Release Notes

New features and Changes in Molconn-Z 4.12

Molconn-Z 4.12 (standalone) was compiled on several platforms including 2 64-bit versions:

Under Irix 6.5 using the -mips3 -n32 compiler directives, and a version using the -mips4 -64 compiler directives.
Under Red Hat Linux Enterprise 3/4 GNU, GCC 3.3 and GCC 4.x.
GNU 4.x 64-bit x86_64 (runs on AMD64 machines).
GNU 4.x 64-bit IA-64 (runs on Itanium 2 machines).
Under Windows2000 (also runs under 95, 98, ME, XP, and Vista).
Under Solaris (SunOS) 5.7.
Under Macintosh OS X

Starting with version 4.10, the existing Keyword "ERRORS" has a new OPTION: "fix". This "fix" option is used to fix "salt" compounds that cause the Error: "Disconnected Graph". Previously these compounds would not be analysed, but skipped with the keyword option "skip". Now, the components of the salt will be separated and separately analysed. This results in additional compounds. For example in the NCI August 2000 database you will get 253_A and 253_B (which appears to be an ammonium borate) with results for the ammonium component and the borate component of the salt. If the salt contains a simple single atom ion like sodium or chloride, the log file will report "Molecule is (heavy atom) monoatomic...", the outfile will report "not_available" for the structure, and no analysis will be done for the single atom component. If the OPTION "skip" is used for the keyword ERRORS, the behavior will be the same as with 4.09. For Example,
```
ALLRECORDS 
HEADERS top 
INPUTFORMAT oelibsmiles 
WARNINGS off                                                                                        
INDEX on                                                                                            
ERRORS fix                                                                                         
GO
```
A bug was discovered in which the descriptor "Xvch8" was improperly named "Xvcp8" in the header. This was corrected in version 4.10. A bug has been discovered that ONLY relates to the use of OELIB as the molecule reading function (for example if you use the option "oelibsmiles" for INPUTFORMAT), but not Daylightsmiles. This bug is caused by some deficiencies in OEBLIB and results in certain 5-membered aromatic ring compounds not being interpreted properly. In some cases, this can be remedied by using a 3-D structure such as a MOL2 file (oelibmol2) and in some cases there is no current fix. In particular, the following compounds give questionable results with versions 4.09 - 4.12 while using oelibsmiles: thiophene, imidazole, thiazole, pryazole and cyclopentadiene anion. If one uses oelibmol2 instead of oelibsmiles for imidazole and pryazole, the results are correct. For thiophene and thiazole, the major problem is that the hydrogen count is wrong, most of the remaining descriptors are correct, but need to be verified. OELIB can not properly interpret cyclopentadiene anion, or probably any other carbanion, properly. For some compounds, OELIB will insist that the compound be charged, so some results (H count) will differ with the daylightsmiles option (daylightsmiles has no problem dealing with uncharged or charged compounds properly). As a result of this OELIB problem, Molconn-Z has H-checking code to make carboxylic acids and guanidines neutral. SMILES strings with neutral carboxylates or anions works fine. However, a side-effect of this is that a carboxylate anion in a MOL2 file (probably SDF and MOL files as well) will be converted to a neutral carboxylic acid as can be seen in demo5.

We will continue to search for solutions for these problems, but we strongly recommend that users consider using Daylight SMILES as an alternative to OELIB. We are considering adding OECHEM from OpenEye Scientific Software to Molconn-Z as a more accurate alternative to OELIB.
People who use the "daylightsmiles" option should note that in this version Molconn-Z is linked with the Daylight version 4.91 of the SMILES toolkit instead of the 4.73 version. We have noticed that while this newer version fixes some bugs (like EZ specification), it is has more stringent SMILES requirements, causing failures which did not occur with 4.73. In particular, version 4.91 will fail on many OELIB/babel generated SMILES structures. Also note that no IA-64 version of Molconn-Z with Daylight support is available because no IA-64 Daylight library is availabe.

In the 4.10 release we introduced new descriptors with the preface "min" and "max" which are applied to the atom E-State, group E-State and group H E-State descriptors. These are the minimum and maximum values of those descriptors within each molecule. As a result, there are an additional 352 descriptors (with place holders for an additional 122) and 28 new "S Records" in version 4.10 compared to 4.09. As a result of these new descriptors, some of the positions of previous descriptors within records and some of the positions of previous "S Records" have changed. The "S Record" and descriptor differences between versions 4.09 and 4.10 are described below and in Appendix I. Please note that the CSVUSEFUL record (which prints a single line of descriptors separated by commas) has been changed slightly in that the group-type H E-State descriptors (35) have been added to the end.


