From: Christoph S. <ste...@eb...> - 2008-05-27 17:04:17
|
Hi everybody, is anyone aware of an open implementation of the following: Electrotopological State Index (E-State): (aus: http://www.ualberta.ca/~csps/JPPS7(1)/R.Carrasco/QSAR.htm#1) The electrotopological state index (E-state) is developed from chemical graph theory and uses the chemical graph (hydrogen-suppressed skeleton) for generation of atom-level structure indices. The index is based on the electronic effect of each atom on the other atoms in the molecule as modified by molecular topology. Any hint appreciated. Cheers, Christoph -- Dr. Christoph Steinbeck Head of Chemoinformatics and Metabolism European Bioinformatics Institute (EBI) Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD UK Phone +44 1223 49 2640 What is man but that lofty spirit - that sense of enterprise. ... Kirk, "I, Mudd," stardate 4513.3.. |
From: Yap C. W. <ph...@nu...> - 2008-06-17 02:32:52
|
Hi, I have just recently written some codes for CDK to calculate electrotopological state indices. How do I upload the codes into CDK? Cheers, Chun Wei YAP Chun Wei (Dr) :: Assistant Professor, Department of Pharmacy :: Faculty of Science :: National University of Singapore :: Blk S4A-02-10, 18 Science Drive 4, Singapore 117543 :: 65-6516 5971 (DID) :: 65-6779 1554 (Fax) :: ph...@nu... <mailto:ph...@nu...> (E) :: padel.nus.edu.sg <http://padel.nus.edu.sg/> (W) :: Company Registration No: 200604346 Important: This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately; you should not copy or use it for any purpose, nor disclose its contents to any other person. Thank you. |
From: Rajarshi G. <rg...@in...> - 2008-07-03 15:53:12
|
-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 On Jun 16, 2008, at 10:32 PM, Yap Chun Wei wrote: > Hi, > > > > I have just recently written some codes for CDK to calculate > electrotopological state indices. How do I upload the codes into CDK > If you can post the code somewhere (along with unit tests) we can take a look at it - ------------------------------------------------------------------- Rajarshi Guha <rg...@in...> GPG Fingerprint: D070 5427 CC5B 7938 929C DD13 66A1 922C 51E7 9E84 - ------------------------------------------------------------------- Do radioactive cats have 18 half-lives? -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.8 (Darwin) iEYEARECAAYFAkhs75YACgkQZqGSLFHnnoRQqwCaArIoftYTH+DL26qDOip6mUmT qNgAn3B/BBWpYZSNZnIJxGkNUgF7VTRd =vXf8 -----END PGP SIGNATURE----- |
From: Egon W. <ego...@gm...> - 2010-12-21 09:56:16
|
Dear Prof. Yap, today I discovered your paper on your PaDEL software: http://chem-bla-ics.blogspot.com/2010/12/re-commercial-or-proprietary.html Please let me know how I can assist porting your new descriptors into the CDK library. Looking forward to hearing from you, with kind regards, Egon On Thu, Jul 3, 2008 at 5:26 PM, Rajarshi Guha <rg...@in...> wrote: > -----BEGIN PGP SIGNED MESSAGE----- > Hash: SHA1 > > > On Jun 16, 2008, at 10:32 PM, Yap Chun Wei wrote: >> Hi, >> >> >> >> I have just recently written some codes for CDK to calculate >> electrotopological state indices. How do I upload the codes into CDK >> > > If you can post the code somewhere (along with unit tests) we can > take a look at it > > - ------------------------------------------------------------------- > Rajarshi Guha <rg...@in...> > GPG Fingerprint: D070 5427 CC5B 7938 929C DD13 66A1 922C 51E7 9E84 > - ------------------------------------------------------------------- > Do radioactive cats have 18 half-lives? > > > -----BEGIN PGP SIGNATURE----- > Version: GnuPG v1.4.8 (Darwin) > > iEYEARECAAYFAkhs75YACgkQZqGSLFHnnoRQqwCaArIoftYTH+DL26qDOip6mUmT > qNgAn3B/BBWpYZSNZnIJxGkNUgF7VTRd > =vXf8 > -----END PGP SIGNATURE----- > > ------------------------------------------------------------------------- > Sponsored by: SourceForge.net Community Choice Awards: VOTE NOW! > Studies have shown that voting for your favorite open source project, > along with a healthy diet, reduces your potential for chronic lameness > and boredom. Vote Now at http://www.sourceforge.net/community/cca08 > _______________________________________________ > Cdk-devel mailing list > Cdk...@li... > https://lists.sourceforge.net/lists/listinfo/cdk-devel > -- Dr E.L. Willighagen Postdoctoral Research Associate University of Cambridge Homepage: http://egonw.github.com/ LinkedIn: http://se.linkedin.com/in/egonw Blog: http://chem-bla-ics.blogspot.com/ PubList: http://www.citeulike.org/user/egonw/tag/papers |
