2021-10-14 * Fix code to handle changes to JDK17. Notably, I needed to reduce the use of the J notation in a nubmer of places in favor of direct calls. * formally deprecated `do.typing` in favor of `set.atom.types` 2020-12-21 Rajarshi Guha * Updated handling of atomic descriptors to resolve a name mismatch bug * Added a test case for atomic descriptors (thanks to Francesca Di Cesare) 2020-09-23 Rajarshi Guha * Updated @export annotation with function name to avoid interpretation as S3 method * Refactored do.typing to set.atom.types and updated to use J notation * Refactored methods to use the renamed function 2020-03-15 Rajarshi Guha * Generate bond order enums and store in rcdk package env * Add a method to retrieve bond order enums * Add unit tests 2013-10-30 Guha * R/fingerprint.R (get.fingerprint): Updated to ensure we call Pubchem fingerprinter with appropriate constructor arguments * R/rcdk.R: Added internal helper method to get a DefaultChemObjectBuilder 2013-10-06 Guha * R/fingerprint.R (get.fingerprint): Included LINGO fingerprinter as an available fingerprint type * man/getfp.Rd: Updated man page to describe feature,count fingeprints. Added reference for signature fingerprint * R/fingerprint.R (get.fingerprint): Added support for the signature fingerprint. We also support the raw and count mode fingerprint types in general. If these modes are requested, the fingerprint is a featvec object 2013-01-05 Guha * man/getfp.Rd: Updated man page for new fingerprints * inst/unitTests/runit.rcdk.R (test.fp): Added some simple fingerprint test cases * R/rcdk.R (get.fingerprint): Updated to use the new IBitFingerprint interface. Added support for the Kelkota Roth and shortest path fingerprinters * Updated to latest CDK master, supporting new atom types 2012-11-17 Rajarshi Guha * R/iterating.R: Updated to use the proper class for iterating over SD files. Thanks to Xavier Arroyo for reporting this 2012-09-01 Rajarshi Guha * R/formula.R (get.mol2formula): Removed a debug statement 2012-07-05 Rajarshi Guha * inst/unitTests/runit.match.R (test.match4): Added a unit test for the new matches update * man/match.Rd: Updated man page for the matches method to describe the new argument and return values * R/matching.R (matches): Updated SMARTS matching method to return the list of atom indices that correspond to the matching substructure 2012-06-20 Rajarshi Guha * R/smiles.R (parse.smiles): Updated code to recognize there is no longer a IMolecule class * R/atoms.R (get.charge): Updated code to recognize there is no longer a IMolecule class * R/desc.R (get.desc.names): Updated code to recognize there is no longer a IMolecule class * R/rcdk.R (get.title): Updated code to recognize there is no longer a IMolecule class * R/props.R (get.properties): Updated code to recognize there is no longer a IMolecule class * R/formula.R (get.mol2formula): Updated code to recognize there is no longer a IMolecule class * inst/unitTests/runit.frags.R (test.frag3): Updated to remove references to IMolecule and Molecule 2012-03-09 Rajarshi Guha * R/atoms.R (get.connected.atoms): Added method to retrieve atoms connected to the specified atom. (get.atom.index): Added method to retrieve index of the atom in a molecule, starting from 0 * R/props.R (get.property): Updated to check for null molecule objects. Also made property retrieval more robust by checking explicitly for exceptions 2012-02-26 Rajarshi Guha * inst/doc/rcdk.Rnw: Updated vignette to not evaluate all descriptors for all molecules. Instead we now hand pick a few descriptors for the example on predictive models 2012-02-23 Rajarshi Guha * man/getfp.Rd: Updated documentation for the new parameters in get.fingerprint and iload.molecules 2012-02-22 Rajarshi Guha * R/rcdk.R (get.fingerprint): Updated to manually check for exceptions and if one occurs optionally print it out (depending on the value of he verbose parameter) 2011-12-13 Rajarshi Guha * Updated NAMESPACE to export the .get.desc.value method 2011-11-01 Rajarshi Guha * Convert package to use a namespace * Updated to use CDK 1.4.5 2011-10-04 Rajarshi Guha * Updated to latest CDK 1.4.x branch, so that SDF writing now properly takes into account aromatic bond types. 2011-08-10 Rajarshi Guha * man/loadmol.Rd: Added examples for using load.molecules * R/iterating.R (hasNext.iload.molecules): Made more robust by checking that the file exists before trying to load it * R/io.R (load.molecules): If non-existant file is specified we now report the error properly 2011-07-23 Rajarshi Guha * Updated to latest CDK library 2011-06-19 Rajarshi Guha * R/formula.R (set.charge.formula): Updated default argument to match docs * man/viewmol2d.Rd: Fixed documentation typo * man/setchargeformula.Rd: Fixed documentation error 2011-06-18 Rajarshi Guha * R/visual.R (view.molecule.2d): Updated some methods to make use of the OS X helper. This allows users on OS X to view single molecules in a Swing window and copy PNG depictions to the system clipboard * man/props.Rd: Updated man page for the new volume method * R/desc.R (get.volume): Added helper method to get molecular volume based on the VABC method. 2011-06-11 Rajarshi Guha * man/getfp.Rd: Updated fingerprint man page for the new one * R/rcdk.R (get.total.formal.charge): Fixed typo in variable name (get.fingerprint): Added support for the new Hybridization fingerprinter * man/viewmol2d.Rd: Updated man page for the new clipboard copy method * R/visual.R (copy.image.to.clipboard): Added function to copy 2D depiction to system clipboard * Updated to latest stable CDK release 2011-05-06 Rajarshi Guha * man/gettotalcharge.Rd: Added man page entry for the total formal charge function. * R/rcdk.R (get.total.formal.charge): Added new function to return the total formal charge. Also updated get.total.charge to recognize when partial charges are unset and in such a case return the sum of formal charges 2011-02-20 Rajarshi Guha * Updated CDK jar file to latest master plus some cherry picks from 1.4 * NAMESPACE: Added a specific export for hasNext 2010-11-08 Rajarshi Guha * R/rcdk.R (get.exact.mass): Updated to check for exception when getting exact mass and print a more useful message. (get.natural.mass): Same as above 2010-11-07 Rajarshi Guha * man/getproperty.Rd: Updated man page for get.title * R/rcdk.R (get.title): Added a helper method to get the title of a molecule. * inst/doc/rcdk.Rnw (section{Input / Output}): Added a description of how to use the iterating version of the molecule loader * R/iterating.R (nextEl): Updated iterator so that we don't skip the first molecule. Also reorganized the code so that it makes more sense 2010-10-21 Rajarshi Guha * Updated to latest CDK (1.4.x) which resolves bugs in formula generation and reading SD tags consisting of single spaces. Also updates to Murkco fragmentatin code which ensures that the proper fragments are returned when requested as molecule objects. This version also includes 3 new descriptors (FMF, acidic group and basic group counts). 2010-05-29 Rajarshi Guha * man/getfp.Rd: Updated docs for the newly included Pubchem fingerprint * R/rcdk.R: Updated fingerprinter to support the Pubchem fingerprints