Package 'rdkitpyr' reference manual

Title:	Task-Oriented Cheminformatics in R Using 'RDKit' via 'Python'
Description:	A task-oriented R interface to the 'RDKit' <https://www.rdkit.org> library through its 'Python' API via 'reticulate'. The package offers high-level cheminformatics functionality, including molecule parsing, descriptor calculation, and fingerprint generation without replicating the native structure of 'RDKit'.
Authors:	Andrey Samokhin [aut, cre, cph] (ORCID: <https://orcid.org/0000-0003-0223-6087>)
Maintainer:	Andrey Samokhin <[email protected]>
License:	MIT + file LICENSE
Version:	0.2.1
Built:	2026-06-04 07:32:52 UTC
Source:	https://github.com/andreysamokhin/rdkitpyr

Check whether RDKit is available

Description

Used in examples and tests to determine whether the Python module rdkit is available via reticulate.

This function is exported to support examples and tests. It is not part of the stable user-facing API and may change without notice.

The result is cached for the duration of the R session to avoid repeated calls to reticulate::py_module_available().

Usage

.IsRdkitAvailable(initialize = TRUE)
.IsRdkitAvailable(initialize = TRUE)

Arguments

initialize

A logical value. If FALSE and Python is not initialized, RDKit is assumed to be unavailable and the corresponding tests and examples are skipped.

Value

A logical value indicating whether the rdkit Python module is available.

Calculate all RDKit molecular descriptors

Description

Calculate all molecular descriptors available in RDKit for a set of molecules.

The descriptors are calculated using the CalcMolDescriptors() function from the rdkit.Chem.Descriptors module in RDKit.

The set of returned descriptors may depend on the installed RDKit version.

Each molecule is represented by a full set of descriptor values returned as a data frame. Invalid molecules are represented by rows containing NA values. Row order is preserved so that the output aligns with the input.

Usage

CalculateAllDescriptors(mols, verbose = FALSE)
CalculateAllDescriptors(mols, verbose = FALSE)

Arguments

mols

A character vector of SMILES or InChI strings, or a list of RDKit Mol objects.

verbose

A logical value. If TRUE, display warning and error messages emitted by the RDKit backend. Default is FALSE.

Value

A data frame with one row per molecule and one column per descriptor. Elements corresponding to invalid molecules are returned as NA. Original RDKit descriptor names are used.

Additionally, the "valid" attribute is attached to indicate which molecules were successfully processed.

Examples


  # Calculate all RDKit descriptors
  smiles <- c("CCO", "c1ccccc1", "invalid_molecule")
  desc <- CalculateAllDescriptors(smiles)

  # Inspect names of first three descriptors
  names(desc)[1:3]
  #> "MaxAbsEStateIndex" "MaxEStateIndex" "MinAbsEStateIndex"

  # Display Molecular weight, LogP, TPSA, and molar refractivity
  desc[c("MolWt", "MolLogP", "TPSA", "MolMR")]
  #>    MolWt MolLogP  TPSA   MolMR
  #> 1 46.069 -0.0014 20.23 12.7598
  #> 2 78.114  1.6866  0.00 26.4420
  #> 3     NA      NA    NA      NA

  # Check which molecules were successfully processed
  attr(desc, "valid")
  #> TRUE TRUE FALSE

# Calculate all RDKit descriptors
  smiles <- c("CCO", "c1ccccc1", "invalid_molecule")
  desc <- CalculateAllDescriptors(smiles)

  # Inspect names of first three descriptors
  names(desc)[1:3]
  #> "MaxAbsEStateIndex" "MaxEStateIndex" "MinAbsEStateIndex"

  # Display Molecular weight, LogP, TPSA, and molar refractivity
  desc[c("MolWt", "MolLogP", "TPSA", "MolMR")]
  #>    MolWt MolLogP  TPSA   MolMR
  #> 1 46.069 -0.0014 20.23 12.7598
  #> 2 78.114  1.6866  0.00 26.4420
  #> 3     NA      NA    NA      NA

  # Check which molecules were successfully processed
  attr(desc, "valid")
  #> TRUE TRUE FALSE

Calculate the exact mass of molecules

Description

Calculate the exact mass (monoisotopic mass) for a set of molecules.