From: Yap C. W. <ph...@nu...> - 2010-12-21 15:40:19
|
Dear Egon, The source code for PaDEL-Descriptor is freely available at http://padel.nus.edu.sg/software/padeldescriptor/PaDEL-Descriptor_src.zip. I have programmed it such that the new descriptors should be easy to port into CDK. You just need to look at the libPaDEL-Descriptor\src\libpadeldescriptor folder. The files to look at are: 1. For atom type EState - EStateAtomTypeDescriptor.java - ElectrotopologicalStateDescriptor.java - HydrogenEStateDescriptor.java - IntrinsicStateDescriptor.java - KierHallElectronegativityDescriptor.java 2. For McGowan volume - McGowanVolumeDescriptor.java 3. For molecular linear free energy relation descriptors - MLFERDescriptor.java 4. For ring counts - RingCountDescriptor.java 5. For number of heavy atoms - HeavyAtomCountDescriptor.java 6. To get count of substructures as fingerprints instead of binary vector - SubstructureFingerprintCount.java In addition, I have made a few modifications to three existing CDK files so that they will be more thread safe. I can't guarantee that they are 100% thread safe yet. I think I have commented the lines which I have changed using // PaDEL - PubchemFingerprinter.java - PaDELPathTools.java - PaDELWeightedPathDescriptor.java I have also modified the PDBReader so that it will read in a small molecule that is saved in pdb format. I think I have commented the lines which I have changed using // PaDEL - PaDELPDBReader.java I have to apologize upfront for the lack of proper commenting in the source code and the lack of unit testing. Do let me know if you need more information. Best regards, Chun Wei YAP Chun Wei (Dr) :: Assistant Professor, Department of Pharmacy :: Faculty of Science :: National University of Singapore :: Blk S7-02-06, 18 Science Drive 4, Singapore 117543 :: 65-6516 5971 (DID) :: 65-6779 1554 (Fax) :: ph...@nu... (E) :: padel.nus.edu.sg (W) :: Company Registration No: 200604346 Important: This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately; you should not copy or use it for any purpose, nor disclose its contents to any other person. Thank you. -----Original Message----- From: Egon Willighagen [mailto:ego...@gm...] Sent: Tuesday, December 21, 2010 5:56 PM To: Rajarshi Guha Cc: Yap Chun Wei; cdk...@li... Subject: Re: [Cdk-devel] Electrotopological State Index - Any open implementation? Dear Prof. Yap, today I discovered your paper on your PaDEL software: http://chem-bla-ics.blogspot.com/2010/12/re-commercial-or-proprietary.html Please let me know how I can assist porting your new descriptors into the CDK library. Looking forward to hearing from you, with kind regards, Egon On Thu, Jul 3, 2008 at 5:26 PM, Rajarshi Guha <rg...@in...> wrote: > -----BEGIN PGP SIGNED MESSAGE----- > Hash: SHA1 > > > On Jun 16, 2008, at 10:32 PM, Yap Chun Wei wrote: >> Hi, >> >> >> >> I have just recently written some codes for CDK to calculate >> electrotopological state indices. How do I upload the codes into CDK >> > > If you can post the code somewhere (along with unit tests) we can > take a look at it > > - ------------------------------------------------------------------- > Rajarshi Guha <rg...@in...> > GPG Fingerprint: D070 5427 CC5B 7938 929C DD13 66A1 922C 51E7 9E84 > - ------------------------------------------------------------------- > Do radioactive cats have 18 half-lives? > > > -----BEGIN PGP SIGNATURE----- > Version: GnuPG v1.4.8 (Darwin) > > iEYEARECAAYFAkhs75YACgkQZqGSLFHnnoRQqwCaArIoftYTH+DL26qDOip6mUmT > qNgAn3B/BBWpYZSNZnIJxGkNUgF7VTRd > =vXf8 > -----END PGP SIGNATURE----- > > ------------------------------------------------------------------------- > Sponsored by: SourceForge.net Community Choice Awards: VOTE NOW! > Studies have shown that voting for your favorite open source project, > along with a healthy diet, reduces your potential for chronic lameness > and boredom. Vote Now at http://www.sourceforge.net/community/cca08 > _______________________________________________ > Cdk-devel mailing list > Cdk...@li... > https://lists.sourceforge.net/lists/listinfo/cdk-devel > -- Dr E.L. Willighagen Postdoctoral Research Associate University of Cambridge Homepage: http://egonw.github.com/ LinkedIn: http://se.linkedin.com/in/egonw Blog: http://chem-bla-ics.blogspot.com/ PubList: http://www.citeulike.org/user/egonw/tag/papers |
