Operations on Atoms

Description

get.symbol returns the chemical symbol for an atom get.point3d returns the 3D coordinates of the atom get.point2d returns the 2D coordinates of the atom get.atomic.number returns the atomic number of the atom get.hydrogen.count returns the number of implicit H’s on the atom. Depending on where the molecule was read from this may be NULL or an integer greater than or equal to 0 get.charge returns the partial charge on the atom. If charges have not been set the return value is NULL, otherwise the appropriate charge. get.formal.charge returns the formal charge on the atom. By default the formal charge will be 0 (i.e., NULL is never returned) is.aromatic returns TRUE if the atom is aromatic, FALSE otherwise is.aliphatic returns TRUE if the atom is part of an aliphatic chain, FALSE otherwise is.in.ring returns TRUE if the atom is in a ring, FALSE otherwise get.atom.index eturns the index of the atom in the molecule (starting from 0) get.connected.atoms returns a list of atoms that are connected to the specified atom

Usage

get.symbol(atom) get.point3d(atom) get.point2d(atom) get.atomic.number(atom) get.hydrogen.count(atom) get.charge(atom) get.formal.charge(atom) get.connected.atoms(atom, mol) get.atom.index(atom, mol) is.aromatic(atom) is.aliphatic(atom) is.in.ring(atom) set.atom.types(mol)

Arguments

atom A jobjRef representing an IAtom object mol A jobjRef representing an IAtomContainer object

Value

In the case of get.point3d the return value is a 3-element vector containing the X, Y and Z co-ordinates of the atom. If the atom does not have 3D coordinates, it returns a vector of the form c(NA,NA,NA). Similarly for get.point2d, in which case the return vector is of length 2.

Author(s)

Rajarshi Guha (rajarshi.guha@gmail.com)

Operations on molecules

Description

Various functions to perform operations on molecules.

get.exact.mass returns the exact mass of a molecule get.natural.mass returns the natural exact mass of a molecule convert.implicit.to.explicit converts implicit hydrogens to explicit hydrogens. This function does not return any value but rather modifies the molecule object passed to it is.neutral returns TRUE if all atoms in the molecule have a formal charge of 0, otherwise FALSE

Details

In some cases, a molecule may not have any hydrogens (such as when read in from an MDL MOLfile that did not have hydrogens). In such cases, convert.implicit.to.explicit will add implicit hydrogens and then convert them to explicit ones. In addition, for such cases, make sure that the molecule has been typed beforehand.

Usage

get.exact.mass(mol) get.natural.mass(mol) convert.implicit.to.explicit(mol) is.neutral(mol)

Arguments

mol A jobjRef representing an IAtomContainer or IMolecule object

Value

get.exact.mass returns a numeric get.natural.mass returns a numeric convert.implicit.to.explicit has no return value is.neutral returns a boolean.

Author(s)

Rajarshi Guha (rajarshi.guha@gmail.com)

See Also

get.atoms, set.atom.types

Boiling Point Data

Description

A dataset containing the structures and associated boiling points for 277 molecules, primarily alkanes and substituted alkanes.

Usage

bpdata

Format

A data frame with 277 rows and 2 columns.:

SMILES

Structure in SMILES format

BP

Boiling point in Kelvin

The names of the molecules are used as the row names.

References

Goll, E.S. and Jurs, P.C.; "Prediction of the Normal Boiling Points of Organic Compounds From Molecular Structures with a Computational Neural Network Model", J. Chem. Inf. Comput. Sci., 1999, 39, 974-983.

Get the current CDK version used in the package.

Description

Get the current CDK version used in the package.

Usage

cdk.version()

Value

Returns a character containing the version of the CDK used in this package

Author(s)

Rajarshi Guha (rajarshi.guha@gmail.com)

Class cdkFormula, ac class for handling molecular formula

Description

This class handles molecular formulae. It provides extra information such as the IMolecularFormula Java object, elements contained and number of them.

Objects from the Class

Objects can be created using new constructor and filled with a specific mass and window accuracy

Author(s)

Miguel Rojas-Cherto (miguelrojasch@yahoo.es)

References

A parallel effort to expand the Chemistry Development Kit: https://cdk.github.io/

See Also

get.formula set.charge.formula get.isotopes.pattern isvalid.formula

Compare isotope patterns.

Description

Computes a similarity score between two different isotope abundance patterns.

Usage

compare.isotope.pattern(iso1, iso2, ips = NULL)

Arguments

Value

A numeric value between 0 and 1 indicating the similarity between the two patterns

Author(s)

Miguel Rojas Cherto

References

http://cdk.github.io/cdk/2.3/docs/api/org/openscience/cdk/formula/IsotopePatternSimilarity.html

See Also

get.isotope.pattern.similarity

Convert implicit hydrogens to explicit.

Description

In some cases, a molecule may not have any hydrogens (such as when read in from an MDL MOL file that did not have hydrogens or SMILES with no explicit hydrogens). In such cases, this method will add implicit hydrogens and then convert them to explicit ones. The newly added H's will not have any 2D or 3D coordinates associated with them. Ensure that the molecule has been typed beforehand.

