Package 'volcalc'

Calculate volatility estimate for a compound

Description

Estimate relative volatility index value and category for specified compounds using group contribution methods.

Usage

calc_vol(
  input,
  from = c("mol_path", "smiles"),
  method = c("meredith", "simpol1"),
  temp_c = 20,
  environment = c("clean", "polluted", "soil"),
  validate = TRUE,
  return_fx_groups = FALSE,
  return_calc_steps = FALSE
)

Arguments

input	A path to a .mol file or a SMILES string.
from	The form of input. Either "mol_path" (default) or "smiles".
method	The method for calculating estimated volatility. See simpol1() for more details.
temp_c	numeric; For methods that allow it, specify temperature (in degrees C) at which log10(P) estimates are calculated.
environment	The environment for calculating relative volatility categories. RVI thresholds for low, moderate, and high volatility are as follows: "clean" (clean atmosphere, default) -2, 0, 2; "polluted" (polluted atmosphere) 0, 2, 4; "soil" 4, 6, 8. For more information about these thresholds see Meredith et al. (2023) and Donahue et al. (2006).
validate	logical; if TRUE (default), results are checked for possible errors in parsing by Open Babel and NAs are returned if possible errors are found. Setting to FALSE bypasses these checks—use at your own risk! Validation is not available on Windows. See Details of get_fx_groups() for more information.
return_fx_groups	When TRUE, the returned tibble includes functional group counts.
return_calc_steps	When TRUE, the returned tibble includes intermediate volatility calculations. See Details.

Details

$\textrm{log}_{10}C^\ast$ is used for the calculated relative volatility index (rvi). $\textrm{log}_{10}C^\ast = \textrm{log}_{10}(PM/RT)$ where $P$ is the estimated vapor pressure for the compound, $M$ is molecular mass of the compound, $R$ is the universal gas constant, and $T$ is temperature (293.14K or 20ºC). When return_calc_steps = TRUE, the log of estimated vapor pressure, log10_P, and $\textrm{log}_{10}(M/RT)$, log_alpha, are also returned.

Value

A tibble with relative volatility index (rvi) and volatility category (category).

References

Donahue, N.M., Robinson, A.L., Stanier, C.O., Pandis, S.N., 2006. Coupled Partitioning, Dilution, and Chemical Aging of Semivolatile Organics. Environ. Sci. Technol. 40, 2635–2643. doi:10.1021/es052297c

Meredith L, Ledford S, Riemer K, Geffre P, Graves K, Honeker L, LeBauer D, Tfaily M, Krechmer J. 2023. Automating methods for estimating metabolite volatility. Frontiers in Microbiology. doi:10.3389/fmicb.2023.1267234

See Also

get_fx_groups(), simpol1()

Examples

mol_paths <- mol_example()
calc_vol(mol_paths)

# Return functional group counts from get_fx_groups()
calc_vol(mol_paths,  return_fx_groups = TRUE)

# Return intermediate calculations
calc_vol(mol_paths, return_calc_steps = TRUE)

---

Count compound functional groups

Description

Returns functional group counts relevant to calculating estimated volatility for specified compounds. Users will not typically interact with this function directly, but rather by using calc_vol().

Usage

get_fx_groups(compound_sdf, validate = TRUE)

Arguments

compound_sdf	a ChemmineR::SDFset object returned by ChemmineR::read.SDFset() or ChemmineR::smiles2sdf(), for example.
validate	logical; if TRUE (default), results are checked for possible errors in parsing by Open Babel and NAs are returned if possible errors are found. Setting to FALSE bypasses these checks—use at your own risk! Validation is not available on Windows. See Details for more information.

Details

For more details on how functional groups are defined, see the smarts_simpol1 data set.

It is unfortunately difficult to capture errors and warnings produced by the command line tool OpenBabel used by ChemmineOB, a dependency of volcalc. These errors and warnings are printed to the R console, but they are not R errors and do not stop code from running and producing potentially incorrect data. validate = TRUE checks the output of certain OpenBabel procedures for the symptoms of these errors, namely missing values for InChI and molecular formula. Unfortunately, since InChI generation is not available with the Windows version of ChemmineOB, this validation step cannot be performed on Windows and validate = TRUE will simply print a warning that can be silenced by setting validate = FALSE.

Value

A tibble with columns of basic compound info and functional group counts.

Note

This function currently does not capture the carbon number on the acid-side of amide, one of the functional groups used in SIMPOL.1. Contributions of SMARTS strings or other methods to capture this "functional group" are welcome.

See Also

calc_vol()

Examples

mol_path <- mol_example()[1]
sdf <- ChemmineR::read.SDFset(mol_path)
get_fx_groups(sdf)

---

Download compound .mol files from KEGG

Description

Downloads mol files corresponding to individual compounds or compounds in a pathway from KEGG.