From: Egon W. <ego...@gm...> - 2010-12-21 15:30:30
|
Dear Yap, On Tue, Dec 21, 2010 at 4:10 PM, Yap Chun Wei <ph...@nu...> wrote: > The source code for PaDEL-Descriptor is freely available at http://padel.nus.edu.sg/software/padeldescriptor/PaDEL-Descriptor_src.zip. I have programmed it such that the new descriptors should be easy to port into CDK. You just need to look at the libPaDEL-Descriptor\src\libpadeldescriptor folder. I already did :) > The files to look at are: > 1. For atom type EState > - EStateAtomTypeDescriptor.java > - ElectrotopologicalStateDescriptor.java > - HydrogenEStateDescriptor.java > - IntrinsicStateDescriptor.java > - KierHallElectronegativityDescriptor.java > > 2. For McGowan volume > - McGowanVolumeDescriptor.java > > 3. For molecular linear free energy relation descriptors > - MLFERDescriptor.java > > 4. For ring counts > - RingCountDescriptor.java > > 5. For number of heavy atoms > - HeavyAtomCountDescriptor.java > > 6. To get count of substructures as fingerprints instead of binary vector > - SubstructureFingerprintCount.java There are all very interesting, and someone from the Open Notebook Science community already asked after the MLFERDescriptor implementation. > In addition, I have made a few modifications to three existing CDK files so that they will be more thread safe. I can't guarantee that they are 100% thread safe yet. But all improvements are very useful. There are a few core issues in the data classes that we still need to overcome too. > I think I have commented the lines which I have changed using // PaDEL > - PubchemFingerprinter.java > - PaDELPathTools.java > - PaDELWeightedPathDescriptor.java > > I have also modified the PDBReader so that it will read in a small molecule that is saved in pdb format. I think I have commented the lines which I have changed using // PaDEL > - PaDELPDBReader.java > > I have to apologize upfront for the lack of proper commenting in the source code and the lack of unit testing. Do let me know if you need more information. That is something we can work on as a community. I noted that some classes you annotated as "LGPL v2.1 or later" as the rest of the CDK code. Is all code you mention above available under that license? All patches must be of course, but also all new code? What we can do is set up a git branch, and start importing your code there, and then see what unit testing and javadoc code improvements we can make. We might be able to recruit external developers too, but you will need to be available for help. Your help is needed to fix some things, but you can expect patches from others too, for which it would be very much appreciated if you can look at those and review/approve them. Are you willing to help with this effort? Egon -- Dr E.L. Willighagen Postdoctoral Research Associate University of Cambridge Homepage: http://egonw.github.com/ LinkedIn: http://se.linkedin.com/in/egonw Blog: http://chem-bla-ics.blogspot.com/ PubList: http://www.citeulike.org/user/egonw/tag/papers |
From: Yap C. W. <ph...@nu...> - 2010-12-21 15:44:38
|
Dear Egon, Sure, I will be willing to help out with the maintenance of the code. For the license issue, I did a lot of copy and paste from existing CDK classes so it may have been copied from somewhere. Anyway, for the record, I release all my code as public domain. There is no license to take note of, except any existing license that the code is supposed to comply with. So if you see any license conditions that is not from the original CDK code, you can safely remove them. Best regards, Chun Wei YAP Chun Wei (Dr) :: Assistant Professor, Department of Pharmacy :: Faculty of Science :: National University of Singapore :: Blk S7-02-06, 18 Science Drive 4, Singapore 117543 :: 65-6516 5971 (DID) :: 65-6779 1554 (Fax) :: ph...@nu... (E) :: padel.nus.edu.sg (W) :: Company Registration No: 200604346 Important: This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately; you should not copy or use it for any purpose, nor disclose its contents to any other person. Thank you. -----Original Message----- From: Egon Willighagen [mailto:ego...@gm...] Sent: Tuesday, December 21, 2010 11:30 PM To: Yap Chun Wei Cc: Rajarshi Guha; cdk...