Toolkit Release Notes -- C# - OpenEye Scientific Software

Toolkit Release Notes – C# 

Release 2013.Oct.3 

OpenEye Scientific Software, Inc. 

October 02, 2013

CONTENTS 

1 OEToolkits 2013.Oct 1 

1.1 OEChem 1.9.3 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 

1.2 OESystem 1.9.3 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2 

1.3 OEPlatform 1.9.3 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3 

1.4 OEGrid 1.4.3 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3 

1.5 OEBrood TK 0.9.0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3 

1.6 OEDepict TK 2.2.1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3 

1.7 OEDocking TK 1.2.1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4 

1.8 Grapheme TK 1.1.0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4 

1.9 GraphSim TK 2.0.6 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6 

1.10 Lexichem TK 2.3.0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6 

1.11 MolProp TK 2.1.7 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7 

1.12 Omega TK 2.5.3 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8 

1.13 QuacPac TK 1.6.4 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8 

1.14 Shape TK 1.9.2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8 

1.15 Spicoli TK 1.2.2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8 

1.16 Szybki TK 1.7.5 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9 

i

CHAPTER 

ONE 

OETOOLKITS 2013.OCT 

This is a new release of the OpenEye Toolkits with versions of the following libraries: 

OEChem TK 1.9.3 

OEBrood TK 0.9.0 

OEDepict TK 2.2.1 

OEDocking TK 1.2.1 

Grapheme TK 1.1.0 

GraphSim TK 2.0.6 

Grid TK 1.4.4 

Lexichem TK 2.3.0 

MolProp TK 2.1.7 

Omega TK 2.5.3 

Quacpac TK 1.6.4 

Shape TK 1.9.2 

Spicoli TK 1.2.2 

Szybki TK 1.7.5 

Zap TK 2.1.6 

• No OpenEye toolkit will call OEErrorHandler.Fatal anymore. All instances have been replaced with 

OEErrorHandler.Error allowing end-users the ability to control whether programs should exit on error 

with OEErrorHandler.SetStrict. It is recommended to use OEThrow.SetStrict(false) inside 

long running services like web servers. 

1.1 OEChem 1.9.3 

1.1.1 New features 

• Added the following atom and bond predicates: 

– OEAtomIsInChain 

– OEBondIsInChain 

– OEIsHetero 

1

Toolkit Release Notes – C#, Release 2013.Oct.3 

– OEIsMetal 

– OEHasHvyDegree 

– OEHasFormalCharge 

1.1.2 Major bug fixes 

• OECreateInChI now passes the following information to the InChI library when calling the 

OECreateInChI function: 

– atom coordinates 

– wedge/hash bond property for single bonds 

– “either” bond property read from MDL file formats for double bonds 

These changes have reduced the number of failure cases to 10 when reading the MDDR database in SDF format 

and testing the InChI strings generated by OECreateInChI against the strings generated by the stand-alone 

InChI application. 

1.1.3 Minor bug fixes 

• The OEIsAtomHybridization.operator() method now checks whether the hybridization was perceived 

and calculates the hybridization of the atom on the fly by calling OEGetHybridization if necessary. 

• The previously release of OEChem, 1.9.2, started considering different isotopes of hydrogen for chirality perception. 

This incorrectly perceived the following molecules as chiral: “C[2H]”, “CC[2H]” and “C([2H])[3H]”. 

Atoms with one or two isotope hydrogen neighbors and at least two implicit hydrogens will no longer be considered 

chiral. 

• When reading MacroModel molecule files (.mmod, .mmd, and .dat), atom serial numbers and HETATM designations 

were not being set, and subsequently saving the molecules in PDB format resulted in poorly formed 

files. This has been corrected so that conversion from MacroModel to PDB files preserves residue information 

properly. 

• OESmilesToMol and OEInChIToMol will now call OEMolBase.Clear before parsing the string into the 

molecule. 

1.1.4 Documentation fixes 

• The OEMMFF* functions are now properly documented. 

1.2 OESystem 1.9.3 


• OEErrorHandlerStream.Msg now calls exit(EXIT_FAILURE) in case of OEErrorLevel.Fatal 

level and calls exit(EXIT_SUCCESS) in case of OEErrorLevel.Usage. 

• OEInterface will no longer strip trailing zero characters from parameters that are non-floating point types. 

For example, “-prefix 1.10” used to return “1.1”. This bug was introduced in OEChem 1.9.0. 

2 Chapter 1. OEToolkits 2013.Oct


1.3 OEPlatform 1.9.3 

• oeistream.gettoken will no longer improperly write a NULL character at buffer[max] location in 

memory in rare circumstances when the token is the exact same size as the buffer. 

1.4 OEGrid 1.4.3 

• Fixed a rare crash when interpolating between grids. This affects many API points, including GridBabel, whenever 

converting a grid to another grid type. 

