChIKey),
                  paste("InChI:", temp_spectra_info$InChI),
                  paste("SMILES:", temp_spectra_info$SMILES),
                  paste("Precursor_type:", temp_spectra_info$Precursor_type),
                  paste("Spectrum_type:", "MS2"),
                  paste("PrecursorMZ:", temp_spectra_info$PrecursorMZ),
                  paste(
                    "Instrument_type:",
                    temp_spectra_info$Instrument.type
                  ),
                  paste("Instrument:", temp_spectra_info$Instrument),
                  paste("Ion_mode:", "NEGATIVE"),
                  paste("Collision_energy:", ce),
                  paste("Formula:", temp_spectra_info$Formula),
                  paste("MW:", temp_spectra_info$MW),
                  paste("ExactMass:", temp_spectra_info$mz),
                  paste("Comments:", temp_spectra_info$Comments),
                  paste("Splash:", temp_spectra_info$Splash),
                  paste("Num Peaks:", nrow(single_spectra))
                )
              single_spectra2 =
                single_spectra %>%
                apply(1, function(x) {
                  paste(x, collapse = " ")
                })
              result =
                c(result, single_spectra2, "")
              cat(
                result,
                file = file.path(path, "spectra_neg.msp"),
                append = TRUE,
                sep = "\n"
              )
              # writeLines(text = result, con = fileConn)
            }
          )
        }
      )
      sink()
      sink(NULL)
      message(crayon::green("Done."))
    }
  }


##------------------------------------------------------------------------------
#' Write MassBank Spectra to MGF Format
#'
#' This function writes positive and negative mode MS2 spectra from a given `databaseClass` object to MGF format files. The spectra are written separately for positive and negative ionization modes.
#'
#' @param database An object of class `databaseClass` containing spectral data and metadata.
#' @param path A character string specifying the directory where the MGF files will be written. Defaults to the current directory (`"."`).
#'
#' @return This function does not return any value. It writes MGF files for positive and negative mode spectra in the specified directory.
#'
#' @details
#' This function extracts the spectra from a `databaseClass` object and writes them into MGF files. The positive mode spectra are written to `spectra_pos.mgf` and the negative mode spectra are written to `spectra_neg.mgf`. Each entry in the MGF file includes information such as the compound name, precursor type, ion mode, collision energy, and the corresponding MS2 spectrum.
#'
#' @examples
#' \dontrun{
#' # Write MGF data from a databaseClass object
#' write_mgf_massbank(database = my_database, path = "output_directory")
#' }
#'
#' @author Xiaotao Shen
#' \email{xiaotao.shen@@outlook.com}
#' @export


# setwd(masstools::get_project_wd())
# load("other_files/all_ms2_database/mike_in_house/msDatabase_hilic0.0.2")
# database = msDatabase_hilic0.0.2
# setwd("other_files/all_ms2_database/mike_in_house")
# write_mgf_massbank(database = database)
# x = read_mgf_mona(file = "spectra_neg.mgf")

write_mgf_massbank <-
  function(database, path = ".") {
    options(warn = -1)
    spectra.info = database@spectra.info
    spectra_pos = database@spectra.data$Spectra.positive
    spectra_neg = database@spectra.data$Spectra.negative
    
    if (length(spectra_pos) == 0 &
        length(spectra_neg) == 0) {
      message("No MS2 spectra.")
    }
    