@li... Subject: Re: [Cdk-devel] Electrotopological State Index - Any open implementation? Dear Yap, On Tue, Dec 21, 2010 at 4:10 PM, Yap Chun Wei <ph...@nu...> wrote: > The source code for PaDEL-Descriptor is freely available at http://padel.nus.edu.sg/software/padeldescriptor/PaDEL-Descriptor_src.zip. I have programmed it such that the new descriptors should be easy to port into CDK. You just need to look at the libPaDEL-Descriptor\src\libpadeldescriptor folder. I already did :) > The files to look at are: > 1. For atom type EState > - EStateAtomTypeDescriptor.java > - ElectrotopologicalStateDescriptor.java > - HydrogenEStateDescriptor.java > - IntrinsicStateDescriptor.java > - KierHallElectronegativityDescriptor.java > > 2. For McGowan volume > - McGowanVolumeDescriptor.java > > 3. For molecular linear free energy relation descriptors > - MLFERDescriptor.java > > 4. For ring counts > - RingCountDescriptor.java > > 5. For number of heavy atoms > - HeavyAtomCountDescriptor.java > > 6. To get count of substructures as fingerprints instead of binary vector > - SubstructureFingerprintCount.java There are all very interesting, and someone from the Open Notebook Science community already asked after the MLFERDescriptor implementation. > In addition, I have made a few modifications to three existing CDK files so that they will be more thread safe. I can't guarantee that they are 100% thread safe yet. But all improvements are very useful. There are a few core issues in the data classes that we still need to overcome too. > I think I have commented the lines which I have changed using // PaDEL > - PubchemFingerprinter.java > - PaDELPathTools.java > - PaDELWeightedPathDescriptor.java > > I have also modified the PDBReader so that it will read in a small molecule that is saved in pdb format. I think I have commented the lines which I have changed using // PaDEL > - PaDELPDBReader.java > > I have to apologize upfront for the lack of proper commenting in the source code and the lack of unit testing. Do let me know if you need more information. That is something we can work on as a community. I noted that some classes you annotated as "LGPL v2.1 or later" as the rest of the CDK code. Is all code you mention above available under that license? All patches must be of course, but also all new code? What we can do is set up a git branch, and start importing your code there, and then see what unit testing and javadoc code improvements we can make. We might be able to recruit external developers too, but you will need to be available for help. Your help is needed to fix some things, but you can expect patches from others too, for which it would be very much appreciated if you can look at those and review/approve them. Are you willing to help with this effort? Egon -- Dr E.L. Willighagen Postdoctoral Research Associate University of Cambridge Homepage: http://egonw.github.com/ LinkedIn: http://se.linkedin.com/in/egonw Blog: http://chem-bla-ics.blogspot.com/ PubList: http://www.citeulike.org/user/egonw/tag/papers |
From: Egon W. <ego...@gm...> - 2010-12-21 17:00:44
|
On Tue, Dec 21, 2010 at 4:40 PM, Yap Chun Wei <ph...@nu...> wrote: > Sure, I will be willing to help out with the maintenance of the code. Do you want your name to show up in the commit messages, as proper author? I could copy in your current code using --author="Yap Chun Wei <ph...@nu..." to effect this... Egon -- Dr E.L. Willighagen Postdoctoral Research Associate University of Cambridge Homepage: http://egonw.github.com/ LinkedIn: http://se.linkedin.com/in/egonw Blog: http://chem-bla-ics.blogspot.com/ PubList: http://www.citeulike.org/user/egonw/tag/papers |
From: Egon W. <ego...@gm...> - 2010-12-21 17:58:29
|
On Tue, Dec 21, 2010 at 6:00 PM, Egon Willighagen <ego...@gm...> wrote: > On Tue, Dec 21, 2010 at 4:40 PM, Yap Chun Wei <ph...@nu...> wrote: >> Sure, I will be willing to help out with the maintenance of the code. > > Do you want your name to show up in the commit messages, as proper > author? I could copy in your current code using --author="Yap Chun Wei > <ph...@nu..." to effect this... Please have a look at the patch I created with you as 'author': https://github.com/cdk/cdk/commits/dev-1.4.x-padel Egon -- Dr E.L. Willighagen Postdoctoral Research Associate University of Cambridge Homepage: http://egonw.github.com/ LinkedIn: http://se.linkedin.com/in/egonw Blog: http://chem-bla-ics.blogspot.com/ PubList: http://www.citeulike.org/user/egonw/tag/papers |
