From: Giovanni C. <gci...@gm...> - 2016-02-11 09:29:56
|
Dear all, I use CDK mainly through KNIME and I found some supposed inconsistencies using the LargestChainDescriptor. I originally posted my doubt in KNIME-CDK forum where I also provided examples: https://tech.knime.org/forum/cdk/cdk-largest-chain-descriptor-inconsistencies#comment-41502 I'm not sure about the purpose of such descriptor. Essentially my doubts are the following: 1. The LargestChainDescriptor count atoms that belong to aliphatic rings. Is that correct or it is a bug? The word "chain" in my opinion can seems opposed to the word "ring". 2. In some cases terminal atoms seems not to be counted as part of the largest chain, while in other cases they are. 3. In some cases iso terminal groups are counted as 2 while in other cases are counted as 3 4. Atoms between rings in some case to be correctly counted, while in other cases they are not Please, can anybody provide some clarification about these issues? Thanks, Gio |
From: John M <joh...@gm...> - 2016-02-11 09:57:58
|
I'll try and have a look this weekend, I must confess it's not entirely clear to me what it's meant to do (i.e. what is correct behavior) - what you've described doesn't sound intuitive. J Regards, John W May joh...@gm... On 11 February 2016 at 09:29, Giovanni Cincilla <gci...@gm...> wrote: > Dear all, > I use CDK mainly through KNIME and I found some supposed inconsistencies > using the LargestChainDescriptor. I originally posted my doubt in KNIME-CDK > forum where I also provided examples: > > > https://tech.knime.org/forum/cdk/cdk-largest-chain-descriptor-inconsistencies#comment-41502 > > I'm not sure about the purpose of such descriptor. Essentially my doubts > are the following: > > 1. The LargestChainDescriptor count atoms that belong to aliphatic > rings. Is that correct or it is a bug? The word "chain" in my opinion can > seems opposed to the word "ring". > 2. In some cases terminal atoms seems not to be counted as part of the > largest chain, while in other cases they are. > 3. In some cases iso terminal groups are counted as 2 while in other > cases are counted as 3 > 4. Atoms between rings in some case to be correctly counted, while in > other cases they are not > > Please, can anybody provide some clarification about these issues? > Thanks, > Gio > > > ------------------------------------------------------------------------------ > Site24x7 APM Insight: Get Deep Visibility into Application Performance > APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month > Monitor end-to-end web transactions and take corrective actions now > Troubleshoot faster and improve end-user experience. Signup Now! > http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140 > _______________________________________________ > Cdk-user mailing list > Cdk...@li... > https://lists.sourceforge.net/lists/listinfo/cdk-user > > |
From: Rajarshi G. <raj...@gm...> - 2016-02-11 12:18:16
|
Could you provide an example where issues 2 & 3 show up? The descriptor is meant to compute the length of the longest aliphatic chain in a molecule On Thu, Feb 11, 2016 at 4:29 AM, Giovanni Cincilla <gci...@gm...> wrote: > Dear all, > I use CDK mainly through KNIME and I found some supposed inconsistencies > using the LargestChainDescriptor. I originally posted my doubt in KNIME-CDK > forum where I also provided examples: > > > https://tech.knime.org/forum/cdk/cdk-largest-chain-descriptor-inconsistencies#comment-41502 > > I'm not sure about the purpose of such descriptor. Essentially my doubts > are the following: > > 1. The LargestChainDescriptor count atoms that belong to aliphatic > rings. Is that correct or it is a bug? The word "chain" in my opinion can > seems opposed to the word "ring". > 2. In some cases terminal atoms seems not to be counted as part of the > largest chain, while in other cases they are. > 3. In some cases iso terminal groups are counted as 2 while in other > cases are counted as 3 > 4. Atoms between rings in some case to be correctly counted, while in > other cases they are not > > Please, can anybody provide some clarification about these issues? > Thanks, > Gio > > > ------------------------------------------------------------------------------ > Site24x7 APM Insight: Get Deep Visibility into Application Performance > APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month > Monitor end-to-end web transactions and take corrective actions now > Troubleshoot faster and improve end-user experience. Signup Now! > http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140 > _______________________________________________ > Cdk-user mailing list > Cdk...@li... > https://lists.sourceforge.net/lists/listinfo/cdk-user > > -- Rajarshi Guha | http://blog.rguha.net NIH Center for Advancing Translational Science |
From: Giovanni C. <gci...@gm...> - 2016-02-11 12:50:56
|
Thank you for your quick reply. Examples are provided in the original KNIME forum thread ( https://tech.knime.org/forum/cdk/cdk-largest-chain-descriptor-inconsistencies#comment-41502), anyway I can report those here: 2. In some cases terminal atoms seems not to be counted as part of the largest chain LC (LC Row0 = 0; LC Row2 = 1), while in other cases they are (LC Row5 = 2; LC Row6 =2). 3. In some cases iso terminal groups are countes as 2 (Row4) while in other cases are counted as 3 (Row8). *Molecules:* "Row0","Cc1nn(c(c1)N)c1nc2c(s1)cccc2" "Row1","Clc1cnn(c(=O)c1Cl)Cc1[nH]c(=O)c2c(n1)c1ccccc1o2" "Row2","Nc1c(cn[nH]1)C#N" "Row3","Fc1ccc(cc1)C(=O)c1ccc(cc1)Oc1ncc(cn1)Br" "Row4","[O-][n+]1ccc(cc1)[N+](=O)[O-]" "Row5","OCc1ccccc1CN" "Row6","COc1ccc(cc1)c1noc(c1)Cn1nc(C)c(c(c1=O)C#N)C" "Row7","Cc1nc(SCc2nc3ccsc3c(=O)[nH]2)c2c(n1)scc2c1cccs1" "Row8","CC(=O)c1cccc(c1)Nc1nc(nc2c1cccc2)c1cccnc1" I hope the examples are quite clear. On Thu, Feb 11, 2016 at 1:18 PM, Rajarshi Guha <raj...@gm...> wrote: > Could you provide an example where issues 2 & 3 show up? > > The descriptor is meant to compute the length of the longest aliphatic > chain in a molecule > > On Thu, Feb 11, 2016 at 4:29 AM, Giovanni Cincilla <gci...@gm...> > wrote: > >> Dear all, >> I use CDK mainly through KNIME and I found some supposed inconsistencies >> using the LargestChainDescriptor. I originally posted my doubt in KNIME-CDK >> forum where I also provided examples: >> >> >> https://tech.knime.org/forum/cdk/cdk-largest-chain-descriptor-inconsistencies#comment-41502 >> >> I'm not sure about the purpose of such descriptor. Essentially my doubts >> are the following: >> >> 1. The LargestChainDescriptor count atoms that belong to aliphatic >> rings. Is that correct or it is a bug? The word "chain" in my opinion can >> seems opposed to the word "ring". >> 2. In some cases terminal atoms seems not to be counted as part of >> the largest chain, while in other cases they are. >> 3. In some cases iso terminal groups are counted as 2 while in other >> cases are counted as 3 >> 4. Atoms between rings in some case to be correctly counted, while in >> other cases they are not >> >> Please, can anybody provide some clarification about these issues? >> Thanks, >> Gio >> >> >> ------------------------------------------------------------------------------ >> Site24x7 APM Insight: Get Deep Visibility into Application Performance >> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month >> Monitor end-to-end web transactions and take corrective actions now >> Troubleshoot faster and improve end-user experience. Signup Now! >> http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140 >> _______________________________________________ >> Cdk-user mailing list >> Cdk...@li... >> https://lists.sourceforge.net/lists/listinfo/cdk-user >> >> > > > -- > Rajarshi Guha | http://blog.rguha.net > NIH Center for Advancing Translational Science > |
From: Rajarshi G. <raj...@gm...> - 2016-02-11 15:47:12