Usage

convert.implicit.to.explicit(mol)

Arguments

Author(s)

Rajarshi Guha (rajarshi.guha@gmail.com)

See Also

get.hydrogen.count, remove.hydrogens, set.atom.types

copy.image.to.clipboard

Description

generate an image and make it available to the system clipboard.

Usage

copy.image.to.clipboard(molecule, depictor = NULL)

Arguments

do.aromaticity

Description

detect aromaticity of an input compound

Usage

do.aromaticity(mol)

Arguments

do.isotopes

Description

configure isotopes

Usage

do.isotopes(mol)

Arguments

Compute descriptors for each atom in a molecule

Description

Compute descriptors for each atom in a molecule

Usage

eval.atomic.desc(molecule, which.desc, verbose = FALSE)

Arguments

Value

A 'data.frame' with atoms in the rows and descriptors in the columns

Author(s)

Rajarshi Guha (rajarshi.guha@gmail.com)

See Also

get.atomic.desc.names

Compute descriptor values for a set of molecules

Description

Compute descriptor values for a set of molecules

Usage

eval.desc(molecules, which.desc, verbose = FALSE)

Arguments

Value

A 'data.frame' with molecules in the rows and descriptors in the columns. If a descriptor value cannot be computed for a molecule, 'NA' is returned.

Author(s)

Rajarshi Guha (rajarshi.guha@gmail.com)

Generate 2D coordinates for a molecule.

Description

Some file formats such as SMILES do not support 2D (or 3D) coordinates for the atoms. Other formats such as SD or MOL have support for coordinates but may not include them. This method will generate reasonable 2D coordinates based purely on connectivity information, overwriting any existing coordinates if present.

Usage

generate.2d.coordinates(mol)

Arguments

Details

Note that when depicting a molecule (view.molecule.2d), 2D coordinates are generated, but since it does not modify the input molecule, we do not have access to the generated coordinates.

Value

The input molecule, with 2D coordinates added

Author(s)

Rajarshi Guha (rajarshi.guha@gmail.com)

See Also

get.point2d, view.molecule.2d

generate.formula

Description

generate.formula

Usage

generate.formula(
  mass,
  window = 0.01,
  elements = list(c("C", 0, 50), c("H", 0, 50), c("N", 0, 50), c("O", 0, 50), c("S", 0,
    50)),
  validation = FALSE,
  charge = 0
)

Arguments

generate.formula.iter

Description

Generate a list of possible formula objects given a mass and a mass tolerance.

Usage

generate.formula.iter(
  mass,
  window = 0.01,
  elements = list(c("C", 0, 50), c("H", 0, 50), c("N", 0, 50), c("O", 0, 50), c("S", 0,
    50)),
  validation = FALSE,
  charge = 0,
  as.string = TRUE
)

Arguments

Get adjacency matrix for a molecule.

Description

The adjacency matrix for a molecule with N non-hydrogen atoms is an N \times N matrix where the element [i,j] is set to 1 if atoms i and j are connected by a bond, otherwise set to 0.

Usage

get.adjacency.matrix(mol)

Arguments

Value

A N \times N numeric matrix

Author(s)

Rajarshi Guha rajarshi.guha@gmail.com

See Also

get.connection.matrix

Examples

m <- parse.smiles("CC=C")[[1]]
get.adjacency.matrix(m)

Compute ALogP for a molecule

Description

Compute ALogP for a molecule

Usage

get.alogp(molecule)

Arguments

Value

A double value representing the ALogP value

Author(s)

Rajarshi Guha (rajarshi.guha@gmail.com)

Get the number of atoms in the molecule.

Description

Get the number of atoms in the molecule.

Usage

get.atom.count(mol)

Arguments

Value

An integer representing the number of atoms in the molecule

Author(s)

Rajarshi Guha (rajarshi.guha@gmail.com)

get.atom.index

Description

Get the index of an atom in a molecule.

Usage

get.atom.index(atom, mol)

Arguments

Details

Acces the index of an atom in the context of an IAtomContainer. Indexing starts from 0. If the index is not known, -1 is returned.

Value

An integer representing the atom index.

Author(s)

Rajarshi Guha (rajarshi.guha@gmail.com)

See Also

get.connected.atom

Get class names for atomic descriptors

Description

Get class names for atomic descriptors

Usage

get.atomic.desc.names(type = "all")

Arguments

Value

A character vector containing class names for atomic descriptors

Author(s)

Rajarshi Guha (rajarshi.guha@gmail.com)

get.atomic.number

Description

Get the atomic number of the atom.

Usage

get.atomic.number(atom)

Arguments

Value

An integer representing the atomic number

Author(s)

Rajarshi Guha (rajarshi.guha@gmail.com)

Get the atoms from a molecule or bond.

Description

Get the atoms from a molecule or bond.