1.5 OEBrood TK 0.9.0 


Providing the following fragmentation functions: 

• OEGetRingChainFragments 

• OEGetRingLinkerSideChainFragments 

• OEGetFuncGroupFragments 

1.6 OEDepict TK 2.2.1 


• Added cubic Bézier drawing method to the following classes: 

– OEImageBase 

– OEImage 

– OEImageFrame 

• Added quadratic Bézier drawing method to the following classes: 

– OEImageBase 

– OEImage 

– OEImageFrame 

• Added rotation angle property to the OEFont class that allows to render text in various angles when calling the 

OEImageBase.DrawText method. 

– OEFont.GetRotationAngle 

– OEFont.SetRotationAngle 

1.3. OEPlatform 1.9.3 3



• When aligning a molecule to a template, atom clashes between the template atoms are ignored. 

• OEPrepareDepiction will now suppress hydrogens even when 2D coordinates are not generated, i.e., 

clearcoords = false. 


• Highlighting a single atom with the OEHighlightStyle.Stick will now work if that atom is bonded to a 

highlighted atom. 

• Fixed problem when the scaling of small molecules resulted in depicting atom labels outside the canvas. 

• Fixed problem that incorrectly positioned the “+” sign between reaction components introduced by the last 

OEDepict TK release, 2.2.0. 

1.6.4 Documentation changes 

• All images in this documentation were automatically regenerated to reflect the changes made since the previous 

release. 

1.7 OEDocking TK 1.2.1 

1.7.1 New Features 

• OEPosit - When full conformer search is turned off, OMEGA is automatically run when the docked ligand 

is not a 3D conformer. 


• OEPosit - Fixed a crash when setting full conformer search to false and docking a ligand with missing hydrogens. 


• Uses of OEThrow.Fatal changed to OEThrow.Error. 

1.8 Grapheme TK 1.1.0 


• Added the following to visualize color forcefields: 

– OEColorForceFieldDisplay 

– OEColorForceFieldLegendDisplayOptions 

– OEDrawColorForceFieldLegend 

• Added the following to visualize the reference molecule of a color and shape overlap: 



– OEShapeOverlapDisplay 

– OEShapeOverlapDisplayOptions 

– OERenderShapeQuery 

• Added the following to visualize shape and color overlaps: 

– OEShapeOverlapDisplay 

– OEShapeOverlapDisplayOptions 

– OERenderShapeOverlap 

– OEColorOverlapDisplayOptions 

– OERenderColorOverlap 

Note: A valid shape license is required to use any of these new shape or color APIs. 

• Added the OEDepictionFrom3DOptions class that allows more advanced customization of the generation 

of 2D coordinates driven by the 3D conformation when calling the OEPrepareDepictionFrom3D function. 

By default, OEPrepareDepictionFrom3D is tuned for generating 2D coordinates for representing 

3D overlays in 2D. This class allows the 2D coordinate generation to choose a set of 2D coordinates that are 

much closer to how the molecule would look in a 3D viewer. 

• Added the following to render user-defined labels when depicting color gradients: 

– OEColorGradientDisplayOptions.AddLabel 

– OEColorGradientDisplayOptions.ClearLabels 

– OEColorGradientDisplayOptions.GetLabels 

• Added OEColorGradientDisplayOptions.ClearBoxRange method to remove the box range previously 

set to a color gradient. 

• Added OEGet2DSurfaceArcs function to return the arcs of the molecule surface of a specific atom with 

the given radius. Varying radii can be passed to generate multiple surfaces in the range specified by the 

OESurfaceArcScale namespace. OEGetMoleculeSurfaceScale can be used to determine the appropriate 

scale for the molecule with the specified radius. 

• Implemented the ShapeOverlap2PDF.cs C# Grapheme TK example. 


• Molecule surface arcs inside macrocycles are no longer returned. See the 

effect of this change in Table: Example of depicting molecule surface. 

1.8. Grapheme TK 1.1.0 5


Grapheme TK 1.0.6 (2013 Jun) 

Table 1.1: Example of depicting molecule surface 

Grapheme TK 1.1.0 (2013 Oct) 

O 

O 

O 

O 


• All images were automatically regenerated to reflect the changes made since the previous release. 

1.9 GraphSim TK 2.0.6 

• Minor internal improvements. 


Adding new images to the: 

• Fingerprint Generation chapter to illustrate the enumeration of fragments of various fingerprints 

• Similarity Measures chapter to show the basic bit count terms of similarity calculation 

• User-defined Fingerprint chapter and OEFPAtomType namespace to visualize the effect of various atom and 

bond typings 

1.10 Lexichem TK 2.3.0 


• Name generation for racemic structures when the ‘MDL AND’ group is present in the MDL V3000 format. 

Stereodescriptors ‘rac’, ‘RS’ and ‘SR’. (Section P-92.1.3 of the IUPAC Nomenclature of Organic Compounds, 

Draft 2004 - Racemates and meso compounds). Racemic stereogenic centers are labeled with ‘RS’ if the CIP 



stereo descriptor is ‘R’ and has the MDL AND group present, else ‘SR’ if the stereogenic centre has the CIP 

stereo descriptor ‘S’ and an MDL AND group present. The prefix ‘rac’ is used in front of a set of descriptors or 

locants, if all stereogenic centres in the molecule are racemic. 