    
    ####positive mode
    if (length(spectra_pos) > 0) {
      message(crayon::yellow("Write positive mode..."))
      unlink(
        x = file.path(path, "spectra_pos.mgf"),
        recursive = TRUE,
        force = TRUE
      )
      sink(file = file.path(path, "spectra_pos.mgf"),
           append = TRUE)
      purrr::walk2(
        .x = names(spectra_pos),
        .y = spectra_pos,
        .f = function(compound_id, spectra) {
          message(compound_id)
          purrr::walk2(
            .x = names(spectra),
            .y = spectra,
            .f = function(ce, single_spectra) {
              temp_spectra_info =
                spectra.info %>%
                dplyr::filter(Lab.ID == compound_id)
              result =
                c(
                  paste("Name:", temp_spectra_info$Compound.name),
                  paste("Synon:", temp_spectra_info$Synon),
                  paste("DB#:", temp_spectra_info$massbank.ID),
                  paste("InChIKey:", temp_spectra_info$InChIKey),
                  paste("InChI:", temp_spectra_info$InChI),
                  paste("SMILES:", temp_spectra_info$SMILES),
                  paste("Precursor_type:", temp_spectra_info$Precursor_type),
                  paste("Spectrum_type:", "MS2"),
                  paste("PrecursorMZ:", temp_spectra_info$PrecursorMZ),
                  paste(
                    "Instrument_type:",
                    temp_spectra_info$Instrument.type
                  ),
                  paste("Instrument:", temp_spectra_info$Instrument),
                  paste("Ion_mode:", "POSITIVE"),
                  paste("Collision_energy:", ce),
                  paste("Formula:", temp_spectra_info$Formula),
                  paste("MW:", temp_spectra_info$MW),
                  paste("ExactMass:", temp_spectra_info$mz),
                  paste("Comments:", temp_spectra_info$Comments),
                  paste("Splash:", temp_spectra_info$Splash),
                  paste("Num Peaks:", nrow(single_spectra))
                )
              single_spectra2 =
                single_spectra %>%
                apply(1, function(x) {
                  paste(x, collapse = " ")
                })
              result =
                c("BEGIN IONS", result, single_spectra2, "END IONS")
              cat(
                result,
                file = file.path(path, "spectra_pos.mgf"),
                append = TRUE,
                sep = "\n"
              )
              # writeLines(text = result, con = fileConn)
            }
          )
        }
      )
      sink()
      sink(NULL)
      message(crayon::green("Done."))
    }
    
    ###negative mode
    if (length(spectra_neg) > 0) {
      message(crayon::yellow("Write negative mode..."))
      unlink(
        x = file.path(path, "spectra_neg.mgf"),
        recursive = TRUE,
        force = TRUE
      )
      sink(file = file.path(path, "spectra_neg.mgf"),
           append = TRUE)
      purrr::walk2(
        .x = names(spectra_neg),
        .y = spectra_neg,
        .f = function(compound_id, spectra) {
          message(compound_id)
          purrr::walk2(
            .x = names(spectra),
            .y = spectra,
            .f = function(ce, single_spectra) {
              temp_spectra_info =
                spectra.info %>%
                dplyr::filter(Lab.ID == compound_id)
              result =
                c(
                  paste("Name:", temp_spectra_info$Compound.name),
                  paste("Synon:", temp_spectra_info$Synon),
                  paste("DB#:", temp_spectra_info$massbank.ID),
                  paste("InChIKey:", temp_spectra_info$InChIKey),
                  paste("InChI:", temp_spectra_info$InChI),
                  paste("SMILES:", temp_spectra_info$SMILES),
                  paste("Precursor_type:", temp_spectra_info$Precursor_type),
                  paste("Spectrum_type:", "MS2"),
                  paste("PrecursorMZ:", temp_spectra_info$PrecursorMZ),
                  paste(
                    "Instrument_type:",
                    temp_spectra_info$Instrument.type
                  ),
                  paste("Instrument:", temp_spectra_info$Instrument),
                  paste("Ion_mode:", "NEGATIVE"),
                  paste("Collision_energy:", ce),
                  paste("Formula:", temp_spectra_info$Formula),
                  paste("MW:", temp_spectra_info$MW),
                  paste("ExactMass:", temp_spectra_info$mz),
                  paste("Comments:", temp_spectra_info$Comments),
                  paste("Splash:", temp_spectra_info$Splash),
                  paste("Num Peaks:", nrow(single_spectra))
                )
              single_spectra2 =
                single_spectra %>%
                apply(1, function(x) {
                  paste(x, collapse = " ")
                })
              result =
                c("BEGIN IONS", result, single_spectra2, "END IONS")
              cat(
                result,
                file = file.path(path, "spectra_neg.mgf"),
                append = TRUE,
                sep = "\n"
              )
              # writeLines(text = result, con = fileConn)
            }
          )
        }
      )
      sink()
      sink(NULL)
      message(crayon::green("Done."))
    }
  }





################################################################################
############################    GNPS      #####################################
################################################################################