|
Yes, it does appear to be a bug. Inspeting the code the LargestChainDescriptor is looking for the longest path that contains non-aromatic, non-ring atoms. For Row0, there are only two non-ring, non-aromatic atoms and so there are two possible chains with a single atom, hence each chain has the value of 0. For Row2, the longest chain according to the definition is the C#N substructure, hence the value should be 2 For Row5 and Row6, the values should also be 2. I've attached a patch against master that fixes this (I wasn't sure how to make a pull request from a local branch) On Thu, Feb 11, 2016 at 7:50 AM, Giovanni Cincilla <gci...@gm...> wrote: > Thank you for your quick reply. > Examples are provided in the original KNIME forum thread ( > https://tech.knime.org/forum/cdk/cdk-largest-chain-descriptor-inconsistencies#comment-41502), > anyway I can report those here: > > 2. In some cases terminal atoms seems not to be counted as part of the > largest chain LC (LC Row0 = 0; LC Row2 = 1), while in other cases they are > (LC Row5 = 2; LC Row6 =2). > 3. In some cases iso terminal groups are countes as 2 (Row4) while in > other cases are counted as 3 (Row8). > > *Molecules:* > "Row0","Cc1nn(c(c1)N)c1nc2c(s1)cccc2" > "Row1","Clc1cnn(c(=O)c1Cl)Cc1[nH]c(=O)c2c(n1)c1ccccc1o2" > "Row2","Nc1c(cn[nH]1)C#N" > "Row3","Fc1ccc(cc1)C(=O)c1ccc(cc1)Oc1ncc(cn1)Br" > "Row4","[O-][n+]1ccc(cc1)[N+](=O)[O-]" > "Row5","OCc1ccccc1CN" > "Row6","COc1ccc(cc1)c1noc(c1)Cn1nc(C)c(c(c1=O)C#N)C" > "Row7","Cc1nc(SCc2nc3ccsc3c(=O)[nH]2)c2c(n1)scc2c1cccs1" > "Row8","CC(=O)c1cccc(c1)Nc1nc(nc2c1cccc2)c1cccnc1" > > I hope the examples are quite clear. > > On Thu, Feb 11, 2016 at 1:18 PM, Rajarshi Guha <raj...@gm...> > wrote: > >> Could you provide an example where issues 2 & 3 show up? >> >> The descriptor is meant to compute the length of the longest aliphatic >> chain in a molecule >> >> On Thu, Feb 11, 2016 at 4:29 AM, Giovanni Cincilla <gci...@gm...> >> wrote: >> >>> Dear all, >>> I use CDK mainly through KNIME and I found some supposed inconsistencies >>> using the LargestChainDescriptor. I originally posted my doubt in KNIME-CDK >>> forum where I also provided examples: >>> >>> >>> https://tech.knime.org/forum/cdk/cdk-largest-chain-descriptor-inconsistencies#comment-41502 >>> >>> I'm not sure about the purpose of such descriptor. Essentially my doubts >>> are the following: >>> >>> 1. The LargestChainDescriptor count atoms that belong to aliphatic >>> rings. Is that correct or it is a bug? The word "chain" in my opinion can >>> seems opposed to the word "ring". >>> 2. In some cases terminal atoms seems not to be counted as part of >>> the largest chain, while in other cases they are. >>> 3. In some cases iso terminal groups are counted as 2 while in other >>> cases are counted as 3 >>> 4. Atoms between rings in some case to be correctly counted, while >>> in other cases they are not >>> >>> Please, can anybody provide some clarification about these issues? >>> Thanks, >>> Gio >>> >>> >>> ------------------------------------------------------------------------------ >>> Site24x7 APM Insight: Get Deep Visibility into Application Performance >>> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month >>> Monitor end-to-end web transactions and take corrective actions now >>> Troubleshoot faster and improve end-user experience. Signup Now! >>> http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140 >>> _______________________________________________ >>> Cdk-user mailing list >>> Cdk...@li... >>> https://lists.sourceforge.net/lists/listinfo/cdk-user >>> >>> >> >> >> -- >> Rajarshi Guha | http://blog.rguha.net >> NIH Center for Advancing Translational Science >> > > -- Rajarshi Guha | http://blog.rguha.net NIH Center for Advancing Translational Science |
From: Rajarshi G. <raj...@gm...> - 2016-02-11 17:04:06
|
you can ignore the patch since I've just made a pull request with this fix On Thu, Feb 11, 2016 at 10:47 AM, Rajarshi Guha <raj...@gm...> wrote: > Yes, it does appear to be a bug. > > Inspeting the code the LargestChainDescriptor is looking for the longest > path that contains non-aromatic, non-ring atoms. > > For Row0, there are only two non-ring, non-aromatic atoms and so there > are two possible chains with a single atom, hence each chain has the value > of 0. > > For Row2, the longest chain according to the definition is the C#N > substructure, hence the value should be 2 > > For Row5 and Row6, the values should also be 2. > > I've attached a patch against master that fixes this (I wasn't sure how to > make a pull request from a local branch) > > > On Thu, Feb 11, 2016 at 7:50 AM, Giovanni Cincilla <gci...@gm...> > wrote: > >> Thank you for your quick reply. >> Examples are provided in the original KNIME forum thread ( >> https://tech.knime.org/forum/cdk/cdk-largest-chain-descriptor-inconsistencies#comment-41502), >> anyway I can report those here: >> >> 2. In some cases terminal atoms seems not to be counted as part of the >> largest chain LC (LC Row0 = 0; LC Row2 = 1), while in other cases they are >> (LC Row5 = 2; LC Row6 =2). >> 3. In some cases iso terminal groups are countes as 2 (Row4) while in >> other cases are counted as 3 (Row8). >> >> *Molecules:* >> "Row0","Cc1nn(c(c1)N)c1nc2c(s1)cccc2" >> "Row1","Clc1cnn(c(=O)c1Cl)Cc1[nH]c(=O)c2c(n1)c1ccccc1o2" >> "Row2","Nc1c(cn[nH]1)C#N" >> "Row3","Fc1ccc(cc1)C(=O)c1ccc(cc1)Oc1ncc(cn1)Br" >> "Row4","[O-][n+]1ccc(cc1)[N+](=O)[O-]" >> "Row5","OCc1ccccc1CN" >> "Row6","COc1ccc(cc1)c1noc(c1)Cn1nc(C)c(c(c1=O)C#N)C" >> "Row7","Cc1nc(SCc2nc3ccsc3c(=O)[nH]2)c2c(n1)scc2c1cccs1" >> "Row8","CC(=O)c1cccc(c1)Nc1nc(nc2c1cccc2)c1cccnc1" >> >> I hope the examples are quite clear. >> >> On Thu, Feb 11, 2016 at 1:18 PM, Rajarshi Guha <raj...@gm...> >> wrote: >> >>> Could you provide an example where issues 2 & 3 show up? >>> >>> The descriptor is meant to compute the length of the longest aliphatic >>> chain in a molecule >>> >>> On Thu, Feb 11, 2016 at 4:29 AM, Giovanni Cincilla <gci...@gm...> >>> wrote: >>> >>>> Dear all, >>>> I use CDK mainly through KNIME and I found some supposed >>>> inconsistencies using the LargestChainDescriptor. I originally posted my >>>> doubt in KNIME-CDK forum where I also provided examples: >>>> >>>> >>>> https://tech.knime.org/forum/cdk/cdk-largest-chain-descriptor-inconsistencies#comment-41502 >>>> >>>> I'm not sure about the purpose of such descriptor. Essentially my >>>> doubts are the following: >>>> >>>> 1. The LargestChainDescriptor count atoms that belong to aliphatic >>>> rings. Is that correct or it is a bug? The word "chain" in my opinion can >>>> seems opposed to the word "ring". >>>> 2. In some cases terminal atoms seems not to be counted as part of >>>> the largest chain, while in other cases they are. >>>> 3. In some cases iso terminal groups are counted as 2 while in >>>> other cases are counted as 3 >>>> 4. Atoms between rings in some case to be correctly counted, while >>>> in other cases they are not >>>> >>>> Please, can anybody provide some clarification about these issues? >>>> Thanks, >>>> Gio >>>> >>>> >>>> ------------------------------------------------------------------------------ >>>> Site24x7 APM Insight: Get Deep Visibility into Application Performance >>>> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month >>>> Monitor end-to-end web transactions and take corrective actions now >>>> Troubleshoot faster and improve end-user experience. Signup Now! >>>> http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140 >>>> _______________________________________________ >>>> Cdk-user mailing list >>>> Cdk...@li... >>>> https://lists.sourceforge.net/lists/listinfo/cdk-user >>>> >>>> >>> >>> >>> -- >>> Rajarshi Guha | http://blog.rguha.net >>> NIH Center for Advancing Translational Science >>> >> >> > > > -- > Rajarshi Guha | http://blog.rguha.net > NIH Center for Advancing Translational Science > -- Rajarshi Guha | http://blog.rguha.net NIH Center for Advancing Translational Science |