From: Yap C. W. <ph...@nu...> - 2010-12-22 02:03:35
|
Dear Egon, Thanks. Not too familiar with Git. Will try it out and let you know. Best regards, Chun Wei YAP Chun Wei (Dr) :: Assistant Professor, Department of Pharmacy :: Faculty of Science :: National University of Singapore :: Blk S7-02-06, 18 Science Drive 4, Singapore 117543 :: 65-6516 5971 (DID) :: 65-6779 1554 (Fax) :: ph...@nu... (E) :: padel.nus.edu.sg (W) :: Company Registration No: 200604346 Important: This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately; you should not copy or use it for any purpose, nor disclose its contents to any other person. Thank you. -----Original Message----- From: Egon Willighagen [mailto:ego...@gm...] Sent: Wednesday, December 22, 2010 1:51 AM To: Yap Chun Wei Cc: Rajarshi Guha; cdk...@li... Subject: Re: [Cdk-devel] Electrotopological State Index - Any open implementation? On Tue, Dec 21, 2010 at 6:00 PM, Egon Willighagen <ego...@gm...> wrote: > On Tue, Dec 21, 2010 at 4:40 PM, Yap Chun Wei <ph...@nu...> wrote: >> Sure, I will be willing to help out with the maintenance of the code. > > Do you want your name to show up in the commit messages, as proper > author? I could copy in your current code using --author="Yap Chun Wei > <ph...@nu..." to effect this... Please have a look at the patch I created with you as 'author': https://github.com/cdk/cdk/commits/dev-1.4.x-padel Egon -- Dr E.L. Willighagen Postdoctoral Research Associate University of Cambridge Homepage: http://egonw.github.com/ LinkedIn: http://se.linkedin.com/in/egonw Blog: http://chem-bla-ics.blogspot.com/ PubList: http://www.citeulike.org/user/egonw/tag/papers |
From: Yap C. W. <ph...@nu...> - 2011-08-01 02:32:38
Attachments:
winmail.dat
|
Dear Rajarshi and Egon, One of my collaborators is having trouble reading hyperchem files (HIN files) with CDK. As I was tracing through the code, I noticed that the code to identify aromatic atoms and bonds in the HINReader.java may not be correct. I have modified it as shown below (lines which were changed were highlighted in red). I am not sure whether this modification is correct but it is working for me so far. Best regards, Chun Wei case 'a': bo = IBond.Order.SINGLE; atom.setFlag(CDKConstants.ISAROMATIC, true); break; } List<Object> ar = new ArrayList<Object>(3); ar.add(atomSerial); ar.add(s); ar.add(bo); cons.add( ar ); } m.addAtom(atom); atomSerial++; line = input.readLine(); } // now just store all the bonds we have for (List<Object> ar : cons) { IAtom s = m.getAtom((Integer) ar.get(0)); IAtom e = m.getAtom((Integer) ar.get(1)); IBond.Order bo = (IBond.Order) ar.get(2); if (!isConnected(m, s, e)) { IBond newBond = null; if (s.getFlag(CDKConstants.ISAROMATIC) || e.getFlag(CDKConstants.ISAROMATIC)) { newBond = file.getBuilder().newInstance(IBond.class,s, e, bo); newBond.setFlag(CDKConstants.ISAROMATIC, true); } else { newBond = file.getBuilder().newInstance(IBond.class,s, e, bo); } m.addBond(newBond); } } |
From: Rajarshi G. <raj...@gm...> - 2011-08-01 04:32:29
|
Hi, thanks for catching this. Would you mind sending a diff of your patch? My mail client removed your formatting and so I can't see the changes easily On Jul 31, 2011, at 10:28 PM, Yap Chun Wei wrote: > Dear Rajarshi and Egon, > > One of my collaborators is having trouble reading hyperchem files > (HIN files) with CDK. As I was tracing through the code, I noticed > that the code to identify aromatic atoms and bonds in the > HINReader.java may not be correct. I have modified it as shown below > (lines which were changed were highlighted in red). I am not sure > whether this modification is correct but it is working for me so far. > > Best regards, > Chun Wei > > case 'a': > bo = IBond.Order.SINGLE; > atom.setFlag(CDKConstants.ISAROMATIC, > true); > break; > } > List<Object> ar = new ArrayList<Object>(3); > ar.add(atomSerial); > ar.add(s); > ar.add(bo); > cons.add( ar ); > } > m.addAtom(atom); > atomSerial++; > line = input.readLine(); > } > > // now just store all the bonds we have > for (List<Object> ar : cons) { > IAtom s = m.getAtom((Integer) ar.get(0)); > IAtom e = m.getAtom((Integer) ar.get(1)); > IBond.Order bo = (IBond.Order) ar.get(2); > if (!isConnected(m, s, e)) > { > IBond newBond = null; > if (s.getFlag(CDKConstants.ISAROMATIC) || > e.getFlag(CDKConstants.ISAROMATIC)) > { > newBond = > file.getBuilder().newInstance(IBond.class,s, e, bo); > newBond.setFlag(CDKConstants.ISAROMATIC, > true); > } > else > { > newBond = > file.getBuilder().newInstance(IBond.class,s, e, bo); > } > m.addBond(newBond); > } > } > <winmail.dat> ---------------------------------------------------- Rajarshi Guha | NIH Chemical Genomics Center http://www.rguha.net | http://ncgc.nih.gov ---------------------------------------------------- Mathematics consists of proving the most obvious thing in the least obvious way. -- George Polya |