Usage

get.atoms(object)

Arguments

Value

A list of 'jobjRef' representing the 'IAtom' objects in the molecule or bond

Author(s)

Rajarshi Guha (rajarshi.guha@gmail.com)

See Also

get.bonds, get.connected.atoms

Get an object representing bond order

Description

This function returns a Java enum representing a bond order. This can be used to modify the order of pre-existing bonds

Usage

get.bond.order(order = "single")

Arguments

Value

A jObjRef representing an 'Order' enum object

Author(s)

Rajarshi Guha (rajarshi.guha@gmail.com)

Examples

## Not run: 
m <- parse.smiles('CCN')[[1]]
b <- get.bonds(m)[[1]]
b$setOrder(get.bond.order("double"))

## End(Not run)

Get the bonds in a molecule.

Description

Get the bonds in a molecule.

Usage

get.bonds(mol)

Arguments

Value

A list of 'jobjRef' representing the bonds ('IBond') objects in the molecule

Author(s)

Rajarshi Guha (rajarshi.guha@gmail.com)

See Also

get.atoms, get.connected.atoms

get.charge

Description

Get the charge on the atom.

Usage

get.charge(atom)

Arguments

Details

This method returns the partial charge on the atom. If charges have not been set the return value is NULL, otherwise the appropriate charge.

Value

An numeric representing the partial charge. If charges have not been set, 'NULL' is returned

Author(s)

Rajarshi Guha (rajarshi.guha@gmail.com)

See Also

get.formal.charge

Get the default chemical object builder.

Description

The CDK employs a builder design pattern to construct instances of new chemical objects (e.g., atoms, bonds, parsers and so on). Many methods require an instance of a builder object to function. While most functions in this package handle this internally, it is useful to be able to get an instance of a builder object when directly working with the CDK API via 'rJava'.

Usage

get.chem.object.builder()

Details

This method returns an instance of the SilentChemObjectBuilder. Note that this is a static object that is created at package load time, and the same instance is returned whenever this function is called.

Value

An instance of SilentChemObjectBuilder

Author(s)

Rajarshi Guha (rajarshi.guha@gmail.com)

Get the atom connected to an atom in a bond.

Description

This function returns the atom that is connected to a specified in a specified bond. Note that this function assumes 2-atom bonds, mainly because the CDK does not currently support other types of bonds

Usage

get.connected.atom(bond, atom)

Arguments

Value

A jObjRef representing an 'IAtom“ object

Author(s)

Rajarshi Guha (rajarshi.guha@gmail.com)

See Also

get.atoms

get.connected.atoms

Description

Get atoms connected to the specified atom

Usage

get.connected.atoms(atom, mol)

Arguments

Details

Returns a 'list“ of atoms that are connected to the specified atom.

Value

A 'list' containing 'IAtom' objects, representing the atoms directly connected to the specified atom

Author(s)

Rajarshi Guha (rajarshi.guha@gmail.com)

Get connection matrix for a molecule.

Description

The connection matrix for a molecule with N non-hydrogen atoms is an N \times N matrix where the element [i,j] is set to the bond order if atoms i and j are connected by a bond, otherwise set to 0.

Usage

get.connection.matrix(mol)

Arguments

Value

A N \times N numeric matrix

Author(s)

Rajarshi Guha rajarshi.guha@gmail.com

See Also

get.adjacency.matrix

Examples

m <- parse.smiles("CC=C")[[1]]
get.connection.matrix(m)

get.depictor

Description

return an RcdkDepictor.

Usage

get.depictor(
  width = 200,
  height = 200,
  zoom = 1.3,
  style = "cow",
  annotate = "off",
  abbr = "on",
  suppressh = TRUE,
  showTitle = FALSE,
  smaLimit = 100,
  sma = NULL,
  fillToFit = FALSE
)

Arguments

List available descriptor categories

Description

List available descriptor categories

Usage

get.desc.categories()

Value

A character vector listing available descriptor categories. This can be used in get.desc.names

Author(s)

Rajarshi Guha (rajarshi.guha@gmail.com)

See Also

get.desc.names

Get descriptor class names

Description

Get descriptor class names

Usage

get.desc.names(type = "all")

Arguments

Author(s)

Rajarshi Guha (rajarshi.guha@gmail.com)

See Also

get.atomic.desc.names

Obtain the type of stereo element support for atom.

Description

Supported elements types are

Bicoordinate

an central atom involved in a cumulated system (not yet supported)

Tricoordinate

an atom at one end of a geometric (double-bond) stereo bond or cumulated system

Tetracoordinate

a tetrahedral atom (could also be square planar in future)

None

the atom is not a (supported) stereo element type

Usage

get.element.types(mol)

Arguments

Value

A factor of length equal in length to the number of atoms, indicating the element type

Author(s)

Rajarshi Guha rajarshi.guha@gmail.com

See Also

get.stereocenters, get.stereo.types

get.exact.mass

Description

get.exact.mass

Usage

get.exact.mass(mol)

Arguments

Generate Bemis-Murcko Fragments

Description

Fragment the input molecule using the Bemis-Murcko scheme

Usage

get.exhaustive.fragments(mols, min.frag.size = 6, as.smiles = TRUE)

Arguments

Details

A variety of methods for fragmenting molecules are available ranging from exhaustive, rings to more specific methods such as Murcko frameworks. Fragmenting a collection of molecules can be a useful for a variety of analyses. In addition fragment based analysis can be a useful and faster alternative to traditional clustering of the whole collection, especially when it is large.