      

4.09 S Record#: changes in 4.10 

      

7: Xvcp8 changed to Xvch8 

      

25: One blank place holder added "n nsLi" changed to "n n nsLi"; ntsC moved from record#25 to record#26 

      

26: ntsC moved from 25 to 26; 2 place holders added "nssssC n n n n n n n n n nsNH3p" 
changed to "nssssC n n n n n n n n n n n nsNH3p"; nssNH naaNH ntN
moved from record#26 to record#27 

      

27: nssNH naaNH ntN moved from record#26 to record#27; ndO nssO naaO
moved from record#27 to record#28 

      

28: ndO nssO naaO moved from record#27 to record#28; nddsP nsssssP n
moved from record#28 to record#29 

      

29: nddsP nsssssP n moved from record#28 to record#29; nssssGe nsAsH2
nssAsH moved from record#29 to record#30 

      

30: nssssGe nsAsH2 nssAsH moved from record#29 to record#30; nssssSn
nsI nsPbH3 moved from record#30 to record#31 

      

31: nssssSn nsI nsPbH3 moved from record#30 to record#31 

      

33: one place holder added "S SsLi" changed to "S S SsLi"; StsC moved to
from record#33 to record#34 

      

34: StsC moved to from record#33 to record#34; 2 place holders added
"SssssC S S S S S S S S S SsNH3p" changed to "SssssC S S S S S S S S S S S SsNH3p"; 
SssNH SaaNH StN moved from record#34 to record#35. 

      

35: SssNH SaaNH StN moved from record#34 to record#35; SdO SssO SaaO
moved from record#35 to record#36. 

      

36: SdO SssO SaaO moved from record#35 to record#36; SddsP SsssssP S
moved from record#36 to record#37. 

      

37: SddsP SsssssP S moved from record#36 to record#37; SssssGe SsAsH2
SssAsH moved from record#37 to record#38. 

      

38: SssssGe SsAsH2 SssAsH moved from record#37 to record#38; SssssSn
SsI SsPbH3 moved from record#38 to record#39. 

      

39: SssssSn SsI SsPbH3 moved from record#38 to record#39. 

      

40: moved to record#56 no changes 

      

41: moved to record#57 no changes 

      

42: moved to record#58 no changes 

      

43: moved to record#59 no changes 

      

44: moved to record#60 no changes 

      

45: moved to record#61 no changes 

      

46: moved to record#68 no changes 

      

47: moved to record#69 no changes 

      

48: moved to record#70 no changes 

      

49: moved to record#77 no changes 

      

50: moved to record#78 no changes 

      

51: moved to record#79 no changes 

      


CSVUSEFUL:

molnumber,errorcode,molname,nvx,nedges,nrings,ncircuits,nclass,nelem,ntpaths,molweight,Xv0,Xv1,Xv2,Xvp3,Xvp4,Xvp5,Xvp6,Xvp7,Xvp8,Xvp9,Xvp10,Xvc3,Xvc4,Xvpc4,Xvch3,Xvch4,Xvch5,Xvch6,Xvch7,Xvch8,Xvch9,Xvch10,ka1,ka2,ka3,phia,sumdelI,sumI,Qv,SHBd,SwHBd,SHBa,SwHBa,hmax,gmax,hmin,gmin,SHBint2,SHBint3,SHBint4,SHBint5,SHBint6,SHBint7,SHBint8,SHBint9,SHBint10,SHsOH,SHdNH,SHsSH,SHsNH2,SHssNH,SHaaNH,SHsNH3p,SHssNH2p,SHsssNHp,SHtCH,SHdCH2,SHdsCH,SHaaCH,SHCHnX,SHCsats,SHCsatu,SHAvin,SHother,SHmisc,SsCH3,SdCH2,SssCH2,StCH,SdsCH,SaaCH,SsssCH,SddC,StsC,SdssC,SaasC,SaaaC,SssssC,SsNH3p,SsNH2,SssNH2p,SdNH,SssNH,SaaNH,StN,SsssNHp,SdsN,SaaN,SsssN,SddsN,SaasN,SssssNp,SsOH,SdO,SssO,SaaO,SaOm,SsOm,SsF,SsPH2,SssPH,SsssP,SdsssP,SddsP,SsssssP,SsSH,SdS,SssS,SaaS,SdssS,SddssS,SssssssS,SsSm,SsCl,SsBr,SsI,Strifluoromethyl,Simine,Samidine,Snitrile,Scarbonyl,Sketone,Saldehyde,Samide,Surea,Scarbamate,Scarbamicacid,Sester,Scarboxylate,Scarboxylicacid,Scarbonate,Sthiocarbonyl,Shydrazine,Sazo,Snitroso,Snitro,Snitrite,Speroxide,Ssulfoxide,Ssulfone,Ssulfonamide,Ssulfinate,Ssulfinicacid,Ssulfonate,Ssulfonicacid,Ssulfate,Ssulfuricacid,Sdisulfide,Sphosphonate,Sphosphonicacid,Sphosphate,Htrifluoromethyl,Himine,Hamidine,Hnitrile,Hcarbonyl,Hketone,Haldehyde,Hamide,Hurea,Hcarbamate,Hcarbamicacid,Hester,Hcarboxylate,Hcarboxylicacid,Hcarbonate,Hthiocarbonyl,Hhydrazine,Hazo,Hnitroso,Hnitro,Hnitrite,Hperoxide,Hsulfoxide,Hsulfone,Hsulfonamide,Hsulfinate,Hsulfinicacid,Hsulfonate,Hsulfonicacid,Hsulfate,Hsulfuricacid,Hdisulfide,Hphosphonate,Hphosphonicacid,Hphosphate