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RAM Cache Environment

Source: R/getcds.R
ram_cache.Rd

An environment used for caching data in RAM.

Usage

ram_cache

Format

An environment with the following elements:

  • CDs: A data frame. The column names of CDs are the chemical descriptors listed in CDFeatures. The rownames in CDs are SMILES strings.

  • CDRowNr: A list. The names of the list elements equal the rownames of CDs. The values are the indices of the rows in the CDs data frame.

Details

This environment is used by getCDsFor1Molecule() to store the results of previous calculations to speed up subsequent calls. It gets initalized upon the first call of getCDsFor1Molecule() with the chemical descriptors for all molecules available in the RP dataset and the HILIC dataset of the Retip package.

References

Retip: Retention Time Prediction for Compound Annotation in Untargeted Metabolomics Paolo Bonini, Tobias Kind, Hiroshi Tsugawa, Dinesh Kumar Barupal, and Oliver Fiehn Analytical Chemistry 2020 92 (11), 7515-7522 DOI: 10.1021/acs.analchem.9b05765

Examples

dim(ram_cache$CDs) # 0 241
#> [1] 1316  241
cds <- getCDsFor1Molecule(cache = TRUE, verbose = TRUE)
#> 2024-08-18 12:17:20.20 Loading chemical descriptors for 'O=C(O)CCCCCCCCCO' from RAM cache
dim(ram_cache$CDs) # 1316 241
#> [1] 1316  241
ram_cache$CDRowNr[["COC1=C(C=CC(=C1)CCN)O"]] # 2
#> [1] 2
ram_cache$CDs[1:10, 1:3]
#>                                                                Fsp3 nSmallRings
#> CCC(C(=O)O)O                                              0.7500000           0
#> COC1=C(C=CC(=C1)CCN)O                                     0.3333333           1
#> C1=NC2=C(N1)C(=NC=N2)N                                    0.0000000           2
#> C1=NC2=C(C(=N1)N)N=CN2C3C(C(C(O3)COP(=O)(O)O)O)O          0.5000000           3
#> C1C2C(C(C(O2)N3C=NC4=C3N=CN=C4N)O)OP(=O)(O1)O             0.5000000           4
#> C1=NC2=C(C(=N1)N)N=CN2C3C(C(C(O3)COP(=O)(O)O)OP(=O)(O)O)O 0.5000000           3
#> [O-]C(=O)C[C@H](O)C[N+](C)(C)C                            0.8571429           0
#> C[N+](C)(CCOP([O-])(OCC(O)CO)=O)C                         1.0000000           0
#> CN1C=C(N=C1)CC(C(=O)O)N                                   0.4285714           1
#> C(CC(=O)O)CN                                              0.7500000           0
#>                                                           nAromRings
#> CCC(C(=O)O)O                                                       0
#> COC1=C(C=CC(=C1)CCN)O                                              1
#> C1=NC2=C(N1)C(=NC=N2)N                                             2
#> C1=NC2=C(C(=N1)N)N=CN2C3C(C(C(O3)COP(=O)(O)O)O)O                   2
#> C1C2C(C(C(O2)N3C=NC4=C3N=CN=C4N)O)OP(=O)(O1)O                      2
#> C1=NC2=C(C(=N1)N)N=CN2C3C(C(C(O3)COP(=O)(O)O)OP(=O)(O)O)O          2
#> [O-]C(=O)C[C@H](O)C[N+](C)(C)C                                     0
#> C[N+](C)(CCOP([O-])(OCC(O)CO)=O)C                                  0
#> CN1C=C(N=C1)CC(C(=O)O)N                                            1
#> C(CC(=O)O)CN                                                       0