(4^{13}C,2,6-^{15}C_{2})nonane 

(3^{14}C)cyclohexatriene(^{13}N,^{15}O)carboxamide 

15 

C 

H 2 

15 C 

H 2 

13 C 

H 2 

14 

C 

H 

13NH 2 15 O 

Generated by OEDepict TK 

Figure 1.1: Isotope Example Depictions 

• Support has been added for name generation for isotopic carbon atoms in chains (e.g. the SMILES: 

C[15CH2]C[13CH2]C[15CH2]CCC will generate the name (4^{13}C,2,6-^{15}C_{2})nonane), 

simple rings and simple suffixes (e.g. the SMILES: [13NH2]C(=[15O])C1=C[14CH]=CC=C1 will generate 

the name (3^{14}C)cyclohexatriene(^{13}N,^{15}O)carboxamide). The chemical structures 

generated from parsing the example SMILES strings into a molecule object are depicted in Figure: Isotope 

Example Depictions. 


• Fixed Lexichem’s thread safety. A global variable in Lexichem that has persisted since its first release in 2005, 

has been removed. This global variable affected the function OEParseIUPACName, used in name to structure 

conversion. Two thread safety issues used in structure to name conversion, namely: double bond (E/Z) CIP 

stereo (thread safety broken in the June 2012TK release) and enhanced relative stereochemistry (thread safety 

broken in the June 2013TK release), that affected the function OECreateIUPACName, have been resolved. 

• OEParseIUPACName will no longer access invalid memory for names of the form ‘(di/tri/tetra)BLAH (ester/hydrazone/oxime/selenoxime/telluroxime/thioxime)’. 

1.11 MolProp TK 2.1.7 


• “MIN_*” and “MAX_*” properties filter rules file no longer have to both be specified to work. Previously, if a 

property filter was specified with “MAX_*”, then the corresponding “MIN_*” filter rule had to also be set for 

the rule to properly function. Now, “MIN_*” and “MAX*” filter rules operate independent of the other. 

1.11. MolProp TK 2.1.7 7


1.12 Omega TK 2.5.3 


• OEAddGlobalFragLib added to allow a given fragment library to be preloaded into the global fragment 

library where it can be shared among all OEOmega instances. 


• The wart symbol has been changed from @ to _ in order to help with parsing SMILES formatting. 

• Bond stereochemistry is now properly perceived when strictstereo is set to false. Previously, there could be an 

OESubSearch warning due to unperceived bond stereochemistry. 

• The OENitrogenEnumeration namespace has been created. The namespace constants should be used in 

place of magic numbers. 

1.13 QuacPac TK 1.6.4 


• The new function OERemoveFormalCharge has been added. This function sets the formal charges on a 

molecule to zero while maintaining a standard valence state. 

• The new function OEGetChargeTypeName has been added. 

OECharges name for the unsigned int passed in. 

This function returns the corresponding 


• The wart symbol has been changed from @ to _ in order to help with parsing SMILES formatting. 

1.14 Shape TK 1.9.2 


• A bug has been fixed where OEBOOrientation.Subrocs was not properly setting starting positions when 

the database molecule was larger than the query molecule. 

• Fixed a rare invalid memory access from the OEOverlapMethod.Analytic2 method. 

1.15 Spicoli TK 1.2.2 

• Minor internal improvements. 



1.16 Szybki TK 1.7.5 


• User partial charges can be used in the combined AMBER-MMFF force field introduced in the version 1.7.3. 

This is done with the method OESzybki.SetUseCurrentCharges which until now could be applied only 

to MMFF94 force field for solvation and protein-ligand interaction. 

• OEOptType:SD_BFGS and OEOptType:SD_CG can now be passed to 

OESzybki.SetOptimizerType to perform pre-optimization with 5 steps of steepest descent before 

either BFGS or CG optimization. 

• OESzybkiEnsembleResults.GetChargeType added to return what type of partial charges were used 

for entropy estimation. 

• OESzybkiResults.GetTotalEnergy() no longer includes the harmonic constraint energy. 

OESzybkiResults.GetTotalEnergyWithHarmConstraint() has been added to return the 

total energy with the harmonic constraint energy included. 


• OESzybki.SetEveryConfAM1BCCCharges will now preserve the existing partial charges from the input 

molecule when using AM1BCC charges for PB, Sheffield and Coulomb protein-ligand interactions. In previous 

versions MMFF94 charges were attached to the output molecule. 

• When calculating ligand entropy, analytical calculation of second order derivatives in solution no longer misses 

the Hessian components coming from solvent forces. 

• OESzybki.GetEntropy will no longer crash whenever a protein was set with OESzybki.SetProtein 

and the environment was not OEEnvType.Protein. 

• Method OESzybki.SetUseCurrentCharges was ignored in Sheffield solvent second derivatives (default 

MMFF94 partial charges were used). This issue has been fixed. 

1.16. Szybki TK 1.7.5 9

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