The calculation is performed using the ExactMolWt() function from the rdkit.Chem.Descriptors module in RDKit.

Usage

CalculateExactMass(mols, verbose = FALSE)
CalculateExactMass(mols, verbose = FALSE)

Arguments

mols

A character vector of SMILES or InChI strings, or a list of RDKit Mol objects.

verbose

A logical value. If TRUE, display warning and error messages emitted by the RDKit backend. Default is FALSE.

Value

A numeric vector containing the exact mass for each molecule. Elements corresponding to invalid molecules are returned as NA.

Examples


  # Calculate exact mass for a set of molecules
  smiles <- c("CCO", "c1ccccc1", "invalid_molecule")
  CalculateExactMass(smiles)
  #> 46.04186 78.04695 NA

# Calculate exact mass for a set of molecules
  smiles <- c("CCO", "c1ccccc1", "invalid_molecule")
  CalculateExactMass(smiles)
  #> 46.04186 78.04695 NA

Calculate MACCS fingerprints for a set of molecules

Description

Calculate MACCS (Molecular ACCess System) fingerprints for a set of molecules. Each fingerprint is a fixed-length binary vector representing the presence or absence of predefined structural features.

The fingerprints are calculated using the GetMACCSKeysFingerprint() function from the rdkit.Chem.rdMolDescriptors module in RDKit.

Invalid molecules are represented by NA vectors. Row order is preserved so that the output aligns with the input.

Usage

CalculateMaccsFingerprints(mols, verbose = FALSE)
CalculateMaccsFingerprints(mols, verbose = FALSE)

Arguments

mols

A character vector of SMILES or InChI strings, or a list of RDKit Mol objects.

verbose

A logical value. If TRUE, display warning and error messages emitted by the RDKit backend. Default is FALSE.

Value

A matrix of integers (0 or 1) with one row per molecule and 167 columns (MACCS keys). Rows corresponding to invalid molecules contain NA.

Additionally, the "valid" attribute is attached to indicate which molecules were successfully processed.

Examples


  # Calculate MACCS fingerprints
  smiles <- c("CCO", "c1ccccc1", "invalid_molecule")
  fps <- CalculateMaccsFingerprints(smiles)

  # Get the number of fingerprints (columns)
  ncol(fps)
  #> 167

  # Check which molecules were successfully processed
  attr(fps, "valid")
  #> TRUE TRUE FALSE

# Calculate MACCS fingerprints
  smiles <- c("CCO", "c1ccccc1", "invalid_molecule")
  fps <- CalculateMaccsFingerprints(smiles)

  # Get the number of fingerprints (columns)
  ncol(fps)
  #> 167

  # Check which molecules were successfully processed
  attr(fps, "valid")
  #> TRUE TRUE FALSE

Calculate the average molecular weight of molecules

Description

Calculate the molecular weight (average mass) for a set of molecules.

The calculation is performed using the MolWt() function from the rdkit.Chem.Descriptors module in RDKit.

Usage

CalculateMolecularWeight(mols, verbose = FALSE)
CalculateMolecularWeight(mols, verbose = FALSE)

Arguments

mols

A character vector of SMILES or InChI strings, or a list of RDKit Mol objects.

verbose

A logical value. If TRUE, display warning and error messages emitted by the RDKit backend. Default is FALSE.

Value

A numeric vector containing the molecular weight for each molecule. Elements corresponding to invalid molecules are returned as NA.

Examples


  # Calculate average molecular weight for a set of molecules
  smiles <- c("CCO", "c1ccccc1", "invalid_molecule")
  CalculateMolecularWeight(smiles)
  #> 46.069 78.114 NA

# Calculate average molecular weight for a set of molecules
  smiles <- c("CCO", "c1ccccc1", "invalid_molecule")
  CalculateMolecularWeight(smiles)
  #> 46.069 78.114 NA

Calculate Morgan fingerprints for a set of molecules

Description

Calculate Morgan (circular) fingerprints for a set of molecules.