##------------------------------------------------------------------------------
#' Write GNPS Spectra to MSP Format
#'
#' This function writes MS2 spectra from a given `databaseClass` object to MSP format files for both positive and negative ion modes. The spectra are written separately for each ion mode, following the format required for GNPS (Global Natural Products Social Molecular Networking).
#'
#' @param database An object of class `databaseClass` containing spectral data and metadata.
#' @param path A character string specifying the directory where the MSP files will be written. Defaults to the current directory (`"."`).
#'
#' @return This function does not return any value. It writes MSP files for positive and negative mode spectra in the specified directory.
#'
#' @details
#' This function extracts the spectra from a `databaseClass` object and writes them into MSP files. The positive mode spectra are written to `spectra_pos.msp` and the negative mode spectra are written to `spectra_neg.msp`. Each entry in the MSP file includes information such as the compound name, precursor type, ion mode, collision energy, and the corresponding MS2 spectrum in the required GNPS format.
#'
#' @examples
#' \dontrun{
#' # Write MSP data from a databaseClass object
#' write_msp_gnps(database = my_database, path = "output_directory")
#' }
#'
#' @author Xiaotao Shen
#' \email{xiaotao.shen@@outlook.com}
#' @export

# setwd(masstools::get_project_wd())
# load("other_files/all_ms2_database/mike_in_house/msDatabase_hilic0.0.2")
# database = msDatabase_hilic0.0.2
# setwd("other_files/all_ms2_database/mike_in_house")
# write_msp_gnps(database = database)
# x = read_msp_gnps(file = "spectra_neg.msp")

write_msp_gnps <-
  function(database, path = ".") {
    options(warn = -1)
    spectra.info = database@spectra.info
    spectra_pos = database@spectra.data$Spectra.positive
    spectra_neg = database@spectra.data$Spectra.negative
    
    if (length(spectra_pos) == 0 &
        length(spectra_neg) == 0) {
      message("No MS2 spectra.")
    }
    
    ####positive mode
    if (length(spectra_pos) > 0) {
      message(crayon::yellow("Write positive mode...\n"))
      unlink(
        x = file.path(path, "spectra_pos.msp"),
        recursive = TRUE,
        force = TRUE
      )
      sink(file = file.path(path, "spectra_pos.msp"),
           append = TRUE)
      purrr::walk2(
        .x = names(spectra_pos),
        .y = spectra_pos,
        .f = function(compound_id, spectra) {
          message(compound_id)
          purrr::walk2(
            .x = names(spectra),
            .y = spectra,
            .f = function(ce, single_spectra) {
              temp_spectra_info =
                spectra.info %>%
                dplyr::filter(Lab.ID == compound_id)
              result =
                c(
                  paste("NAME:", temp_spectra_info$Compound.name),
                  paste("PRECURSORMZ:", temp_spectra_info$PRECURSORMZ),
                  paste("PRECURSORTYPE:", temp_spectra_info$PRECURSORTYPE),
                  paste("FORMULA:", temp_spectra_info$Formula),
                  paste("Ontology:", temp_spectra_info$Ontology),
                  paste("INCHIKEY:", temp_spectra_info$InChIKey),
                  paste("SMILES:", temp_spectra_info$SMILES),
                  paste(
                    "RETENTIONTIME: CCS:",
                    temp_spectra_info$RETENTIONTIME
                  ),
                  paste("IONMODE:", "Positive"),
                  paste(
                    "INSTRUMENTTYPE:",
                    temp_spectra_info$Instrument.type
                  ),
                  paste("INSTRUMENT:", temp_spectra_info$Instrument),
                  paste("COLLISIONENERGY:", ce),
                  paste("Comment:", temp_spectra_info$Comment),
                  paste("Num Peaks:", nrow(single_spectra))
                )
              single_spectra2 =
                single_spectra %>%
                apply(1, function(x) {
                  paste(x, collapse = "\t")
                })
              result =
                c(result, single_spectra2, "", "")
              cat(
                result,
                file = file.path(path, "spectra_pos.msp"),
                append = TRUE,
                sep = "\n"
              )
              # writeLines(text = result, con = fileConn)
            }
          )
        }
      )
      sink()
      sink(NULL)
      message(crayon::green("Done."))
    }
    