Note that exhaustive fragmentation of large molecules (with many single bonds) can become time consuming.

Value

returns a list of length equal to the number of input molecules. Each element is a character vector of SMILES strings or a list of 'jobjRef' objects.

Author(s)

Rajarshi Guha (rajarshi.guha@gmail.com)

See Also

[get.murcko.fragments()]

Examples

mol <- parse.smiles('c1ccc(cc1)CN(c2cc(ccc2[N+](=O)[O-])c3c(nc(nc3CC)N)N)C')[[1]]
mf1 <- get.murcko.fragments(mol, as.smiles=TRUE, single.framework=TRUE)
mf1 <- get.murcko.fragments(mol, as.smiles=TRUE, single.framework=FALSE)

Generate molecular fingerprints

Description

'get.fingerprint' returns a 'fingerprint' object representing molecular fingerprint of the input molecule.

Usage

get.fingerprint(
  molecule,
  type = "standard",
  fp.mode = "bit",
  depth = 6,
  size = 1024,
  substructure.pattern = character(),
  circular.type = "ECFP6",
  verbose = FALSE
)

Arguments

Value

an S4 object of class fingerprint-class or featvec-class, which can be manipulated with the fingerprint package.

Author(s)

Rajarshi Guha (rajarshi.guha@gmail.com)

Examples

## get some molecules
sp <- get.smiles.parser()
smiles <- c('CCC', 'CCN', 'CCN(C)(C)', 'c1ccccc1Cc1ccccc1','C1CCC1CC(CN(C)(C))CC(=O)CC')
mols <- parse.smiles(smiles)

## get a single fingerprint using the standard
## (hashed, path based) fingerprinter
fp <- get.fingerprint(mols[[1]])

## get MACCS keys for all the molecules
fps <- lapply(mols, get.fingerprint, type='maccs')

## get Signature fingerprint
## feature, count fingerprinter
fps <- lapply(mols, get.fingerprint, type='signature', fp.mode='raw')
## get Substructure fingerprint for functional group fragments
fps <- lapply(mols, get.fingerprint, type='substructure')

## get Substructure count fingerprint for user defined fragments
mol1 <- parse.smiles("c1ccccc1CCC")[[1]]
smarts <- c("c1ccccc1", "[CX4H3][#6]", "[CX2]#[CX2]")
fps <- get.fingerprint(mol1, type='substructure', fp.mode='count',
    substructure.pattern=smarts)

## get ECFP0 count fingerprints 
mol2 <- parse.smiles("C1=CC=CC(=C1)CCCC2=CC=CC=C2")[[1]]
fps <- get.fingerprint(mol2, type='circular', fp.mode='count', circular.type='ECFP0')

get.formal.charge

Description

Get the formal charge on the atom.

Usage

get.formal.charge(atom)

Arguments

Details

By default the formal charge will be 0 (i.e., NULL is never returned).

Value

An integer representing the formal charge

Author(s)

Rajarshi Guha (rajarshi.guha@gmail.com)

See Also

get.charge

get.formula

Description

obtain molecular formula from formula string

Usage

get.formula(mf, charge = 0)

Arguments

get.hydrogen.count

Description

Get the implicit hydrogen count for the atom.

Usage

get.hydrogen.count(atom)

Arguments

Details

This method returns the number of implicit H's on the atom. Depending on where the molecule was read from this may be NULL or an integer greater than or equal to 0

Value

An integer representing the hydrogen count

Author(s)

Rajarshi Guha (rajarshi.guha@gmail.com)

Construct an isotope pattern generator.

Description

Constructs an instance of the CDK IsotopePatternGenerator, with an optional minimum abundance specified. This object can be used to generate all combinatorial chemical isotopes given a structure.

Usage

get.isotope.pattern.generator(minAbundance = NULL)

Arguments

Value

A jobjRef corresponding to an instance of IsotopePatternGenerator

Author(s)

Miguel Rojas Cherto

References

http://cdk.github.io/cdk/1.5/docs/api/org/openscience/cdk/formula/IsotopePatternGenerator.html

Construct an isotope pattern similarity calculator.

Description

A method that returns an instance of the CDK IsotopePatternSimilarity class which can be used to compute similarity scores between pairs of isotope abundance patterns.

Usage

get.isotope.pattern.similarity(tol = NULL)

Arguments

Value

A jobjRef corresponding to an instance of IsotopePatternSimilarity

Author(s)

Miguel Rojas Cherto

References

http://cdk.github.io/cdk/1.5/docs/api/org/openscience/cdk/formula/IsotopePatternSimilarity.html

See Also

compare.isotope.pattern

get.isotopes.pattern

Description

Generate the isotope pattern given a formula class

Usage

get.isotopes.pattern(formula, minAbund = 0.1)

Arguments

Gets the largest component in a disconnected molecular graph.