The fingerprints are calculated using the GetMorganGenerator() function from the rdkit.Chem.rdFingerprintGenerator module in RDKit.

Invalid molecules are represented by NA vectors. Row order is preserved so that the output aligns with the input.

Usage

CalculateMorganFingerprints(
  mols,
  radius = 3L,
  fp_size = 2048L,
  count_simulation = FALSE,
  include_chirality = FALSE,
  use_bond_types = TRUE,
  include_ring_membership = TRUE,
  verbose = FALSE
)
CalculateMorganFingerprints(
  mols,
  radius = 3L,
  fp_size = 2048L,
  count_simulation = FALSE,
  include_chirality = FALSE,
  use_bond_types = TRUE,
  include_ring_membership = TRUE,
  verbose = FALSE
)

Arguments

mols

A character vector of SMILES or InChI strings, or a list of RDKit Mol objects.

radius

An integer value. Bond radius defining the size of circular substructures.

fp_size

An integer value. Number of bits in the fingerprint.

count_simulation

A logical value. If set, use count simulation while generating the fingerprint.

include_chirality

A logical value. If set, chirality information will be added to the generated fingerprint.

use_bond_types

A logical value. If set, bond types will be included as a part of the default bond invariants.

include_ring_membership

A logical value. If set, whether or not the atom is in a ring will be used in the invariant list.

verbose

A logical value. If TRUE, display warning and error messages emitted by the RDKit backend. Default is FALSE.

Value

A matrix of integers (0 or 1) with one row per molecule and fp_size columns. Rows corresponding to invalid molecules contain NA.

Additionally, the "valid" attribute is attached to indicate which molecules were successfully processed.

Examples


  # Calculate Morgan fingerprints
  smiles <- c("CCO", "c1ccccc1", "invalid_molecule")
  fps <- CalculateMorganFingerprints(smiles)

  # Get the number of fingerprints (columns)
  ncol(fps)
  #> 2048

  # Check which molecules were successfully processed
  attr(fps, "valid")
  #> TRUE TRUE FALSE

# Calculate Morgan fingerprints
  smiles <- c("CCO", "c1ccccc1", "invalid_molecule")
  fps <- CalculateMorganFingerprints(smiles)

  # Get the number of fingerprints (columns)
  ncol(fps)
  #> 2048

  # Check which molecules were successfully processed
  attr(fps, "valid")
  #> TRUE TRUE FALSE

Calculate RDKit topological fingerprints for a set of molecules

Description

Calculate RDKit topological (path-based) fingerprints for a set of molecules.

The fingerprints are calculated using the RDKFingerprint() function from the rdkit.Chem.rdmolops module in RDKit.

Invalid molecules are represented by NA vectors. Row order is preserved so that the output aligns with the input.

Usage

CalculateRdkitFingerprints(
  mols,
  min_path = 1L,
  max_path = 7L,
  fp_size = 2048L,
  n_bits_per_hash = 2L,
  use_hydrogens = TRUE,
  target_density = 0,
  min_size = 128L,
  branched_paths = TRUE,
  use_bond_order = TRUE,
  verbose = FALSE
)
CalculateRdkitFingerprints(
  mols,
  min_path = 1L,
  max_path = 7L,
  fp_size = 2048L,
  n_bits_per_hash = 2L,
  use_hydrogens = TRUE,
  target_density = 0,
  min_size = 128L,
  branched_paths = TRUE,
  use_bond_order = TRUE,
  verbose = FALSE
)

Arguments

mols

A character vector of SMILES or InChI strings, or a list of RDKit Mol objects.

min_path

An integer value. Minimum number of bonds to include in the subgraphs.

max_path

An integer value. Maximum number of bonds to include in the subgraphs.

fp_size

An integer value. Number of bits in the fingerprint.

n_bits_per_hash

An integer value. Number of bits to set per path.

use_hydrogens

A logical value. Include paths involving hydrogens in the fingerprint if the molecule has explicit hydrogens.

target_density

A numeric value. Fold the fingerprint until this minimum density has been reached.

min_size

An integer value. The minimum size the fingerprint will be folded to when trying to reach target_density.

branched_paths

A logical value. If set, both branched and unbranched paths will be used in the fingerprint.

use_bond_order

A logical value. If set, both bond orders will be used in the path hashes.

verbose

A logical value. If TRUE, display warning and error messages emitted by the RDKit backend. Default is FALSE.