From: Yap C. W. <ph...@nu...> - 2011-08-01 03:54:19
Attachments:
winmail.dat
|
Discovered an error in my modifications. Should be case 'a': bo = IBond.Order.SINGLE; atom.setFlag(CDKConstants.ISAROMATIC, true); break; } List<Object> ar = new ArrayList<Object>(3); ar.add(atomSerial); ar.add(s); ar.add(bo); cons.add( ar ); } m.addAtom(atom); atomSerial++; line = input.readLine(); } // now just store all the bonds we have for (List<Object> ar : cons) { IAtom s = m.getAtom((Integer) ar.get(0)); IAtom e = m.getAtom((Integer) ar.get(1)); IBond.Order bo = (IBond.Order) ar.get(2); if (!isConnected(m, s, e)) { IBond newBond = null; if (s.getFlag(CDKConstants.ISAROMATIC) && e.getFlag(CDKConstants.ISAROMATIC)) { newBond = file.getBuilder().newInstance(IBond.class,s, e, bo); newBond.setFlag(CDKConstants.ISAROMATIC, true); } else { newBond = file.getBuilder().newInstance(IBond.class,s, e, bo); } m.addBond(newBond); } } Best regards, Chun Wei From: Yap Chun Wei Sent: Monday, August 01, 2011 10:28 AM To: 'Egon Willighagen'; 'Rajarshi Guha' Cc: 'cdk...@li...' Subject: [Cdk-devel] HINReader error Dear Rajarshi and Egon, One of my collaborators is having trouble reading hyperchem files (HIN files) with CDK. As I was tracing through the code, I noticed that the code to identify aromatic atoms and bonds in the HINReader.java may not be correct. I have modified it as shown below (lines which were changed were highlighted in red). I am not sure whether this modification is correct but it is working for me so far. Best regards, Chun Wei case 'a': bo = IBond.Order.SINGLE; atom.setFlag(CDKConstants.ISAROMATIC, true); break; } List<Object> ar = new ArrayList<Object>(3); ar.add(atomSerial); ar.add(s); ar.add(bo); cons.add( ar ); } m.addAtom(atom); atomSerial++; line = input.readLine(); } // now just store all the bonds we have for (List<Object> ar : cons) { IAtom s = m.getAtom((Integer) ar.get(0)); IAtom e = m.getAtom((Integer) ar.get(1)); IBond.Order bo = (IBond.Order) ar.get(2); if (!isConnected(m, s, e)) { IBond newBond = null; if (s.getFlag(CDKConstants.ISAROMATIC) || e.getFlag(CDKConstants.ISAROMATIC)) { newBond = file.getBuilder().newInstance(IBond.class,s, e, bo); newBond.setFlag(CDKConstants.ISAROMATIC, true); } else { newBond = file.getBuilder().newInstance(IBond.class,s, e, bo); } m.addBond(newBond); } } |
From: Rajarshi G. <raj...@gm...> - 2011-08-01 04:45:21
|
Hi, thanks for catching this. Would you mind sending a diff of your patch? My mail client removed your formatting and so I can't see the changes easily On Jul 31, 2011, at 10:28 PM, Yap Chun Wei wrote: > Dear Rajarshi and Egon, > > One of my collaborators is having trouble reading hyperchem files > (HIN files) with CDK. As I was tracing through the code, I noticed > that the code to identify aromatic atoms and bonds in the > HINReader.java may not be correct. I have modified it as shown below > (lines which were changed were highlighted in red). I am not sure > whether this modification is correct but it is working for me so far. > > Best regards, > Chun Wei > > case 'a': > bo = IBond.Order.SINGLE; > atom.setFlag(CDKConstants.ISAROMATIC, > true); > break; > } > List<Object> ar = new ArrayList<Object>(3); > ar.add(atomSerial); > ar.add(s); > ar.add(bo); > cons.add( ar ); > } > m.addAtom(atom); > atomSerial++; > line = input.readLine(); > } > > // now just store all the bonds we have > for (List<Object> ar : cons) { > IAtom s = m.getAtom((Integer) ar.get(0)); > IAtom e = m.getAtom((Integer) ar.get(1)); > IBond.Order bo = (IBond.Order) ar.get(2); > if (!isConnected(m, s, e)) > { > IBond newBond = null; > if (s.getFlag(CDKConstants.ISAROMATIC) || > e.getFlag(CDKConstants.ISAROMATIC)) > { > newBond = > file.getBuilder().newInstance(IBond.class,s, e, bo); > newBond.setFlag(CDKConstants.ISAROMATIC, > true); > } > else > { > newBond = > file.getBuilder().newInstance(IBond.class,s, e, bo); > } > m.addBond(newBond); > } > } > <winmail.dat> ---------------------------------------------------- Rajarshi Guha | NIH Chemical Genomics Center http://www.rguha.net | http://ncgc.nih.gov ---------------------------------------------------- Mathematics consists of proving the most obvious thing in the least obvious way. -- George Polya |