Description

A molecule may be represented as a disconnected graph, such as when read in as a salt form. This method will return the larges connected component or if there is only a single component (i.e., the molecular graph is complete or fully connected), that component is returned.

Usage

get.largest.component(mol)

Arguments

Value

The largest component as an 'IAtomContainer' object or else the input molecule itself

Author(s)

Rajarshi Guha (rajarshi.guha@gmail.com)

See Also

is.connected

Examples

m <- parse.smiles("CC.CCCCCC.CCCC")[[1]]
largest <- get.largest.component(m)
length(get.atoms(largest)) == 6

get.mcs

Description

get.mcs

Usage

get.mcs(mol1, mol2, as.molecule = TRUE)

Arguments

get.mol2formula

Description

get.mol2formula

Usage

get.mol2formula(molecule, charge = 0)

Arguments

Generate Bemis-Murcko Fragments

Description

Fragment the input molecule using the Bemis-Murcko scheme

Usage

get.murcko.fragments(
  mols,
  min.frag.size = 6,
  as.smiles = TRUE,
  single.framework = FALSE
)

Arguments

Details

A variety of methods for fragmenting molecules are available ranging from exhaustive, rings to more specific methods such as Murcko frameworks. Fragmenting a collection of molecules can be a useful for a variety of analyses. In addition fragment based analysis can be a useful and faster alternative to traditional clustering of the whole collection, especially when it is large.

Note that exhaustive fragmentation of large molecules (with many single bonds) can become time consuming.

Value

Returns a list with each element being a list with two elements: 'rings' and 'frameworks'. Each of these elements is either a character vector of SMILES strings or a list of 'IAtomContainer' objects.

Author(s)

Rajarshi Guha (rajarshi.guha@gmail.com)

See Also

[get.exhuastive.fragments()]

Examples

mol <- parse.smiles('c1ccc(cc1)CN(c2cc(ccc2[N+](=O)[O-])c3c(nc(nc3CC)N)N)C')[[1]]
mf1 <- get.murcko.fragments(mol, as.smiles=TRUE, single.framework=TRUE)
mf1 <- get.murcko.fragments(mol, as.smiles=TRUE, single.framework=FALSE)

get.natural.mass

Description

get.natural.mass

Usage

get.natural.mass(mol)

Arguments

get.point2d

Description

Get the 2D coordinates of the atom.

Usage

get.point2d(atom)

Arguments

Details

In case, coordinates are unavailable (e.g., molecule was read in from a SMILES file) or have not been generated yet, ‘NA'’s are returned for the X & Y coordinates.

Value

A 2-element numeric vector representing the X & Y coordinates.

Author(s)

Rajarshi Guha (rajarshi.guha@gmail.com)

See Also

get.point3d

Examples

## Not run: 
atoms <- get.atoms(mol)
coords <- do.call('rbind', lapply(apply, get.point2d))

## End(Not run)

get.point3d

Description

Get the 3D coordinates of the atom.

Usage

get.point3d(atom)

Arguments

Details

In case, coordinates are unavailable (e.g., molecule was read in from a SMILES file) or have not been generated yet, ‘NA'’s are returned for the X, Y and Z coordinates.

Value

A 3-element numeric vector representing the X, Y and Z coordinates.

Author(s)

Rajarshi Guha (rajarshi.guha@gmail.com)

See Also

get.point2d

Examples

## Not run: 
atoms <- get.atoms(mol)
coords <- do.call('rbind', lapply(apply, get.point3d))

## End(Not run)

Get all properties associated with a molecule.

Description

In this context a property is a value associated with a key and stored with the molecule. This method returns a list of all the properties of a molecule. The names of the list are set to the property names.

Usage

get.properties(molecule)

Arguments

Value

A named 'list' with the property values. Element names are the keys for each property. If no properties have been defined, an empty list.

Author(s)

Rajarshi Guha (rajarshi.guha@gmail.com)

See Also

set.property, get.property, remove.property

Examples

mol <- parse.smiles("CC1CC(C=O)CCC1")[[1]]
set.property(mol, 'prop1', 23.45)
set.property(mol, 'prop2', 'inactive')
get.properties(mol)

Get a property value of the molecule.

Description

This function retrieves the value of a keyed property that has previously been set on the molecule. Properties enable us to associate arbitrary pieces of data with a molecule. Such data can be text, numeric or a Java object (represented as a 'jobjRef').

Usage

get.property(molecule, key)

Arguments

Value

The value of the property. If there is no property with the specified key, 'NA' is returned

Author(s)

Rajarshi Guha (rajarshi.guha@gmail.com)

See Also

set.property, get.properties

Examples

mol <- parse.smiles("CC1CC(C=O)CCC1")[[1]]
set.property(mol, 'prop1', 23.45)
set.property(mol, 'prop2', 'inactive')
get.property(mol, 'prop1')

Generate a SMILES representation of a molecule.

