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/rcdk/CHANGELOG

http://github.com/rajarshi/cdkr
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  12013-10-30  Guha  <guhar@HG-01881061-LM8.local>
  2
  3	* R/fingerprint.R (get.fingerprint): Updated to ensure we call
  4	Pubchem fingerprinter with appropriate constructor arguments
  5
  6	* R/rcdk.R: Added internal helper method to get a DefaultChemObjectBuilder
  7
  82013-10-06  Guha  <guhar@HG-01881061-LM8.local>
  9
 10	* R/fingerprint.R (get.fingerprint): Included LINGO fingerprinter
 11	as an available fingerprint type
 12
 13	* man/getfp.Rd: Updated man page to describe feature,count
 14	fingeprints. Added reference for signature fingerprint
 15
 16	* R/fingerprint.R (get.fingerprint): Added support for the
 17	signature fingerprint. We also support the raw and count mode
 18	fingerprint types in general. If these modes are requested, the
 19	fingerprint is a featvec object
 20
 212013-01-05  Guha  <guhar@citdnstjonesr.cit.nih.gov>
 22
 23	* man/getfp.Rd: Updated man page for new fingerprints
 24
 25	* inst/unitTests/runit.rcdk.R (test.fp): Added some simple
 26	fingerprint test cases
 27
 28	* R/rcdk.R (get.fingerprint): Updated to use the new
 29	IBitFingerprint interface. Added support for the Kelkota Roth and shortest
 30	path fingerprinters
 31
 32	* Updated to latest CDK master, supporting new atom types
 33
 342012-11-17 Rajarshi Guha
 35
 36	* R/iterating.R: Updated to use the proper class for iterating
 37	over SD files. Thanks to Xavier Arroyo for reporting this
 38
 392012-09-01  Rajarshi Guha  <guhar@Rajarshi-Guha-MacBook-Pro.local>
 40
 41	* R/formula.R (get.mol2formula): Removed a debug statement
 42
 432012-07-05  Rajarshi Guha  <guhar@OfficeMac.local>
 44
 45	* inst/unitTests/runit.match.R (test.match4): Added a unit test
 46	for the new matches update
 47
 48	* man/match.Rd: Updated man page for the matches method
 49	to describe the new argument and return values
 50
 51	* R/matching.R (matches): Updated SMARTS matching method to return
 52	the list of atom indices that correspond to the matching substructure
 53
 542012-06-20  Rajarshi Guha  <guhar@hg-01716957-lwx.nhgri.nih.gov>
 55
 56	* R/smiles.R (parse.smiles): Updated code to recognize there
 57	is no longer a IMolecule class
 58
 59	* R/atoms.R (get.charge): Updated code to recognize there
 60	is no longer a IMolecule class
 61
 62	* R/desc.R (get.desc.names): Updated code to recognize there
 63	is no longer a IMolecule class
 64
 65	* R/rcdk.R (get.title): Updated code to recognize there
 66	is no longer a IMolecule class
 67
 68	* R/props.R (get.properties): Updated code to recognize there
 69	is no longer a IMolecule class
 70
 71	* R/formula.R (get.mol2formula): Updated code to recognize there
 72	is no longer a IMolecule class
 73
 74	* inst/unitTests/runit.frags.R (test.frag3): Updated to remove
 75	references to IMolecule and Molecule
 76
 772012-03-09  Rajarshi Guha  <guhar@Rajarshi-Guha-MacBook-Pro.local>
 78
 79	* R/atoms.R (get.connected.atoms): Added method to retrieve atoms
 80	connected to the specified atom.
 81	(get.atom.index): Added method to retrieve index of the atom in a
 82	molecule, starting from 0
 83
 84	* R/props.R (get.property): Updated to check for null molecule
 85	objects. Also made property retrieval more robust by checking
 86	explicitly for exceptions
 87
 882012-02-26  Rajarshi Guha  <guhar@niaaa-lptroach.niaaa.nih.gov>
 89
 90	* inst/doc/rcdk.Rnw: Updated vignette to not evaluate all descriptors for all molecules. 
 91	Instead we now hand pick a few descriptors for the example on predictive models
 92
 932012-02-23  Rajarshi Guha  <guhar@dk31r9a06lp5a.niddk.nih.gov>
 94
 95	* man/getfp.Rd: Updated documentation for the new parameters in
 96	get.fingerprint and iload.molecules
 97
 982012-02-22  Rajarshi Guha  <guhar@Rajarshi-Guha-MacBook-Pro.local>
 99
100	* R/rcdk.R (get.fingerprint): Updated to manually check for
101	exceptions and if one occurs optionally print it out (depending on
102	the value of he verbose parameter)
103
1042011-12-13  Rajarshi Guha  <guhar@citdcssgoldi7lt.cit.nih.gov>
105
106	* Updated NAMESPACE to export the .get.desc.value method
107
1082011-11-01  Rajarshi Guha  <guhar@OfficeMac.local>
109	
110	* Convert package to use a namespace
111	
112	* Updated to use CDK 1.4.5
113
1142011-10-04  Rajarshi Guha  <guhar@OfficeMac.local>
115
116	* Updated to latest CDK 1.4.x branch, so that SDF writing now
117	properly takes into account aromatic bond types.