From: Yap C. W. <ph...@nu...> - 2011-08-02 02:03:13
Attachments:
HINReader.patch
|
Hi, attached is the patch file. Best regards, Chun Wei -----Original Message----- From: Rajarshi Guha [mailto:raj...@gm...] Sent: Monday, August 01, 2011 12:44 PM To: Yap Chun Wei Cc: Egon Willighagen; Rajarshi Guha; cdk...@li... Subject: Re: [Cdk-devel] HINReader error Hi, thanks for catching this. Would you mind sending a diff of your patch? My mail client removed your formatting and so I can't see the changes easily On Jul 31, 2011, at 10:28 PM, Yap Chun Wei wrote: > Dear Rajarshi and Egon, > > One of my collaborators is having trouble reading hyperchem files > (HIN files) with CDK. As I was tracing through the code, I noticed > that the code to identify aromatic atoms and bonds in the > HINReader.java may not be correct. I have modified it as shown below > (lines which were changed were highlighted in red). I am not sure > whether this modification is correct but it is working for me so far. > > Best regards, > Chun Wei > > case 'a': > bo = IBond.Order.SINGLE; > atom.setFlag(CDKConstants.ISAROMATIC, > true); > break; > } > List<Object> ar = new ArrayList<Object>(3); > ar.add(atomSerial); > ar.add(s); > ar.add(bo); > cons.add( ar ); > } > m.addAtom(atom); > atomSerial++; > line = input.readLine(); > } > > // now just store all the bonds we have > for (List<Object> ar : cons) { > IAtom s = m.getAtom((Integer) ar.get(0)); > IAtom e = m.getAtom((Integer) ar.get(1)); > IBond.Order bo = (IBond.Order) ar.get(2); > if (!isConnected(m, s, e)) > { > IBond newBond = null; > if (s.getFlag(CDKConstants.ISAROMATIC) || > e.getFlag(CDKConstants.ISAROMATIC)) > { > newBond = > file.getBuilder().newInstance(IBond.class,s, e, bo); > newBond.setFlag(CDKConstants.ISAROMATIC, > true); > } > else > { > newBond = > file.getBuilder().newInstance(IBond.class,s, e, bo); > } > m.addBond(newBond); > } > } > <winmail.dat> ---------------------------------------------------- Rajarshi Guha | NIH Chemical Genomics Center http://www.rguha.net | http://ncgc.nih.gov ---------------------------------------------------- Mathematics consists of proving the most obvious thing in the least obvious way. -- George Polya |
From: Rajarshi G. <raj...@gm...> - 2011-09-05 21:32:36
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Sorry for getting to this after so long. Could you send me a HIN file for which the current code fails or is wrong. On Aug 1, 2011, at 9:58 PM, Yap Chun Wei wrote: > Hi, > > attached is the patch file. > > Best regards, > Chun Wei > > > -----Original Message----- > From: Rajarshi Guha [mailto:raj...@gm...] > Sent: Monday, August 01, 2011 12:44 PM > To: Yap Chun Wei > Cc: Egon Willighagen; Rajarshi Guha; cdk...@li... > Subject: Re: [Cdk-devel] HINReader error > > Hi, thanks for catching this. Would you mind sending a diff of your > patch? My mail client removed your formatting and so I can't see the > changes easily > > On Jul 31, 2011, at 10:28 PM, Yap Chun Wei wrote: > >> Dear Rajarshi and Egon, >> >> One of my collaborators is having trouble reading hyperchem files >> (HIN files) with CDK. As I was tracing through the code, I noticed >> that the code to identify aromatic atoms and bonds in the >> HINReader.java may not be correct. I have modified it as shown below >> (lines which were changed were highlighted in red). I am not sure >> whether this modification is correct but it is working for me so far. >> >> Best regards, >> Chun Wei >> >> case 'a': >> bo = IBond.Order.SINGLE; >> atom.setFlag(CDKConstants.ISAROMATIC, >> true); >> break; >> } >> List<Object> ar = new ArrayList<Object>(3); >> ar.add(atomSerial); >> ar.add(s); >> ar.add(bo); >> cons.add( ar ); >> } >> m.addAtom(atom); >> atomSerial++; >> line = input.readLine(); >> } >> >> // now just store all the bonds we have >> for (List<Object> ar : cons) { >> IAtom s = m.getAtom((Integer) ar.get(0)); >> IAtom e = m.getAtom((Integer) ar.get(1)); >> IBond.Order bo = (IBond.Order) ar.get(2); >> if (!isConnected(m, s, e)) >> { >> IBond newBond = null; >> if (s.getFlag(CDKConstants.ISAROMATIC) || >> e.getFlag(CDKConstants.ISAROMATIC)) >> { >> newBond = >> file.getBuilder().newInstance(IBond.class,s, e, bo); >> newBond.setFlag(CDKConstants.ISAROMATIC, >> true); >> } >> else >> { >> newBond = >> file.getBuilder().newInstance(IBond.class,s, e, bo); >> } >> m.addBond(newBond); >> } >> } >> <winmail.dat> > > ---------------------------------------------------- > Rajarshi Guha | NIH Chemical Genomics Center > http://www.rguha.net | http://ncgc.nih.gov > ---------------------------------------------------- > Mathematics consists of proving the most obvious thing > in the least obvious way. > -- George Polya > > > <HINReader.patch> ---------------------------------------------------- Rajarshi Guha | NIH Chemical Genomics Center http://www.rguha.net | http://ncgc.nih.gov ---------------------------------------------------- Finally I am becoming stupider no more - Paul Erdos' epitaph |
From: Yap C. W. <ph...@nu...> - 2011-09-06 02:57:49
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Dear Rajarshi, Attached are the HIN files. When using these HIN files to calculate molecular descriptors, certain descriptors such as ALogP, ATSp1-5, BCUT, cannot be calculated. Best regards, Chun Wei -----Original Message----- From: Rajarshi Guha [mailto:raj...@gm...] Sent: Tuesday, September 06, 2011 5:32 AM To: Yap Chun Wei Cc: Egon Willighagen; Rajarshi Guha; cdk...@li... Subject: Re: [Cdk-devel] HINReader error Sorry for getting to this after so long. Could you send me a HIN file for which the current code fails or is wrong. On Aug 1, 2011, at 9:58 PM, Yap Chun Wei wrote: > Hi, > > attached is the patch file. > > Best regards, > Chun Wei > > > -----Original Message----- > From: Rajarshi Guha [mailto:raj...@gm...] > Sent: Monday, August 01, 2011 12:44 PM > To: Yap Chun Wei > Cc: Egon Willighagen; Rajarshi Guha; cdk...@li... > Subject: Re: [Cdk-devel] HINReader error > > Hi, thanks for catching this. Would you mind sending a diff of your > patch? My mail client removed your formatting and so I can't see the > changes easily > > On Jul 31, 2011, at 10:28 PM, Yap Chun Wei wrote: > >> Dear Rajarshi and Egon, >> >> One of my collaborators is having trouble reading hyperchem files >> (HIN files) with CDK. As I was tracing through the code, I noticed >> that the code to identify aromatic atoms and bonds in the >> HINReader.java may not be correct. I have modified it as shown below >> (lines which were changed were highlighted in red). I am not sure >> whether this modification is correct but it is working for me so far. >> >> Best regards, >> Chun Wei >> >> case 'a': >> bo = IBond.Order.SINGLE; >> atom.setFlag(CDKConstants.ISAROMATIC, >> true); >> break; >> } >> List<Object> ar = new ArrayList<Object>(3); >> ar.add(atomSerial); >> ar.add(s); >> ar.add(bo); >> cons.add( ar ); >> } >> m.addAtom(atom); >> atomSerial++; >> line = input.readLine(); >> } >> >> // now just store all the bonds we have >> for (List<Object> ar : cons) { >> IAtom s = m.getAtom((Integer) ar.get(0)); >> IAtom e = m.getAtom((Integer) ar.get(1)); >> IBond.Order bo = (IBond.Order) ar.get(2); >> if (!isConnected(m, s, e)) >> { >> IBond newBond = null; >> if (s.getFlag(CDKConstants.ISAROMATIC) || >> e.getFlag(CDKConstants.ISAROMATIC)) >> { >> newBond = >> file.getBuilder().newInstance(IBond.class,s, e, bo); >> newBond.setFlag(CDKConstants.ISAROMATIC, >> true); >> } >> else >> { >> newBond = >> file.getBuilder().newInstance(IBond.class,s, e, bo); >> } >> m.addBond(newBond); >> } >> } >> <winmail.dat> > > ---------------------------------------------------- > Rajarshi Guha | NIH Chemical Genomics Center > http://www.rguha.net | http://ncgc.nih.gov > ---------------------------------------------------- > Mathematics consists of proving the most obvious thing > in the least obvious way. > -- George Polya > > > <HINReader.patch> ---------------------------------------------------- Rajarshi Guha | NIH Chemical Genomics Center http://www.rguha.net | http://ncgc.nih.gov ---------------------------------------------------- Finally I am becoming stupider no more - Paul Erdos' epitaph |