    ###negative mode
    if (length(spectra_neg) > 0) {
      message(crayon::yellow("Write negative mode..."))
      unlink(
        x = file.path(path, "spectra_neg.msp"),
        recursive = TRUE,
        force = TRUE
      )
      sink(file = file.path(path, "spectra_neg.msp"),
           append = TRUE)
      purrr::walk2(
        .x = names(spectra_neg),
        .y = spectra_neg,
        .f = function(compound_id, spectra) {
          message(compound_id)
          purrr::walk2(
            .x = names(spectra),
            .y = spectra,
            .f = function(ce, single_spectra) {
              temp_spectra_info =
                spectra.info %>%
                dplyr::filter(Lab.ID == compound_id)
              result =
                c(
                  paste("NAME:", temp_spectra_info$Compound.name),
                  paste("PRECURSORMZ:", temp_spectra_info$PRECURSORMZ),
                  paste("PRECURSORTYPE:", temp_spectra_info$PRECURSORTYPE),
                  paste("FORMULA:", temp_spectra_info$Formula),
                  paste("Ontology:", temp_spectra_info$Ontology),
                  paste("INCHIKEY:", temp_spectra_info$InChIKey),
                  paste("SMILES:", temp_spectra_info$SMILES),
                  paste(
                    "RETENTIONTIME: CCS:",
                    temp_spectra_info$RETENTIONTIME
                  ),
                  paste("IONMODE:", "Positive"),
                  paste(
                    "INSTRUMENTTYPE:",
                    temp_spectra_info$Instrument.type
                  ),
                  paste("INSTRUMENT:", temp_spectra_info$Instrument),
                  paste("COLLISIONENERGY:", ce),
                  paste("Comment:", temp_spectra_info$Comment),
                  paste("Num Peaks:", nrow(single_spectra))
                )
              single_spectra2 =
                single_spectra %>%
                apply(1, function(x) {
                  paste(x, collapse = "\t")
                })
              result =
                c(result, single_spectra2, "", "")
              cat(
                result,
                file = file.path(path, "spectra_neg.msp"),
                append = TRUE,
                sep = "\n"
              )
              # writeLines(text = result, con = fileConn)
            }
          )
        }
      )
      sink()
      sink(NULL)
      message(crayon::green("Done."))
    }
  }


##------------------------------------------------------------------------------
#' Write GNPS Spectra to MGF Format
#'
#' This function writes MS2 spectra from a given `databaseClass` object to MGF format files for both positive and negative ion modes. The spectra are written separately for each ion mode, following the format required for GNPS (Global Natural Products Social Molecular Networking).
#'
#' @param database An object of class `databaseClass` containing spectral data and metadata.
#' @param path A character string specifying the directory where the MGF files will be written. Defaults to the current directory (`"."`).
#'
#' @return This function does not return any value. It writes MGF files for positive and negative mode spectra in the specified directory.
#'
#' @details
#' This function extracts the spectra from a `databaseClass` object and writes them into MGF files. The positive mode spectra are written to `spectra_pos.mgf` and the negative mode spectra are written to `spectra_neg.mgf`. Each entry in the MGF file includes information such as the compound name, precursor type, ion mode, retention time, and the corresponding MS2 spectrum in the required GNPS format.
#'
#' @examples
#' \dontrun{
#' # Write MGF data from a databaseClass object
#' write_mgf_gnps(database = my_database, path = "output_directory")
#' }
#'
#' @author Xiaotao Shen
#' \email{xiaotao.shen@@outlook.com}
#' @export
# setwd(masstools::get_project_wd())
# load("other_files/all_ms2_database/mike_in_house/msDatabase_hilic0.0.2")
# database = msDatabase_hilic0.0.2
# setwd("other_files/all_ms2_database/mike_in_house")
# write_mgf_gnps(database = database)
# x = read_mgf_gnps(file = "spectra_pos.mgf")

write_mgf_gnps <-
  function(database, path = ".") {
    options(warn = -1)
    spectra.info = database@spectra.info
    spectra_pos = database@spectra.data$Spectra.positive
    spectra_neg = database@spectra.data$Spectra.negative
    
    if (length(spectra_pos) == 0 &
        length(spectra_neg) == 0) {
      message("No MS2 spectra.")
    }
    
