From:
<a.s...@ch...> - 2006-02-15 15:30:26
Attachments:
buggy_mols.sdf
log.txt
|
Hi all, I'm working on a Java program that converts a library of chemical compounds to Markush structures. It parses an input SD file and replaces any occurence of found pre-defined chemical substructures by a substituent, which normally is an R-atom (pseudo atom). The substitution procedure is a follows: 1.) The substitution residue (normally the pseudo atom 'R') is added to the molecule by molecule.add(substituent); 2.) The R-residue is connected with the molecule by redirecting all bonds to the leaving group to the R-residue by bond.setAtomAt(substituent.getFirstAtom(), i); 3.) The leaving group and all connected electron containers are removed by molecule.removeAtomAndConnectedElectronContainers(atom); Example for an alcohol: Molecule: CCCCO Substituent: R Resulting molecule: CCCCR This procedure is followed by a call to StructureDiagramGenerator to calculate coordinates for the added subsitutent. Unfortunately all my test runs fail with a NullPointerException in StructureDiagramGenerator (exception and logger ouput is attached). The test database is a collection of 3745 building blocks in SD format. The exception is reproducable but not always with the same molecule. So far the exception occured at molecules #746, #951 and #1075 (see attached SD file). Interestingly performing a test run with only those three problematic molecules completes flawlessly and the resulting markush molecules look as expected. Any help is appreciated. Cheers, Andreas P.S.: The CDK version used is the release 'cdk-20050826'. ---------------------------- Java exception: java.lang.NullPointerException at org.openscience.cdk.layout.StructureDiagramGenerator.layoutNextRingSystem(StructureDiagramGenerator.java:636) at org.openscience.cdk.layout.StructureDiagramGenerator.generateCoordinates(StructureDiagramGenerator.java:420) at org.openscience.cdk.layout.StructureDiagramGenerator.generateCoordinates(StructureDiagramGenerator.java:437) -- PhD student in the research group of Prof. Dr. Gisbert Schneider Institute for Organic Chemistry and Chemical Biology Chair for Chemo- and Bioinformatics Beilstein-endowed Chair for Chemoinformatics Johann Wolfgang Goethe University Siesmayerstr. 70 60323 Frankfurt am Main Germany Tel.: +49-69-798-24879 Fax: +49-69-798-24880 http://www.modlab.de/ |
From: Christoph S. <c.s...@un...> - 2006-02-15 16:56:07
|
Andreas, I cannot deduce anything from your provided data. Without the full code and full dataset and a reproducible behavior, nothi= ng can=20 be done, I'm afraid. Is it possible to boil down the case to, say, an SDF file with 10 of your= =20 molecules? If you supply me with code(!) and data, where the bug reproduc= ibly=20 occurs, I'm willing to look at it and see what I can do. Cheers, Chris Andreas Sch=FCller wrote: > Hi all, >=20 > I'm working on a Java program that converts a library of chemical > compounds to Markush structures. It parses an input SD file and replace= s > any occurence of found pre-defined chemical substructures by a=20 > substituent, which normally is an R-atom (pseudo atom). >=20 > The substitution procedure is a follows: > 1.) The substitution residue (normally the pseudo atom 'R') is added to= =20 > the molecule by molecule.add(substituent); > 2.) The R-residue is connected with the molecule by redirecting all=20 > bonds to the leaving group to the R-residue by=20 > bond.setAtomAt(substituent.getFirstAtom(), i); > 3.) The leaving group and all connected electron containers are removed= =20 > by molecule.removeAtomAndConnectedElectronContainers(atom); >=20 > Example for an alcohol: > Molecule: CCCCO > Substituent: R > Resulting molecule: CCCCR >=20 > This procedure is followed by a call to StructureDiagramGenerator to=20 > calculate coordinates for the added subsitutent. >=20 > Unfortunately all my test runs fail with a NullPointerException in=20 > StructureDiagramGenerator (exception and logger ouput is attached). > The test database is a collection of 3745 building blocks in SD format. > The exception is reproducable but not always with the same molecule. So= =20 > far the exception occured at molecules #746, #951 and #1075 (see=20 > attached SD file). Interestingly performing a test run with only those=20 > three problematic molecules completes flawlessly and the resulting=20 > markush molecules look as expected. >=20 > Any help is appreciated. >=20 > Cheers, > Andreas >=20 > P.S.: The CDK version used is the release 'cdk-20050826'. >=20 > ---------------------------- >=20 > Java exception: >=20 > java.lang.NullPointerException > at > org.openscience.cdk.layout.StructureDiagramGenerator.layoutNextRingSyst= em(StructureDiagramGenerator.java:636)=20 >=20 > at > org.openscience.cdk.layout.StructureDiagramGenerator.generateCoordinate= s(StructureDiagramGenerator.java:420)=20 >=20 > at > org.openscience.cdk.layout.StructureDiagramGenerator.generateCoordinate= s(StructureDiagramGenerator.java:437)=20 >=20 >=20 >=20 > -----------------------------------------------------------------------= - >=20 >=20 > MOE2005 2D >=20 > 29 31 0 0 0 0 0 0 0 0999 V2000 > 0.9790 0.4630 0.0000 N 0 0 3 0 0 0 0 0 0 0 0 0 > 1.4500 1.1460 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 1.4880 -0.2170 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 2.2790 0.0630 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 > 2.2540 0.9130 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0 > 2.9170 -0.