{ "_id": "6a1e948c1d7bb097a0a6b366", "Package": "rcdk", "Version": "3.8.2", "Date": "2025-11-30", "Title": "Interface to the 'CDK' Libraries", "Authors@R": "c(\nperson('Rajarshi', 'Guha', ,'rajarshi.guha@gmail.com', role=c('aut',\"cph\"),\ncomment = c(ORCID = \"0000-0001-7403-8819\")),\nperson('Zachary', 'Charlop-Powers', ,'zach.charlop.powers@gmail.com',role=c('cre'),\ncomment = c(ORCID = \"0000-0001-8816-4680\")),\nperson('Emma', 'Schymanski', ,'schymane@gmail.com', role=c('ctb'),\ncomment = c(ORCID = \"0000-0001-6868-8145\")),\nperson('Egon', 'Willighagen', ,'egon.willighagen@maastrichtuniversity.nl', role=c('ctb'),\ncomment = c(ORCID = \"0000-0001-7542-0286\")))", "License": "LGPL", "URL": "https://github.com/CDK-R/cdkr", "LazyLoad": "yes", "LazyData": "true", "SystemRequirements": "Java (>= 8)", "BugReports": "https://github.com/CDK-R/cdkr/issues", "Description": "Allows the user to access functionality in the 'CDK', a\nJava framework for cheminformatics. This allows the user to\nload molecules, evaluate fingerprints, calculate molecular\ndescriptors and so on. In addition, the 'CDK' API allows the\nuser to view structures in 2D.", "RoxygenNote": "7.3.3", "VignetteBuilder": "knitr", "Encoding": "UTF-8", "Config/pak/sysreqs": "make default-jdk libpng-dev", "Repository": "https://cdk-r.r-universe.dev", "Date/Publication": "2025-11-30 16:36:40 UTC", "RemoteUrl": "https://github.com/cdk-r/cdkr", "RemoteRef": "HEAD", "RemoteSha": "ecb5eaa5dec5a99484ea9846579525eb11c07809", "RemoteSubdir": "rcdk", "NeedsCompilation": "no", "Packaged": { "Date": "2026-06-02 08:24:44 UTC", "User": "root" }, "Author": "Rajarshi Guha [aut, cph] (ORCID:\n),\nZachary Charlop-Powers [cre] (ORCID:\n),\nEmma Schymanski [ctb] (ORCID: ),\nEgon Willighagen [ctb] (ORCID: )", "Maintainer": "Zachary Charlop-Powers ", "MD5sum": "6aee180cc0b7632ca7980dda4a108f57", "_user": "cdk-r", "_type": "src", "_file": "rcdk_3.8.2.tar.gz", "_fileid": "64f3381d156e964d76760275b0ccdfdfd0152fb25517cac2558ba8fb7e0f549c", "_filesize": 672055, "_sha256": 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tests\n\n* Remove expensive tests when on CRAN\n\n* Using MACCs in our examples to speed calculation\n\n* update cran_comments\n\n* update the linux CRAN detection\n\n* fix one more URL\n\n* update CRAN submission markdown\n\n* fix: URL moved permanently\n\n* fix: set CPUs to 1 inside of CHECK environments\n\n* fix: run all tests during the check now that CPU usage has been limited in CHECK envs\n\n* fix update CRAN submission docs\n\n* spelling\n\n* update the date\n\n* Correct first name\n\n* Setup JAVA for single threaded testing to avoid triggering warning on CRAN\n\n* prep for resubmission\n\n* rebuild docs\n\n---------\n\nCo-authored-by: Egon Willighagen ", "time": 1764520600 }, "_maintainer": { "name": "Zachary Charlop-Powers", "email": "zach.charlop.powers@gmail.com", "login": "zachcp", "description": "", "uuid": 1260667, "orcid": "0000-0001-8816-4680" }, "_registered": true, "_dependencies": [ { "package": "rcdklibs", "version": ">= 2.9", "role": "Depends" }, { "package": 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"fields": [ "SMILES", "BP" ], "rows": 277, "table": true, "tojson": true } ], "_help": [ { "page": "Atoms", "title": "Operations on Atoms", "topics": [ "rcdk-package", "Atoms" ] }, { "page": "bpdata", "title": "Boiling Point Data", "topics": [ "bpdata" ] }, { "page": "cdk.version", "title": "Get the current CDK version used in the package.", "topics": [ "cdk.version" ] }, { "page": "cdkFormula-class", "title": "Class cdkFormula, ac class for handling molecular formula", "topics": [ "cdkFormula-class", "show,cdkFormula-method" ] }, { "page": "compare.isotope.pattern", "title": "Compare