/rcdk/CHANGELOG

2013-10-30  Guha  <guhar@HG-01881061-LM8.local>

	* 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  <guhar@HG-01881061-LM8.local>

	* 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  <guhar@citdnstjonesr.cit.nih.gov>

	* 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  <guhar@Rajarshi-Guha-MacBook-Pro.local>

	* R/formula.R (get.mol2formula): Removed a debug statement

2012-07-05  Rajarshi Guha  <guhar@OfficeMac.local>

	* 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  <guhar@hg-01716957-lwx.nhgri.nih.gov>

	* 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  <guhar@Rajarshi-Guha-MacBook-Pro.local>

	* 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  <guhar@niaaa-lptroach.niaaa.nih.gov>

	* 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  <guhar@dk31r9a06lp5a.niddk.nih.gov>

	* man/getfp.Rd: Updated documentation for the new parameters in
	get.fingerprint and iload.molecules

2012-02-22  Rajarshi Guha  <guhar@Rajarshi-Guha-MacBook-Pro.local>

	* 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  <guhar@citdcssgoldi7lt.cit.nih.gov>

	* Updated NAMESPACE to export the .get.desc.value method

2011-11-01  Rajarshi Guha  <guhar@OfficeMac.local>
	
	* Convert package to use a namespace
	
	* Updated to use CDK 1.4.5

2011-10-04  Rajarshi Guha  <guhar@OfficeMac.local>

	* 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  <guhar@Rajarshi-Guha-MacBook-Pro.local>

	* 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  <guhar@Rajarshi-Guha-MacBook-Pro.local>
	
	* Updated to latest CDK library

2011-06-19  Rajarshi Guha  <guhar@Rajarshi-Guha-MacBook-Pro.local>

	* 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  <guhar@Rajarshi-Guha-MacBook-Pro.local>

	* 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  <guhar@nida01768669-lt.nida.nih.gov>

	* 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  <guhar@guest-193-062-206-199.wtgc.org>

	* 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  <guhar@Rajarshi-Guha-MacBook-Pro.local>

	* 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  <guhar@office>

	* 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  <guhar@Rajarshi-Guha-MacBook-Pro.local>

	* 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  <guhar@Rajarshi-Guha-MacBook-Pro.local>

	* 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  <guhar@OfficeMac.local>

	* man/getfp.Rd: Updated docs for the newly included Pubchem fingerprint

	* R/rcdk.R: Updated fingerprinter to support the Pubchem fingerprints