118
1192011-08-10  Rajarshi Guha  <guhar@Rajarshi-Guha-MacBook-Pro.local>
120
121	* man/loadmol.Rd: Added examples for using load.molecules
122
123	* R/iterating.R (hasNext.iload.molecules): Made more robust by
124	checking that the file exists before trying to load it
125
126	* R/io.R (load.molecules): If non-existant file is specified we
127	now report the error properly
128
1292011-07-23  Rajarshi Guha  <guhar@Rajarshi-Guha-MacBook-Pro.local>
130	
131	* Updated to latest CDK library
132
1332011-06-19  Rajarshi Guha  <guhar@Rajarshi-Guha-MacBook-Pro.local>
134
135	* R/formula.R (set.charge.formula): Updated default argument to
136	match docs
137
138	* man/viewmol2d.Rd: Fixed documentation typo
139
140	* man/setchargeformula.Rd: Fixed documentation error
141
1422011-06-18  Rajarshi Guha  <guhar@Rajarshi-Guha-MacBook-Pro.local>
143
144	* R/visual.R (view.molecule.2d): Updated some methods to make use
145	of the OS X helper. This allows users on OS X to view single
146	molecules in a Swing window and copy PNG depictions to the system clipboard
147
148	* man/props.Rd: Updated man page for the new volume method
149
150	* R/desc.R (get.volume): Added helper method to get molecular
151	volume based on the VABC method.
152
1532011-06-11  Rajarshi Guha  <guhar@nida01768669-lt.nida.nih.gov>
154
155	* man/getfp.Rd: Updated fingerprint man page for the new one
156
157	* R/rcdk.R (get.total.formal.charge): Fixed typo in variable name
158	(get.fingerprint): Added support for the new Hybridization fingerprinter
159
160	* man/viewmol2d.Rd: Updated man page for the new clipboard
161	copy method
162
163	* R/visual.R (copy.image.to.clipboard): Added function
164	to copy 2D depiction to system clipboard
165
166	* Updated to latest stable CDK release
167
1682011-05-06  Rajarshi Guha  <guhar@guest-193-062-206-199.wtgc.org>
169
170	* man/gettotalcharge.Rd: Added man page entry for the total
171	formal charge function.
172
173	* R/rcdk.R (get.total.formal.charge): Added new function to 
174	return the total formal charge. Also updated get.total.charge
175	to recognize when partial charges are unset and in such a case
176	return the sum of formal charges
177
1782011-02-20  Rajarshi Guha  <guhar@Rajarshi-Guha-MacBook-Pro.local>
179
180	* Updated CDK jar file to latest master plus some
181	cherry picks from 1.4
182
183	* NAMESPACE: Added a specific export for hasNext
184
1852010-11-08  Rajarshi Guha  <guhar@office>
186
187	* R/rcdk.R (get.exact.mass): Updated to check for exception when
188	getting exact mass and print a more useful message.
189	(get.natural.mass): Same as above
190
1912010-11-07  Rajarshi Guha  <guhar@Rajarshi-Guha-MacBook-Pro.local>
192
193	* man/getproperty.Rd: Updated man page for get.title
194
195	* R/rcdk.R (get.title): Added a helper method to get the title
196	of a molecule.
197
198	* inst/doc/rcdk.Rnw (section{Input / Output}): Added a description
199	of how to use the iterating version of the molecule loader
200
201	* R/iterating.R (nextEl): Updated iterator so that we don't skip 
202	the first molecule. Also reorganized the code so that it makes
203	more sense
204
2052010-10-21  Rajarshi Guha  <guhar@Rajarshi-Guha-MacBook-Pro.local>
206
207	* Updated to latest CDK (1.4.x) which resolves bugs in formula
208	generation and reading SD tags consisting of single spaces. Also
209	updates to Murkco fragmentatin code which ensures that the proper
210	fragments are returned when requested as molecule objects. This
211	version also includes 3 new descriptors (FMF, acidic group and
212	basic group counts). 
213	
214
2152010-05-29  Rajarshi Guha  <guhar@OfficeMac.local>
216
217	* man/getfp.Rd: Updated docs for the newly included Pubchem fingerprint
218
219	* R/rcdk.R: Updated fingerprinter to support the Pubchem fingerprints
220