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 > 0.1040 0.4500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > -4.0960 -0.9790 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > -1.1460 1.1960 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 1.1670 1.9330 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0 > -0.2960 1.1960 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > -3.6630 -0.2670 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > -1.5630 0.4710 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 > 1.2500 -1.0540 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 > -2.8210 -0.2670 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 3.7380 -0.2040 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > -2.4130 0.4710 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > -3.7000 -1.7170 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 > -1.5460 1.9330 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 > 4.3880 -0.7500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > -4.9210 -0.9880 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 > 5.1790 -0.4790 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 5.8290 -1.0040 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0 0 > -4.0830 0.4630 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > -3.6630 1.1830 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 4.6790 0.9000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 3.8790 0.6210 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > -2.8330 1.1960 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 5.3170 0.3500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 1 7 1 0 0 0 0 > 1 3 1 0 0 0 0 > 1 2 1 0 0 0 0 > 2 10 2 0 0 0 0 > 2 5 1 0 0 0 0 > 3 4 1 0 0 0 0 > 3 14 2 0 0 0 0 > 4 5 1 0 0 0 0 > 4 6 2 0 0 0 0 > 6 16 1 0 0 0 0 > 7 11 1 0 0 0 0 > 8 12 1 0 0 0 0 > 8 18 2 0 0 0 0 > 8 21 1 0 0 0 0 > 9 11 1 0 0 0 0 > 9 13 1 0 0 0 0 > 9 19 2 0 0 0 0 > 12 15 2 0 0 0 0 > 12 24 1 0 0 0 0 > 13 17 1 0 0 0 0 > 15 17 1 0 0 0 0 > 16 20 2 0 0 0 0 > 16 27 1 0 0 0 0 > 17 28 2 0 0 0 0 > 20 22 1 0 0 0 0 > 22 23 1 0 0 0 0 > 22 29 2 0 0 0 0 > 24 25 2 0 0 0 0 > 25 28 1 0 0 0 0 > 26 29 1 0 0 0 0 > 26 27 2 0 0 0 0 > M END >> <Amides> > x >=20 >> <Grade> > 3 >=20 >> <IDNUMBER> > F0726-0049 >=20 >> <LOGP> > 3.984 >=20 >> <WEIGHT> > 0 >=20 > $$$$ >=20 > MOE2005 2D >=20 > 28 30 0 0 0 0 0 0 0 0999 V2000 > 0.1290 2.0000 0.0000 N 0 0 3 0 0 0 0 0 0 0 0 0 > -0.2500 1.4630 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > -0.2710 2.5460 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > -0.8960 2.3210 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 > -0.8960 1.6630 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0 > -1.4130 2.7830 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 > 0.8040 2.0210 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 1.1500 1.4460 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 3.8540 0.2830 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > -0.0130 0.8000 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0 > 3.1880 0.2830 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 1.8290 1.4460 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 > -0.0710 3.2080 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 > 2.8500 0.8630 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > -2.0710 2.5460 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 2.1670 0.8630 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 4.2040 0.8500 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 > 0.8040 0.8630 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 > -2.1960 1.8630 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 4.2040 -0.2880 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 > -2.8130 1.6210 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > -2.9130 0.9460 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0 0 > 2.8500 -0.3000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 2.1670 -0.3170 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > -3.2330 2.7210 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > -2.5960 2.9630 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 1.8290 0.2630 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > -3.3330 2.0630 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 1 7 1 0 0 0 0 > 1 3 1 0 0 0 0 > 1 2 1 0 0 0 0 > 2 10 2 0 0 0 0 > 2 5 1 0 0 0 0 > 3 4 1 0 0 0 0 > 3 13 2 0 0 0 0 > 4 5 1 0 0 0 0 > 4 6 2 0 0 0 0 > 6 15 1 0 0 0 0 > 7 8 1 0 0 0 0 > 8 12 1 0 0 0 0 > 8 18 2 0 0 0 0 > 9 11 1 0 0 0 0 > 9 17 2 0 0 0 0 > 9 20 1 0 0 0 0 > 11 14 2 0 0 0 0 > 11 23 1 0 0 0 0 > 12 16 1 0 0 0 0 > 14 16 1 0 0 0 0 > 15 19 2 0 0 0 0 > 15 26 1 0 0 0 0 > 16 27 2 0 0 0 0 > 19 21 1 0 0 0 0 > 21 22 1 0 0 0 0 > 21 28 2 0 0 0 0 > 23 24 2 0 0 0 0 > 24 27 1 0 0 0 0 > 25 28 1 0 0 0 0 > 25 26 2 0 0 0 0 > M END >> <Amides> > x >=20 >> <Grade> > 3 >=20 >> <IDNUMBER> > F0822-0114 >=20 >> <LOGP> > 3.896 >=20 >> <WEIGHT> > 0 >=20 > $$$$ >=20 > MOE2005 2D >=20 > 35 38 0 0 0 0 0 0 0 0999 V2000 > -2.5710 -1.3790 0.0000 N 0 0 3 0 0 0 0 0 0 0 0 0 > -0.9960 -1.3790 0.0000 N 0 0 3 0 0 0 0 0 0 0 0 0 > -3.3500 -1.3790 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 > 0.9880 -0.7000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 2.1670 0.