R/data_dna_phyche.R

In genomaths/GenomAutomorphism: Compute the automorphisms between DNA's Abelian group representations

## Copyright (C) 2021-2024 Robersy Sanchez <https://genomaths.com/>
## Author: Robersy Sanchez This file is part of the R package
## 'GenomAutomorphism'.  'GenomAutomorphism' is a 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
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## 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/>.

#' Some Physicochemical Properties of DNA bases
#' 
#' This data set carries some relevant physicochemical properties of the 
#' DNA bases. Available properties are:
#' \describe{
#'   \item{"proton_affinity: "}{It is an indicatio of the thermodynamic 
#'    gradient between a molecule and the anionic form of that molecule upon
#'    removal of a proton from it
#'    (\href{https://en.wikipedia.org/wiki/Proton_affinity}{Wikipedia}). The
#'    proton affinity values, given in kJ/mol, were taken from reference (1),
#'    also available in Wolfram Alpha at https://www.wolframalpha.com/ and in
#'    the cell phone App 'Wolfram Alpha'.. Reference (2) provides several
#'    measurements accomplished by several computational and experimental
#'    approaches.
#'   }       
#'   \item{"partition_coef: "}{1-octanol/water partition coefficients, logP. 
#'   In the physical sciences, a partition coefficient (P) or distribution 
#'   coefficient (D) is the ratio of concentrations of a compound in a mixture
#'   of two immiscible solvents at equilibrium (3). The partition coefficient 
#'   measures how hydrophilic ("water-loving") or hydrophobic ("water-fearing")
#'   a chemical substance is. Partition coefficients are useful in estimating 
#'   the distribution of drugs within the body. Hydrophobic drugs with high 
#'   octanol-water partition coefficients are mainly distributed to hydrophobic
#'   areas such as lipid bilayers of cells. Conversely, hydrophilic drugs 
#'   (low octanol/water partition coefficients) are found primarily in aqueous
#'   regions such as blood serum. The partition coefficient values included
#'   here were taken from reference (1), also available in Wolfram Alpha at
#'   https://www.wolframalpha.com/  and in the cell phone App 'Wolfram Alpha'.
#'   }  
#'   \item{"dipole_moment: "}{Dipole-dipole, dipole-induced-dipole and London 
#'   force interactions among the bases in the helix are large, and make the 
#'   free energy of the helix depend on the base composition and sequence. The
#'   dipole moment values were taken from reference (4). The dipole moment of 
#'   DNA bases refers to the measure of polarity in the chemical bonds between
#'   atoms within the nucleobases. Dipole moments arise due to differences in 
#'   electronegativity between the bonded atoms. In DNA bases, these dipole 
#'   moments can influence the orientation of the bases when interacting with
#'   other molecules or surfaces, such as graphene/h-BN interfaces. The concept
#'   of dipole moments has been applied to analyze the electric moments of 
#'   RNA-binding proteins, which can help identify DNA-binding proteins and 
#'   provide insights into their mechanisms and prediction.
#'   }
#'   \item{"tautomerization_energy: "}{The term “tautomerism” is usually 
#'   defined as structural isomerism with a low barrier to interconversion
#'   between the isomers, for example, the enol/imino forms for cytosine and
#'   guanine. Tautomerization is a process where the chemical structure of a
#'   molecule, such as DNA bases, undergoes a rearrangement of its atoms. This
#'   rearrangement results in the formation of different isomers, called
#'   tautomers, which can exist in solution or in a cell. The DNA bases can
#'   undergo tautomeric shifts, which can potentially contribute to mutagenic
#'   mispairings during DNA replication. The energy required for
#'   tautomerization of DNA bases is known as tautomerization energy. These
#'   values were taken from reference (2) and the value for each base
#'   corresponds to the average of the values estimated from different
#'   measurement approaches.
#'   }
#' }
#' @references 
#' 1. Wolfram Research (2007), ChemicalData, Wolfram Language function, 
#' https://reference.wolfram.com/language/ref/ChemicalData.html (updated 2016).
#' 2. Moser A, Range K, York DM. Accurate proton affinity and gas-phase 
#' basicity values for molecules important in biocatalysis. J Phys Chem B. 
#' 2010;114: 13911–13921. doi:10.1021/jp107450n.
#' 3. Leo A, Hansch C, Elkins D. Partition coefficients and their uses. Chem
#' Rev. 1971;71: 525–616. doi:10.1021/cr60274a001.
#' 4. Vovusha H, Amorim RG, Scheicher RH, Sanyal B. Controlling the orientation
#' of nucleobases by dipole moment interaction with graphene/h-BN interfaces. 
#' RSC Adv. Royal Society of Chemistry; 2018;8: 6527–6531. 
#' doi:10.1039/c7ra11664k.
#' @usage 
#' data("dna_phyche", package = "GenomAutomorphism")
#' 
#' @format A data frame object.
#' @examples
#' data("dna_phyche", package = "GenomAutomorphism")
#' dna_phyche
#' 
#' ## Select DNA base tautomerization energy
#' te <- as.list(dna_phyche$tautomerization_energy)
#' names(te) <- rownames(dna_phyche)
#' 
#' ## Let's create DNAStringSet-class object
#' base <- DNAStringSet(x = c( seq1 ='ACGTGATCAAGT',
#'                             seq2 = 'GTGTGATCCAGT'))
#' 
#' dna_phychem(seqs = base, phychem = te,
#'             index_name = "Tautomerization-Energy")
#' 
"dna_phyche"