isotope patterns.", "topics": [ "compare.isotope.pattern" ] }, { "page": "convert.implicit.to.explicit", "title": "Convert implicit hydrogens to explicit.", "topics": [ "convert.implicit.to.explicit" ] }, { "page": "copy.image.to.clipboard", "title": "copy.image.to.clipboard", "topics": [ "copy.image.to.clipboard" ] }, { "page": "do.aromaticity", "title": "do.aromaticity", "topics": [ "do.aromaticity" ] }, { "page": "do.isotopes", "title": "do.isotopes", "topics": [ "do.isotopes" ] }, { "page": "eval.atomic.desc", "title": "Compute descriptors for each atom in a molecule", "topics": [ "eval.atomic.desc" ] }, { "page": "eval.desc", "title": "Compute descriptor values for a set of molecules", "topics": [ "eval.desc" ] }, { "page": "generate.2d.coordinates", "title": "Generate 2D coordinates for a molecule.", "topics": [ "generate.2d.coordinates" ] }, { "page": "generate.formula", "title": "generate.formula", "topics": [ "generate.formula" ] }, { "page": "generate.formula.iter", "title": "generate.formula.iter", "topics": [ "generate.formula.iter" ] }, { "page": "get.adjacency.matrix", "title": "Get adjacency matrix for a molecule.", "topics": [ "get.adjacency.matrix" ] }, { "page": "get.alogp", "title": "Compute ALogP for a molecule", "topics": [ "get.alogp" ] }, { "page": "get.atom.count", "title": "Get the number of atoms in the molecule.", "topics": [ "get.atom.count" ] }, { "page": "get.atom.index", "title": "get.atom.index", "topics": [ "get.atom.index" ] }, { "page": "get.atomic.desc.names", "title": "Get class names for atomic descriptors", "topics": [ "get.atomic.desc.names" ] }, { "page": "get.atomic.number", "title": "get.atomic.number", "topics": [ "get.atomic.number" ] }, { "page": "get.atoms", "title": "Get the atoms from a molecule or bond.", "topics": [ "get.atoms" ] }, { "page": "get.bond.order", "title": "Get an object representing bond order", "topics": [ "get.bond.order" ] }, { "page": "get.bonds", "title": "Get the bonds in a molecule.", "topics": [ "get.bonds" ] }, { "page": "get.charge", "title": "get.charge", "topics": [ "get.charge" ] }, { "page": "get.chem.object.builder", "title": "Get the default chemical object builder.", "topics": [ "get.chem.object.builder" ] }, { "page": "get.connected.atom", "title": "Get the atom connected to an atom in a bond.", "topics": [ "get.connected.atom" ] }, { "page": "get.connected.atoms", "title": "get.connected.atoms", "topics": [ "get.connected.atoms" ] }, { "page": "get.connection.matrix", "title": "Get connection matrix for a molecule.", "topics": [ "get.connection.matrix" ] }, { "page": "get.depictor", "title": "get.depictor", "topics": [ "get.depictor" ] }, { "page": "get.desc.categories", "title": "List available descriptor categories", "topics": [ "get.desc.categories" ] }, { "page": "get.desc.names", "title": "Get descriptor class names", "topics": [ "get.desc.names" ] }, { "page": "get.element.types", "title": "Obtain the type of stereo element support for atom.", "topics": [ "get.element.types" ] }, { "page": "get.exact.mass", "title": "get.exact.mass", "topics": [ "get.exact.mass" ] }, { "page": "get.exhaustive.fragments", "title": "Generate Bemis-Murcko Fragments", "topics": [ "get.exhaustive.fragments" ] }, { "page": "get.fingerprint", "title": "Generate molecular fingerprints", "topics": [ "get.fingerprint" ] }, { "page": "get.formal.charge", "title": "get.formal.charge", "topics": [ "get.formal.charge" ] }, { "page": "get.formula", "title": "get.formula", "topics": [ "get.formula" ] }, { "page": "get.hydrogen.count", "title": "get.hydrogen.count", "topics": [ "get.hydrogen.count", "hydrogen" ] }, { "page": "get.isotope.pattern.generator", "title": "Construct