Re: [Jmol-users] Jmol smarts/smiles upgrade
It is correct on the simple example I have been testing. Phil On May 10, 2010, at 6:02 PM, Robert Hanson wrote: > Phil, there was a miscalculation of hybridization on the adding of H atoms > there. Try the stereochemistry again and see if it's correct now. > > http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm > > and > > http://chemapps.stolaf.edu/jmol/docs/examples-11/Jmol-11.zip > > > On Sun, May 9, 2010 at 9:38 PM, Robert Hanson wrote: > sending JME strings. Jmol 12.0.RC10 is at the usual place -- > http://jmol.sourceforge.net/download/ > > > On Sun, May 9, 2010 at 9:06 PM, Philip Bays wrote: > OK. I sent you two files from the old version and now have tested on your > page. The stereochemistry is different in the old unless you add the > implicit hydrogens at the stereo centers but the same in the new without the > hydrogens. > > Where do I find the Jmol 12 files? What are you sending from JME to Jmol: > smiles strings, JME strings, smarts strings? > > I was looking the other day and only saw the 11. Perhaps I am blind:-( It > is getting late. > > Phil > > On May 9, 2010, at 9:39 PM, Robert Hanson wrote: > >> Hi, Phil. First, let me point out that we're still discovering the nuances >> of this, and the more help we can get, the better. So do keep testing. The >> latest JAR files were just released as Jmol 12.0.RC10. So be sure to use >> those. >> >> Stereochemistry and JME. Of course this is quite tricky, and I don't know >> that we have Jmol totally optimized for that. What works best is if you can >> work at http://chemapps.stolaf.edu/jmol/docs/examples-11/JmeToJmol.htm and >> then, when you have something to show us, click on save and then send us >> that link. For example: >> >> http://chemapps.stolaf.edu/jmol/docs/examples-11/JmeToJmol.htm?load=7%206%20C%209.42%20-6.02%20C%208.29%20-5.19%20C%207.16%20-6.02%20C%2010.75%20-5.58%20C%2011.79%20-6.52%20C%2010.59%20-4.19%20C%2011.50%20-7.89%201%202%201%202%203%201%201%204%201%204%205%201%204%206%20-1%205%207%201 >> >> so we can compare notes. >> >> >> On Sun, May 9, 2010 at 2:14 PM, Philip Bays wrote: >> >> Here is the issue I am faced with. If I use JME to construct, for example, >> 2-bromo-3-pentanol I can get several correct smiles strings out of JME, >> depending upon how I draw the structure. In these cases I show the >> stereochemistry of the H's on carbons 2 and 3. If on the other hand I >> simple show all the heavy atoms, with appropriate "above and below" wedges, >> Jmol gets the stereochemistry wrong. I have read that adding hydrogens to >> the carbons in JME using the X icon gives a different smiles type of H which >> leads to the multiple strings. >> >> >> I need some good examples of that. >> >> You mentioned that Jmol can compare molecules. Do you do that via smiles >> strings or how is it done? Is it a javascript function, or part of the >> applet itself? Is there a function that can assign a IUPAC name to small >> molecules, including stereochemistry (which Marvin Sketch can do)? >> >> >> So now Jmol can compare two sets of atoms structurally -- atom positions -- >> provided you know the correlation from one atom to another. But that's not >> going to work for differently drawn conformations. In addition, Jmol can >> search a SMILES string for a subset or equivalent SMILES string. HOWEVER, as >> I think about that, it won't work for stereochemistry. So there's still more >> work to do. >> >> Certainly can't assign IUPAC names. >> >> >> Define the problem -- what you'd really like to be able to do. >> >> Bob >> >> Feel free to respond off line if you think others are not interested. >> >> Phil Bays >> >> >> >> >> On May 6, 2010, at 12:22 PM, Robert Hanson wrote: >> >>> Not by Jmol. In principle, the SMILES with stereochemistry does describe >>> the topology correctly. >>> >>> On Wed, May 5, 2010 at 11:40 PM, Egon Willighagen >>> wrote: >>> On Thu, May 6, 2010 at 4:34 AM, Robert Hanson wrote: >>> > What the heck! Might as well do them all! >>> >>> So, can these chiral SMILES also be used to create a 3D model? Where >>> the stereo is correctly applied? >>> >>> Egon >>> >>> -- >>> Post-doc @ Uppsala University >>> Proteochemometrics / Bioclipse Group of Prof. Jarl Wikberg >>> Homepage: http://egonw.github.com/ >>> Blog: http://chem-bla-ics.blogspot.com/ >>> PubList: http://www.citeulike.org/user/egonw/tag/papers >>> >>> -- >>> ___ >>> Jmol-users mailing list >>> Jmol-users@lists.sourceforge.net >>> https://lists.sourceforge.net/lists/listinfo/jmol-users >>> >>> >>> >>> -- >>> Robert M. Hanson >>> Professor of Chemistry >>> St. Olaf College >>> 1520 St. Olaf Ave. >>> Northfield, MN 55057 >>> http://www.stolaf.edu/people/hansonr >>> phone: 507-786-3107 >>> >>> >>> If nature does not answer first what we want, >>>