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 > 0.1880 -0.7000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 2.1670 2.7210 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 1.3670 2.7210 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > -2.1710 -0.7000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > -2.1710 -2.0540 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 1.3670 0.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 > 2.5500 2.0460 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 1.3670 -1.3790 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 > -0.1960 -1.3790 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > -3.7500 -2.0540 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > -3.7500 -0.7000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 0.9880 2.0460 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > -1.3960 -2.0540 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > -1.3960 -0.7000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 2.5500 0.6830 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 2.1670 1.3630 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 1.3670 1.3630 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 2.5790 3.3960 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 > 0.9670 3.4000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 > -4.5330 -0.7000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > -3.3500 -2.7380 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > -3.3500 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > -4.5330 -2.0540 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 3.3670 3.3830 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > -3.7500 -3.4170 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > -4.9330 -2.7380 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > -4.9330 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > -3.7500 0.6830 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > -4.5330 -3.4170 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > -4.5330 0.6830 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 1 10 1 0 0 0 0 > 1 9 1 0 0 0 0 > 1 3 1 0 0 0 0 > 2 18 1 0 0 0 0 > 2 19 1 0 0 0 0 > 2 14 1 0 0 0 0 > 3 15 1 0 0 0 0 > 3 16 1 0 0 0 0 > 4 6 1 0 0 0 0 > 4 11 1 0 0 0 0 > 4 13 2 0 0 0 0 > 5 11 1 0 0 0 0 > 5 20 2 0 0 0 0 > 6 14 1 0 0 0 0 > 7 8 2 0 0 0 0 > 7 23 1 0 0 0 0 > 7 12 1 0 0 0 0 > 8 17 1 0 0 0 0 > 8 24 1 0 0 0 0 > 9 19 1 0 0 0 0 > 10 18 1 0 0 0 0 > 12 21 2 0 0 0 0 > 15 26 2 0 0 0 0 > 15 28 1 0 0 0 0 > 16 25 2 0 0 0 0 > 16 27 1 0 0 0 0 > 17 22 2 0 0 0 0 > 20 21 1 0 0 0 0 > 21 22 1 0 0 0 0 > 23 29 1 0 0 0 0 > 25 32 1 0 0 0 0 > 26 30 1 0 0 0 0 > 27 33 2 0 0 0 0 > 28 31 2 0 0 0 0 > 30 34 2 0 0 0 0 > 31 34 1 0 0 0 0 > 32 35 2 0 0 0 0 > 33 35 1 0 0 0 0 > M END >> <Grade> > 3 >=20 >> <IDNUMBER> > F0840-0120 >=20 >> <LOGP> > 4.775 >=20 >> <WEIGHT> > 0 >=20 > $$$$ >=20 >=20 > -----------------------------------------------------------------------= - >=20 > 2006-02-14 16:23:17,765 [main] DEBUG org.openscience.cdk.layout.Structu= reDiagramGenerator - Entry point of generatorCoordinates() > 2006-02-14 16:23:17,765 [main] DEBUG org.openscience.cdk.layout.Structu= reDiagramGenerator - We have a molecules with 28 atoms. > 2006-02-14 16:23:17,765 [main] DEBUG org.openscience.cdk.layout.Structu= reDiagramGenerator - Molecule is connected. > 2006-02-14 16:23:17,765 [main] DEBUG org.openscience.cdk.layout.Structu= reDiagramGenerator - Initializing TemplateHandler > 2006-02-14 16:23:17,765 [main] DEBUG org.openscience.cdk.layout.Structu= reDiagramGenerator - TemplateHander initialized > 2006-02-14 16:23:17,765 [main] DEBUG org.openscience.cdk.layout.Structu= reDiagramGenerator - Now starting Template Detection in Molecule... > 2006-02-14 16:23:17,765 [main] DEBUG org.openscience.cdk.layout.Structu= reDiagramGenerator - Template Detection finished > 2006-02-14 16:23:17,765 [main] DEBUG org.openscience.cdk.layout.Structu= reDiagramGenerator - Template found: false > 2006-02-14 16:23:17,765 [main] DEBUG org.openscience.cdk.layout.Structu= reDiagramGenerator - *** Start of handling rings. *** > 2006-02-14 16:23:17,765 [main] DEBUG org.openscience.cdk.layout.Structu= reDiagramGenerator - We have 3 ring system(s). > 2006-02-14 16:23:17,765 [main] DEBUG org.openscience.cdk.layout.Structu= reDiagramGenerator - RingSet 0 has size 1 > 2006-02-14 16:23:17,765 [main] DEBUG org.openscience.cdk.layout.Structu= reDiagramGenerator - RingSet 1 has size 1 > 2006-02-14 16:23:17,765 [main] DEBUG org.openscience.cdk.layout.Structu= reDiagramGenerator - RingSet 2 has size 1 > 2006-02-14 16:23:17,765 [main] DEBUG org.openscience.cdk.layout.Structu= reDiagramGenerator - Largest RingSystem is at RingSet collection's positi= on 0 > 2006-02-14 16:23:17,765 [main] DEBUG