Re: [Rdkit-discuss] Problem of install of RDkit in Ubuntu
Dear Markus, Yes it is not their its lost. Will install again and see. Abhik Seal Indiana University Bloomington Department of Chemical Informatics abs...@indiana.edu *OSDD CHEMINFORMATICS* +18123699097 http://mypage.iu.edu/~abseal/index.htm On Tue, Jul 24, 2012 at 8:46 PM, Abhik Seal abhik1...@gmail.com wrote: Dear Greg, The error is no module named rdkit Well i am using the windows installer of ubuntu.I guess it should be problem of that. If had been path problem then should the rdkit runned and passed all test? Abhik Seal Indiana University Bloomington Department of Chemical Informatics abs...@indiana.edu *OSDD CHEMINFORMATICS* +18123699097 http://mypage.iu.edu/~abseal/index.htm On Tue, Jul 24, 2012 at 8:34 PM, Markus Sitzmann sitzm...@helix.nih.govwrote: Hi Abhik, are you maybe doing this on a virtual machine and/or are you booting Ubuntu just from an ISO image? Markus On 7/24/2012 9:32 AM, Abhik Seal wrote: Dear All, I have a peculiar problem of RDKit installation I installed RDKit in ubuntu 11.06 with all the 76 test passed and also i started working in it. But it happened three times to me that when i use RDkit after 2-3 days later then i found that it cannot recognise the command in python from rdkit import Chem showing error Which means that i again have to install RDkit ? It happened three times to me . I didn't upgraded my ubuntu but i installed some other free tools. Did anybody found this problem? Abhik Seal Indiana University Bloomington Department of Chemical Informatics abs...@indiana.edu mailto:abs...@indiana.edu *OSDD CHEMINFORMATICS* +18123699097 http://mypage.iu.edu/~abseal/index.htm -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss -- Markus Sitzmann, Ph.D. Chemical Biology Laboratory Center for Cancer Research National Cancer Institute National Institutes of Health 376 Boyles St Frederick, MD 21702, USA 301-846-5974 (office) 301-846-6033 (fax) sitzm...@helix.nih.gov http://www.linkedin.com/pub/1/7b8/342 http://www.xing.com/profile/Markus_Sitzmann -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
[Rdkit-discuss] Problem of install of RDkit in Ubuntu
Dear All, I have a peculiar problem of RDKit installation I installed RDKit in ubuntu 11.06 with all the 76 test passed and also i started working in it. But it happened three times to me that when i use RDkit after 2-3 days later then i found that it cannot recognise the command in python from rdkit import Chem showing error Which means that i again have to install RDkit ? It happened three times to me . I didn't upgraded my ubuntu but i installed some other free tools. Did anybody found this problem? Abhik Seal Indiana University Bloomington Department of Chemical Informatics abs...@indiana.edu *OSDD CHEMINFORMATICS* +18123699097 http://mypage.iu.edu/~abseal/index.htm -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Problem of install of RDkit in Ubuntu
Hi Abhik, are you maybe doing this on a virtual machine and/or are you booting Ubuntu just from an ISO image? Markus On 7/24/2012 9:32 AM, Abhik Seal wrote: Dear All, I have a peculiar problem of RDKit installation I installed RDKit in ubuntu 11.06 with all the 76 test passed and also i started working in it. But it happened three times to me that when i use RDkit after 2-3 days later then i found that it cannot recognise the command in python from rdkit import Chem showing error Which means that i again have to install RDkit ? It happened three times to me . I didn't upgraded my ubuntu but i installed some other free tools. Did anybody found this problem? Abhik Seal Indiana University Bloomington Department of Chemical Informatics abs...@indiana.edu mailto:abs...@indiana.edu *OSDD CHEMINFORMATICS* +18123699097 http://mypage.iu.edu/~abseal/index.htm -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss -- Markus Sitzmann, Ph.D. Chemical Biology Laboratory Center for Cancer Research National Cancer Institute National Institutes of Health 376 Boyles St Frederick, MD 21702, USA 301-846-5974 (office) 301-846-6033 (fax) sitzm...@helix.nih.gov http://www.linkedin.com/pub/1/7b8/342 http://www.xing.com/profile/Markus_Sitzmann -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Problem of install of RDkit in Ubuntu