Usage

get_mol_kegg(compound_ids, pathway_ids, dir, force = FALSE)

Arguments

compound_ids	Character vector of KEGG compound IDs—5 digits prepended with a "C".
pathway_ids	Character vector of KEGG pathway or pathway module IDs—5 digits prepended with "map" or "M", respectively.
dir	Path to a folder to save .mol files in. Folder will be created if it does not already exist.
force	Logical; by default (FALSE), .mol files will not be downloaded if they are found in dir. Set this to TRUE to download and overwrite existing files.

Value

A tibble with the columns compound_ids, pathway_ids (if used), and mol_paths (paths to downloaded .mol files).

Note

For additional functionality for interacting with KEGG, try the KEGGREST package, which this function was inspired by.

Examples

## Not run: 
get_mol_kegg(compound_ids = c("C16181", "C06074"), dir = tempdir())
get_mol_kegg(pathway_ids = "map00253", dir = tempdir())

## End(Not run)

---

Example .mol files

Description

volcalc comes bundled with some example .mol files in its inst/extdata directory. This function provides easy access to them.

Usage

mol_example()

Details

File names are the KEGG identifiers. Compound names are as follows:

• C00031: D-Glucose

• C00157: Phosphatidylcholine

• C08491: (-)-Jasmonic acid

• C16181: beta-2,3,4,5,6-Pentachlorocyclohexanol

• C16286: Geosmin

• C16521: Isoprene

Value

File paths to installed example .mol files.

Examples

#return paths to all example .mol files
mol_example()

#examine the contents of a file
readLines(mol_example()[1])

---

SIMPOL.1 method for calculating estimated volatility

Description

Implements the SIMPOL.1 group contribution method for predicting liquid vapor pressure of organic compounds as described in Pankow & Asher (2008) and a modified version described in Meredith et al. (2023). Users will not usually use this function directly, but rather through calc_vol().

Usage

simpol1(fx_groups, meredith = TRUE, temp_c = 20)

Arguments

fx_groups	A data.frame or tibble with counts of functional groups produced by get_fx_groups() (or manually, with the same column names).
meredith	Logical; FALSE: use the original SIMPOL.1 method. TRUE: use the modified version in Meredith et al. (2023).
temp_c	Numeric; the temperature at which to calculate volatility estimates in °C.

Details

The output includes a column for log10_P where $\textrm{log}_{10} P_{\textrm{L},i}^\circ(T) = \sum_k\nu_{k,i}b_k(T)$, or the sum of the counts of functional groups ($\nu_{k,i}$) times the coefficients for each functional group ($b_K(T)$). Units are in log10 atmospheres.

The modified method in Meredith et al. (2023) adds the following additional functional groups:

Using the same coefficient as nitrate

• Phosphoric acid

• Phosphoric ester

• Sulfate

• Sulfonate

• Thiol

Using the same coefficient as ester

• Carbothioester

Value

The fx_groups tibble with the additional log10_P column.

Note

The method described in Pankow & Asher (2008) was developed using data between 0 °C and 120 °C, so extrapolating beyond that range is not recommended.

References

Meredith L, Ledford S, Riemer K, Geffre P, Graves K, Honeker L, LeBauer D, Tfaily M, Krechmer J. 2023. Automating methods for estimating metabolite volatility. Frontiers in Microbiology. doi:10.3389/fmicb.2023.1267234

Pankow, J.F., Asher, W.E. 2008. SIMPOL.1: a simple group contribution method for predicting vapor pressures and enthalpies of vaporization of multifunctional organic compounds. Atmos. Chem. Phys. doi:10.5194/acp-8-2773-2008

See Also

calc_vol()

Examples

mol_path <- mol_example()[3]
sdf <- ChemmineR::read.SDFset(mol_path)
fx_groups <- get_fx_groups(sdf)
simpol1(fx_groups)

---

Search patterns used for SIMPOL.1 functional groups

Description

This dataframe documents how functional groups for the SIMPOL.1 and Meredith et al. method are defined using SMARTS strings or ChemmineR functions.

Usage

smarts_simpol1

Format

method

Either "simpol1" for functional groups only used with the SIMPOL.1 method, or "meredith" for additional groups used in the Meredith et al. method.

functional_groups

These correspond to matching column names in the results of get_fx_groups().

description

Functional group description from Table 5 of Pankow & Asher (2008)

smarts

SMARTS strings used to capture groups, when applicable

fun

The function used to capture the functional group. When smarts is not NA, this is always "ChemmineR::smartsSearchOB". Other groups are captured with other ChemmineR functions or as calculations using other functional groups.

notes

Notes including how any functional group counts are corrected when there is overlap. E.g. when one SMARTS pattern is a subset of another pattern, but the two groups are counted separately without overlap in the SIMPOL.1 method.

References

Meredith L, Ledford S, Riemer K, Geffre P, Graves K, Honeker L, LeBauer D, Tfaily M, Krechmer J. 2023. Automating methods for estimating metabolite volatility. Frontiers in Microbiology. doi:10.3389/fmicb.2023.1267234

Pankow, J.F., Asher, W.E. 2008. SIMPOL.1: a simple group contribution method for predicting vapor pressures and enthalpies of vaporization of multifunctional organic compounds. Atmos. Chem. Phys. doi:10.5194/acp-8-2773-2008

---