R/check_golden_rules2.R

In yufree/xMSannotator: xMSannotator: R package for network based annotation of metabolomics data.

check_golden_rules2 <- function(curformula, NOPS_check = FALSE) {
    
    
    # curformula<-d2$Formula[1]
    curformula <- as.character(curformula)
    strsplit_var <- strsplit(curformula, split = "")
    
    g1 <- gregexpr(curformula, pattern = "N[0-9]*")
    
    regexp_len <- attr(g1[[1]], "match.length")
    
    if (regexp_len > 0) {
        
        if (regexp_len == 1) {
            numnitrogens <- 1
            
        } else {
            numnitrogens <- paste(strsplit_var[[1]][(g1[[1]][1] + 
                1):(g1[[1]][1] + regexp_len - 1)], collapse = "")
            numnitrogens <- as.numeric(numnitrogens)
        }
    } else {
        numnitrogens <- 0
        
    }
    
    
    g1 <- gregexpr(curformula, pattern = "C[0-9]*")
    
    regexp_len <- attr(g1[[1]], "match.length")
    numcarbons <- 0
    if (regexp_len > 0) {
        if (regexp_len == 1) {
            numcarbons <- 1
            
        } else {
            numcarbons <- paste(strsplit_var[[1]][(g1[[1]][1] + 
                1):(g1[[1]][1] + regexp_len - 1)], collapse = "")
            numcarbons <- as.numeric(numcarbons)
        }
    } else {
        numcarbons <- 0
        
    }
    
    
    
    g1 <- gregexpr(curformula, pattern = "O[0-9]*")
    regexp_len <- attr(g1[[1]], "match.length")
    
    if (regexp_len > 0) {
        if (regexp_len == 1) {
            numoxygens <- 1
            
        } else {
            numoxygens <- paste(strsplit_var[[1]][(g1[[1]][1] + 
                1):(g1[[1]][1] + regexp_len - 1)], collapse = "")
            numoxygens <- as.numeric(numoxygens)
        }
    } else {
        numoxygens <- 0
        
    }
    
    g3 <- gregexpr(curformula, pattern = "H[0-9]*")
    regexp_len3 <- attr(g3[[1]], "match.length")
    numhydrogens <- 0
    if (regexp_len3 > 0) {
        if (regexp_len3 == 1) {
            numhydrogens <- 1
            
        } else {
            numhydrogens <- paste(strsplit_var[[1]][(g3[[1]][1] + 
                1):(g3[[1]][1] + regexp_len3 - 1)], collapse = "")
            numhydrogens <- as.numeric(numhydrogens)
        }
    } else {
        numhydrogens <- 0
        
    }
    
    
    
    g3 <- gregexpr(curformula, pattern = "P[0-9]*")
    
    regexp_len3 <- attr(g3[[1]], "match.length")
    
    if (regexp_len3 > 0) {
        
        if (regexp_len3 == 1) {
            numphos <- 1
            
        } else {
            numphos <- paste(strsplit_var[[1]][(g3[[1]][1] + 
                1):(g3[[1]][1] + regexp_len3 - 1)], collapse = "")
            
            numphos <- as.numeric(numphos)
            
        }
    } else {
        numphos <- 0
        
    }
    
    
    
    g3 <- gregexpr(curformula, pattern = "S[0-9]*")
    
    regexp_len3 <- attr(g3[[1]], "match.length")
    
    if (regexp_len3 > 0) {
        
        if (regexp_len3 == 1) {
            numsulphur <- 1
            
        } else {
            numsulphur <- paste(strsplit_var[[1]][(g3[[1]][1] + 
                1):(g3[[1]][1] + regexp_len3 - 1)], collapse = "")
            
            numsulphur <- as.numeric(numsulphur)
            
        }
    } else {
        numsulphur <- 0
        
    }
    
    
    
    if (numcarbons < 1) {
        
        bool_check <- 0
    } else {
        
        max_hydrogens <- (2 * numcarbons) + numnitrogens + 
            2
        
        nitrogen_to_carbon_ratio <- numnitrogens/numcarbons
        
        oxygen_to_carbon_ratio <- numoxygens/numcarbons
        
        phosphorus_to_carbon_ratio <- numphos/numcarbons
        
        sulphur_to_carbon_ratio <- numsulphur/numcarbons
        
        hydrogens_to_carbon_ratio <- numhydrogens/numcarbons
        
        bool_check <- 1
        
        
        
        if (hydrogens_to_carbon_ratio < 0.1 | hydrogens_to_carbon_ratio > 
            6) {
            
            bool_check = 0
        }
        
        if (nitrogen_to_carbon_ratio > 4) {
            
            bool_check = 0
        }
        
        if (oxygen_to_carbon_ratio > 3) {
            
            bool_check = 0
        }
        
        if (phosphorus_to_carbon_ratio > 2) {
            
            bool_check = 0
        }
        
        if (sulphur_to_carbon_ratio > 3) {
            
            bool_check = 0
        }
        
        if (NOPS_check == TRUE) {
            # NOPS>1
            if (numnitrogens > 1 & numoxygens > 1 & numphos > 
                1 & numsulphur > 1) {
                if (numnitrogens > 10 | numoxygens > 20 | 
                  numphos > 4 | numsulphur > 3) {
                  
                  bool_check <- 0
                }
                
            }
            
            
            # NOP>3
            if (numnitrogens > 3 & numoxygens > 3 & numphos > 
                3) {
                if (numnitrogens > 11 | numoxygens > 22 | 
                  numphos > 6) {
                  
                  bool_check <- 0
                }
                
            }
            
            # OPS>1
            if (numoxygens > 1 & numphos > 1 & numsulphur > 
                1) {
                if (numoxygens > 14 | numphos > 3 | numsulphur > 
                  3) {
                  
                  bool_check <- 0
                }
                
            }
            
            # PSN>1
            if (numnitrogens > 1 & numphos > 1 & numsulphur > 
                1) {
                if (numnitrogens > 4 | numphos > 3 | numsulphur > 
                  3) {
                  
                  bool_check <- 0
                }
                
            }
            
            # NOS>6
            if (numnitrogens > 6 & numoxygens > 6 & numsulphur > 
                6) {
                if (numnitrogens > 19 | numoxygens > 14 | 
                  numsulphur > 8) {
                  
                  bool_check <- 0
                }
                
            }
            
        }
        
        
    }
    res <- cbind(curformula, bool_check)
    res <- as.data.frame(res)
    return(res)
    
}