Value

A matrix of integers (0 or 1) with one row per molecule and fp_size columns. Rows corresponding to invalid molecules contain NA.

Additionally, the "valid" attribute is attached to indicate which molecules were successfully processed.

Examples


  # Calculate RDKit fingerprints
  smiles <- c("CCO", "c1ccccc1", "invalid_molecule")
  fps <- CalculateRdkitFingerprints(smiles)

  # Get the number of fingerprints (columns)
  ncol(fps)
  #> 2048

  # Check which molecules were successfully processed
  attr(fps, "valid")
  #> TRUE TRUE FALSE

# Calculate RDKit fingerprints
  smiles <- c("CCO", "c1ccccc1", "invalid_molecule")
  fps <- CalculateRdkitFingerprints(smiles)

  # Get the number of fingerprints (columns)
  ncol(fps)
  #> 2048

  # Check which molecules were successfully processed
  attr(fps, "valid")
  #> TRUE TRUE FALSE

Convert molecules to InChI strings

Description

Convert molecules to InChI strings.

InChI identifiers can technically be provided as input. In this case, the output is expected to be identical to the input. This can be useful only to test RDKit's consistency with challenging molecules.

Usage

ConvertToInchi(mols, verbose = FALSE)
ConvertToInchi(mols, verbose = FALSE)

Arguments

mols

A character vector of SMILES or InChI strings, or a list of RDKit Mol objects.

verbose

A logical value. If TRUE, display warning and error messages emitted by the RDKit backend. Default is FALSE.

Value

A character vector. InChI strings. Elements that cannot be converted are returned as NA.

Examples


  # Convert a vector of SMILES to InChI identifiers
  smiles <- c("CC", "CCC")
  ConvertToInchi(smiles)
  #> "InChI=1S/C2H6/c1-2/h1-2H3"
  #> "InChI=1S/C3H8/c1-3-2/h3H2,1-2H3"

  # Providing InChI as input returns identical output
  ConvertToInchi("InChI=1S/CH4/h1H4")
  #> "InChI=1S/CH4/h1H4"

# Convert a vector of SMILES to InChI identifiers
  smiles <- c("CC", "CCC")
  ConvertToInchi(smiles)
  #> "InChI=1S/C2H6/c1-2/h1-2H3"
  #> "InChI=1S/C3H8/c1-3-2/h3H2,1-2H3"

  # Providing InChI as input returns identical output
  ConvertToInchi("InChI=1S/CH4/h1H4")
  #> "InChI=1S/CH4/h1H4"

Convert molecules to InChIKey strings

Description

Convert molecules to InChIKey strings.

Conversion of an InChI string to an InChIKey relies on the IUPAC library, allowing conversion without creating intermediate RDKit Mol objects.

Usage

ConvertToInchikey(mols, verbose = FALSE)
ConvertToInchikey(mols, verbose = FALSE)

Arguments

mols

A character vector of SMILES or InChI strings, or a list of RDKit Mol objects.

verbose

A logical value. If TRUE, display warning and error messages emitted by the RDKit backend. Default is FALSE.

Value

A character vector. InChIKey strings. Elements that cannot be converted are returned as NA.