    
    ####positive mode
    if (length(spectra_pos) > 0) {
      message(crayon::yellow("Write positive mode..."))
      unlink(
        x = file.path(path, "spectra_pos.mgf"),
        recursive = TRUE,
        force = TRUE
      )
      sink(file = file.path(path, "spectra_pos.mgf"),
           append = TRUE)
      purrr::walk2(
        .x = names(spectra_pos),
        .y = spectra_pos,
        .f = function(compound_id, spectra) {
          message(compound_id)
          purrr::walk2(
            .x = names(spectra),
            .y = spectra,
            .f = function(ce, single_spectra) {
              temp_spectra_info =
                spectra.info %>%
                dplyr::filter(Lab.ID == compound_id)
              result =
                result =
                c(
                  paste("NAME:", temp_spectra_info$Compound.name),
                  paste("PRECURSORMZ:", temp_spectra_info$PRECURSORMZ),
                  paste("PRECURSORTYPE:", temp_spectra_info$PRECURSORTYPE),
                  paste("FORMULA:", temp_spectra_info$Formula),
                  paste("Ontology:", temp_spectra_info$Ontology),
                  paste("INCHIKEY:", temp_spectra_info$InChIKey),
                  paste("SMILES:", temp_spectra_info$SMILES),
                  paste(
                    "RETENTIONTIME: CCS:",
                    temp_spectra_info$RETENTIONTIME
                  ),
                  paste("IONMODE:", "Positive"),
                  paste(
                    "INSTRUMENTTYPE:",
                    temp_spectra_info$Instrument.type
                  ),
                  paste("INSTRUMENT:", temp_spectra_info$Instrument),
                  paste("COLLISIONENERGY:", ce),
                  paste("Comment:", temp_spectra_info$Comment),
                  paste("Num Peaks:", nrow(single_spectra))
                )
              single_spectra2 =
                single_spectra %>%
                apply(1, function(x) {
                  paste(x, collapse = "\t")
                })
              
              result =
                c("BEGIN IONS", result, single_spectra2, "END IONS", "", "")
              cat(
                result,
                file = file.path(path, "spectra_pos.mgf"),
                append = TRUE,
                sep = "\n"
              )
              # writeLines(text = result, con = fileConn)
            }
          )
        }
      )
      sink()
      sink(NULL)
      message(crayon::green("Done."))
    }
    
    ###negative mode
    if (length(spectra_neg) > 0) {
      message(crayon::yellow("Write negative mode..."))
      unlink(
        x = file.path(path, "spectra_neg.mgf"),
        recursive = TRUE,
        force = TRUE
      )
      sink(file = file.path(path, "spectra_neg.mgf"),
           append = TRUE)
      purrr::walk2(
        .x = names(spectra_neg),
        .y = spectra_neg,
        .f = function(compound_id, spectra) {
          message(compound_id)
          purrr::walk2(
            .x = names(spectra),
            .y = spectra,
            .f = function(ce, single_spectra) {
              temp_spectra_info =
                spectra.info %>%
                dplyr::filter(Lab.ID == compound_id)
              result =
                result =
                c(
                  paste("NAME:", temp_spectra_info$Compound.name),
                  paste("PRECURSORMZ:", temp_spectra_info$PRECURSORMZ),
                  paste("PRECURSORTYPE:", temp_spectra_info$PRECURSORTYPE),
                  paste("FORMULA:", temp_spectra_info$Formula),
                  paste("Ontology:", temp_spectra_info$Ontology),
                  paste("INCHIKEY:", temp_spectra_info$InChIKey),
                  paste("SMILES:", temp_spectra_info$SMILES),
                  paste(
                    "RETENTIONTIME: CCS:",
                    temp_spectra_info$RETENTIONTIME
                  ),
                  paste("IONMODE:", "Positive"),
                  paste(
                    "INSTRUMENTTYPE:",
                    temp_spectra_info$Instrument.type
                  ),
                  paste("INSTRUMENT:", temp_spectra_info$Instrument),
                  paste("COLLISIONENERGY:", ce),
                  paste("Comment:", temp_spectra_info$Comment),
                  paste("Num Peaks:", nrow(single_spectra))
                )
              single_spectra2 =
                single_spectra %>%
                apply(1, function(x) {
                  paste(x, collapse = "\t")
                })
              
              result =
                c("BEGIN IONS", result, single_spectra2, "END IONS", "", "")
              cat(
                result,
                file = file.path(path, "spectra_neg.mgf"),
                append = TRUE,
                sep = "\n"
              )
              # writeLines(text = result, con = fileConn)
            }
          )
        }
      )
      sink()
      sink(NULL)
      message(crayon::green("Done."))
    }
  }