Re: [Jmol-users] Jmol smarts/smiles upgrade
Phil, there was a miscalculation of hybridization on the adding of H atoms there. Try the stereochemistry again and see if it's correct now. http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm and http://chemapps.stolaf.edu/jmol/docs/examples-11/Jmol-11.zip On Sun, May 9, 2010 at 9:38 PM, Robert Hanson wrote: > sending JME strings. Jmol 12.0.RC10 is at the usual place -- > http://jmol.sourceforge.net/download/ > > > On Sun, May 9, 2010 at 9:06 PM, Philip Bays wrote: > >> OK. I sent you two files from the old version and now have tested on your >> page. The stereochemistry is different in the old unless you add the >> implicit hydrogens at the stereo centers but the same in the new without the >> hydrogens. >> >> Where do I find the Jmol 12 files? What are you sending from JME to >> Jmol: smiles strings, JME strings, smarts strings? >> >> I was looking the other day and only saw the 11. Perhaps I am blind:-( >> It is getting late. >> >> Phil >> >> On May 9, 2010, at 9:39 PM, Robert Hanson wrote: >> >> Hi, Phil. First, let me point out that we're still discovering the nuances >> of this, and the more help we can get, the better. So do keep testing. The >> latest JAR files were just released as Jmol 12.0.RC10. So be sure to use >> those. >> >> Stereochemistry and JME. Of course this is quite tricky, and I don't know >> that we have Jmol totally optimized for that. What works best is if you can >> work at http://chemapps.stolaf.edu/jmol/docs/examples-11/JmeToJmol.htmand >> then, when you have something to show us, click on save and then send us >> that link. For example: >> >> >> http://chemapps.stolaf.edu/jmol/docs/examples-11/JmeToJmol.htm?load=7%206%20C%209.42%20-6.02%20C%208.29%20-5.19%20C%207.16%20-6.02%20C%2010.75%20-5.58%20C%2011.79%20-6.52%20C%2010.59%20-4.19%20C%2011.50%20-7.89%201%202%201%202%203%201%201%204%201%204%205%201%204%206%20-1%205%207%201 >> >> so we can compare notes. >> >> >> On Sun, May 9, 2010 at 2:14 PM, Philip Bays wrote: >> >>> >>> Here is the issue I am faced with. If I use JME to construct, for >>> example, 2-bromo-3-pentanol I can get several correct smiles strings out of >>> JME, depending upon how I draw the structure. In these cases I show the >>> stereochemistry of the H's on carbons 2 and 3. If on the other hand I >>> simple show all the heavy atoms, with appropriate "above and below" wedges, >>> Jmol gets the stereochemistry wrong. I have read that adding hydrogens to >>> the carbons in JME using the X icon gives a different smiles type of H which >>> leads to the multiple strings. >>> >>> >> I need some good examples of that. >> >> >>> You mentioned that Jmol can compare molecules. Do you do that via >>> smiles strings or how is it done? Is it a javascript function, or part of >>> the applet itself? Is there a function that can assign a IUPAC name to >>> small molecules, including stereochemistry (which Marvin Sketch can do)? >>> >>> >> So now Jmol can compare two sets of atoms structurally -- atom positions >> -- provided you know the correlation from one atom to another. But that's >> not going to work for differently drawn conformations. In addition, Jmol can >> search a SMILES string for a subset or equivalent SMILES string. HOWEVER, as >> I think about that, it won't work for stereochemistry. So there's still more >> work to do. >> >> Certainly can't assign IUPAC names. >> >> >> Define the problem -- what you'd really like to be able to do. >> >> Bob >> >> >>> Feel free to respond off line if you think others are not interested. >>> >>> Phil Bays >>> >>> >>> >>> >>> On May 6, 2010, at 12:22 PM, Robert Hanson wrote: >>> >>> Not by Jmol. In principle, the SMILES with stereochemistry does describe >>> the topology correctly. >>> >>> On Wed, May 5, 2010 at 11:40 PM, Egon Willighagen < >>> egon.willigha...