Examples


  # Convert a vector of InChI to InChIKey identifiers
  inchi <- c("InChI=1S/C2H6/c1-2/h1-2H3",
             "InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H")
  ConvertToInchikey(inchi)
  #> "OTMSDBZUPAUEDD-UHFFFAOYSA-N"
  #> "UHOVQNZJYSORNB-UHFFFAOYSA-N"

  # Convert a vector of SMILES to InChIKey identifiers
  smiles <- c("CC", "c1ccccc1")
  ConvertToInchikey(smiles)
  #> "OTMSDBZUPAUEDD-UHFFFAOYSA-N"
  #> "UHOVQNZJYSORNB-UHFFFAOYSA-N"

# Convert a vector of InChI to InChIKey identifiers
  inchi <- c("InChI=1S/C2H6/c1-2/h1-2H3",
             "InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H")
  ConvertToInchikey(inchi)
  #> "OTMSDBZUPAUEDD-UHFFFAOYSA-N"
  #> "UHOVQNZJYSORNB-UHFFFAOYSA-N"

  # Convert a vector of SMILES to InChIKey identifiers
  smiles <- c("CC", "c1ccccc1")
  ConvertToInchikey(smiles)
  #> "OTMSDBZUPAUEDD-UHFFFAOYSA-N"
  #> "UHOVQNZJYSORNB-UHFFFAOYSA-N"

Convert molecules to SMILES strings

Description

Convert molecules to SMILES strings.

SMILES strings can be provided as input to obtain their canonical form or to remove stereochemistry.

Usage

ConvertToSmiles(
  mols,
  isomeric = TRUE,
  kekule = FALSE,
  canonical = TRUE,
  explicit_bonds = FALSE,
  explicit_hydrogens = FALSE,
  verbose = FALSE
)
ConvertToSmiles(
  mols,
  isomeric = TRUE,
  kekule = FALSE,
  canonical = TRUE,
  explicit_bonds = FALSE,
  explicit_hydrogens = FALSE,
  verbose = FALSE
)

Arguments

mols

A character vector of SMILES or InChI strings, or a list of RDKit Mol objects.

isomeric

A logical value. If TRUE, include stereochemistry in the output.

kekule

A logical value. If TRUE, kekulize aromatic bonds.

canonical

A logical value. If TRUE, generate canonical SMILES.

explicit_bonds

A logical value. If TRUE, make all bonds explicit.

explicit_hydrogens

A logical value. If TRUE, make all hydrogens explicit.

verbose

A logical value. If TRUE, display warning and error messages emitted by the RDKit backend. Default is FALSE.

Value

A character vector. SMILES strings. Elements that cannot be converted are returned as NA.

Examples


  # Convert a vector of InChI identifiers to canonical SMILES
  inchi <- c("InChI=1S/C2H6/c1-2/h1-2H3",
             "InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H")
  ConvertToSmiles(inchi)
  #> "CC"
  #> "c1ccccc1"

  # Convert a vector of SMILES to SMILES with Kekulized aromatic bonds
  smiles <- c("c1ccccc1", "c1ccc2ccccc2c1")
  ConvertToSmiles(smiles, kekule = TRUE)
  #> "C1=CC=CC=C1"
  #> "C1=CC=C2C=CC=CC2=C1"

# Convert a vector of InChI identifiers to canonical SMILES
  inchi <- c("InChI=1S/C2H6/c1-2/h1-2H3",
             "InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H")
  ConvertToSmiles(inchi)
  #> "CC"
  #> "c1ccccc1"

  # Convert a vector of SMILES to SMILES with Kekulized aromatic bonds
  smiles <- c("c1ccccc1", "c1ccc2ccccc2c1")
  ConvertToSmiles(smiles, kekule = TRUE)
  #> "C1=CC=CC=C1"
  #> "C1=CC=C2C=CC=CC2=C1"

Get information about the currently used Python environment

Description

Get details about the Python interpreter, numpy and rdkit packages.

Usage

GetPythonInfo(verbose = TRUE)
GetPythonInfo(verbose = TRUE)

Arguments

verbose

A logical value. If TRUE (default), function prints information about currently used Python environemt.

Value

Invisibly return a named list with the following components:

python_path: Full path to the Python executable.
python_version: Version of the Python interpreter.
numpy_version: Installed version of the numpy package.
rdkit_version: Installed version of the rdkit package.
forced_by: If applicable, indicates whether the Python interpreter was forced via RETICULATE_PYTHON, use_*(), or py_require().