From: John M <joh...@gm...> - 2016-02-11 17:57:21
|
Cheers for patch Rajarshi, added some clean up the code: https://github.com/cdk/cdk/pull/195 but get a test failure on, "CC=CC(C)=O" expected longest path is 6 but I get 5? 5 looks correct to me? John Regards, John W May joh...@gm... On 11 February 2016 at 17:03, Rajarshi Guha <raj...@gm...> wrote: > you can ignore the patch since I've just made a pull request with this fix > > On Thu, Feb 11, 2016 at 10:47 AM, Rajarshi Guha <raj...@gm...> > wrote: > >> Yes, it does appear to be a bug. >> >> Inspeting the code the LargestChainDescriptor is looking for the longest >> path that contains non-aromatic, non-ring atoms. >> >> For Row0, there are only two non-ring, non-aromatic atoms and so there >> are two possible chains with a single atom, hence each chain has the value >> of 0. >> >> For Row2, the longest chain according to the definition is the C#N >> substructure, hence the value should be 2 >> >> For Row5 and Row6, the values should also be 2. >> >> I've attached a patch against master that fixes this (I wasn't sure how >> to make a pull request from a local branch) >> >> >> On Thu, Feb 11, 2016 at 7:50 AM, Giovanni Cincilla <gci...@gm...> >> wrote: >> >>> Thank you for your quick reply. >>> Examples are provided in the original KNIME forum thread ( >>> https://tech.knime.org/forum/cdk/cdk-largest-chain-descriptor-inconsistencies#comment-41502), >>> anyway I can report those here: >>> >>> 2. In some cases terminal atoms seems not to be counted as part of the >>> largest chain LC (LC Row0 = 0; LC Row2 = 1), while in other cases they are >>> (LC Row5 = 2; LC Row6 =2). >>> 3. In some cases iso terminal groups are countes as 2 (Row4) while in >>> other cases are counted as 3 (Row8). >>> >>> *Molecules:* >>> "Row0","Cc1nn(c(c1)N)c1nc2c(s1)cccc2" >>> "Row1","Clc1cnn(c(=O)c1Cl)Cc1[nH]c(=O)c2c(n1)c1ccccc1o2" >>> "Row2","Nc1c(cn[nH]1)C#N" >>> "Row3","Fc1ccc(cc1)C(=O)c1ccc(cc1)Oc1ncc(cn1)Br" >>> "Row4","[O-][n+]1ccc(cc1)[N+](=O)[O-]" >>> "Row5","OCc1ccccc1CN" >>> "Row6","COc1ccc(cc1)c1noc(c1)Cn1nc(C)c(c(c1=O)C#N)C" >>> "Row7","Cc1nc(SCc2nc3ccsc3c(=O)[nH]2)c2c(n1)scc2c1cccs1" >>> "Row8","CC(=O)c1cccc(c1)Nc1nc(nc2c1cccc2)c1cccnc1" >>> >>> I hope the examples are quite clear. >>> >>> On Thu, Feb 11, 2016 at 1:18 PM, Rajarshi Guha <raj...@gm...> >>> wrote: >>> >>>> Could you provide an example where issues 2 & 3 show up? >>>> >>>> The descriptor is meant to compute the length of the longest aliphatic >>>> chain in a molecule >>>> >>>> On Thu, Feb 11, 2016 at 4:29 AM, Giovanni Cincilla <gci...@gm... >>>> > wrote: >>>> >>>>> Dear all, >>>>> I use CDK mainly through KNIME and I found some supposed >>>>> inconsistencies using the LargestChainDescriptor. I originally posted my >>>>> doubt in KNIME-CDK forum where I also provided examples: >>>>> >>>>> >>>>> https://tech.knime.org/forum/cdk/cdk-largest-chain-descriptor-inconsistencies#comment-41502 >>>>> >>>>> I'm not sure about the purpose of such descriptor. Essentially my >>>>> doubts are the following: >>>>> >>>>> 1. The LargestChainDescriptor count atoms that belong to aliphatic >>>>> rings. Is that correct or it is a bug? The word "chain" in my opinion can >>>>> seems opposed to the word "ring". >>>>> 2. In some cases terminal atoms seems not to be counted as part of >>>>> the largest chain, while in other cases they are. >>>>> 3. In some cases iso terminal groups are counted as 2 while in >>>>> other cases are counted as 3 >>>>> 4. Atoms between rings in some case to be correctly counted, while >>>>> in other cases they are not >>>>> >>>>> Please, can anybody provide some clarification about these issues? >>>>> Thanks, >>>>> Gio >>>>> >>>>> >>>>> ------------------------------------------------------------------------------ >>>>> Site24x7 APM Insight: Get Deep Visibility into Application Performance >>>>> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month >>>>> Monitor end-to-end web transactions and take corrective actions now >>>>> Troubleshoot faster and improve end-user experience. Signup Now! >>>>> http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140 >>>>> _______________________________________________ >>>>> Cdk-user mailing list >>>>> Cdk...@li... >>>>> https://lists.sourceforge.net/lists/listinfo/cdk-user >>>>> >>>>> >>>> >>>> >>>> -- >>>> Rajarshi Guha | http://blog.rguha.net >>>> NIH Center for Advancing Translational Science >>>> >>> >>> >> >> >> -- >> Rajarshi Guha | http://blog.rguha.net >> NIH Center for Advancing Translational Science >> > > > > -- > Rajarshi Guha | http://blog.rguha.net > NIH Center for Advancing Translational Science > > > ------------------------------------------------------------------------------ > Site24x7 APM Insight: Get Deep Visibility into Application Performance > APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month > Monitor end-to-end web transactions and take corrective actions now > Troubleshoot faster and improve end-user experience. Signup Now! > http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140 > _______________________________________________ > Cdk-user mailing list > Cdk...@li... > https://lists.sourceforge.net/lists/listinfo/cdk-user > > |
From: Rajarshi G. <raj...@gm...> - 2016-02-11 17:58:35
|
Yes, 5 should be the value for this On Thu, Feb 11, 2016 at 12:57 PM, John M <joh...@gm...> wrote: > Cheers for patch Rajarshi, added some clean up the code: > https://github.com/cdk/cdk/pull/195 but get a test failure on, > "CC=CC(C)=O" expected longest path is 6 but I get 5? > > 5 looks correct to me? > > John > > Regards, > John W May > joh...@gm... > > On 11 February 2016 at 17:03, Rajarshi Guha <raj...@gm...> > wrote: > >> you can ignore the patch since I've just made a pull request with this fix >> >> On Thu, Feb 11, 2016 at 10:47 AM, Rajarshi Guha <raj...@gm...> >> wrote: >> >>> Yes, it does appear to be a bug. >>> >>> Inspeting the code the LargestChainDescriptor is looking for the longest >>> path that contains non-aromatic, non-ring atoms. >>> >>> For Row0, there are only two non-ring, non-aromatic atoms and so there >>> are two possible chains with a single atom, hence each chain has the value >>> of 0. >>> >>> For Row2, the longest chain according to the definition is the C#N >>> substructure, hence the value should be 2 >>> >>> For Row5 and Row6, the values should also be 2. >>> >>> I've attached a patch against master that fixes this (I wasn't sure how >>> to make a pull request from a local branch) >>> >>> >>> On Thu, Feb 11, 2016 at 7:50 AM, Giovanni Cincilla <gci...@gm...> >>> wrote: >>> >>>> Thank you for your quick reply. >>>> Examples are provided in the original KNIME forum thread ( >>>> https://tech.knime.org/forum/cdk/cdk-largest-chain-descriptor-inconsistencies#comment-41502), >>>> anyway I can report those here: >>>> >>>> 2. In some cases terminal atoms seems not to be counted as part of the >>>> largest chain LC (LC Row0 = 0; LC Row2 = 1), while in other cases they are >>>> (LC Row5 = 2; LC Row6 =2). >>>> 3. In some cases iso terminal groups are countes as 2 (Row4) while in >>>> other cases are counted as 3 (Row8). >>>> >>>> *Molecules:* >>>> "Row0","Cc1nn(c(c1)N)c1nc2c(s1)cccc2" >>>> "Row1","Clc1cnn(c(=O)c1Cl)Cc1[nH]c(=O)c2c(n1)c1ccccc1o2" >>>> "Row2","Nc1c(cn[nH]1)C#N" >>>> "Row3","Fc1ccc(cc1)C(=O)c1ccc(cc1)Oc1ncc(cn1)Br" >>>> "Row4","[O-][n+]1ccc(cc1)[N+](=O)[O-]" >>>> "Row5","OCc1ccccc1CN" >>>> "Row6","COc1ccc(cc1)c1noc(c1)Cn1nc(C)c(c(c1=O)C#N)C" >>>> "Row7","Cc1nc(SCc2nc3ccsc3c(=O)[nH]2)c2c(n1)scc2c1cccs1" >>>> "Row8","CC(=O)c1cccc(c1)Nc1nc(nc2c1cccc2)c1cccnc1" >>>> >>>> I hope the examples are quite clear. >>>> >>>> On Thu, Feb 11, 2016 at 1:18 PM, Rajarshi Guha <raj...