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Author SHA1 Message Date
Noel O'Boyle
3b86b037b4 Move the setting and resetting of the DL open flags to where 'import _openbabel' occurs in openbabel.py 2018-02-11 08:31:02 +00:00
Noel O'Boyle
e287255158 Reset the DL open flags after loading the plugins. 2018-02-08 21:09:53 +00:00
Noel O'Boyle
28dbe451d7 Merge pull request #1757 from mcs07/cmake-testdir-fix 
Fix TESTDIR definition to allow space in path
 2018-01-18 08:00:25 +00:00
Geoff Hutchison
d5842841a0 Merge pull request #1755 from yishutu/master 
Solving #1569
 2018-01-17 15:48:41 -05:00
Matt Swain
5162f49936 Remove unneeded TESTDIR definition 2018-01-16 15:40:24 +00:00
Matt Swain
af9c5019cd Fix TESTDIR definition to allow space in path 2018-01-16 14:22:52 +00:00
Yi-Shu Tu
daf4a0b594 change EOF comparison when skipping tail blank lines. 2018-01-15 11:11:08 +08:00
Yi-Shu Tu
3e2cd4e9c2 The codes removing tailing blank lines were rewritten to solve issue #1569. 2018-01-15 10:44:58 +08:00
Geoff Hutchison
c094a42463 Merge pull request #1747 from baoilleach/FixWarnings 
Fix GCC warnings
 2018-01-11 13:55:01 -05:00
Geoff Hutchison
4736189bf6 Merge pull request #1749 from baoilleach/fastsearchbug 
Fix warning in fastsearch substructure fingerprint screen
 2018-01-11 13:54:10 -05:00
Geoff Hutchison
5904179c83 Merge pull request #1751 from mmghahremanpour/gaussformat-ReadingExactPolarizability 
Reading Exact Polairzability from Gaussian log file
 2018-01-11 13:53:39 -05:00
Noel O'Boyle
a6c84d5a15 Use a portable way to mark variables as unused. Hopefully fix MSVC build. 2018-01-11 08:03:25 +00:00
Noel O'Boyle
3934c5e356 Rebase and fix error. 2018-01-10 20:41:54 +00:00
Noel O'Boyle
1cfaebddce Add back the dtor I removed so that things compile. 2018-01-10 20:39:38 +00:00
Noel O'Boyle
ba49902efd Get rid of warning about unused variable. 2018-01-10 20:39:38 +00:00
Noel O'Boyle
b6e1394f36 Fix reorder initialization warning 2018-01-10 20:39:38 +00:00
Noel O'Boyle
a223ee2318 Fix signed/unsigned comp 2018-01-10 20:39:37 +00:00
Noel O'Boyle
1cf13c017e Fix a warning about an unused param by trimming down a bunch of no-longer used methods in OBAromaticTyper. To begin with, this no longer needed to inherit from OBGlobalDatabase, and so I removed that, and the associated private variables and public methods. In the end, it's essentially a single function and could be turned into that, but I've left it as it is. 2018-01-10 20:39:37 +00:00
Noel O'Boyle
0300b92741 Fix signed/unsigned. Also initialization reorder. 2018-01-10 20:39:37 +00:00
Noel O'Boyle
c6625285e5 Fix signed/unsigned by changing the parameter type for StripSalts and GetConformer. Fix warning about type qualifiers being ignored for 'internal' function DeleteStereoOnAtom by changing 'const' to 'static' (presumably a mistype (pun alert)) 2018-01-10 20:39:37 +00:00
Noel O'Boyle
f3d4c755e4 Change API for OBVirtualBond to use unsigned ints for bgn,end,order. I'm not sure that we really need this class in the first place, but if we do, it should use unsigned ints. This fixes a signed/unsigned comparison warning in mol.cpp. 2018-01-10 20:39:37 +00:00
Noel O'Boyle
38f2b416c9 An API change to two OBStereo functions to avoid signed/unsigned comparison. Why allow signed integers as a parameter if negative values are not allowed? 2018-01-10 20:39:37 +00:00
Noel O'Boyle
51d81cc89c Fix signed/unsigned comps. 2018-01-10 20:39:37 +00:00
Noel O'Boyle
8df5c9e0d6 Fix warnings. Signed/unsigned. Parameter init order. Suggested parentheses in expression. 2018-01-10 20:39:37 +00:00
Noel O'Boyle
24915b6107 Fix signed/unsigned comp. 2018-01-10 20:39:37 +00:00
Noel O'Boyle
8fd7fa0feb Fix signed/unsigned. Also unused function parameter of OBBond* in OBRotor::SetRings() - fixed by removing it. I'm not sure that this function needs to be in the public API at all though. 2018-01-10 20:39:37 +00:00