Examples


  # Print information about the Python environment
  GetPythonInfo()

  # Access programmatically
  py_env <- GetPythonInfo(verbose = FALSE)
  py_env$python_version
  py_env$rdkit_version

# Print information about the Python environment
  GetPythonInfo()

  # Access programmatically
  py_env <- GetPythonInfo(verbose = FALSE)
  py_env$python_version
  py_env$rdkit_version

Parse SMILES and InChI strings into RDKit Mol objects

Description

Parse SMILES and InChI strings into RDKit Mol objects

This function converts a character vector of molecular representations (SMILES or InChI) into a list of RDKit Mol objects (Python-backed pointers via reticulate). The resulting objects can be reused in subsequent operations without repeated conversion from SMILES or InChI. This is particularly useful when multiple cheminformatics tasks are performed on the same set of molecules, improving efficiency by avoiding repeated parsing steps.

Usage

ParseMolecules(mols, verbose = FALSE)
ParseMolecules(mols, verbose = FALSE)

Arguments

mols

A character vector of SMILES or InChI strings.

verbose

A logical value. If TRUE, display warning and error messages emitted by the RDKit backend. Default is FALSE.

Value

A list of RDKit Mol objects.

Examples


  # Convert a vector of SMILES to RDKit Mol objects
  mols <- ParseMolecules(c("CC", "CCC"))
  print(mols[[1L]])
  #> <rdkit.Chem.rdchem.Mol object at 0x000001CC4D60F4C0>

  # Convert a list of RDKit Mol objects to InChI identifiers
  ConvertToInchi(mols)
  #> "InChI=1S/C2H6/c1-2/h1-2H3"
  #> "InChI=1S/C3H8/c1-3-2/h3H2,1-2H3"

# Convert a vector of SMILES to RDKit Mol objects
  mols <- ParseMolecules(c("CC", "CCC"))
  print(mols[[1L]])
  #> <rdkit.Chem.rdchem.Mol object at 0x000001CC4D60F4C0>

  # Convert a list of RDKit Mol objects to InChI identifiers
  ConvertToInchi(mols)
  #> "InChI=1S/C2H6/c1-2/h1-2H3"
  #> "InChI=1S/C3H8/c1-3-2/h3H2,1-2H3"

Test compounds

Description

A small reference set of chemical compounds extracted from the PubChem database. Despite its limited size, the dataset covers a broad range of chemical properties, including:

neutral, charged, and radical species;
aromatic and aliphatic compounds;
molecules containing heteroatoms;
isotopically labeled compounds;
stereochemistry;
species with disconnected fragments.

Usage

test_compounds
test_compounds

Format

A data frame.

pubchem_cid: PubChem compound identifier (CID).
name: Compound name (as reported in the PubChem database).
smiles: SMILES identifier.
inchi: InChI identifier.
inchikey: InChIKey identifier.
n_labeled_atoms: Number of isotopically labeled atoms.
charge: The total charge of a molecule.
exact_mass: Exact monoisotopic mass.
molecular_weight: Average molecular weight.
formula: Molecular formula.
formula_isotopes: Molecular formula with explicit isotopes.

Package 'rdkitpyr'

Help Index

Check whether RDKit is available

Description

Usage

Arguments

Value

Calculate all RDKit molecular descriptors

Description

Usage

Arguments

Value

Examples

Calculate the exact mass of molecules

Description

Usage

Arguments

Value

Examples

Calculate MACCS fingerprints for a set of molecules

Description

Usage

Arguments

Value

Examples

Calculate the average molecular weight of molecules

Description

Usage

Arguments

Value

Examples

Calculate Morgan fingerprints for a set of molecules

Description

Usage

Arguments

Value

Examples

Calculate RDKit topological fingerprints for a set of molecules

Description

Usage

Arguments

Value

Examples

Convert molecules to InChI strings

Description

Usage

Arguments

Value

Examples

Convert molecules to InChIKey strings

Description

Usage

Arguments

Value

Examples

Convert molecules to SMILES strings

Description

Usage

Arguments

Value

Examples

Get information about the currently used Python environment

Description

Usage

Arguments

Value

Examples

Parse SMILES and InChI strings into RDKit Mol objects

Description

Usage

Arguments

Value

Examples

Test compounds

Description

Usage

Format