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updating fork #1

Merged

schymane merged 142 commits into schymane:master from CDK-R:master

Nov 10, 2018

Owner

schymane commented Nov 10, 2018

No description provided.

rajarshi and others added some commits Feb 21, 2017


      Added extra args to view methods

Updated rcdk jar file

ebc9bbe


      Added more args to control 2D depictions.

Updated man page

ae80170


      Update viewmol2d.Rd

Added missing \ to \code{\link{readPNG}}

29d298a


      Merge pull request CDK-R#42 from schymane/patch-1

Update viewmol2d.Rd

3a1fcb1


      Merge branch 'master' of github.com:rajarshi/cdkr

482ef8a


      Added wwrapper for CDK depictions

d3e1678


      Added public methods, hide depiction generation process

aa4e4d1


      Added helper method

Removed some testing code

0da258d


      Ensure helper method is static

5f3e32d


      Refactored to use depiction wrapper class

26cfa93


      Cleaned up helper code

a44a286


      Updated depiction code so that everything is refactored to use the ne…

…w depiction wrapper

Updated man page

20fe1d5


      Made depiction method input args consistent

06ea7a3


      fixed some missing args

1529ba6


      Update viewmol2d.Rd

depictor => dep

609118e


      Merge pull request CDK-R#43 from schymane/patch-2

Update viewmol2d.Rd

b1cd0c2


      Added Emma as contributor

ff5e790


      Merge branch 'master' of github.com:rajarshi/cdkr

5e5e681


      updated depends/imports

Fixed global var issue in depiction code

f5bbd62


      Fixed missing doc errors

Fixed function refs in vignette

f2f1616


      update cdk Jar files

9d21c93


      rebuilt rcdk on cdk2.0 libs

987fad1


      updated JARfiel to reomve pdb and 3d mods. see README_DEV.md

f2a5a11


      add devfile describing how to build CDK2.0

0d8c087


      update cdk2 jarfile

eb32903


      update DESCRIPTION file. Version bump. Date Bump. CRAN fixes

2dc4629


      Merge pull request CDK-R#46 from zachcp/master

Update cdklibs to 2.0 release

74cfc89


      rebuild rcdklibs and update DESCRIPTION files

48a6e93


      Return NULL rather than NA if SMILES parsing fails

Bumped version number

fd2977e


      Added help method to get SMILES flavors

Updated SMILES generator to use flavors

702adb9

Rajarshi Guha and others added some commits Sep 16, 2018


      Some code cleanup

0cb1744


      Updated rcdklibs to latest CDK snapshot

15df3e5


      Updated to latest CDK snapshot

0983a0c


      fixed wrong var name

3aa6a3e


      Add travis (CDK-R#78)

* Start adding travis

* Setup for R pkgs in subdirs, add java dep

* Another attempt to install JDK

* Attempt to install rJava

* Attempt to install devtools prior to dependencies

* Another attempt to install devtools prior to dependencies

* Add rcdk as well

* Debug dep installation on travis

* Fix package root for newer R version

2ac7f5a


      update java check to allow working with Java 11

b19c96b


      - Update the CDK Jar to the 2.2 release.

- Update the version/date
- Update Readme in thr source directory

935d241


      force build

2745e14


      fix bug in generate.2d.coordinates

ba63db8


      another molecule <--> mol bug

c992fe6


      another bug mol <--> molecule

d608692


      update rcdk build jar

99edf5c


      Change the code in .cdkFormula.createObject to handle cases where we …

…were getting null values.

3d6573f


      remove prints

c29ae52


      the code for descriptors is currently broken. Will need to fix this. …

…Commenting it out so that builds can proceed

0c49635


      Merge pull request CDK-R#80 from zachcp/j11

Update for J11 and Miscellaneous fixed

d91d34d


      Adding the build badge

This adds the link with the Travis build results to the README.md and hence the cdkr page users see first.

067f863


      Merge pull request CDK-R#81 from sneumann/patch-3

Adding the build badge

f1dee01


      Handle the FractionalCSP3Descriptor Case

7e06586


      restore vignette

7ab345c


      update JAR files

69d21fb


      a few more molecule typos picked up from unit tests

7ec5524


      Merge pull request CDK-R#82 from zachcp/descriptorfixes

Descriptorfixes

416ac83


      calculate mass by passing through the molecular formula. The advantag…

…e here is that the formula manipulator handles isotope assignment of the atoms in the molecule. Isotope assignment (or lack therof_ was causing mass calculations to fail

65b546b


      fix molecule->mol

2f15087


      Merge pull request CDK-R#83 from zachcp/getmassfix

calculate mass by passing through the molecular formula. The advantag…

7930c4e


      Fix a test to CDK .silent classes, fix examples to include element na…

…me. Passing R CMD check now without errors, bump version number

7840cd4


      Merge pull request CDK-R#84 from sneumann/fixCheck

Fix a test to CDK .silent classes,

dd0886f

schymane merged commit `b9c2647` into schymane:master Nov 10, 2018

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