an isotope pattern generator.", "topics": [ "get.isotope.pattern.generator" ] }, { "page": "get.isotope.pattern.similarity", "title": "Construct an isotope pattern similarity calculator.", "topics": [ "get.isotope.pattern.similarity" ] }, { "page": "get.isotopes.pattern", "title": "get.isotopes.pattern", "topics": [ "get.isotopes.pattern" ] }, { "page": "get.largest.component", "title": "Gets the largest component in a disconnected molecular graph.", "topics": [ "get.largest.component" ] }, { "page": "get.mcs", "title": "get.mcs", "topics": [ "get.mcs" ] }, { "page": "get.mol2formula", "title": "get.mol2formula", "topics": [ "get.mol2formula" ] }, { "page": "get.murcko.fragments", "title": "Generate Bemis-Murcko Fragments", "topics": [ "get.murcko.fragments" ] }, { "page": "get.natural.mass", "title": "get.natural.mass", "topics": [ "get.natural.mass" ] }, { "page": "get.point2d", "title": "get.point2d", "topics": [ "get.point2d" ] }, { "page": "get.point3d", "title": "get.point3d", "topics": [ "get.point3d" ] }, { "page": "get.properties", "title": "Get all properties associated with a molecule.", "topics": [ "get.properties" ] }, { "page": "get.property", "title": "Get a property value of the molecule.", "topics": [ "get.property" ] }, { "page": "get.smiles", "title": "Generate a SMILES representation of a molecule.", "topics": [ "get.smiles" ] }, { "page": "get.smiles.parser", "title": "Get a SMILES parser object.", "topics": [ "get.smiles.parser" ] }, { "page": "get.stereo.types", "title": "Obtain the stereocenter type for atom.", "topics": [ "get.stereo.types" ] }, { "page": "get.stereocenters", "title": "Identify which atoms are stereocenters.", "topics": [ "get.stereocenters" ] }, { "page": "get.symbol", "title": "get.symbol", "topics": [ "get.symbol" ] }, { "page": "get.title", "title": "Get the title of the molecule.", "topics": [ "get.title" ] }, { "page": "get.total.charge", "title": "get.total.charge", "topics": [ "get.total.charge" ] }, { "page": "get.total.formal.charge", "title": "get.total.formal.charge", "topics": [ "get.total.formal.charge" ] }, { "page": "get.total.hydrogen.count", "title": "Get total number of implicit hydrogens in the molecule.", "topics": [ "get.total.hydrogen.count" ] }, { "page": "get.tpsa", "title": "Compute TPSA for a molecule", "topics": [ "get.tpsa" ] }, { "page": "get.volume", "title": "Compute volume of a molecule", "topics": [ "get.volume" ] }, { "page": "get.xlogp", "title": "Compute XLogP for a molecule", "topics": [ "get.xlogp" ] }, { "page": "iload.molecules", "title": "Load molecules using an iterator.", "topics": [ "iload.molecules" ] }, { "page": "is.aliphatic", "title": "is.aliphatic", "topics": [ "is.aliphatic" ] }, { "page": "is.aromatic", "title": "is.aromatic", "topics": [ "is.aromatic" ] }, { "page": "is.connected", "title": "Tests whether the molecule is fully connected.", "topics": [ "is.connected" ] }, { "page": "is.in.ring", "title": "is.in.ring", "topics": [ "is.in.ring" ] }, { "page": "is.neutral", "title": "Tests whether the molecule is neutral.", "topics": [ "charge", "is.neutral" ] }, { "page": "isvalid.formula", "title": "isvalid.formula", "topics": [ "isvalid.formula" ] }, { "page": "load.molecules", "title": "Load molecular structures from disk or URL", "topics": [ "load.molecules" ] }, { "page": "matches", "title": "matches", "topics": [ "match-SMARTS", "matches" ] }, { "page": "Molecule", "title": "Operations on molecules", "topics": [ "Molecule" ] }, { "page": "parse.smiles", "title": "Parse SMILES strings into molecule objects.", "topics": [ "parse.smiles" ] }, { "page": "rcdk-deprecated", "title": "Deprecated functions 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