org.openscience.cdk.layout.Structu= reDiagramGenerator - Size of Largest RingSystem: 1 > 2006-02-14 16:23:17,765 [main] DEBUG org.openscience.cdk.layout.Structu= reDiagramGenerator - Start of layoutRingSet > 2006-02-14 16:23:17,765 [main] DEBUG org.openscience.cdk.layout.Structu= reDiagramGenerator - placeFirstBondOfFirstRing->bondVector.length():1.0 > 2006-02-14 16:23:17,765 [main] DEBUG org.openscience.cdk.layout.Structu= reDiagramGenerator - placeFirstBondOfFirstRing->bondVector.length() after= scaling:1.5 > 2006-02-14 16:23:17,765 [main] DEBUG org.openscience.cdk.layout.Structu= reDiagramGenerator - Atom 1 of first Bond: 2 > 2006-02-14 16:23:17,765 [main] DEBUG org.openscience.cdk.layout.Structu= reDiagramGenerator - Atom 2 of first Bond: 1 > 2006-02-14 16:23:17,765 [main] DEBUG org.openscience.cdk.layout.RingPla= cer - placeRing -> sharedAtomCount: 2 > 2006-02-14 16:23:17,765 [main] DEBUG org.openscience.cdk.layout.RingPla= cer - RingPlacer.placeFusedRing() start > 2006-02-14 16:23:17,765 [main] DEBUG org.openscience.cdk.layout.RingPla= cer - placeFusedRing->: ringCenterVector.length()1.0 > 2006-02-14 16:23:17,765 [main] DEBUG org.openscience.cdk.layout.RingPla= cer - placeFusedRing->occupiedAngle: 72.0 > 2006-02-14 16:23:17,765 [main] DEBUG org.openscience.cdk.layout.RingPla= cer - placeFusedRing->remainingAngle: 288.0 > 2006-02-14 16:23:17,765 [main] DEBUG org.openscience.cdk.layout.RingPla= cer - placeFusedRing->addAngle: 72.0 > 2006-02-14 16:23:17,765 [main] DEBUG org.openscience.cdk.layout.RingPla= cer - placeFusedRing->Bond is vertical > 2006-02-14 16:23:17,765 [main] DEBUG org.openscience.cdk.layout.RingPla= cer - placeFusedRing->startAngle: 36.0 > 2006-02-14 16:23:17,765 [main] DEBUG org.openscience.cdk.layout.RingPla= cer - placeFusedRing->addAngle: 72.0 > 2006-02-14 16:23:17,765 [main] DEBUG org.openscience.cdk.layout.RingPla= cer - placeFusedRing->startAtom is: 1 > 2006-02-14 16:23:17,765 [main] DEBUG org.openscience.cdk.layout.RingPla= cer - AtomsToDraw: Numbers: 3 4 5=20 > 2006-02-14 16:23:17,765 [main] DEBUG org.openscience.cdk.layout.AtomPla= cer - populatePolygonCorners->startAngle: 36.0 > 2006-02-14 16:23:17,765 [main] DEBUG org.openscience.cdk.layout.AtomPla= cer - centerX:-1.03228644035338 > 2006-02-14 16:23:17,765 [main] DEBUG org.openscience.cdk.layout.AtomPla= cer - centerY:0.7500000000000001 > 2006-02-14 16:23:17,765 [main] DEBUG org.openscience.cdk.layout.AtomPla= cer - radius :1.2759762125280598 > 2006-02-14 16:23:17,765 [main] DEBUG org.openscience.cdk.layout.AtomPla= cer - populatePolygonCorners->angle: 108.0 > 2006-02-14 16:23:17,765 [main] DEBUG org.openscience.cdk.layout.AtomPla= cer - newX:-1.42658477444273 > 2006-02-14 16:23:17,765 [main] DEBUG org.openscience.cdk.layout.AtomPla= cer - newY:1.9635254915624212 > 2006-02-14 16:23:17,765 [main] DEBUG org.openscience.cdk.layout.AtomPla= cer - populatePolygonCorners->angle: 180.0 > 2006-02-14 16:23:17,765 [main] DEBUG org.openscience.cdk.layout.AtomPla= cer - newX:-2.3082626528814396 > 2006-02-14 16:23:17,765 [main] DEBUG org.openscience.cdk.layout.AtomPla= cer - newY:0.7500000000000002 > 2006-02-14 16:23:17,765 [main] DEBUG org.openscience.cdk.layout.AtomPla= cer - populatePolygonCorners->angle: 252.0 > 2006-02-14 16:23:17,765 [main] DEBUG org.openscience.cdk.layout.AtomPla= cer - newX:-1.4265847744427305 > 2006-02-14 16:23:17,765 [main] DEBUG org.openscience.cdk.layout.AtomPla= cer - newY:-0.46352549156242084 > 2006-02-14 16:23:17,765 [main] DEBUG org.openscience.cdk.layout.Structu= reDiagramGenerator - End of layoutRingSet > 2006-02-14 16:23:17,765 [main] DEBUG org.openscience.cdk.layout.Structu= reDiagramGenerator - First RingSet placed > 2006-02-14 16:23:17,765 [main] DEBUG org.openscience.cdk.layout.RingPla= cer - RingPlacer.placeRingSubstituents() start > 2006-02-14 16:23:17,765 [main] DEBUG org.openscience.cdk.layout.RingPla= cer - placeRingSubstituents->unplacedPartners: 7 > 2006-02-14 16:23:17,765 [main] DEBUG org.openscience.cdk.layout.AtomPla= cer - distributePartners->occupiedDirection.lenght(): 1.2759762125280596 > 2006-02-14 16:23:17,765 [main] DEBUG org.openscience.cdk.layout.AtomPla= cer - Number of shared atoms: 2 > 2006-02-14 16:23:17,765 [main] DEBUG org.openscience.cdk.layout.AtomPla= cer - distributePartners->newDirection.lenght(): 1.5000000000000002 > 2006-02-14 16:23:17,765 [main] DEBUG org.openscience.cdk.layout.AtomPla= cer - distributePartners->sortedAtoms[0]: 3 > 2006-02-14 16:23:17,765 [main] DEBUG org.openscience.cdk.layout.AtomPla= cer - distributePartners->sortedAtoms[1]: 2 > 2006-02-14 16:23:17,765 [main] DEBUG org.openscience.cdk.layout.AtomPla= cer - distributePartners->angle1: 162.0 > 2006-02-14 16:23:17,765 [main] DEBUG org.openscience.cdk.layout.AtomPla= cer - distributePartners->angle2: 270.0 > 2006-02-14 16:23:17,765 [main] DEBUG org.openscience.cdk.layout.AtomPla= cer - distributePartners->startAtom: 2 > 2006-02-14 16:23:17,765 [main] DEBUG org.openscience.cdk.layout.AtomPla= cer - distributePartners->remainingAngle: 252.0 > 2006-02-14 16:23:17,765 [main] DEBUG org.openscience.cdk.layout.AtomPla= cer - distributePartners->addAngle: 126.0 > 2006-02-14 16:23:17,765 [main] DEBUG org.openscience.cdk.layout.AtomPla= cer - distributePartners-> partners.getAtomCount(): 1 > 2006-02-14 16:23:17,765 [main] DEBUG org.openscience.cdk.layout.AtomPla= cer - Before check: distributePartners->startAngle: 4.71238898038469 > 2006-02-14 16:23:17,765 [main] DEBUG org.openscience.cdk.layout.AtomPla= cer - After check: distributePartners->startAngle: 4.71238898038469 > 2006-02-14 16:23:17,765 [main] DEBUG org.openscience.cdk.layout.AtomPla= cer - populatePolygonCorners->startAngle: 270.0 > 2006-02-14 16:23:17,765 [main] DEBUG org.openscience.cdk.layout.AtomPla= cer - centerX:0.0 > 2006-02-14 16:23:17,765 [main] DEBUG org.openscience.cdk.layout.AtomPla= cer - centerY:1.5 > 2006-02-14 16:23:17,765 [main] DEBUG org.openscience.cdk.layout.AtomPla= cer - radius :1.5 > 2006-02-14 16:23:17,765 [main] DEBUG org.openscience.cdk.layout.AtomPla= cer - populatePolygonCorners->angle: 36.0 > 2006-02-14 16:23:17,765 [main] DEBUG org.openscience.cdk.layout.AtomPla= cer - newX:1.2135254915624212 > 2006-02-14 16:23:17,765 [main] DEBUG org.openscience.cdk.layout.AtomPla= cer - newY:2.3816778784387096 > 2006-02-14 16:23:17,765 [main] DEBUG org.openscience.cdk.layout.RingPla= cer - placeRingSubstituents->unplacedPartners: 10 > 2006-02-14 16:23:17,765 [main] DEBUG org.openscience.cdk.layout.AtomPla= cer - distributePartners->occupiedDirection.lenght(): 1.27597621252806 > 2006-02-14 16:23:17,765 [main] DEBUG org.openscience.cdk.layout.AtomPla= cer - Number of shared atoms: 2 > 2006-02-14 16:23:17,765 [main] DEBUG org.openscience.cdk.layout.AtomPla= cer - distributePartners->newDirection.lenght(): 1.4999999999999998 > 2006-02-14 16:23:17,765 [main] DEBUG org.openscience.cdk.layout.AtomPla= cer - distributePartners->sortedAtoms[0]: 5 > 2006-02-14 16:23:17,765 [main] DEBUG org.openscience.cdk.layout.AtomPla= cer - distributePartners->sortedAtoms[1]: 1 > 2006-02-14 16:23:17,765 [main] DEBUG org.openscience.cdk.layout.AtomPla= cer - distributePartners->angle1: 198.00000000000003 > 2006-02-14 16:23:17,765 [main] DEBUG org.openscience.cdk.layout.AtomPla= cer - distributePartners->angle2: 90.0 > 2006-02-14 16:23:17,765 [main] DEBUG org.openscience.cdk.layout.AtomPla= cer - distributePartners->startAtom: 5 > 2006-02-14 16:23:17,765 [main] DEBUG org.openscience.cdk.layout.AtomPla= cer - distributePartners->remainingAngle: 252.0 > 2006-02-14 16:23:17,765 [main] DEBUG org.openscience.cdk.layout.AtomPla= cer - distributePartners->addAngle: 126.0 > 2006-02-14 16:23:17,765 [main] DEBUG org.openscience.cdk.layout.AtomPla= cer - distributePartners-> partners.getAtomCount(): 1 > 2006-02-14 16:23:17,765 [main] DEBUG org.openscience.cdk.layout.AtomPla= cer - Before check: distributePartners->startAngle: 3.4557519189487724 > 2006-02-14 16:23:17,765 [main] DEBUG org.openscience.cdk.layout.AtomPla= cer - After check: distributePartners->startAngle: 3.4557519189487724 > 2006-02-14 16:23:17,765 [main] DEBUG org.openscience.cdk.layout.AtomPla= cer - populatePolygonCorners->startAngle: 198.00000000000003 > 2006-02-14 16:23:17,765 [main] DEBUG org.openscience.cdk.layout.AtomPla= cer - centerX:0.0 > 2006-02-14 16:23:17,765 [main] DEBUG org.openscience.cdk.layout.AtomPla= cer - centerY:0.0 > 2006-02-14 16:23:17,765 [main] DEBUG org.openscience.cdk.layout.AtomPla= cer - radius :1.5 > 2006-02-14 16:23:17,765 [main] DEBUG org.openscience.cdk.layout.AtomPla= cer - populatePolygonCorners->angle: 324.0 > 2006-02-14 16:23:17,765 [main] DEBUG org.openscience.cdk.layout.AtomPla= cer - newX:1.213525491562421 > 2006-02-14 16:23:17,765 [main] DEBUG org.openscience.cdk.layout.AtomPla= cer - newY:-0.88167787843871 > 2006-02-14 16:23:17,781 [main] DEBUG org.openscience.cdk.layout.RingPla= cer - placeRingSubstituents->unplacedPartners: 6 > 2006-02-14 16:23:17,781 [main] DEBUG org.openscience.cdk.layout.AtomPla= cer - distributePartners->occupiedDirection.lenght(): 1.2759762125280596 > 2006-02-14 16:23:17,781 [main] DEBUG org.openscience.cdk.layout.AtomPla= cer - Number of shared atoms: 2 > 2006-02-14 16:23:17,781 [main] DEBUG org.openscience.cdk.layout.AtomPla= cer - distributePartners->newDirection.lenght(): 1.5 > 2006-02-14 16:23:17,781 [main] DEBUG org.openscience.cdk.layout.AtomPla= cer - distributePartners->sortedAtoms[0]: 5 > 2006-02-14 16:23:17,781 [main] DEBUG org.openscience.cdk.layout.AtomPla= cer - distributePartners->sortedAtoms[1]: 3 > 2006-02-14 16:23:17,781 [main] DEBUG org.openscience.cdk.layout.AtomPla= cer - distributePartners->angle1: 306.0 > 2006-02-14 16:23:17,781 [main] DEBUG org.openscience.cdk.layout.AtomPla= cer - distributePartners->angle2: 54.0 > 2006-02-14 16:23:17,781 [main] DEBUG org.openscience.cdk.layout.AtomPla= cer - distributePartners->startAtom: 3 > 2006-02-14 16:23:17,781 [main] DEBUG org.openscience.cdk.layout.AtomPla= cer - distributePartners->remainingAngle: 252.0 > 2006-02-14 16:23:17,781 [main] DEBUG org.openscience.cdk.layout.AtomPla= cer - distributePartners->addAngle: 126.0 > 2006-02-14 16:23:17,781 [main] DEBUG org.openscience.cdk.layout.AtomPla= cer - distributePartners-> partners.getAtomCount(): 1 > 2006-02-14 16:23:17,781 [main] DEBUG org.openscience.cdk.layout.AtomPla= cer - Before check: distributePartners->startAngle: 0.9424777960769379 > 2006-02-14 16:23:17,781 [main] DEBUG org.openscience.cdk.layout.AtomPla= cer - After check: distributePartners->startAngle: 0.9424777960769379 > 2006-02-14 16:23:17,781 [main] DEBUG org.openscience.cdk.layout.AtomPla= cer - populatePolygonCorners->startAngle: 54.0 > 2006-02-14 16:23:17,781 [main] DEBUG org.openscience.cdk.layout.AtomPla= cer - centerX:-2.3082626528814396 > 2006-02-14 16:23:17,781 [main] DEBUG org.openscience.cdk.layout.AtomPla= cer - centerY:0.7500000000000002 > 2006-02-14 16:23:17,781 [main] DEBUG org.openscience.cdk.layout.AtomPla= cer - radius :1.5 > 2006-02-14 16:23:17,781 [main] DEBUG org.openscience.cdk.layout.AtomPla= cer - populatePolygonCorners->angle: 180.0 > 2006-02-14 16:23:17,781 [main] DEBUG org.openscience.cdk.layout.AtomPla= cer - newX:-3.8082626528814396 > 2006-02-14 16:23:17,781 [main] DEBUG org.openscience.cdk.layout.AtomPla= cer - newY:0.7500000000000004 > 2006-02-14 16:23:17,781 [main] DEBUG org.openscience.cdk.layout.RingPla= cer - placeRingSubstituents->unplacedPartners: 13 > 2006-02-14 16:23:17,781 [main] DEBUG org.openscience.cdk.layout.AtomPla= cer - distributePartners->occupiedDirection.lenght(): 1.2759762125280596 > 2006-02-14 16:23:17,781 [main] DEBUG org.openscience.cdk.layout.AtomPla= cer - Number of shared atoms: 2 > 2006-02-14 16:23:17,781 [main] DEBUG org.openscience.cdk.layout.AtomPla= cer - distributePartners->newDirection.lenght(): 1.5000000000000002 > 2006-02-14 16:23:17,781 [main] DEBUG org.openscience.cdk.layout.AtomPla= cer - distributePartners->sortedAtoms[0]: 1 > 2006-02-14 16:23:17,781 [main] DEBUG org.openscience.cdk.layout.AtomPla= cer - distributePartners->sortedAtoms[1]: 4 > 2006-02-14 16:23:17,781 [main] DEBUG org.openscience.cdk.layout.AtomPla= cer - distributePartners->angle1: 342.0 > 2006-02-14 16:23:17,781 [main] DEBUG org.openscience.cdk.layout.AtomPla= cer - distributePartners->angle2: 234.0 > 2006-02-14 16:23:17,781 [main] DEBUG org.openscience.cdk.layout.AtomPla= cer - distributePartners->startAtom: 1 > 2006-02-14 16:23:17,781 [main] DEBUG org.openscience.cdk.layout.AtomPla= cer - distributePartners->remainingAngle: 252.0 > 2006-02-14 16:23:17,781 [main] DEBUG org.openscience.cdk.layout.AtomPla= cer - distributePartners->addAngle: 126.0 > 2006-02-14 16:23:17,781 [main] DEBUG org.openscience.cdk.layout.AtomPla= cer - distributePartners-> partners.getAtomCount(): 1 > 2006-02-14 16:23:17,781 [main] DEBUG org.openscience.cdk.layout.AtomPla= cer - Before check: distributePartners->startAngle: 5.969026041820607 > 2006-02-14 16:23:17,781 [main] DEBUG org.openscience.cdk.layout.AtomPla= cer - After check: distributePartners->startAngle: 5.969026041820607 > 2006-02-14 16:23:17,781 [main] DEBUG org.openscience.cdk.layout.AtomPla= cer - populatePolygonCorners->startAngle: 342.0 > 2006-02-14 16:23:17,781 [main] DEBUG org.openscience.cdk.layout.AtomPla= cer - centerX:-1.42658477444273 > 2006-02-14 16:23:17,781 [main] DEBUG org.openscience.cdk.layout.AtomPla= cer - centerY:1.9635254915624212 > 2006-02-14 16:23:17,781 [main] DEBUG org.openscience.cdk.layout.AtomPla= cer - radius :1.5 > 2006-02-14 16:23:17,781 [main] DEBUG org.openscience.cdk.layout.AtomPla= cer - populatePolygonCorners->angle: 108.0 > 2006-02-14 16:23:17,781 [main] DEBUG org.openscience.cdk.layout.AtomPla= cer - newX:-1.890110266005151 > 2006-02-14 16:23:17,781 [main] DEBUG org.openscience.cdk.layout.AtomPla= cer - newY:3.3901102660051516 > 2006-02-14 16:23:17,781 [main] DEBUG org.openscience.cdk.layout.RingPla= cer - RingPlacer.placeRingSubstituents() end > 2006-02-14 16:23:17,781 [main] DEBUG org.openscience.cdk.layout.Structu= reDiagramGenerator - *** Start of handling the rest of the molecule. *** > 2006-02-14 16:23:17,781 [main] DEBUG org.openscience.cdk.layout.AtomPla= cer - Start of getLongestUnplacedChain. > 2006-02-14 16:23:17,781 [main] DEBUG org.openscience.cdk.layout.AtomPla= cer - Start of breadthFirstSearch > 2006-02-14 16:23:17,781 [main] DEBUG org.openscience.cdk.layout.AtomPla= cer - BreadthFirstSearch around atom 7 > 2006-02-14 16:23:17,781 [main] DEBUG org.openscience.cdk.layout.AtomPla= cer - BreadthFirstSearch is meeting new atom 8 > 2006-02-14 16:23:17,781 [main] DEBUG org.openscience.cdk.layout.AtomPla= cer - Making copy of path 7 to form new path 8 > 2006-02-14 16:23:17,781 [main] DEBUG org.openscience.cdk.layout.AtomPla= cer - Old path 7 looks like: Numbers: 7=20 > 2006-02-14 16:23:17,781 [main] DEBUG org.openscience.cdk.layout.AtomPla= cer - Copied path 8 looks like: Numbers: 7=20 > 2006-02-14 16:23:17,781 [main] DEBUG org.openscience.cdk.layout.AtomPla= cer - Adding atom 8 to path 8 > 2006-02-14 16:23:17,781 [main] DEBUG org.openscience.cdk.layout.AtomPla= cer - New path 8 looks like: Numbers: 7 8=20 > 2006-02-14 16:23:17,781 [main] DEBUG org.openscience.cdk.layout.AtomPla= cer - Start of breadthFirstSearch > 2006-02-14 16:23:17,781 [main] DEBUG org.openscience.cdk.layout.AtomPla= cer - BreadthFirstSearch around atom 8 > 2006-02-14 16:23:17,781 [main] DEBUG org.openscience.cdk.layout.AtomPla= cer - BreadthFirstSearch is meeting new atom 12 > 2006-02-14 16:23:17,781 [main] DEBUG org.openscience.cdk.layout.AtomPla= cer - Making copy of path 8 to form