@gmail.com> wrote: >>> On Thu, May 6, 2010 at 4:34 AM, Robert Hanson wrote: > What the heck! Might as well do them all! So, can these chiral SMILES also be used to create a 3D model? Where the stereo is correctly applied? Egon -- Post-doc @ Uppsala University Proteochemometrics / Bioclipse Group of Prof. Jarl Wikberg Homepage: http://egonw.github.com/ Blog: http://chem-bla-ics.blogspot.com/ PubList: http://www.citeulike.org/user/egonw/tag/papers -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users >>> >>> >>> >>> -- >>> Robert M. Hanson >>> Professor of Chemistry >>> St. Olaf College >>> 1520 St. Olaf Ave. >>> Northfield, MN 55057 >>> http://www.stolaf.edu/people/hansonr >>> phone: 507-786-3107 >>> >>> >>> If nature does not answer first what we want, >>> it is better to take what answer we get. >>> >>> -- Josiah Willard Gibbs, Lecture XXX, Monday
Re: [Jmol-users] Jmol smarts/smiles upgrade
sending JME strings. Jmol 12.0.RC10 is at the usual place -- http://jmol.sourceforge.net/download/ On Sun, May 9, 2010 at 9:06 PM, Philip Bays wrote: > OK. I sent you two files from the old version and now have tested on your > page. The stereochemistry is different in the old unless you add the > implicit hydrogens at the stereo centers but the same in the new without the > hydrogens. > > Where do I find the Jmol 12 files? What are you sending from JME to Jmol: > smiles strings, JME strings, smarts strings? > > I was looking the other day and only saw the 11. Perhaps I am blind:-( It > is getting late. > > Phil > > On May 9, 2010, at 9:39 PM, Robert Hanson wrote: > > Hi, Phil. First, let me point out that we're still discovering the nuances > of this, and the more help we can get, the better. So do keep testing. The > latest JAR files were just released as Jmol 12.0.RC10. So be sure to use > those. > > Stereochemistry and JME. Of course this is quite tricky, and I don't know > that we have Jmol totally optimized for that. What works best is if you can > work at http://chemapps.stolaf.edu/jmol/docs/examples-11/JmeToJmol.htm and > then, when you have something to show us, click on save and then send us > that link. For example: > > > http://chemapps.stolaf.edu/jmol/docs/examples-11/JmeToJmol.htm?load=7%206%20C%209.42%20-6.02%20C%208.29%20-5.19%20C%207.16%20-6.02%20C%2010.75%20-5.58%20C%2011.79%20-6.52%20C%2010.59%20-4.19%20C%2011.50%20-7.89%201%202%201%202%203%201%201%204%201%204%205%201%204%206%20-1%205%207%201 > > so we can compare notes. > > > On Sun, May 9, 2010 at 2:14 PM, Philip Bays wrote: > >> >> Here is the issue I am faced with. If I use JME to construct, for >> example, 2-bromo-3-pentanol I can get several correct smiles strings out of >> JME, depending upon how I draw the structure. In these cases I show the >> stereochemistry of the H's on carbons 2 and 3. If on the other hand I >> simple show all the heavy atoms, with appropriate "above and below" wedges, >> Jmol gets the stereochemistry wrong. I have read that adding hydrogens to >> the carbons in JME using the X icon gives a different smiles type of H which >> leads to the multiple strings. >> >> > I need some good examples of that. > > >> You mentioned that Jmol can compare molecules. Do you do that via smiles >> strings or how is it done? Is it a javascript function, or part of the >> applet itself? Is there a function that can assign a IUPAC name to small >> molecules, including stereochemistry (which Marvin Sketch can do)? >> >> > So now Jmol can compare two sets of atoms structurally -- atom positions -- > provided you know the correlation from one atom to another. But that's not > going to work for differently drawn conformations. In addition, Jmol can > search a SMILES string for a subset or equivalent SMILES string. HOWEVER, as > I think about that, it won't work for stereochemistry. So there's still more > work to do. > > Certainly can't assign IUPAC names. > > > Define the problem -- what you'd really like to be able to do. > > Bob > > >> Feel free to respond off line if you think others are not interested. >> >> Phil Bays >> >> >> >> >> On May 6, 2010, at 12:22 PM, Robert Hanson wrote: >> >> Not by Jmol. In principle, the SMILES with stereochemistry does describe >> the topology correctly. >> >> On Wed, May 5, 2010 at 11:40 PM, Egon Willighagen < >> egon.willigha...