@gm... >>>> > wrote: >>>> >>>>> Could you provide an example where issues 2 & 3 show up? >>>>> >>>>> The descriptor is meant to compute the length of the longest aliphatic >>>>> chain in a molecule >>>>> >>>>> On Thu, Feb 11, 2016 at 4:29 AM, Giovanni Cincilla < >>>>> gci...@gm...> wrote: >>>>> >>>>>> Dear all, >>>>>> I use CDK mainly through KNIME and I found some supposed >>>>>> inconsistencies using the LargestChainDescriptor. I originally posted my >>>>>> doubt in KNIME-CDK forum where I also provided examples: >>>>>> >>>>>> >>>>>> https://tech.knime.org/forum/cdk/cdk-largest-chain-descriptor-inconsistencies#comment-41502 >>>>>> >>>>>> I'm not sure about the purpose of such descriptor. Essentially my >>>>>> doubts are the following: >>>>>> >>>>>> 1. The LargestChainDescriptor count atoms that belong to >>>>>> aliphatic rings. Is that correct or it is a bug? The word "chain" in my >>>>>> opinion can seems opposed to the word "ring". >>>>>> 2. In some cases terminal atoms seems not to be counted as part >>>>>> of the largest chain, while in other cases they are. >>>>>> 3. In some cases iso terminal groups are counted as 2 while in >>>>>> other cases are counted as 3 >>>>>> 4. Atoms between rings in some case to be correctly counted, >>>>>> while in other cases they are not >>>>>> >>>>>> Please, can anybody provide some clarification about these issues? >>>>>> Thanks, >>>>>> Gio >>>>>> >>>>>> >>>>>> ------------------------------------------------------------------------------ >>>>>> Site24x7 APM Insight: Get Deep Visibility into Application Performance >>>>>> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month >>>>>> Monitor end-to-end web transactions and take corrective actions now >>>>>> Troubleshoot faster and improve end-user experience. Signup Now! >>>>>> http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140 >>>>>> _______________________________________________ >>>>>> Cdk-user mailing list >>>>>> Cdk...@li... >>>>>> https://lists.sourceforge.net/lists/listinfo/cdk-user >>>>>> >>>>>> >>>>> >>>>> >>>>> -- >>>>> Rajarshi Guha | http://blog.rguha.net >>>>> NIH Center for Advancing Translational Science >>>>> >>>> >>>> >>> >>> >>> -- >>> Rajarshi Guha | http://blog.rguha.net >>> NIH Center for Advancing Translational Science >>> >> >> >> >> -- >> Rajarshi Guha | http://blog.rguha.net >> NIH Center for Advancing Translational Science >> >> >> ------------------------------------------------------------------------------ >> Site24x7 APM Insight: Get Deep Visibility into Application Performance >> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month >> Monitor end-to-end web transactions and take corrective actions now >> Troubleshoot faster and improve end-user experience. Signup Now! >> http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140 >> _______________________________________________ >> Cdk-user mailing list >> Cdk...@li... >> https://lists.sourceforge.net/lists/listinfo/cdk-user >> >> > -- Rajarshi Guha | http://blog.rguha.net NIH Center for Advancing Translational Science |
From: John M <joh...@gm...> - 2016-02-11 18:06:25
|
Hmm.. should we deprecate one of LargestChainDescriptor or LongestAliphaticChainDescriptor? Same purpose as far as I can set. John Regards, John W May joh...@gm... On 11 February 2016 at 17:58, Rajarshi Guha <raj...@gm...> wrote: > Yes, 5 should be the value for this > > On Thu, Feb 11, 2016 at 12:57 PM, John M <joh...@gm...> > wrote: > >> Cheers for patch Rajarshi, added some clean up the code: >> https://github.com/cdk/cdk/pull/195 but get a test failure on, >> "CC=CC(C)=O" expected longest path is 6 but I get 5? >> >> 5 looks correct to me? >> >> John >> >> Regards, >> John W May >> joh...@gm... >> >> On 11 February 2016 at 17:03, Rajarshi Guha <raj...@gm...> >> wrote: >> >>> you can ignore the patch since I've just made a pull request with this >>> fix >>> >>> On Thu, Feb 11, 2016 at 10:47 AM, Rajarshi Guha <raj...@gm... >>> > wrote: >>> >>>> Yes, it does appear to be a bug. >>>> >>>> Inspeting the code the LargestChainDescriptor is looking for the >>>> longest path that contains non-aromatic, non-ring atoms. >>>> >>>> For Row0, there are only two non-ring, non-aromatic atoms and so there >>>> are two possible chains with a single atom, hence each chain has the value >>>> of 0. >>>> >>>> For Row2, the longest chain according to the definition is the C#N >>>> substructure, hence the value should be 2 >>>> >>>> For Row5 and Row6, the values should also be 2. >>>> >>>> I've attached a patch against master that fixes this (I wasn't sure how >>>> to make a pull request from a local branch) >>>> >>>> >>>> On Thu, Feb 11, 2016 at 7:50 AM, Giovanni Cincilla <gci...@gm... >>>> > wrote: >>>> >>>>> Thank you for your quick reply. >>>>> Examples are provided in the original KNIME forum thread ( >>>>> https://tech.knime.org/forum/cdk/cdk-largest-chain-descriptor-inconsistencies#comment-41502), >>>>> anyway I can report those here: >>>>> >>>>> 2. In some cases terminal atoms seems not to be counted as part of >>>>> the largest chain LC (LC Row0 = 0; LC Row2 = 1), while in other cases they >>>>> are (LC Row5 = 2; LC Row6 =2). >>>>> 3. In some cases iso terminal groups are countes as 2 (Row4) while in >>>>> other cases are counted as 3 (Row8). >>>>> >>>>> *Molecules:* >>>>> "Row0","Cc1nn(c(c1)N)c1nc2c(s1)cccc2" >>>>> "Row1","Clc1cnn(c(=O)c1Cl)Cc1[nH]c(=O)c2c(n1)c1ccccc1o2" >>>>> "Row2","Nc1c(cn[nH]1)C#N" >>>>> "Row3","Fc1ccc(cc1)C(=O)c1ccc(cc1)Oc1ncc(cn1)Br" >>>>> "Row4","[O-][n+]1ccc(cc1)[N+](=O)[O-]" >>>>> "Row5","OCc1ccccc1CN" >>>>> "Row6","COc1ccc(cc1)c1noc(c1)Cn1nc(C)c(c(c1=O)C#N)C" >>>>> "Row7","Cc1nc(SCc2nc3ccsc3c(=O)[nH]2)c2c(n1)scc2c1cccs1" >>>>> "Row8","CC(=O)c1cccc(c1)Nc1nc(nc2c1cccc2)c1cccnc1" >>>>> >>>>> I hope the examples are quite clear. >>>>> >>>>> On Thu, Feb 11, 2016 at 1:18 PM, Rajarshi Guha < >>>>> raj...@gm...> wrote: >>>>> >>>>>> Could you provide an example where issues 2 & 3 show up? >>>>>> >>>>>> The descriptor is meant to compute the length of the longest >>>>>> aliphatic chain in a molecule >>>>>> >>>>>> On Thu, Feb 11, 2016 at 4:29 AM, Giovanni Cincilla < >>>>>> gci...@gm...> wrote: >>>>>> >>>>>>> Dear all, >>>>>>> I use CDK mainly through KNIME and I found some supposed >>>>>>> inconsistencies using the LargestChainDescriptor. I originally posted my >>>>>>> doubt in KNIME-CDK forum where I also provided examples: >>>>>>> >>>>>>> >>>>>>> https://tech.knime.org/forum/cdk/cdk-largest-chain-descriptor-inconsistencies#comment-41502 >>>>>>> >>>>>>> I'm not sure about the purpose of such descriptor. Essentially my >>>>>>> doubts are the following: >>>>>>> >>>>>>> 1. The LargestChainDescriptor count atoms that belong to >>>>>>> aliphatic rings. Is that correct or it is a bug? The word "chain" in my >>>>>>> opinion can seems opposed to the word "ring". >>>>>>> 2. In some cases terminal atoms seems not to be counted as part >>>>>>> of the largest chain, while in other cases they are. >>>>>>> 3. In some cases iso terminal groups are counted as 2 while in >>>>>>> other cases are counted as 3 >>>>>>> 4. Atoms between rings in some case to be correctly counted, >>>>>>> while in other cases they are not >>>>>>> >>>>>>> Please, can anybody provide some clarification about these issues? >>>>>>> Thanks, >>>>>>> Gio >>>>>>> >>>>>>> >>>>>>> ------------------------------------------------------------------------------ >>>>>>> Site24x7 APM Insight: Get Deep Visibility into Application >>>>>>> Performance >>>>>>> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month >>>>>>> Monitor end-to-end web transactions and take corrective actions now >>>>>>> Troubleshoot faster and improve end-user experience. Signup Now! >>>>>>> http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140 >>>>>>> _______________________________________________ >>>>>>> Cdk-user mailing list >>>>>>> Cdk...@li... >>>>>>> https://lists.sourceforge.net/lists/listinfo/cdk-user >>>>>>> >>>>>>> >>>>>> >>>>>> >>>>>> -- >>>>>> Rajarshi Guha | http://blog.rguha.net >>>>>> NIH Center for Advancing Translational Science >>>>>> >>>>> >>>>> >>>> >>>> >>>> -- >>>> Rajarshi Guha | http://blog.rguha.net >>>> NIH Center for Advancing Translational Science >>>> >>> >>> >>> >>> -- >>> Rajarshi Guha | http://blog.rguha.net >>> NIH Center for Advancing Translational Science >>> >>> >>> ------------------------------------------------------------------------------ >>> Site24x7 APM Insight: Get Deep Visibility into Application Performance >>> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month >>> Monitor end-to-end web transactions and take corrective actions now >>> Troubleshoot faster and improve end-user experience. Signup Now! >>> http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140 >>> _______________________________________________ >>> Cdk-user mailing list >>> Cdk...@li... >>> https://lists.sourceforge.net/lists/listinfo/cdk-user >>> >>> >> > > > -- > Rajarshi Guha | http://blog.rguha.net > NIH Center for Advancing Translational Science > |