Dear Greg, The error is no module named rdkit Well i am using the windows installer of ubuntu.I guess it should be problem of that. If had been path problem then should the rdkit runned and passed all test? Abhik Seal Indiana University Bloomington Department of Chemical Informatics abs...@indiana.edu *OSDD CHEMINFORMATICS* +18123699097 http://mypage.iu.edu/~abseal/index.htm On Tue, Jul 24, 2012 at 8:34 PM, Markus Sitzmann sitzm...@helix.nih.govwrote: Hi Abhik, are you maybe doing this on a virtual machine and/or are you booting Ubuntu just from an ISO image? Markus On 7/24/2012 9:32 AM, Abhik Seal wrote: Dear All, I have a peculiar problem of RDKit installation I installed RDKit in ubuntu 11.06 with all the 76 test passed and also i started working in it. But it happened three times to me that when i use RDkit after 2-3 days later then i found that it cannot recognise the command in python from rdkit import Chem showing error Which means that i again have to install RDkit ? It happened three times to me . I didn't upgraded my ubuntu but i installed some other free tools. Did anybody found this problem? Abhik Seal Indiana University Bloomington Department of Chemical Informatics abs...@indiana.edu mailto:abs...@indiana.edu *OSDD CHEMINFORMATICS* +18123699097 http://mypage.iu.edu/~abseal/index.htm -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss -- Markus Sitzmann, Ph.D. Chemical Biology Laboratory Center for Cancer Research National Cancer Institute National Institutes of Health 376 Boyles St Frederick, MD 21702, USA 301-846-5974 (office) 301-846-6033 (fax) sitzm...@helix.nih.gov http://www.linkedin.com/pub/1/7b8/342 http://www.xing.com/profile/Markus_Sitzmann -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Problem of install of RDkit in Ubuntu
Hi Abhik, I am not entirely sure how this windows installer of ubuntu works, but probably you have to make sure that you install RDkit in the right place (a directory that is actually written to the disk). Your problem is probably that you install RDKit only virtually, i.e. in a part of the directory tree that is coming from the ISO image underlying your Ubuntu installation, so RDKit is gone after each reboot (it is only present as long as your Ubuntu installation is not rebooted). Markus On 7/24/2012 11:16 AM, Abhik Seal wrote: Dear Greg, The error is no module named rdkit Well i am using the windows installer of ubuntu.I guess it should be problem of that. If had been path problem then should the rdkit runned and passed all test? Abhik Seal Indiana University Bloomington Department of Chemical Informatics abs...@indiana.edu mailto:abs...@indiana.edu *OSDD CHEMINFORMATICS* +18123699097 http://mypage.iu.edu/~abseal/index.htm On Tue, Jul 24, 2012 at 8:34 PM, Markus Sitzmann sitzm...@helix.nih.gov mailto:sitzm...@helix.nih.gov wrote: Hi Abhik, are you maybe doing this on a virtual machine and/or are you booting Ubuntu just from an ISO image? Markus On 7/24/2012 9:32 AM, Abhik Seal wrote: Dear All, I have a peculiar problem of RDKit installation I installed RDKit in ubuntu 11.06 with all the 76 test passed and also i started working in it. But it happened three times to me that when i use RDkit after 2-3 days later then i found that it cannot recognise the command in python from rdkit import Chem showing error Which means that i again have to install RDkit ? It happened three times to me . I didn't upgraded my ubuntu but i installed some other free tools. Did anybody found this problem? Abhik Seal Indiana University Bloomington Department of Chemical Informatics abs...@indiana.edu mailto:abs...@indiana.edu mailto:abs...@indiana.edu mailto:abs...@indiana.edu *OSDD CHEMINFORMATICS* +18123699097 tel:%2B18123699097 http://mypage.iu.edu/~abseal/index.htm -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net mailto:Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss -- Markus Sitzmann, Ph.D. Chemical Biology Laboratory Center for Cancer Research National Cancer Institute National Institutes of Health 376 Boyles St Frederick, MD 21702, USA 301-846-5974 tel:301-846-5974 (office) 301-846-6033 tel:301-846-6033 (fax) sitzm...@helix.nih.gov mailto:sitzm...@helix.nih.gov http://www.linkedin.com/pub/1/7b8/342 http://www.xing.com/profile/Markus_Sitzmann -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net mailto:Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss -- Markus Sitzmann, Ph.D. Chemical Biology Laboratory Center for Cancer Research National Cancer Institute National Institutes of Health 376 Boyles St Frederick, MD 21702, USA 301-846-5974 (office) 301-846-6033 (fax) sitzm...@helix.nih.gov http://www.linkedin.com/pub/1/7b8/342