new path 12 > 2006-02-14 16:23:17,781 [main] DEBUG org.openscience.cdk.layout.AtomPla= cer - Old path 8 looks like: Numbers: 7 8=20 > 2006-02-14 16:23:17,781 [main] DEBUG org.openscience.cdk.layout.AtomPla= cer - Copied path 12 looks like: Numbers: 7 8=20 > 2006-02-14 16:23:17,781 [main] DEBUG org.openscience.cdk.layout.AtomPla= cer - Adding atom 12 to path 12 > 2006-02-14 16:23:17,781 [main] DEBUG org.openscience.cdk.layout.AtomPla= cer - New path 12 looks like: Numbers: 7 8 12=20 > 2006-02-14 16:23:17,781 [main] DEBUG org.openscience.cdk.layout.AtomPla= cer - BreadthFirstSearch is meeting new atom 18 > 2006-02-14 16:23:17,781 [main] DEBUG org.openscience.cdk.layout.AtomPla= cer - Making copy of path 8 to form new path 18 > 2006-02-14 16:23:17,781 [main] DEBUG org.openscience.cdk.layout.AtomPla= cer - Old path 8 looks like: Numbers: 7 8=20 > 2006-02-14 16:23:17,781 [main] DEBUG org.openscience.cdk.layout.AtomPla= cer - Copied path 18 looks like: Numbers: 7 8=20 > 2006-02-14 16:23:17,781 [main] DEBUG org.openscience.cdk.layout.AtomPla= cer - Adding atom 18 to path 18 > 2006-02-14 16:23:17,781 [main] DEBUG org.openscience.cdk.layout.AtomPla= cer - New path 18 looks like: Numbers: 7 8 18=20 > 2006-02-14 16:23:17,781 [main] DEBUG org.openscience.cdk.layout.AtomPla= cer - Start of breadthFirstSearch > 2006-02-14 16:23:17,781 [main] DEBUG org.openscience.cdk.layout.AtomPla= cer - BreadthFirstSearch around atom 12 > 2006-02-14 16:23:17,781 [main] DEBUG org.openscience.cdk.layout.AtomPla= cer - BreadthFirstSearch is meeting new atom 16 > 2006-02-14 16:23:17,781 [main] DEBUG org.openscience.cdk.layout.AtomPla= cer - Making copy of path 12 to form new path 16 > 2006-02-14 16:23:17,781 [main] DEBUG org.openscience.cdk.layout.AtomPla= cer - Old path 12 looks like: Numbers: 7 8 12=20 > 2006-02-14 16:23:17,781 [main] DEBUG org.openscience.cdk.layout.AtomPla= cer - Copied path 16 looks like: Numbers: 7 8 12=20 > 2006-02-14 16:23:17,781 [main] DEBUG org.openscience.cdk.layout.AtomPla= cer - Adding atom 16 to path 16 > 2006-02-14 16:23:17,781 [main] DEBUG org.openscience.cdk.layout.AtomPla= cer - New path 16 looks like: Numbers: 7 8 12 16=20 > 2006-02-14 16:23:17,781 [main] DEBUG org.openscience.cdk.layout.AtomPla= cer - Start of breadthFirstSearch > 2006-02-14 16:23:17,781 [main] DEBUG org.openscience.cdk.layout.AtomPla= cer - End of breadthFirstSearch > 2006-02-14 16:23:17,781 [main] DEBUG org.openscience.cdk.layout.AtomPla= cer - End of breadthFirstSearch > 2006-02-14 16:23:17,781 [main] DEBUG org.openscience.cdk.layout.AtomPla= cer - End of breadthFirstSearch > 2006-02-14 16:23:17,781 [main] DEBUG org.openscience.cdk.layout.AtomPla= cer - End of breadthFirstSearch > 2006-02-14 16:23:17,781 [main] DEBUG org.openscience.cdk.layout.AtomPla= cer - End of getLongestUnplacedChain. > 2006-02-14 16:23:17,781 [main] DEBUG org.openscience.cdk.layout.Structu= reDiagramGenerator - ---start of longest unplaced chain--- > 2006-02-14 16:23:17,781 [main] DEBUG org.openscience.cdk.layout.Structu= reDiagramGenerator - Start at atom no. 7 > 2006-02-14 16:23:17,781 [main] DEBUG org.openscience.cdk.layout.Structu= reDiagramGenerator - Numbers: 7 8 12 16=20 > 2006-02-14 16:23:17,781 [main] DEBUG org.openscience.cdk.layout.Structu= reDiagramGenerator - ---end of longest unplaced chain--- > 2006-02-14 16:23:17,781 [main] DEBUG org.openscience.cdk.layout.Structu= reDiagramGenerator - Less than one atoms placed already > 2006-02-14 16:23:17,781 [main] DEBUG org.openscience.cdk.layout.Structu= reDiagramGenerator - Trying to get next bond vector. > 2006-02-14 16:23:17,781 [main] DEBUG org.openscience.cdk.layout.AtomPla= cer - Entering AtomPlacer.getNextBondVector() > 2006-02-14 16:23:17,781 [main] DEBUG org.openscience.cdk.layout.AtomPla= cer - Arguments are atom: Atom(2553100, C, H:2, SP:0, 2D:[(1.213525491562= 4212, 2.3816778784387096)], 3D:[null], Fract3D:[null], C:0.0, FC:0, AtomT= ype(null, MBO:0.0, BOS:0.0, FC:0, H:0, NC:0, CR:0.0, VDWR:0.0, EV:0, A:fa= lse, D:false, ChemicalGroupCode:0, RingSize:0, Aromatic:false, SphericalD= escriptor:null, Isotope(12, EM:12.0, AB:100.0, Element(C, ID:null, AN:6))= )), previousAtom: Atom(29250150, N, H:0, SP:0, 2D:[(0.0, 1.5)], 3D:[null]= , Fract3D:[null], C:0.0, FC:0, AtomType(null, MBO:0.0, BOS:0.0, FC:0, H:0= , NC:0, CR:0.0, VDWR:0.0, EV:0, A:false, D:false, ChemicalGroupCode:0, Ri= ngSize:0, Aromatic:false, SphericalDescriptor:null, Isotope(14, EM:14.003= 074, AB:100.0, Element(N, ID:null, AN:7)))), distanceMeasure: (-0.9369726= 819476275, 1.0433455851116837) > 2006-02-14 16:23:17,781 [main] DEBUG org.openscience.cdk.layout.AtomPla= cer - Exiting AtomPlacer.getNextBondVector() > 2006-02-14 16:23:17,781 [main] DEBUG org.openscience.cdk.layout.AtomPla= cer - Placing linear chain of length 4 > 2006-02-14 16:23:17,781 [main] DEBUG org.openscience.cdk.layout.AtomPla= cer - Entering AtomPlacer.getNextBondVector() > 2006-02-14 16:23:17,781 [main] DEBUG org.openscience.cdk.layout.AtomPla= cer - Arguments are atom: Atom(27391563, C, H:0, SP:0, 2D:[(2.58384367802= 6322, 1.7715729138250083)], 3D:[null], Fract3D:[null], C:0.0, FC:0, AtomT= ype(null, MBO:0.0, BOS:0.0, FC:0, H:0, NC:0, CR:0.0, VDWR:0.0, EV:0, A:fa= lse, D:false, ChemicalGroupCode:0, RingSize:0, Aromatic:false, SphericalD= escriptor:null, Isotope(12, EM:12.0, AB:100.0, Element(C, ID:null, AN:6))= )), previousAtom: Atom(2553100, C, H:2, SP:0, 2D:[(1.2135254915624212, 2.