From: Rajarshi G. <raj...@gm...> - 2016-02-11 18:10:43
|
well the first looks at all atoms, the other only considers carbon chains. I'd say keep them both in for now (though the first could be parametrized on element, in which case we'd only need one) On Thu, Feb 11, 2016 at 1:06 PM, John M <joh...@gm...> wrote: > Hmm.. should we deprecate one of LargestChainDescriptor > or LongestAliphaticChainDescriptor? Same purpose as far as I can set. > > John > > Regards, > John W May > joh...@gm... > > On 11 February 2016 at 17:58, Rajarshi Guha <raj...@gm...> > wrote: > >> Yes, 5 should be the value for this >> >> On Thu, Feb 11, 2016 at 12:57 PM, John M <joh...@gm...> >> wrote: >> >>> Cheers for patch Rajarshi, added some clean up the code: >>> https://github.com/cdk/cdk/pull/195 but get a test failure on, >>> "CC=CC(C)=O" expected longest path is 6 but I get 5? >>> >>> 5 looks correct to me? >>> >>> John >>> >>> Regards, >>> John W May >>> joh...@gm... >>> >>> On 11 February 2016 at 17:03, Rajarshi Guha <raj...@gm...> >>> wrote: >>> >>>> you can ignore the patch since I've just made a pull request with this >>>> fix >>>> >>>> On Thu, Feb 11, 2016 at 10:47 AM, Rajarshi Guha < >>>> raj...@gm...> wrote: >>>> >>>>> Yes, it does appear to be a bug. >>>>> >>>>> Inspeting the code the LargestChainDescriptor is looking for the >>>>> longest path that contains non-aromatic, non-ring atoms. >>>>> >>>>> For Row0, there are only two non-ring, non-aromatic atoms and so >>>>> there are two possible chains with a single atom, hence each chain has the >>>>> value of 0. >>>>> >>>>> For Row2, the longest chain according to the definition is the C#N >>>>> substructure, hence the value should be 2 >>>>> >>>>> For Row5 and Row6, the values should also be 2. >>>>> >>>>> I've attached a patch against master that fixes this (I wasn't sure >>>>> how to make a pull request from a local branch) >>>>> >>>>> >>>>> On Thu, Feb 11, 2016 at 7:50 AM, Giovanni Cincilla < >>>>> gci...@gm...> wrote: >>>>> >>>>>> Thank you for your quick reply. >>>>>> Examples are provided in the original KNIME forum thread ( >>>>>> https://tech.knime.org/forum/cdk/cdk-largest-chain-descriptor-inconsistencies#comment-41502), >>>>>> anyway I can report those here: >>>>>> >>>>>> 2. In some cases terminal atoms seems not to be counted as part of >>>>>> the largest chain LC (LC Row0 = 0; LC Row2 = 1), while in other cases they >>>>>> are (LC Row5 = 2; LC Row6 =2). >>>>>> 3. In some cases iso terminal groups are countes as 2 (Row4) while >>>>>> in other cases are counted as 3 (Row8). >>>>>> >>>>>> *Molecules:* >>>>>> "Row0","Cc1nn(c(c1)N)c1nc2c(s1)cccc2" >>>>>> "Row1","Clc1cnn(c(=O)c1Cl)Cc1[nH]c(=O)c2c(n1)c1ccccc1o2" >>>>>> "Row2","Nc1c(cn[nH]1)C#N" >>>>>> "Row3","Fc1ccc(cc1)C(=O)c1ccc(cc1)Oc1ncc(cn1)Br" >>>>>> "Row4","[O-][n+]1ccc(cc1)[N+](=O)[O-]" >>>>>> "Row5","OCc1ccccc1CN" >>>>>> "Row6","COc1ccc(cc1)c1noc(c1)Cn1nc(C)c(c(c1=O)C#N)C" >>>>>> "Row7","Cc1nc(SCc2nc3ccsc3c(=O)[nH]2)c2c(n1)scc2c1cccs1" >>>>>> "Row8","CC(=O)c1cccc(c1)Nc1nc(nc2c1cccc2)c1cccnc1" >>>>>> >>>>>> I hope the examples are quite clear. >>>>>> >>>>>> On Thu, Feb 11, 2016 at 1:18 PM, Rajarshi Guha < >>>>>> raj...@gm...> wrote: >>>>>> >>>>>>> Could you provide an example where issues 2 & 3 show up? >>>>>>> >>>>>>> The descriptor is meant to compute the length of the longest >>>>>>> aliphatic chain in a molecule >>>>>>> >>>>>>> On Thu, Feb 11, 2016 at 4:29 AM, Giovanni Cincilla < >>>>>>> gci...@gm...> wrote: >>>>>>> >>>>>>>> Dear all, >>>>>>>> I use CDK mainly through KNIME and I found some supposed >>>>>>>> inconsistencies using the LargestChainDescriptor. I originally posted my >>>>>>>> doubt in KNIME-CDK forum where I also provided examples: >>>>>>>> >>>>>>>> >>>>>>>> https://tech.knime.org/forum/cdk/cdk-largest-chain-descriptor-inconsistencies#comment-41502 >>>>>>>> >>>>>>>> I'm not sure about the purpose of such descriptor. Essentially my >>>>>>>> doubts are the following: >>>>>>>> >>>>>>>> 1. The LargestChainDescriptor count atoms that belong to >>>>>>>> aliphatic rings. Is that correct or it is a bug? The word "chain" in my >>>>>>>> opinion can seems opposed to the word "ring". >>>>>>>> 2. In some cases terminal atoms seems not to be counted as part >>>>>>>> of the largest chain, while in other cases they are. >>>>>>>> 3. In some cases iso terminal groups are counted as 2 while in >>>>>>>> other cases are counted as 3 >>>>>>>> 4. Atoms between rings in some case to be correctly counted, >>>>>>>> while in other cases they are not >>>>>>>> >>>>>>>> Please, can anybody provide some clarification about these issues? >>>>>>>> Thanks, >>>>>>>> Gio >>>>>>>> >>>>>>>> >>>>>>>> ------------------------------------------------------------------------------ >>>>>>>> Site24x7 APM Insight: Get Deep Visibility into Application >>>>>>>> Performance >>>>>>>> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month >>>>>>>> Monitor end-to-end web transactions and take corrective actions now >>>>>>>> Troubleshoot faster and improve end-user experience. Signup Now! >>>>>>>> http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140 >>>>>>>> _______________________________________________ >>>>>>>> Cdk-user mailing list >>>>>>>> Cdk...@li... >>>>>>>> https://lists.sourceforge.net/lists/listinfo/cdk-user >>>>>>>> >>>>>>>> >>>>>>> >>>>>>> >>>>>>> -- >>>>>>> Rajarshi Guha | http://blog.rguha.net >>>>>>> NIH Center for Advancing Translational Science >>>>>>> >>>>>> >>>>>> >>>>> >>>>> >>>>> -- >>>>> Rajarshi Guha | http://blog.rguha.net >>>>> NIH Center for Advancing Translational Science >>>>> >>>> >>>> >>>> >>>> -- >>>> Rajarshi Guha | http://blog.rguha.net >>>> NIH Center for Advancing Translational Science >>>> >>>> >>>> ------------------------------------------------------------------------------ >>>> Site24x7 APM Insight: Get Deep Visibility into Application Performance >>>> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month >>>> Monitor end-to-end web transactions and take corrective actions now >>>> Troubleshoot faster and improve end-user experience. Signup Now! >>>> http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140 >>>> _______________________________________________ >>>> Cdk-user mailing list >>>> Cdk...@li... >>>> https://lists.sourceforge.net/lists/listinfo/cdk-user >>>> >>>> >>> >> >> >> -- >> Rajarshi Guha | http://blog.rguha.net >> NIH Center for Advancing Translational Science >> > > -- Rajarshi Guha | http://blog.rguha.net NIH Center for Advancing Translational Science |
From: Giovanni C. <gci...@gm...> - 2016-02-12 19:20:09
|