Noel O'Boyle
65074163ee Compiling the Python bindings (at least) failed as OBBitVec was not yet defined. I've moved it before the mol.h include. 2018-01-10 20:39:37 +00:00
Noel O'Boyle
b15bf4199d Get rid of warning about unused static functions. Get rid of signed/unsigned warning. 2018-01-10 20:39:37 +00:00
Noel O'Boyle
3d8301d8bc Update PDB-based file formats for change to AssignBonds() function 2018-01-10 20:39:37 +00:00
Noel O'Boyle
51cebb6962 Get rid of warning about signed/unsigned comparison. 2018-01-10 20:39:37 +00:00
Noel O'Boyle
c84e1b5d50 Get rid of warning about unused parameter by removing it. It is part of the API but is already marked as deprecated in the doxygen description. 2018-01-10 20:39:37 +00:00
Noel O'Boyle
80d2c3f055 Get rid of warnings about uninitialized variables. 2018-01-10 20:39:37 +00:00
Noel O'Boyle
633bafe6c6 Get rid of warning about initialization order (by reordering the parameter list). Get rid of warning about unused parameter by removing the parameter. 2018-01-10 20:39:37 +00:00
Noel O'Boyle
d28a2c4ce9 Get rid of warnings about multiline comments (comments that end with a backslash). Get rid of warning about possibly uninitialized value. 2018-01-10 20:39:37 +00:00
Noel O'Boyle
766e3d9787 Get rid of warning about signed/unsigned comparison in that key convenience function, OBAtom::HighestBondOrder() 2018-01-10 20:39:36 +00:00
Noel O'Boyle
43dd0ac883 Get rid of warning about unused parameters for OpGenAlias. 2018-01-10 20:39:36 +00:00
Noel O'Boyle
dd3306cedc Fix signed/unsigned comparison warning. There was a mismatch between the type of stored value of the HOMO and the type of the parameter in some of the functions. 2018-01-10 20:39:36 +00:00
Noel O'Boyle
e33e14a972 Fix warning about signed/unsigned comparison 2018-01-10 20:39:36 +00:00
Noel O'Boyle
4b684c64e9 Merge pull request #1750 from Acpharis/numCompare 
Fix #1684
 2018-01-10 20:30:09 +00:00
mohammad-ghahremanpour
7d74d738b7 Reading Exact Polairzability from Gaussian log file 2018-01-10 09:52:23 +01:00
David Hall
58774501ed Fix #1684 
When figuring out if a filter value is numeric by casting to double, Mac and Linux
set the failbit if the cast cannot be done, so peek returns -1. This checks for
said failbit.
 2018-01-09 17:26:50 -05:00
Noel O'Boyle
8fd19840c6 Fix warning about evaluation order being undefined due to use of ppat and ppat++ in the same statement. Made slightly faster, I think too, but this is not the slow part of substructure searching. 2018-01-09 20:47:06 +00:00
Geoff Hutchison
eb408c7e65 Merge pull request #1746 from baoilleach/Fix1731New 
Fix for 1731. Store atom classes in CML atomids by appending _ATOMCLASS.
 2018-01-09 13:58:35 -05:00
Mohammad Ghahremanpour
2be791c805 Gaussformat reading electrostatic potentials (#1748) 
* Reading Electrostatic Potentials from Gaussian log files
 2018-01-09 13:58:11 -05:00
Noel O'Boyle
a7aaeb9bf6 Fix for #1731. Changes how atom class information is used in CML. If we must hack it into the atomid, let's do it in a very simple way by appending _ATOMCLASS to the end of the atomid. 2018-01-06 19:49:30 +00:00
Noel O'Boyle
771b917388 Merge pull request #1745 from baoilleach/Fix1676 
Fix error in VASPformat found by static code analysis
 2018-01-04 09:41:29 +00:00
Noel O'Boyle
ee11c98a65 Merge pull request #1744 from baoilleach/FixUnsignedChar 
Ensure portability to ARM platforms
 2018-01-04 09:39:02 +00:00
Noel O'Boyle
48fe969e51 Fix error in code. Should have been using (*it) in loop, not atom. 2018-01-04 07:51:31 +00:00
Noel O'Boyle
8d707b8ebb Fix yasara compile 2018-01-04 07:16:48 +00:00
Noel O'Boyle
e26491017e Fix #1689 by using positive values and explicitly stating unsigned char 2018-01-03 21:27:53 +00:00