@gmail.com> wrote: >> >>> On Thu, May 6, 2010 at 4:34 AM, Robert Hanson >>> wrote: >>> > What the heck! Might as well do them all! >>> >>> So, can these chiral SMILES also be used to create a 3D model? Where >>> the stereo is correctly applied? >>> >>> Egon >>> >>> -- >>> Post-doc @ Uppsala University >>> Proteochemometrics / Bioclipse Group of Prof. Jarl Wikberg >>> Homepage: http://egonw.github.com/ >>> Blog: http://chem-bla-ics.blogspot.com/ >>> PubList: http://www.citeulike.org/user/egonw/tag/papers >>> >>> >>> -- >>> ___ >>> Jmol-users mailing list >>> Jmol-users@lists.sourceforge.net >>> https://lists.sourceforge.net/lists/listinfo/jmol-users >>> >> >> >> >> -- >> Robert M. Hanson >> Professor of Chemistry >> St. Olaf College >> 1520 St. Olaf Ave. >> Northfield, MN 55057 >> http://www.stolaf.edu/people/hansonr >> phone: 507-786-3107 >> >> >> If nature does not answer first what we want, >> it is better to take what answer we get. >> >> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 >> >> -- >> ___ >> Jmol-users mailing list >> Jmol-users@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/jmol-users >> >> >> J. Philip Bays >> Professor of Chemistry >> Department of Chemistry and Physics >> Saint Mary's College >> Notre Dame, IN 46556 >> (574) 284-4663 >> pb...@saintmarys.edu
Re: [Jmol-users] Jmol smarts/smiles upgrade
OK. I sent you two files from the old version and now have tested on your page. The stereochemistry is different in the old unless you add the implicit hydrogens at the stereo centers but the same in the new without the hydrogens. Where do I find the Jmol 12 files? What are you sending from JME to Jmol: smiles strings, JME strings, smarts strings? I was looking the other day and only saw the 11. Perhaps I am blind:-( It is getting late. Phil On May 9, 2010, at 9:39 PM, Robert Hanson wrote: > Hi, Phil. First, let me point out that we're still discovering the nuances of > this, and the more help we can get, the better. So do keep testing. The > latest JAR files were just released as Jmol 12.0.RC10. So be sure to use > those. > > Stereochemistry and JME. Of course this is quite tricky, and I don't know > that we have Jmol totally optimized for that. What works best is if you can > work at http://chemapps.stolaf.edu/jmol/docs/examples-11/JmeToJmol.htm and > then, when you have something to show us, click on save and then send us that > link. For example: > > http://chemapps.stolaf.edu/jmol/docs/examples-11/JmeToJmol.htm?load=7%206%20C%209.42%20-6.02%20C%208.29%20-5.19%20C%207.16%20-6.02%20C%2010.75%20-5.58%20C%2011.79%20-6.52%20C%2010.59%20-4.19%20C%2011.50%20-7.89%201%202%201%202%203%201%201%204%201%204%205%201%204%206%20-1%205%207%201 > > so we can compare notes. > > > On Sun, May 9, 2010 at 2:14 PM, Philip Bays wrote: > > Here is the issue I am faced with. If I use JME to construct, for example, > 2-bromo-3-pentanol I can get several correct smiles strings out of JME, > depending upon how I draw the structure. In these cases I show the > stereochemistry of the H's on carbons 2 and 3. If on the other hand I simple > show all the heavy atoms, with appropriate "above and below" wedges, Jmol > gets the stereochemistry wrong. I have read that adding hydrogens to the > carbons in JME using the X icon gives a different smiles type of H which > leads to the multiple strings. > > > I need some good examples of that. > > You mentioned that Jmol can compare molecules. Do you do that via smiles > strings or how is it done? Is it a javascript function, or part of the > applet itself? Is there a function that can assign a IUPAC name to small > molecules, including stereochemistry (which Marvin Sketch can do)? > > > So now Jmol can compare two sets of atoms structurally -- atom positions -- > provided you know the correlation from one atom to another. But that's not > going to work for differently drawn conformations. In addition, Jmol can > search a SMILES string for a subset or equivalent SMILES string. HOWEVER, as > I think about that, it won't work for stereochemistry. So there's still more > work to do. > > Certainly can't assign IUPAC names. > > > Define the problem -- what you'd really like to be able to do. > > Bob > > Feel free to respond off line if you think others are not interested. > > Phil Bays > > > > > On May 6, 2010, at 12:22 PM, Robert Hanson wrote: > >> Not by Jmol. In principle, the SMILES with stereochemistry does describe the >> topology correctly. >> >> On Wed, May 5, 2010 at 11:40 PM, Egon Willighagen >> wrote: >> On Thu, May 6, 2010 at 4:34 AM, Robert Hanson wrote: >> > What the heck! Might as well do them all! >> >> So, can these chiral SMILES also be used to create a 3D model? Where >> the stereo is correctly applied? >> >> Egon >> >> -- >> Post-doc @ Uppsala University >> Proteochemometrics / Bioclipse Group of Prof. Jarl Wikberg >> Homepage: http://egonw.github.com/ >> Blog: http://chem-bla-ics.blogspot.com/ >> PubList: http://www.citeulike.org/user/egonw/tag/papers >> >> -- >> ___ >> Jmol-users mailing list >> Jmol-users@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/jmol-users >> >> >> >> -- >> Robert M. Hanson >> Professor of Chemistry >> St. Olaf College >> 1520 St. Olaf Ave. >> Northfield, MN 55057 >> http://www.stolaf.edu/people/hansonr >> phone: 507-786-3107 >> >> >> If nature does not answer first what we want, >> it is better to take what answer we get. >> >> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 >> -- >> ___ >> Jmol-users mailing list >> Jmol-users@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/jmol-users > > J. Philip Bays > Professor of Chemistry > Department of Chemistry and Physics > Saint Mary's College > Notre Dame, IN 46556 > (574) 284-4663 > pb...@saintmarys.edu > > > > > -- > > > ___ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > https:
Re: [Jmol-users] Jmol smarts/smiles upgrade
Hi, Phil. First, let me point out that we're still discovering the nuances of this, and the more help we can get, the better. So do keep testing. The latest JAR files were just released as Jmol 12.0.RC10. So be sure to use those. Stereochemistry and JME. Of course this is quite tricky, and I don't know that we have Jmol totally optimized for that. What works best is if you can work at http://chemapps.stolaf.edu/jmol/docs/examples-11/JmeToJmol.htm and then, when you have something to show us, click on save and then send us that link. For example: http://chemapps.stolaf.edu/jmol/docs/examples-11/JmeToJmol.htm?load=7%206%20C%209.42%20-6.02%20C%208.29%20-5.19%20C%207.16%20-6.02%20C%2010.75%20-5.58%20C%2011.79%20-6.52%20C%2010.59%20-4.19%20C%2011.50%20-7.89%201%202%201%202%203%201%201%204%201%204%205%201%204%206%20-1%205%207%201 so we can compare notes. On Sun, May 9, 2010 at 2:14 PM, Philip Bays wrote: > > Here is the issue I am faced with. If I use JME to construct, for example, > 2-bromo-3-pentanol I can get several correct smiles strings out of JME, > depending upon how I draw the structure. In these cases I show the > stereochemistry of the H's on carbons 2 and 3. If on the other hand I > simple show all the heavy atoms, with appropriate "above and below" wedges, > Jmol gets the stereochemistry wrong. I have read that adding hydrogens to > the carbons in JME using the X icon gives a different smiles type of H which > leads to the multiple strings. > > I need some good examples of that. > You mentioned that Jmol can compare molecules. Do you do that via smiles > strings or how is it done? Is it a javascript function, or part of the > applet itself? Is there a function that can assign a IUPAC name to small > molecules, including stereochemistry (which Marvin Sketch can do)? > > So now Jmol can compare two sets of atoms structurally -- atom positions -- provided you know the correlation from one atom to another. But that's not going to work for differently drawn conformations. In addition, Jmol can search a SMILES string for a subset or equivalent SMILES string. HOWEVER, as I think about that, it won't work for stereochemistry. So there's still more work to do. Certainly can't assign IUPAC names. Define the problem -- what you'd really like to be able to do. Bob > Feel free to respond off line if you think others are not interested. > > Phil Bays > > > > > On May 6, 2010, at 12:22 PM, Robert Hanson wrote: > > Not by Jmol. In principle, the SMILES with stereochemistry does describe > the topology correctly. > > On Wed, May 5, 2010 at 11:40 PM, Egon Willighagen < > egon.willigha...