Very good guys! You are great. So I suppose the bug-free version will be available in the next CDK release, isn't it? Can you please me specify which version it will be? Please can you also confirm me that the purpose of the LargestChainDescriptor is to provide the longest path that contains non-aromatic, non-ring atoms? In other words: should the parameter *checkRingSystem* always be set = true in this description. I'm asking you this because it seems that in the current KNIME-CDK version this is currently not the case. Thank you in advance for your feedback! Gio On Thu, Feb 11, 2016 at 7:10 PM, Rajarshi Guha <raj...@gm...> wrote: > well the first looks at all atoms, the other only considers carbon chains. > > I'd say keep them both in for now (though the first could be parametrized > on element, in which case we'd only need one) > > On Thu, Feb 11, 2016 at 1:06 PM, John M <joh...@gm...> > wrote: > >> Hmm.. should we deprecate one of LargestChainDescriptor >> or LongestAliphaticChainDescriptor? Same purpose as far as I can set. >> >> John >> >> Regards, >> John W May >> joh...@gm... >> >> On 11 February 2016 at 17:58, Rajarshi Guha <raj...@gm...> >> wrote: >> >>> Yes, 5 should be the value for this >>> >>> On Thu, Feb 11, 2016 at 12:57 PM, John M <joh...@gm...> >>> wrote: >>> >>>> Cheers for patch Rajarshi, added some clean up the code: >>>> https://github.com/cdk/cdk/pull/195 but get a test failure on, >>>> "CC=CC(C)=O" expected longest path is 6 but I get 5? >>>> >>>> 5 looks correct to me? >>>> >>>> John >>>> >>>> Regards, >>>> John W May >>>> joh...@gm... >>>> >>>> On 11 February 2016 at 17:03, Rajarshi Guha <raj...@gm...> >>>> wrote: >>>> >>>>> you can ignore the patch since I've just made a pull request with this >>>>> fix >>>>> >>>>> On Thu, Feb 11, 2016 at 10:47 AM, Rajarshi Guha < >>>>> raj...@gm...> wrote: >>>>> >>>>>> Yes, it does appear to be a bug. >>>>>> >>>>>> Inspeting the code the LargestChainDescriptor is looking for the >>>>>> longest path that contains non-aromatic, non-ring atoms. >>>>>> >>>>>> For Row0, there are only two non-ring, non-aromatic atoms and so >>>>>> there are two possible chains with a single atom, hence each chain has the >>>>>> value of 0. >>>>>> >>>>>> For Row2, the longest chain according to the definition is the C#N >>>>>> substructure, hence the value should be 2 >>>>>> >>>>>> For Row5 and Row6, the values should also be 2. >>>>>> >>>>>> I've attached a patch against master that fixes this (I wasn't sure >>>>>> how to make a pull request from a local branch) >>>>>> >>>>>> >>>>>> On Thu, Feb 11, 2016 at 7:50 AM, Giovanni Cincilla < >>>>>> gci...@gm...> wrote: >>>>>> >>>>>>> Thank you for your quick reply. >>>>>>> Examples are provided in the original KNIME forum thread ( >>>>>>> https://tech.knime.org/forum/cdk/cdk-largest-chain-descriptor-inconsistencies#comment-41502), >>>>>>> anyway I can report those here: >>>>>>> >>>>>>> 2. In some cases terminal atoms seems not to be counted as part of >>>>>>> the largest chain LC (LC Row0 = 0; LC Row2 = 1), while in other cases they >>>>>>> are (LC Row5 = 2; LC Row6 =2). >>>>>>> 3. In some cases iso terminal groups are countes as 2 (Row4) while >>>>>>> in other cases are counted as 3 (Row8). >>>>>>> >>>>>>> *Molecules:* >>>>>>> "Row0","Cc1nn(c(c1)N)c1nc2c(s1)cccc2" >>>>>>> "Row1","Clc1cnn(c(=O)c1Cl)Cc1[nH]c(=O)c2c(n1)c1ccccc1o2" >>>>>>> "Row2","Nc1c(cn[nH]1)C#N" >>>>>>> "Row3","Fc1ccc(cc1)C(=O)c1ccc(cc1)Oc1ncc(cn1)Br" >>>>>>> "Row4","[O-][n+]1ccc(cc1)[N+](=O)[O-]" >>>>>>> "Row5","OCc1ccccc1CN" >>>>>>> "Row6","COc1ccc(cc1)c1noc(c1)Cn1nc(C)c(c(c1=O)C#N)C" >>>>>>> "Row7","Cc1nc(SCc2nc3ccsc3c(=O)[nH]2)c2c(n1)scc2c1cccs1" >>>>>>> "Row8","CC(=O)c1cccc(c1)Nc1nc(nc2c1cccc2)c1cccnc1" >>>>>>> >>>>>>> I hope the examples are quite clear. >>>>>>> >>>>>>> On Thu, Feb 11, 2016 at 1:18 PM, Rajarshi Guha < >>>>>>> raj...@gm...> wrote: >>>>>>> >>>>>>>> Could you provide an example where issues 2 & 3 show up? >>>>>>>> >>>>>>>> The descriptor is meant to compute the length of the longest >>>>>>>> aliphatic chain in a molecule >>>>>>>> >>>>>>>> On Thu, Feb 11, 2016 at 4:29 AM, Giovanni Cincilla < >>>>>>>> gci...@gm...> wrote: >>>>>>>> >>>>>>>>> Dear all, >>>>>>>>> I use CDK mainly through KNIME and I found some supposed >>>>>>>>> inconsistencies using the LargestChainDescriptor. I originally posted my >>>>>>>>> doubt in KNIME-CDK forum where I also provided examples: >>>>>>>>> >>>>>>>>> >>>>>>>>> https://tech.knime.org/forum/cdk/cdk-largest-chain-descriptor-inconsistencies#comment-41502 >>>>>>>>> >>>>>>>>> I'm not sure about the purpose of such descriptor. Essentially my >>>>>>>>> doubts are the following: >>>>>>>>> >>>>>>>>> 1. The LargestChainDescriptor count atoms that belong to >>>>>>>>> aliphatic rings. Is that correct or it is a bug? The word "chain" in my >>>>>>>>> opinion can seems opposed to the word "ring". >>>>>>>>> 2. In some cases terminal atoms seems not to be counted as >>>>>>>>> part of the largest chain, while in other cases they are. >>>>>>>>> 3. In some cases iso terminal groups are counted as 2 while in >>>>>>>>> other cases are counted as 3 >>>>>>>>> 4. Atoms between rings in some case to be correctly counted, >>>>>>>>> while in other cases they are not >>>>>>>>> >>>>>>>>> Please, can anybody provide some clarification about these issues? >>>>>>>>> Thanks, >>>>>>>>> Gio >>>>>>>>> >>>>>>>>> >>>>>>>>> ------------------------------------------------------------------------------ >>>>>>>>> Site24x7 APM Insight: Get Deep Visibility into Application >>>>>>>>> Performance >>>>>>>>> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month >>>>>>>>> Monitor end-to-end web transactions and take corrective actions now >>>>>>>>> Troubleshoot faster and improve end-user experience. Signup Now! >>>>>>>>> http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140 >>>>>>>>> _______________________________________________ >>>>>>>>> Cdk-user mailing list >>>>>>>>> Cdk...@li... >>>>>>>>> https://lists.sourceforge.net/lists/listinfo/cdk-user >>>>>>>>> >>>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> -- >>>>>>>> Rajarshi Guha | http://blog.rguha.net >>>>>>>> NIH Center for Advancing Translational Science >>>>>>>> >>>>>>> >>>>>>> >>>>>> >>>>>> >>>>>> -- >>>>>> Rajarshi Guha | http://blog.rguha.net >>>>>> NIH Center for Advancing Translational Science >>>>>> >>>>> >>>>> >>>>> >>>>> -- >>>>> Rajarshi Guha | http://blog.rguha.net >>>>> NIH Center for Advancing Translational Science >>>>> >>>>> >>>>> ------------------------------------------------------------------------------ >>>>> Site24x7 APM Insight: Get Deep Visibility into Application Performance >>>>> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month >>>>> Monitor end-to-end web transactions and take corrective actions now >>>>> Troubleshoot faster and improve end-user experience. Signup Now! >>>>> http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140 >>>>> _______________________________________________ >>>>> Cdk-user mailing list >>>>> Cdk...@li... >>>>> https://lists.sourceforge.net/lists/listinfo/cdk-user >>>>> >>>>> >>>> >>> >>> >>> -- >>> Rajarshi Guha | http://blog.rguha.net >>> NIH Center for Advancing Translational Science >>> >> >> > > > -- > Rajarshi Guha | http://blog.rguha.net > NIH Center for Advancing Translational Science > |
From: John M <joh...@gm...> - 2016-02-12 19:53:13
|