= 3816778784387096)], 3D:[null], Fract3D:[null], C:0.0, FC:0, AtomType(null= , MBO:0.0, BOS:0.0, FC:0, H:0, NC:0, CR:0.0, VDWR:0.0, EV:0, A:false, D:f= alse, ChemicalGroupCode:0, RingSize:0, Aromatic:false, SphericalDescripto= r:null, Isotope(12, EM:12.0, AB:100.0, Element(C, ID:null, AN:6)))), dist= anceMeasure: (-0.5848910459502326, 1.1161683179830162) > 2006-02-14 16:23:17,781 [main] DEBUG org.openscience.cdk.layout.AtomPla= cer - Exiting AtomPlacer.getNextBondVector() > 2006-02-14 16:23:17,781 [main] DEBUG org.openscience.cdk.layout.AtomPla= cer - Entering AtomPlacer.getNextBondVector() > 2006-02-14 16:23:17,781 [main] DEBUG org.openscience.cdk.layout.AtomPla= cer - Arguments are atom: Atom(5270634, N, H:1, SP:0, 2D:[(3.797369169588= 745, 2.6532507922637154)], 3D:[null], Fract3D:[null], C:0.0, FC:0, AtomTy= pe(null, MBO:0.0, BOS:0.0, FC:0, H:0, NC:0, CR:0.0, VDWR:0.0, EV:0, A:fal= se, D:false, ChemicalGroupCode:0, RingSize:0, Aromatic:false, SphericalDe= scriptor:null, Isotope(14, EM:14.003074, AB:100.0, Element(N, ID:null, AN= :7)))), previousAtom: Atom(27391563, C, H:0, SP:0, 2D:[(2.583843678026322= , 1.7715729138250083)], 3D:[null], Fract3D:[null], C:0.0, FC:0, AtomType(= null, MBO:0.0, BOS:0.0, FC:0, H:0, NC:0, CR:0.0, VDWR:0.0, EV:0, A:false,= D:false, ChemicalGroupCode:0, RingSize:0, Aromatic:false, SphericalDescr= iptor:null, Isotope(12, EM:12.0, AB:100.0, Element(C, ID:null, AN:6)))), = distanceMeasure: (-0.18650375362850724, 1.2559030883721707) > 2006-02-14 16:23:17,781 [main] DEBUG org.openscience.cdk.layout.AtomPla= cer - Exiting AtomPlacer.getNextBondVector() > 2006-02-14 16:23:17,781 [main] DEBUG org.openscience.cdk.layout.AtomPla= cer - Entering AtomPlacer.getNextBondVector() > 2006-02-14 16:23:17,781 [main] DEBUG org.openscience.cdk.layout.AtomPla= cer - Arguments are atom: Atom(969695, C, H:0, SP:0, 2D:[(5.1676873560526= 45, 2.0431458276500116)], 3D:[null], Fract3D:[null], C:0.0, FC:0, AtomTyp= e(null, MBO:0.0, BOS:0.0, FC:0, H:0, NC:0, CR:0.0, VDWR:0.0, EV:0, A:fals= e, D:false, ChemicalGroupCode:0, RingSize:0, Aromatic:false, SphericalDes= criptor:null, Isotope(12, EM:12.0, AB:100.0, Element(C, ID:null, AN:6))))= , previousAtom: Atom(5270634, N, H:1, SP:0, 2D:[(3.797369169588745, 2.653= 2507922637154)], 3D:[null], Fract3D:[null], C:0.0, FC:0, AtomType(null, M= BO:0.0, BOS:0.0, FC:0, H:0, NC:0, CR:0.0, VDWR:0.0, EV:0, A:false, D:fals= e, ChemicalGroupCode:0, RingSize:0, Aromatic:false, SphericalDescriptor:n= ull, Isotope(14, EM:14.003074, AB:100.0, Element(N, ID:null, AN:7)))), di= stanceMeasure: (0.2596788388449221, 1.3215066499786574) > 2006-02-14 16:23:17,781 [main] DEBUG org.openscience.cdk.layout.AtomPla= cer - Exiting AtomPlacer.getNextBondVector() > 2006-02-14 16:23:17,781 [main] DEBUG org.openscience.cdk.layout.AtomPla= cer - Start of getLongestUnplacedChain. > 2006-02-14 16:23:17,781 [main] DEBUG org.openscience.cdk.layout.AtomPla= cer - Start of breadthFirstSearch > 2006-02-14 16:23:17,781 [main] DEBUG org.openscience.cdk.layout.AtomPla= cer - End of breadthFirstSearch > 2006-02-14 16:23:17,781 [main] DEBUG org.openscience.cdk.layout.AtomPla= cer - End of getLongestUnplacedChain. > 2006-02-14 16:23:17,781 [main] DEBUG org.openscience.cdk.layout.Structu= reDiagramGenerator - ---start of longest unplaced chain--- > 2006-02-14 16:23:17,781 [main] DEBUG org.openscience.cdk.layout.Structu= reDiagramGenerator - Start at atom no. 16 > 2006-02-14 16:23:17,781 [main] DEBUG org.openscience.cdk.layout.Structu= reDiagramGenerator - Numbers: 16=20 > 2006-02-14 16:23:17,781 [main] DEBUG org.openscience.cdk.layout.Structu= reDiagramGenerator - ---end of longest unplaced chain--- > 2006-02-14 16:23:17,781 [main] DEBUG org.openscience.cdk.layout.Structu= reDiagramGenerator - Start of layoutNextRingSystem() > 2006-02-14 16:23:17,781 [main] DEBUG org.openscience.cdk.layout.Structu= reDiagramGenerator - Ring with 6 atoms is not placed. > 2006-02-14 16:23:17,781 [main] DEBUG org.openscience.cdk.layout.Structu= reDiagramGenerator - Ring with 6 atoms is not placed. > 2006-02-14 16:23:17,781 [main] DEBUG org.openscience.cdk.layout.Structu= reDiagramGenerator - There are 2 Rings. > 2006-02-14 16:23:17,781 [main] DEBUG org.openscience.cdk.layout.Structu= reDiagramGenerator - Computing rotation of new ringset to fit old attachm= ent bond orientation... > 2006-02-14 16:23:17,781 [main] DEBUG org.openscience.cdk.layout.Structu= reDiagramGenerator - oldPoint1: (-3.8082626528814396, 0.7500000000000004) > 2006-02-14 16:23:17,781 [main] DEBUG org.openscience.cdk.layout.Structu= reDiagramGenerator - oldPoint2: null --=20 Priv. Doz. Dr. Christoph Steinbeck (c.s...@un...) Head of the Research Group for Molecular Informatics Cologne University BioInformatics Center (http://almost.cubic.uni-koeln.d= e) Z=FClpicher Str. 47, 50674 Cologne Tel: +49(0)221-470-7426 Fax: +49 (0) 221-470-7786 What is man but that lofty spirit - that sense of enterprise. ... Kirk, "I, Mudd," stardate 4513.3.. |