@gmail.com> wrote: > >> On Thu, May 6, 2010 at 4:34 AM, Robert Hanson wrote: >> > What the heck! Might as well do them all! >> >> So, can these chiral SMILES also be used to create a 3D model? Where >> the stereo is correctly applied? >> >> Egon >> >> -- >> Post-doc @ Uppsala University >> Proteochemometrics / Bioclipse Group of Prof. Jarl Wikberg >> Homepage: http://egonw.github.com/ >> Blog: http://chem-bla-ics.blogspot.com/ >> PubList: http://www.citeulike.org/user/egonw/tag/papers >> >> >> -- >> ___ >> Jmol-users mailing list >> Jmol-users@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/jmol-users >> > > > > -- > Robert M. Hanson > Professor of Chemistry > St. Olaf College > 1520 St. Olaf Ave. > Northfield, MN 55057 > http://www.stolaf.edu/people/hansonr > phone: 507-786-3107 > > > If nature does not answer first what we want, > it is better to take what answer we get. > > -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 > > -- > ___ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users > > > J. Philip Bays > Professor of Chemistry > Department of Chemistry and Physics > Saint Mary's College > Notre Dame, IN 46556 > (574) 284-4663 > pb...@saintmarys.edu > > > > > > -- > > > ___ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users > > -- Robert M. Hanson Professor of Chemistry St. Olaf College 1520 St. Olaf Ave. Northfield, MN 55057 http://www.stolaf.edu/people/hansonr phone: 507-786-3107 If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol smarts/smiles upgrade
I have been out of the loop for a couple of weeks and am very interested in this issue. To top it off, our IT department mucked around with the campus spam filter resulting in catching, and I fear discarding, a series of conversations. So what I have to ask or say may be redundant:-( I am primarily interested in how to get consistent smiles strings to represent a single stereochemical structure. I have been playing the last couple of days with the JME/Jmol interaction that Bob posted a couple of weeks ago. Again, if that has been improved upon, let me know. Here is the issue I am faced with. If I use JME to construct, for example, 2-bromo-3-pentanol I can get several correct smiles strings out of JME, depending upon how I draw the structure. In these cases I show the stereochemistry of the H's on carbons 2 and 3. If on the other hand I simple show all the heavy atoms, with appropriate "above and below" wedges, Jmol gets the stereochemistry wrong. I have read that adding hydrogens to the carbons in JME using the X icon gives a different smiles type of H which leads to the multiple strings. You mentioned that Jmol can compare molecules. Do you do that via smiles strings or how is it done? Is it a javascript function, or part of the applet itself? Is there a function that can assign a IUPAC name to small molecules, including stereochemistry (which Marvin Sketch can do)? Feel free to respond off line if you think others are not interested. Phil Bays On May 6, 2010, at 12:22 PM, Robert Hanson wrote: > Not by Jmol. In principle, the SMILES with stereochemistry does describe the > topology correctly. > > On Wed, May 5, 2010 at 11:40 PM, Egon Willighagen > wrote: > On Thu, May 6, 2010 at 4:34 AM, Robert Hanson wrote: > > What the heck! Might as well do them all! > > So, can these chiral SMILES also be used to create a 3D model? Where > the stereo is correctly applied? > > Egon > > -- > Post-doc @ Uppsala University > Proteochemometrics / Bioclipse Group of Prof. Jarl Wikberg > Homepage: http://egonw.github.com/ > Blog: http://chem-bla-ics.blogspot.com/ > PubList: http://www.citeulike.org/user/egonw/tag/papers > > -- > ___ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users > > > > -- > Robert M. Hanson > Professor of Chemistry > St. Olaf College > 1520 St. Olaf Ave. > Northfield, MN 55057 > http://www.stolaf.edu/people/hansonr > phone: 507-786-3107 > > > If nature does not answer first what we want, > it is better to take what answer we get. > > -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 > -- > ___ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users J. Philip Bays Professor of Chemistry Department of Chemistry and Physics Saint Mary's College Notre Dame, IN 46556 (574) 284-4663 pb...@saintmarys.edu -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol smarts/smiles upgrade