Hi Gio, Next release is 1.5.13. Probably do it soon, not a huge number of changes but I know a few patches people are waiting (this now being added as one of them). Please can you also confirm me that the purpose > of the LargestChainDescriptor is to provide the longest path that contains > non-aromatic, non-ring atoms? Yes... but it now no longer checks aromaticity. Since an atom is only aromatic if it's in a ring we just need to check the non-ring atoms. John Regards, John W May joh...@gm... On 12 February 2016 at 19:20, Giovanni Cincilla <gci...@gm...> wrote: > Very good guys! You are great. So I suppose the bug-free version will be > available in the next CDK release, isn't it? Can you please me specify > which version it will be? > Please can you also confirm me that the purpose > of the LargestChainDescriptor is to provide the longest path that contains > non-aromatic, non-ring atoms? In other words: should the parameter > *checkRingSystem* always be set = true in this description. I'm asking > you this because it seems that in the current KNIME-CDK version this is > currently not the case. > Thank you in advance for your feedback! > Gio > > On Thu, Feb 11, 2016 at 7:10 PM, Rajarshi Guha <raj...@gm...> > wrote: > >> well the first looks at all atoms, the other only considers carbon chains. >> >> I'd say keep them both in for now (though the first could be parametrized >> on element, in which case we'd only need one) >> >> On Thu, Feb 11, 2016 at 1:06 PM, John M <joh...@gm...> >> wrote: >> >>> Hmm.. should we deprecate one of LargestChainDescriptor >>> or LongestAliphaticChainDescriptor? Same purpose as far as I can set. >>> >>> John >>> >>> Regards, >>> John W May >>> joh...@gm... >>> >>> On 11 February 2016 at 17:58, Rajarshi Guha <raj...@gm...> >>> wrote: >>> >>>> Yes, 5 should be the value for this >>>> >>>> On Thu, Feb 11, 2016 at 12:57 PM, John M <joh...@gm...> >>>> wrote: >>>> >>>>> Cheers for patch Rajarshi, added some clean up the code: >>>>> https://github.com/cdk/cdk/pull/195 but get a test failure on, >>>>> "CC=CC(C)=O" expected longest path is 6 but I get 5? >>>>> >>>>> 5 looks correct to me? >>>>> >>>>> John >>>>> >>>>> Regards, >>>>> John W May >>>>> joh...@gm... >>>>> >>>>> On 11 February 2016 at 17:03, Rajarshi Guha <raj...@gm...> >>>>> wrote: >>>>> >>>>>> you can ignore the patch since I've just made a pull request with >>>>>> this fix >>>>>> >>>>>> On Thu, Feb 11, 2016 at 10:47 AM, Rajarshi Guha < >>>>>> raj...@gm...> wrote: >>>>>> >>>>>>> Yes, it does appear to be a bug. >>>>>>> >>>>>>> Inspeting the code the LargestChainDescriptor is looking for the >>>>>>> longest path that contains non-aromatic, non-ring atoms. >>>>>>> >>>>>>> For Row0, there are only two non-ring, non-aromatic atoms and so >>>>>>> there are two possible chains with a single atom, hence each chain has the >>>>>>> value of 0. >>>>>>> >>>>>>> For Row2, the longest chain according to the definition is the C#N >>>>>>> substructure, hence the value should be 2 >>>>>>> >>>>>>> For Row5 and Row6, the values should also be 2. >>>>>>> >>>>>>> I've attached a patch against master that fixes this (I wasn't sure >>>>>>> how to make a pull request from a local branch) >>>>>>> >>>>>>> >>>>>>> On Thu, Feb 11, 2016 at 7:50 AM, Giovanni Cincilla < >>>>>>> gci...@gm...> wrote: >>>>>>> >>>>>>>> Thank you for your quick reply. >>>>>>>> Examples are provided in the original KNIME forum thread ( >>>>>>>> https://tech.knime.org/forum/cdk/cdk-largest-chain-descriptor-inconsistencies#comment-41502), >>>>>>>> anyway I can report those here: >>>>>>>> >>>>>>>> 2. In some cases terminal atoms seems not to be counted as part of >>>>>>>> the largest chain LC (LC Row0 = 0; LC Row2 = 1), while in other cases they >>>>>>>> are (LC Row5 = 2; LC Row6 =2). >>>>>>>> 3. In some cases iso terminal groups are countes as 2 (Row4) while >>>>>>>> in other cases are counted as 3 (Row8). >>>>>>>> >>>>>>>> *Molecules:* >>>>>>>> "Row0","Cc1nn(c(c1)N)c1nc2c(s1)cccc2" >>>>>>>> "Row1","Clc1cnn(c(=O)c1Cl)Cc1[nH]c(=O)c2c(n1)c1ccccc1o2" >>>>>>>> "Row2","Nc1c(cn[nH]1)C#N" >>>>>>>> "Row3","Fc1ccc(cc1)C(=O)c1ccc(cc1)Oc1ncc(cn1)Br" >>>>>>>> "Row4","[O-][n+]1ccc(cc1)[N+](=O)[O-]" >>>>>>>> "Row5","OCc1ccccc1CN" >>>>>>>> "Row6","COc1ccc(cc1)c1noc(c1)Cn1nc(C)c(c(c1=O)C#N)C" >>>>>>>> "Row7","Cc1nc(SCc2nc3ccsc3c(=O)[nH]2)c2c(n1)scc2c1cccs1" >>>>>>>> "Row8","CC(=O)c1cccc(c1)Nc1nc(nc2c1cccc2)c1cccnc1" >>>>>>>> >>>>>>>> I hope the examples are quite clear. >>>>>>>> >>>>>>>> On Thu, Feb 11, 2016 at 1:18 PM, Rajarshi Guha < >>>>>>>> raj...@gm...> wrote: >>>>>>>> >>>>>>>>> Could you provide an example where issues 2 & 3 show up? >>>>>>>>> >>>>>>>>> The descriptor is meant to compute the length of the longest >>>>>>>>> aliphatic chain in a molecule >>>>>>>>> >>>>>>>>> On Thu, Feb 11, 2016 at 4:29 AM, Giovanni Cincilla < >>>>>>>>> gci...@gm...> wrote: >>>>>>>>> >>>>>>>>>> Dear all, >>>>>>>>>> I use CDK mainly through KNIME and I found some supposed >>>>>>>>>> inconsistencies using the LargestChainDescriptor. I originally posted my >>>>>>>>>> doubt in KNIME-CDK forum where I also provided examples: >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> https://tech.knime.org/forum/cdk/cdk-largest-chain-descriptor-inconsistencies#comment-41502 >>>>>>>>>> >>>>>>>>>> I'm not sure about the purpose of such descriptor. Essentially my >>>>>>>>>> doubts are the following: >>>>>>>>>> >>>>>>>>>> 1. The LargestChainDescriptor count atoms that belong to >>>>>>>>>> aliphatic rings. Is that correct or it is a bug? The word "chain" in my >>>>>>>>>> opinion can seems opposed to the word "ring". >>>>>>>>>> 2. In some cases terminal atoms seems not to be counted as >>>>>>>>>> part of the largest chain, while in other cases they are. >>>>>>>>>> 3. In some cases iso terminal groups are counted as 2 while >>>>>>>>>> in other cases are counted as 3 >>>>>>>>>> 4. Atoms between rings in some case to be correctly counted, >>>>>>>>>> while in other cases they are not >>>>>>>>>> >>>>>>>>>> Please, can anybody provide some clarification about these issues? >>>>>>>>>> Thanks, >>>>>>>>>> Gio >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> ------------------------------------------------------------------------------ >>>>>>>>>> Site24x7 APM Insight: Get Deep Visibility into Application >>>>>>>>>> Performance >>>>>>>>>> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month >>>>>>>>>> Monitor end-to-end web transactions and take corrective actions >>>>>>>>>> now >>>>>>>>>> Troubleshoot faster and improve end-user experience. Signup Now! >>>>>>>>>> http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140 >>>>>>>>>> _______________________________________________ >>>>>>>>>> Cdk-user mailing list >>>>>>>>>> Cdk...@li... >>>>>>>>>> https://lists.sourceforge.net/lists/listinfo/cdk-user >>>>>>>>>> >>>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> -- >>>>>>>>> Rajarshi Guha | http://blog.rguha.net >>>>>>>>> NIH Center for Advancing Translational Science >>>>>>>>> >>>>>>>> >>>>>>>> >>>>>>> >>>>>>> >>>>>>> -- >>>>>>> Rajarshi Guha | http://blog.rguha.net >>>>>>> NIH Center for Advancing Translational Science >>>>>>> >>>>>> >>>>>> >>>>>> >>>>>> -- >>>>>> Rajarshi Guha | http://blog.rguha.net >>>>>> NIH Center for Advancing Translational Science >>>>>> >>>>>> >>>>>> ------------------------------------------------------------------------------ >>>>>> Site24x7 APM Insight: Get Deep Visibility into Application Performance >>>>>> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month >>>>>> Monitor end-to-end web transactions and take corrective actions now >>>>>> Troubleshoot faster and improve end-user experience. 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From: Giovanni C. <gci...@gm...> - 2016-02-15 07:40:09