Re: [Rdkit-discuss] Problem of install of RDkit in Ubuntu
Dear Markus, Well i agree then but what about other tools like cdk,open babel they are working well Abhik Seal Indiana University Bloomington Department of Chemical Informatics abs...@indiana.edu *OSDD CHEMINFORMATICS* +18123699097 http://mypage.iu.edu/~abseal/index.htm On Tue, Jul 24, 2012 at 9:31 PM, Markus Sitzmann sitzm...@helix.nih.govwrote: Hi Abhik, I am not entirely sure how this windows installer of ubuntu works, but probably you have to make sure that you install RDkit in the right place (a directory that is actually written to the disk). Your problem is probably that you install RDKit only virtually, i.e. in a part of the directory tree that is coming from the ISO image underlying your Ubuntu installation, so RDKit is gone after each reboot (it is only present as long as your Ubuntu installation is not rebooted). Markus On 7/24/2012 11:16 AM, Abhik Seal wrote: Dear Greg, The error is no module named rdkit Well i am using the windows installer of ubuntu.I guess it should be problem of that. If had been path problem then should the rdkit runned and passed all test? Abhik Seal Indiana University Bloomington Department of Chemical Informatics abs...@indiana.edu mailto:abs...@indiana.edu *OSDD CHEMINFORMATICS* +18123699097 http://mypage.iu.edu/~abseal/index.htm On Tue, Jul 24, 2012 at 8:34 PM, Markus Sitzmann sitzm...@helix.nih.gov mailto:sitzm...@helix.nih.gov wrote: Hi Abhik, are you maybe doing this on a virtual machine and/or are you booting Ubuntu just from an ISO image? Markus On 7/24/2012 9:32 AM, Abhik Seal wrote: Dear All, I have a peculiar problem of RDKit installation I installed RDKit in ubuntu 11.06 with all the 76 test passed and also i started working in it. But it happened three times to me that when i use RDkit after 2-3 days later then i found that it cannot recognise the command in python from rdkit import Chem showing error Which means that i again have to install RDkit ? It happened three times to me . I didn't upgraded my ubuntu but i installed some other free tools. Did anybody found this problem? Abhik Seal Indiana University Bloomington Department of Chemical Informatics abs...@indiana.edu mailto:abs...@indiana.edu mailto:abs...@indiana.edu mailto:abs...@indiana.edu *OSDD CHEMINFORMATICS* +18123699097 tel:%2B18123699097 http://mypage.iu.edu/~abseal/index.htm -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net mailto:Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss -- Markus Sitzmann, Ph.D. Chemical Biology Laboratory Center for Cancer Research National Cancer Institute National Institutes of Health 376 Boyles St Frederick, MD 21702, USA 301-846-5974 tel:301-846-5974 (office) 301-846-6033 tel:301-846-6033 (fax) sitzm...@helix.nih.gov mailto:sitzm...@helix.nih.gov http://www.linkedin.com/pub/1/7b8/342 http://www.xing.com/profile/Markus_Sitzmann -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net mailto:Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
Re: [Rdkit-discuss] Problem of install of RDkit in Ubuntu