Not by Jmol. In principle, the SMILES with stereochemistry does describe the topology correctly. On Wed, May 5, 2010 at 11:40 PM, Egon Willighagen < egon.willigha...@gmail.com> wrote: > On Thu, May 6, 2010 at 4:34 AM, Robert Hanson wrote: > > What the heck! Might as well do them all! > > So, can these chiral SMILES also be used to create a 3D model? Where > the stereo is correctly applied? > > Egon > > -- > Post-doc @ Uppsala University > Proteochemometrics / Bioclipse Group of Prof. Jarl Wikberg > Homepage: http://egonw.github.com/ > Blog: http://chem-bla-ics.blogspot.com/ > PubList: http://www.citeulike.org/user/egonw/tag/papers > > > -- > ___ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users > -- Robert M. Hanson Professor of Chemistry St. Olaf College 1520 St. Olaf Ave. Northfield, MN 55057 http://www.stolaf.edu/people/hansonr phone: 507-786-3107 If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol smarts/smiles upgrade
On Thu, May 6, 2010 at 4:34 AM, Robert Hanson wrote: > What the heck! Might as well do them all! So, can these chiral SMILES also be used to create a 3D model? Where the stereo is correctly applied? Egon -- Post-doc @ Uppsala University Proteochemometrics / Bioclipse Group of Prof. Jarl Wikberg Homepage: http://egonw.github.com/ Blog: http://chem-bla-ics.blogspot.com/ PubList: http://www.citeulike.org/user/egonw/tag/papers -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol smarts/smiles upgrade
What the heck! Might as well do them all! OK, Jmol 12.0.RC10_dev has all the SMILES/SMARTS stereochemistry descriptors described at http://www.daylight.com/dayhtml/doc/theory/theory.smiles.html#RTFToC24 This includes allenes, cumulenes, tetrahedral, square planar, trigonal bipyramidal, and octahedral stereochemistry. All structures on that page have been tested using the example SMILES strings given there. The files relating to that page are available in the Spartan datafiles directory, http://jmol.svn.sourceforge.net/viewvc/jmol/trunk/Jmol-datafiles/spartan http://chemapps.stolaf.edu/jmol/docs/examples-11/Jmol-11.zip is uploading now. Bob On Wed, May 5, 2010 at 2:09 PM, Egon Willighagen wrote: > On Wed, May 5, 2010 at 9:03 PM, Robert Hanson wrote: > > those should all be fine. They are similar to all the ones I tested. It's > a > > full range of [...@1] [...@th2] [C@@] [...@h] etc. The parser accepts the > > defaults for two-, four-, five-, and six-bond situations (AL, TH, TP, > OC), > > but the matcher does not yet process SP, TP, or OC. I'm figuring I will > > implement just the minimal versions of those. Shouldn't be too terribly > > difficult. > > Bob++ > > Egon > > -- > Post-doc @ Uppsala University > Proteochemometrics / Bioclipse Group of Prof. Jarl Wikberg > Homepage: http://egonw.github.com/ > Blog: http://chem-bla-ics.blogspot.com/ > PubList: http://www.citeulike.org/user/egonw/tag/papers > > > -- > ___ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users > -- Robert M. Hanson Professor of Chemistry St. Olaf College 1520 St. Olaf Ave. Northfield, MN 55057 http://www.stolaf.edu/people/hansonr phone: 507-786-3107 If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol smarts/smiles upgrade
On Wed, May 5, 2010 at 9:03 PM, Robert Hanson wrote: > those should all be fine. They are similar to all the ones I tested. It's a > full range of [...@1] [...@th2] [C@@] [...@h] etc. The parser accepts the > defaults for two-, four-, five-, and six-bond situations (AL, TH, TP, OC), > but the matcher does not yet process SP, TP, or OC. I'm figuring I will > implement just the minimal versions of those. Shouldn't be too terribly > difficult. Bob++ Egon -- Post-doc @ Uppsala University Proteochemometrics / Bioclipse Group of Prof. Jarl Wikberg Homepage: http://egonw.github.com/ Blog: http://chem-bla-ics.blogspot.com/ PubList: http://www.citeulike.org/user/egonw/tag/papers -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol smarts/smiles upgrade
On Wed, May 5, 2010 at 1:17 PM, Egon Willighagen wrote:
> Hi Bob,
>
> I'm impresses, once more... and don't want to spoil the news of this
> powerful API! But...
>
> On Wed, May 5, 2010 at 8:07 PM, Robert Hanson wrote:
> > select smarts("C(F)[...@](Cl)H")
>
> ... this molecule is not chiral...
>
yeah, yeah:
> select smarts("c...@](Cl)(F)H")
>
How does your lib handle the SMILES listed by Noel:
>
> http://baoilleach.blogspot.com/2009/03/clockwisdom-of-smiles-part-ii.html
>
>
those should all be fine. They are similar to all the ones I tested. It's a
full range of [...@1] [...@th2] [C@@] [...@h] etc. The parser accepts the
defaults for two-, four-, five-, and six-bond situations (AL, TH, TP, OC),
but the matcher does not yet process SP, TP, or OC. I'm figuring I will
implement just the minimal versions of those. Shouldn't be too terribly
difficult.