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OK, thank you for the clarification! Cheers On Fri, Feb 12, 2016 at 8:52 PM, John M <joh...@gm...> wrote: > Hi Gio, > > Next release is 1.5.13. Probably do it soon, not a huge number of changes > but I know a few patches people are waiting (this now being added as one of > them). > > Please can you also confirm me that the purpose >> of the LargestChainDescriptor is to provide the longest path that contains >> non-aromatic, non-ring atoms? > > > Yes... but it now no longer checks aromaticity. Since an atom is only > aromatic if it's in a ring we just need to check the non-ring atoms. > > John > > Regards, > John W May > joh...@gm... > > On 12 February 2016 at 19:20, Giovanni Cincilla <gci...@gm...> > wrote: > >> Very good guys! You are great. So I suppose the bug-free version will be >> available in the next CDK release, isn't it? Can you please me specify >> which version it will be? >> Please can you also confirm me that the purpose >> of the LargestChainDescriptor is to provide the longest path that contains >> non-aromatic, non-ring atoms? In other words: should the parameter >> *checkRingSystem* always be set = true in this description. I'm asking >> you this because it seems that in the current KNIME-CDK version this is >> currently not the case. >> Thank you in advance for your feedback! >> Gio >> >> On Thu, Feb 11, 2016 at 7:10 PM, Rajarshi Guha <raj...@gm...> >> wrote: >> >>> well the first looks at all atoms, the other only considers carbon >>> chains. >>> >>> I'd say keep them both in for now (though the first could be >>> parametrized on element, in which case we'd only need one) >>> >>> On Thu, Feb 11, 2016 at 1:06 PM, John M <joh...@gm...> >>> wrote: >>> >>>> Hmm.. should we deprecate one of LargestChainDescriptor >>>> or LongestAliphaticChainDescriptor? Same purpose as far as I can set. >>>> >>>> John >>>> >>>> Regards, >>>> John W May >>>> joh...@gm... >>>> >>>> On 11 February 2016 at 17:58, Rajarshi Guha <raj...@gm...> >>>> wrote: >>>> >>>>> Yes, 5 should be the value for this >>>>> >>>>> On Thu, Feb 11, 2016 at 12:57 PM, John M <joh...@gm...> >>>>> wrote: >>>>> >>>>>> Cheers for patch Rajarshi, added some clean up the code: >>>>>> https://github.com/cdk/cdk/pull/195 but get a test failure on, >>>>>> "CC=CC(C)=O" expected longest path is 6 but I get 5? >>>>>> >>>>>> 5 looks correct to me? >>>>>> >>>>>> John >>>>>> >>>>>> Regards, >>>>>> John W May >>>>>> joh...@gm... >>>>>> >>>>>> On 11 February 2016 at 17:03, Rajarshi Guha <raj...@gm...> >>>>>> wrote: >>>>>> >>>>>>> you can ignore the patch since I've just made a pull request with >>>>>>> this fix >>>>>>> >>>>>>> On Thu, Feb 11, 2016 at 10:47 AM, Rajarshi Guha < >>>>>>> raj...@gm...> wrote: >>>>>>> >>>>>>>> Yes, it does appear to be a bug. >>>>>>>> >>>>>>>> Inspeting the code the LargestChainDescriptor is looking for the >>>>>>>> longest path that contains non-aromatic, non-ring atoms. >>>>>>>> >>>>>>>> For Row0, there are only two non-ring, non-aromatic atoms and so >>>>>>>> there are two possible chains with a single atom, hence each chain has the >>>>>>>> value of 0. >>>>>>>> >>>>>>>> For Row2, the longest chain according to the definition is the C#N >>>>>>>> substructure, hence the value should be 2 >>>>>>>> >>>>>>>> For Row5 and Row6, the values should also be 2. >>>>>>>> >>>>>>>> I've attached a patch against master that fixes this (I wasn't sure >>>>>>>> how to make a pull request from a local branch) >>>>>>>> >>>>>>>> >>>>>>>> On Thu, Feb 11, 2016 at 7:50 AM, Giovanni Cincilla < >>>>>>>> gci...@gm...> wrote: >>>>>>>> >>>>>>>>> Thank you for your quick reply. >>>>>>>>> Examples are provided in the original KNIME forum thread ( >>>>>>>>> https://tech.knime.org/forum/cdk/cdk-largest-chain-descriptor-inconsistencies#comment-41502), >>>>>>>>> anyway I can report those here: >>>>>>>>> >>>>>>>>> 2. In some cases terminal atoms seems not to be counted as part >>>>>>>>> of the largest chain LC (LC Row0 = 0; LC Row2 = 1), while in other cases >>>>>>>>> they are (LC Row5 = 2; LC Row6 =2). >>>>>>>>> 3. In some cases iso terminal groups are countes as 2 (Row4) >>>>>>>>> while in other cases are counted as 3 (Row8). >>>>>>>>> >>>>>>>>> *Molecules:* >>>>>>>>> "Row0","Cc1nn(c(c1)N)c1nc2c(s1)cccc2" >>>>>>>>> "Row1","Clc1cnn(c(=O)c1Cl)Cc1[nH]c(=O)c2c(n1)c1ccccc1o2" >>>>>>>>> "Row2","Nc1c(cn[nH]1)C#N" >>>>>>>>> "Row3","Fc1ccc(cc1)C(=O)c1ccc(cc1)Oc1ncc(cn1)Br" >>>>>>>>> "Row4","[O-][n+]1ccc(cc1)[N+](=O)[O-]" >>>>>>>>> "Row5","OCc1ccccc1CN" >>>>>>>>> "Row6","COc1ccc(cc1)c1noc(c1)Cn1nc(C)c(c(c1=O)C#N)C" >>>>>>>>> "Row7","Cc1nc(SCc2nc3ccsc3c(=O)[nH]2)c2c(n1)scc2c1cccs1" >>>>>>>>> "Row8","CC(=O)c1cccc(c1)Nc1nc(nc2c1cccc2)c1cccnc1" >>>>>>>>> >>>>>>>>> I hope the examples are quite clear. >>>>>>>>> >>>>>>>>> On Thu, Feb 11, 2016 at 1:18 PM, Rajarshi Guha < >>>>>>>>> raj...@gm...> wrote: >>>>>>>>> >>>>>>>>>> Could you provide an example where issues 2 & 3 show up? >>>>>>>>>> >>>>>>>>>> The descriptor is meant to compute the length of the longest >>>>>>>>>> aliphatic chain in a molecule >>>>>>>>>> >>>>>>>>>> On Thu, Feb 11, 2016 at 4:29 AM, Giovanni Cincilla < >>>>>>>>>> gci...@gm...> wrote: >>>>>>>>>> >>>>>>>>>>> Dear all, >>>>>>>>>>> I use CDK mainly through KNIME and I found some supposed >>>>>>>>>>> inconsistencies using the LargestChainDescriptor. I originally posted my >>>>>>>>>>> doubt in KNIME-CDK forum where I also provided examples: >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> https://tech.knime.org/forum/cdk/cdk-largest-chain-descriptor-inconsistencies#comment-41502 >>>>>>>>>>> >>>>>>>>>>> I'm not sure about the purpose of such descriptor. Essentially >>>>>>>>>>> my doubts are the following: >>>>>>>>>>> >>>>>>>>>>> 1. The LargestChainDescriptor count atoms that belong to >>>>>>>>>>> aliphatic rings. Is that correct or it is a bug? The word "chain" in my >>>>>>>>>>> opinion can seems opposed to the word "ring". >>>>>>>>>>> 2. In some cases terminal atoms seems not to be counted as >>>>>>>>>>> part of the largest chain, while in other cases they are. >>>>>>>>>>> 3. In some cases iso terminal groups are counted as 2 while >>>>>>>>>>> in other cases are counted as 3 >>>>>>>>>>> 4. Atoms between rings in some case to be correctly counted, >>>>>>>>>>> while in other cases they are not >>>>>>>>>>> >>>>>>>>>>> Please, can anybody provide some clarification about these >>>>>>>>>>> issues? >>>>>>>>>>> Thanks, >>>>>>>>>>> Gio >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> ------------------------------------------------------------------------------ >>>>>>>>>>> Site24x7 APM Insight: Get Deep Visibility into Application >>>>>>>>>>> Performance >>>>>>>>>>> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month >>>>>>>>>>> Monitor end-to-end web transactions and take corrective actions >>>>>>>>>>> now >>>>>>>>>>> Troubleshoot faster and improve end-user experience. Signup Now! >>>>>>>>>>> http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140 >>>>>>>>>>> _______________________________________________ >>>>>>>>>>> Cdk-user mailing list >>>>>>>>>>> Cdk...@li... >>>>>>>>>>> https://lists.sourceforge.net/lists/listinfo/cdk-user >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> -- >>>>>>>>>> Rajarshi Guha | http://blog.rguha.net >>>>>>>>>> NIH Center for Advancing Translational Science >>>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> -- >>>>>>>> Rajarshi Guha | http://blog.rguha.net >>>>>>>> NIH Center for Advancing Translational Science >>>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> -- >>>>>>> Rajarshi Guha | http://blog.rguha.net >>>>>>> NIH Center for Advancing Translational Science >>>>>>> >>>>>>> >>>>>>> ------------------------------------------------------------------------------ >>>>>>> Site24x7 APM Insight: Get Deep Visibility into Application >>>>>>> Performance >>>>>>> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month >>>>>>> Monitor end-to-end web transactions and take corrective actions now >>>>>>> Troubleshoot faster and improve end-user experience. Signup Now! >>>>>>> http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140 >>>>>>> _______________________________________________ >>>>>>> Cdk-user mailing list >>>>>>> Cdk...@li... >>>>>>> https://lists.sourceforge.net/lists/listinfo/cdk-user >>>>>>> >>>>>>> >>>>>> >>>>> >>>>> >>>>> -- >>>>> Rajarshi Guha | http://blog.rguha.net >>>>> NIH Center for Advancing Translational Science >>>>> >>>> >>>> >>> >>> >>> -- >>> Rajarshi Guha | http://blog.rguha.net >>> NIH Center for Advancing Translational Science >>> >> >> > |