Hi Abhik, well, now it is getting odd, of course, but it still could be that something got lost that way (I remember that I ran into exactly these kind problem when I was experimenting with Linux on Virtual Machines and the likes). My bet would be, that /usr/lib/python2.x/site-packages/rdkit got lost. Can you maybe try locate site-packages/rdkit on a shell, whether it finds something. Markus On 7/24/2012 12:09 PM, Abhik Seal wrote: Dear Markus, Well i agree then but what about other tools like cdk,open babel they are working well Abhik Seal Indiana University Bloomington Department of Chemical Informatics abs...@indiana.edu mailto:abs...@indiana.edu *OSDD CHEMINFORMATICS* +18123699097 http://mypage.iu.edu/~abseal/index.htm On Tue, Jul 24, 2012 at 9:31 PM, Markus Sitzmann sitzm...@helix.nih.gov mailto:sitzm...@helix.nih.gov wrote: Hi Abhik, I am not entirely sure how this windows installer of ubuntu works, but probably you have to make sure that you install RDkit in the right place (a directory that is actually written to the disk). Your problem is probably that you install RDKit only virtually, i.e. in a part of the directory tree that is coming from the ISO image underlying your Ubuntu installation, so RDKit is gone after each reboot (it is only present as long as your Ubuntu installation is not rebooted). Markus On 7/24/2012 11:16 AM, Abhik Seal wrote: Dear Greg, The error is no module named rdkit Well i am using the windows installer of ubuntu.I guess it should be problem of that. If had been path problem then should the rdkit runned and passed all test? Abhik Seal Indiana University Bloomington Department of Chemical Informatics abs...@indiana.edu mailto:abs...@indiana.edu mailto:abs...@indiana.edu mailto:abs...@indiana.edu *OSDD CHEMINFORMATICS* +18123699097 tel:%2B18123699097 http://mypage.iu.edu/~abseal/index.htm On Tue, Jul 24, 2012 at 8:34 PM, Markus Sitzmann sitzm...@helix.nih.gov mailto:sitzm...@helix.nih.gov mailto:sitzm...@helix.nih.gov mailto:sitzm...@helix.nih.gov wrote: Hi Abhik, are you maybe doing this on a virtual machine and/or are you booting Ubuntu just from an ISO image? Markus On 7/24/2012 9:32 AM, Abhik Seal wrote: Dear All, I have a peculiar problem of RDKit installation I installed RDKit in ubuntu 11.06 with all the 76 test passed and also i started working in it. But it happened three times to me that when i use RDkit after 2-3 days later then i found that it cannot recognise the command in python from rdkit import Chem showing error Which means that i again have to install RDkit ? It happened three times to me . I didn't upgraded my ubuntu but i installed some other free tools. Did anybody found this problem? Abhik Seal Indiana University Bloomington Department of Chemical Informatics abs...@indiana.edu mailto:abs...@indiana.edu mailto:abs...@indiana.edu mailto:abs...@indiana.edu mailto:abs...@indiana.edu mailto:abs...@indiana.edu mailto:abs...@indiana.edu mailto:abs...@indiana.edu *OSDD CHEMINFORMATICS* +18123699097 tel:%2B18123699097 tel:%2B18123699097 http://mypage.iu.edu/~abseal/index.htm -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net mailto:Rdkit-discuss@lists.sourceforge.net mailto:Rdkit-discuss@lists.sourceforge.net mailto:Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss -- Markus Sitzmann, Ph.D. Chemical Biology Laboratory Center for Cancer Research National Cancer Institute National Institutes of Health 376 Boyles St Frederick, MD 21702, USA 301-846-5974 tel:301-846-5974 tel:301-846-5974 tel:301-846-5974 (office) 301-846-6033 tel:301-846-6033 tel:301-846-6033
Re: [Rdkit-discuss] Problem of install of RDkit in Ubuntu
Can you specify what other free tools you installed? Some tools have a tendency to install their own python, causing problems. A common culprit for this is autodock tools. Can you run `which python` and see what python you are running? If it is not /usr/bin/python , it probably was installed by one of these tools -David On Tue, Jul 24, 2012 at 9:32 AM, Abhik Seal abhik1...@gmail.com wrote: Dear All, I have a peculiar problem of RDKit installation I installed RDKit in ubuntu 11.06 with all the 76 test passed and also i started working in it. But it happened three times to me that when i use RDkit after 2-3 days later then i found that it cannot recognise the command in python from rdkit import Chem showing error Which means that i again have to install RDkit ? It happened three times to me . I didn't upgraded my ubuntu but i installed some other free tools. Did anybody found this problem? Abhik Seal Indiana University Bloomington Department of Chemical Informatics abs...@indiana.edu OSDD CHEMINFORMATICS +18123699097 http://mypage.iu.edu/~abseal/index.htm -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
