OMEGA Release 2.5.1.4 OpenEye Scientific Software, Inc.
OMEGA Release 2.5.1.4 OpenEye Scientific Software, Inc.
OMEGA Release 2.5.1.4 OpenEye Scientific Software, Inc.
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13.1 <strong>OMEGA</strong> 2.5.1 (May 2013)<br />
13.1.1 New features<br />
CHAPTER<br />
THIRTEEN<br />
RELEASE NOTES<br />
• FILTER is now completely bundled into the <strong>OMEGA</strong> package. The manuals have been consolidated into this<br />
single manual and FILTER has taken on the <strong>OMEGA</strong> version number.<br />
• An option has been added to allow hydrogen atoms in -OH, -SH, and amines to take part in conformational<br />
sampling. This new option can be enabled via the -sampleHydrogens parameter. By default, hydrogen atoms<br />
are not sampled. [Case #13115]<br />
• A -warts option has been added to flipper. [Case #10655]<br />
13.1.2 Major bug fixes<br />
• Now using -fixsmarts without -fixmol will rematch for every input structure. Previously, this would only match<br />
the first input structure and reuse that match for the rest of the calculation. Using both -fixsmarts and -fixmol<br />
will continue to match against the fixmol and use that match for the entire calculation. [Case #14518]<br />
• Partial ring matching with -fixsmarts or -fixmol could cause a crash. Now only full ring systems may be specified<br />
and any attempt at matching a partial ring system will fail gracefully.<br />
• Planar molecules could have problems sprouting hydrogens when using -fromCT false because <strong>OMEGA</strong> was<br />
treating them as 2D. Now <strong>OMEGA</strong> will assume that planar molecules are properly defined 3D coordinates in<br />
this situation. [Case #15737]<br />
• Stereochemistry at the attachment points of rings with four or less atoms could be lost. Now stereochemistry is<br />
saved for rings of all sizes. [Case #3553]<br />
• A bug has been fixed where exceptionally long torsion rules could get cutoff early. [Case #16115]<br />
• A bug has been fixed where older TK licenses in the license file could cause the <strong>OMEGA</strong> application to fail.<br />
[Case #13466]<br />
13.1.3 Minor bug fixes<br />
• Only 3D coordinates were being cleared in FLIPPER. Now 2D coordinates are cleared as well. [Case #13378]<br />
• Fragment generation during an <strong>OMEGA</strong> calculation with strictfrags parameter enabled could yield slightly<br />
different fragments than the MAKEFRAGLIB app. This has been corrected for consistency. [Case #13115]<br />
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