Description

The function will generate a SMILES representation of an 'IAtomContainer' object. The default parameters of the CDK SMILES generator are used. This can mean that for large ring systems the method may fail. See CDK Javadocs for more information

Usage

get.smiles(molecule, flavor = smiles.flavors(c("Generic")), smigen = NULL)

Arguments

Value

A character string containing the generated SMILES

Author(s)

Rajarshi Guha (rajarshi.guha@gmail.com)

References

SmilesGenerator

See Also

parse.smiles, smiles.flavors

Examples

m <- parse.smiles('C1C=CCC1N(C)c1ccccc1')[[1]]
get.smiles(m)
get.smiles(m, smiles.flavors(c('Generic','UseAromaticSymbols')))

Get a SMILES parser object.

Description

This function returns a reference to a SMILES parser object. If you are parsing multiple SMILES strings using multiple calls to parse.smiles, it is preferable to create your own parser and supply it to parse.smiles rather than forcing that function to instantiate a new parser for each call

Usage

get.smiles.parser()

Value

A 'jobjRef' object corresponding to the CDK SmilesParser class

Author(s)

Rajarshi Guha (rajarshi.guha@gmail.com)

See Also

get.smiles, parse.smiles

Obtain the stereocenter type for atom.

Description

Supported stereo center types are

True

the atom has constitutionally different neighbors

Para

the atom resembles a stereo centre but has constitutionally equivalent neighbors (e.g. inositol, decalin). The stereocenter depends on the configuration of one or more stereocenters.

Potential

the atom can supported stereo chemistry but has not be shown ot be a true or para center

Non

the atom is not a stereocenter (e.g. methane)

Usage

get.stereo.types(mol)

Arguments

Value

A factor of length equal in length to the number of atoms indicating the stereocenter type.

Author(s)

Rajarshi Guha rajarshi.guha@gmail.com

See Also

get.stereocenters, get.element.types

Identify which atoms are stereocenters.

Description

This method identifies stereocenters based on connectivity.

Usage

get.stereocenters(mol)

Arguments

Value

A logical vector of length equal in length to the number of atoms. The i'th element is TRUE if the i'th element is identified as a stereocenter

Author(s)

Rajarshi Guha rajarshi.guha@gmail.com

See Also

get.element.types, get.stereo.types

get.symbol

Description

Get the atomic symbol of the atom.

Usage

get.symbol(atom)

Arguments

Value

A character representing the atomic symbol

Author(s)

Rajarshi Guha (rajarshi.guha@gmail.com)

Get the title of the molecule.

Description

Some molecules may not have a title (such as when parsing in a SMILES with not title).

Usage

get.title(mol)

Arguments

Value

A character string with the title, 'NA' is no title is specified

Author(s)

Rajarshi Guha (rajarshi.guha@gmail.com)

See Also

set.title

get.total.charge

Description

get.total.charge

Usage

get.total.charge(mol)

Arguments

get.total.formal.charge

Description

get.total.formal.charge

Usage

get.total.formal.charge(mol)

Arguments

Get total number of implicit hydrogens in the molecule.

Description

Counts the number of hydrogens on the provided molecule. As this method will sum all implicit hydrogens on each atom it is important to ensure the molecule has already been configured (and thus each atom has an implicit hydrogen count).

Usage

get.total.hydrogen.count(mol)

Arguments

Value

An integer representing the total number of implicit hydrogens

Author(s)

Rajarshi Guha (rajarshi.guha@gmail.com)

See Also

get.hydrogen.count, remove.hydrogens

Compute TPSA for a molecule

Description

Compute TPSA for a molecule

Usage

get.tpsa(molecule)

Arguments

Value

A double value representing the TPSA value

Author(s)

Rajarshi Guha (rajarshi.guha@gmail.com)

Compute volume of a molecule

Description

This method does not require 3D coordinates. As a result its an approximation

Usage

get.volume(molecule)

Arguments

Value

A double value representing the volume

Author(s)

Rajarshi Guha (rajarshi.guha@gmail.com)

Compute XLogP for a molecule

Description

Compute XLogP for a molecule

Usage

get.xlogp(molecule)

Arguments

Value

A double value representing the XLogP value

Author(s)

Rajarshi Guha (rajarshi.guha@gmail.com)

Load molecules using an iterator.

Description

The CDK can read a variety of molecular structure formats. Some file formats support multiple molecules in a single file. If read using load.molecules, all are read into memory. For very large structure files, this can lead to out of memory errors. Instead it is recommended to use the iterating version of the loader so that only a single molecule is read at a time.

Usage

iload.molecules(
  molfile,
  type = "smi",
  aromaticity = TRUE,
  typing = TRUE,
  isotopes = TRUE,
  skip = TRUE
)

Arguments

Details

Note that the iterating loader only supports SDF and SMILES file formats.