Bob
>
> --
> Post-doc @ Uppsala University
> Proteochemometrics / Bioclipse Group of Prof. Jarl Wikberg
> Homepage: http://egonw.github.com/
> Blog: http://chem-bla-ics.blogspot.com/
> PubList: http://www.citeulike.org/user/egonw/tag/papers
>
>
> --
> ___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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Re: [Jmol-users] Jmol smarts/smiles upgrade
On Wed, May 5, 2010 at 8:17 PM, Egon Willighagen
wrote:
> On Wed, May 5, 2010 at 8:07 PM, Robert Hanson wrote:
>> select smarts("C(F)[...@](Cl)H")
>
> ... this molecule is not chiral...
But then again, it's a SMARTS, not SMILES... so, it's fine that the
chiral atom lacks the fourth non-hydrogen side chain... /me is
embarrassed...
Egon
--
Post-doc @ Uppsala University
Proteochemometrics / Bioclipse Group of Prof. Jarl Wikberg
Homepage: http://egonw.github.com/
Blog: http://chem-bla-ics.blogspot.com/
PubList: http://www.citeulike.org/user/egonw/tag/papers
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Re: [Jmol-users] Jmol smarts/smiles upgrade
Hi Bob,
I'm impresses, once more... and don't want to spoil the news of this
powerful API! But...
On Wed, May 5, 2010 at 8:07 PM, Robert Hanson wrote:
> select smarts("C(F)[...@](Cl)H")
... this molecule is not chiral...
How does your lib handle the SMILES listed by Noel:
http://baoilleach.blogspot.com/2009/03/clockwisdom-of-smiles-part-ii.html
Egon
--
Post-doc @ Uppsala University
Proteochemometrics / Bioclipse Group of Prof. Jarl Wikberg
Homepage: http://egonw.github.com/
Blog: http://chem-bla-ics.blogspot.com/
PubList: http://www.citeulike.org/user/egonw/tag/papers
--
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[Jmol-users] Jmol smarts/smiles upgrade
Although I don't have demo pages, the latest prerelease of Jmol, 12.0.RC10
at http://chemapps.stolaf.edu/jmol/docs/examples-11/Jmol-11.jar should have
greatly expanded SMILES and SMARTS capability. Two new functions:
select smiles("..")
and
select smarts("..")
are added, which deprecate
select substructure("")
The problem with substructure() is that it uses SMILES strings, which are
really whole-molecule descriptors and not meant for substructure searching.
That's what SMARTS are for [
http://www.daylight.com/dayhtml/doc/theory/theory.smarts.html]. So while I'm
not saying I've fully implemented SMARTS or SMILES, some important
improvements are now in place. In particular:
select smarts("...")
allows a more natural search:
select smarts("C(C)=CC")
rather than
select smiles("[C]([C])=[C][C]")
More importantly, double bond, tetrahedral, and allenic stereochemistry are
now available. So you can quickly find out, for example, if a double bond is
cis or trans:
select smarts("C/C=C/C") # trans only
select smarts("C/C=C\\C") # cis only
And you can check stereochemistry around a tetrahedral or allenic center:
select smarts("C(F)[...@](Cl)H")
select smarts("C(F)(H)=[C@@]=C(Cl)H")
The more general form of this function allows finding ALL matches:
allTrans = {*}.find("smarts","C/C=C/C")
Note that now you can also find SMILES or SMARTS within smiles strings, so
the following allows a quick test of the equivalence of two SMILES strings:
print "CCC(O)C".find("smiles",anotherSmilesString)
If anotherSmilesString is functionally identical to "CCC(O)C", no matter how
it is written, Jmol will report "1", otherwise it will report "0".
FIND with the "smarts" option allows a simple substructure search of SMILES
strings:
print "".find("smarts","CCC")
prints "1" meaning it was found;
print "".find("smarts","CCC", true)
prints "2" meaning there are two total;
If this is done on an atom selection instead of a string, then the return is
one or more atom sets:
print {atomno < 18}.find("smarts","CC")
({6 7})
({8 16})
({9 11})
({9 15})
({10 12})
({13 14})
print {atomno < 18}.find("smarts","CC")[2]
({8 16})
I suppose at some point I need to make Jmol create SMILES strings, but I
don't have that yet.
Useful?
Bob
--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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