Author(s)

Rajarshi Guha (rajarshi.guha@gmail.com)

See Also

write.molecules, load.molecules, parse.smiles

Examples

## Not run: 
moliter <- iload.molecules("big.sdf", type="sdf")
while(hasNext(moliter)) {
mol <- nextElem(moliter)
  print(get.property(mol, "cdk:Title"))
}

## End(Not run)

is.aliphatic

Description

Tests whether an atom is aliphatic.

Usage

is.aliphatic(atom)

Arguments

Details

This assumes that the molecule containing the atom has been appropriately configured.

Value

'TRUE' is the atom is aliphatic, 'FALSE' otherwise

Author(s)

Rajarshi Guha (rajarshi.guha@gmail.com)

See Also

is.in.ring, is.aromatic

is.aromatic

Description

Tests whether an atom is aromatic.

Usage

is.aromatic(atom)

Arguments

Details

This assumes that the molecule containing the atom has been appropriately configured.

Value

'TRUE' is the atom is aromatic, 'FALSE' otherwise

Author(s)

Rajarshi Guha (rajarshi.guha@gmail.com)

See Also

is.aliphatic, is.in.ring, do.aromaticity

Tests whether the molecule is fully connected.

Description

A single molecule will be represented as a complete graph. In some cases, such as for molecules in salt form, or after certain operations such as bond splits, the molecular graph may contained disconnected components. This method can be used to tested whether the molecule is complete (i.e. fully connected).

Usage

is.connected(mol)

Arguments

Value

'TRUE' if molecule is complete, 'FALSE' otherwise

Author(s)

Rajarshi Guha (rajarshi.guha@gmail.com)

See Also

get.largest.component

Examples

m <- parse.smiles("CC.CCCCCC.CCCC")[[1]]
is.connected(m)

is.in.ring

Description

Tests whether an atom is in a ring.

Usage

is.in.ring(atom)

Arguments

Details

This assumes that the molecule containing the atom has been appropriately configured.

Value

'TRUE' is the atom is in a ring, 'FALSE' otherwise

Author(s)

Rajarshi Guha (rajarshi.guha@gmail.com)

See Also

is.aliphatic, is.aromatic

Tests whether the molecule is neutral.

Description

The test checks whether all atoms in the molecule have a formal charge of 0.

Usage

is.neutral(mol)

Arguments

Value

'TRUE' if molecule is neutral, 'FALSE' otherwise

Author(s)

Rajarshi Guha (rajarshi.guha@gmail.com)

isvalid.formula

Description

Validate a cdkFormula.

Usage

isvalid.formula(formula, rule = c("nitrogen", "RDBE"))

Arguments

Load molecular structures from disk or URL

Description

The CDK can read a variety of molecular structure formats. This function encapsulates the calls to the CDK API to load a structure given its filename or a URL to a structure file.

Usage

load.molecules(
  molfiles = NA,
  aromaticity = TRUE,
  typing = TRUE,
  isotopes = TRUE,
  verbose = FALSE
)

Arguments

Details

Note that this method will load all molecules into memory. For files containing tens of thousands of molecules this may lead to out of memory errors. In such situations consider using the iterating file readers.

Note that if molecules are read in from formats that do not have rules for handling implicit hydrogens (such as MDL MOL), the molecule will not have implicit or explicit hydrogens. To add explicit hydrogens, make sure that the molecule has been typed (this is 'TRUE' by default for this function) and then call convert.implicit.to.explicit. On the other hand for a format such as SMILES, implicit or explicit hydrogens will be present.

Value

A 'list' of CDK 'IAtomContainer' objects, represented as 'jobjRef' objects in R, which can be used in other 'rcdk' functions

Author(s)

Rajarshi Guha (rajarshi.guha@gmail.com)

See Also

write.molecules, parse.smiles, iload.molecules

Examples

## Not run: 
sdffile <- system.file("molfiles/dhfr00008.sdf", package="rcdk")
mols <- load.molecules(c('mol1.sdf', 'mol2.smi', sdfile))

## End(Not run)

matches

Description

matches

Usage

matches(query, target, return.matches = FALSE)

Arguments

Parse SMILES strings into molecule objects.

Description

This function parses a vector of SMILES strings to generate a list of 'IAtomContainer' objects. Note that the resultant molecule will not have any 2D or 3D coordinates. Note that the molecules obtained from this method will not have any aromaticity perception (unless aromatic symbols are encountered, in which case the relevant atoms are automatically set to aromatic), atom typing or isotopic configuration done on them. This is in contrast to the load.molecules method. Thus, you should perform these steps manually on the molecules.

Usage

parse.smiles(smiles, kekulise = TRUE, omit.nulls = FALSE, smiles.parser = NULL)

Arguments

Value

A 'list' of 'jobjRef's to their corresponding CDK 'IAtomContainer' objects. If a SMILES string could not be parsed and 'omit.nulls=TRUE' it is omited from the output list.

Author(s)

Rajarshi Guha (rajarshi.guha@gmail.com)

See Also

get.smiles, parse.smiles

Deprecated functions in the rcdk package.

Description

These functions are provided for compatibility with older version of the phyloseq package. They may eventually be completely removed.

Usage

deprecated_rcdk_function(x, value, ...)

Arguments

Details

Remove explicit hydrogens.

Description

Create an copy of the original structure with explicit hydrogens removed. Stereochemistry is updated but up and down bonds in a depiction may need to be recalculated. This can also be useful for descriptor calculations.

Usage

remove.hydrogens(mol)

Arguments

Value

A copy of the original molecule, with explicit hydrogens removed

Author(s)

Rajarshi Guha (rajarshi.guha@gmail.com)

See Also

get.hydrogen.count, get.total.hydrogen.count

Remove a property associated with a molecule.

Description

In this context a property is a value associated with a key and stored with the molecule. This methd will remove the property defined by the key. If there is such key, a warning is raised.

Usage

remove.property(molecule, key)

Arguments

Author(s)

Rajarshi Guha (rajarshi.guha@gmail.com)

See Also

set.property, get.property, get.properties

Examples

mol <- parse.smiles("CC1CC(C=O)CCC1")[[1]]
set.property(mol, 'prop1', 23.45)
set.property(mol, 'prop2', 'inactive')
get.properties(mol)
remove.property(mol, 'prop2')
get.properties(mol)

set.atom.types

Description

Set the CDK atom types for all atoms in the molecule.

Usage

set.atom.types(mol)

Arguments

Details

Calling this method will overwrite any pre-existing type information. Currently there is no way to choose other atom typing schemes

Value

Nothing is returned, the molecule is modified in place

Author(s)

Rajarshi Guha (rajarshi.guha@gmail.com)

set.charge.formula

Description

Set the charge to a cdkFormula function.

Usage

set.charge.formula(formula, charge = -1)

Arguments

Set a property value of the molecule.

Description

This function sets the value of a keyed property on the molecule. Properties enable us to associate arbitrary pieces of data with a molecule. Such data can be text, numeric or a Java object (represented as a 'jobjRef').

Usage

set.property(molecule, key, value)

Arguments

Author(s)

Rajarshi Guha (rajarshi.guha@gmail.com)

See Also

get.property, get.properties, remove.property

Examples

mol <- parse.smiles("CC1CC(C=O)CCC1")[[1]]
set.property(mol, 'prop1', 23.45)
set.property(mol, 'prop2', 'inactive')
get.property(mol, 'prop1')

Set the title of the molecule.

Description

Set the title of the molecule.

Usage

set.title(mol, title = "")

Arguments

Author(s)

Rajarshi Guha (rajarshi.guha@gmail.com)

See Also

get.title

Generate flag for customizing SMILES generation.

Description

The CDK supports a variety of customizations for SMILES generation including the use of lower case symbols for aromatic compounds to the use of the ChemAxon CxSmiles format. Each 'flavor' is represented by an integer and multiple customizations are bitwise OR'ed. This method accepts the names of one or more customizations and returns the bitwise OR of them. See CDK documentation for the list of flavors and what they mean.

Usage

smiles.flavors(flavors = c("Generic"))

Arguments

Value

A numeric representing the bitwise 'OR“ of the specified flavors

Author(s)

Rajarshi Guha rajarshi.guha@gmail.com

References

CDK documentation

See Also

get.smiles

Examples

m <- parse.smiles('C1C=CCC1N(C)c1ccccc1')[[1]]
get.smiles(m)
get.smiles(m, smiles.flavors(c('Generic','UseAromaticSymbols')))

m <- parse.smiles("OS(=O)(=O)c1ccc(cc1)C(CC)CC |Sg:n:13:m:ht,Sg:n:11:n:ht|")[[1]]
get.smiles(m,flavor = smiles.flavors(c("CxSmiles")))
get.smiles(m,flavor = smiles.flavors(c("CxSmiles","UseAromaticSymbols")))

view.image.2d

Description

view.image.2d

Usage

view.image.2d(molecule, depictor = NULL)

Arguments

view.molecule.2d

Description

Create a 2D depiction of a molecule. If there are more than one molecules supplied, return a grid woth ncol columns,.

Usage

view.molecule.2d(
  molecule,
  ncol = 4,
  width = 200,
  height = 200,
  depictor = NULL
)

Arguments

view.table

Description

Create a tabular view of a set of molecules (in 2D) and associated data columns

Usage

view.table(molecules, dat, depictor = NULL)

Arguments

Write molecules to disk.

Description

This function writes one or more molecules to an SD file on disk, which can be of the single- or multi-molecule variety. In addition, if the molecule has keyed properties, they can also be written out as SD tags.

Usage

write.molecules(mols, filename, together = TRUE, write.props = FALSE)

Arguments

Details

In case individual SD files are desired the together argument can be set ot FALSE. In this case, the value of filename is used as a prefix, to which a numeric identifier and the suffix of ".sdf" is appended.

Author(s)

Rajarshi Guha (rajarshi.guha@gmail.com)

See Also

load.molecules, parse.smiles, iload.molecules