From: E.L. W. (Egon) <eg...@sc...> - 2003-07-18 06:27:43
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Christoph, how can I generate missing 2D coordinates? This is now possible for 3D, but maybe also possible for 2D? Egon |
From: Peter Murray-R. <pm...@ca...> - 2003-07-18 13:15:30
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At 08:28 18/07/2003 +0200, E.L. Willighagen (Egon) wrote: >Christoph, > >how can I generate missing 2D coordinates? This is now possible for 3D, but >maybe also possible for 2D? This may be irrelevant to what you are wanting, but after we talked in Cambridge I wrote the following interface to the 2D coordinates generator: /** * generates and adds 2D coordinates * @param molecule the molecule to edit * @exception ??? * @return CMLMolecule molecule after adding 2D coordinates */ public CMLMolecule add2DCoordinates(CMLMolecule cmlMolecule) throws CMLException { Molecule molecule = MolUtil.createCDKMolecule(cmlMolecule); StructureDiagramGenerator sdg = new StructureDiagramGenerator(molecule); try { sdg.generateCoordinates(); } catch (Exception e) {throw new CMLException(e.toString());} molecule = sdg.getMolecule(); cmlMolecule = MolUtil.createCMLMolecule(molecule); return cmlMolecule; } It generates a CDKMolecule and adds 2D coordinates and works. P. >Egon > > >------------------------------------------------------- >This SF.net email is sponsored by: VM Ware >With VMware you can run multiple operating systems on a single machine. >WITHOUT REBOOTING! Mix Linux / Windows / Novell virtual machines at the >same time. Free trial click here: http://www.vmware.com/wl/offer/345/0 >_______________________________________________ >Cdk-devel mailing list >Cdk...@li... >https://lists.sourceforge.net/lists/listinfo/cdk-devel |
From: E.L. W. (Egon) <eg...@sc...> - 2003-07-18 13:21:20
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On Friday 18 July 2003 15:14, Peter Murray-Rust wrote: > At 08:28 18/07/2003 +0200, E.L. Willighagen (Egon) wrote: > >how can I generate missing 2D coordinates? This is now possible for 3D, > > but maybe also possible for 2D? > > This may be irrelevant to what you are wanting, but after we talked in > Cambridge I wrote the following interface to the 2D coordinates generator: <snip> > It generates a CDKMolecule and adds 2D coordinates and works. Does it remain the already known coordinates? Because that is what I want in JChemPaint... Egon |
From: Peter Murray-R. <pm...@ca...> - 2003-07-18 15:18:13
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At 15:21 18/07/2003 +0200, E.L. Willighagen (Egon) wrote: >On Friday 18 July 2003 15:14, Peter Murray-Rust wrote: > > At 08:28 18/07/2003 +0200, E.L. Willighagen (Egon) wrote: > > >how can I generate missing 2D coordinates? This is now possible for 3D, > > > but maybe also possible for 2D? > > > > This may be irrelevant to what you are wanting, but after we talked in > > Cambridge I wrote the following interface to the 2D coordinates generator: > ><snip> > > > It generates a CDKMolecule and adds 2D coordinates and works. > >Does it remain the already known coordinates? Because that is what I want in >JChemPaint... Well it could quite easily but I doubt that is what you want. I posted this because this is what I wanted when we were talking. I assume that what you want is to clean up a structure in which an author has added or moved some atoms. That doesn't seem to be completely automatic. If the new atoms are in a substituent then that could be laid out separately and oriented/joined on the current 2D vector. That would be relatively easy though might overlap with current structure. If the new atoms alter a ring nucleus then I can't see an alternative to recomputing the whole nucleus and probably the whole structure. As a simple example, join the 1,6 atoms of cyclodecane with a 1 atom bridge. Do you just want to layout the bridge? P. >Egon |
From: E.L. W. (Egon) <eg...@sc...> - 2003-07-18 16:08:58
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On Friday 18 July 2003 17:16, Peter Murray-Rust wrote: > At 15:21 18/07/2003 +0200, E.L. Willighagen (Egon) wrote: > >On Friday 18 July 2003 15:14, Peter Murray-Rust wrote: > > > It generates a CDKMolecule and adds 2D coordinates and works. > > > >Does it remain the already known coordinates? Because that is what I want > > in JChemPaint... > > Well it could quite easily but I doubt that is what you want. I posted this > because this is what I wanted when we were talking. Ack. I haven't gotten around to fixing the cdk-fileconvertor yet to do the layout step... > I assume that what you want is to clean up a structure in which an author > has added or moved some atoms. That doesn't seem to be completely > automatic. Right. What I actually want is this: JCP now has to option to add hydrogens, and but the now get the 2D coordinates of the atom to which they are added. Only for the new H atoms, I want to calculate 2D coordinates... > If the new atoms are in a substituent then that could be laid out > separately and oriented/joined on the current 2D vector. Haven't thought of that... just making a new AtomContainer with the new atoms, and then do a layout... > That would be > relatively easy though might overlap with current structure. If the new > atoms alter a ring nucleus then I can't see an alternative to recomputing > the whole nucleus and probably the whole structure. As a simple example, > join the 1,6 atoms of cyclodecane with a 1 atom bridge. Do you just want to > layout the bridge? Maybe... a future option I want to add to JCP too, is the relayout of the selected atoms... and that might involve a situation like to one you gave as an example... Egon |
From: Peter Murray-R. <pm...@ca...> - 2003-07-18 16:43:24
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At 18:09 18/07/2003 +0200, E.L. Willighagen (Egon) wrote: > > I assume that what you want is to clean up a structure in which an author > > has added or moved some atoms. That doesn't seem to be completely > > automatic. > >Right. What I actually want is this: JCP now has to option to add hydrogens, >and but the now get the 2D coordinates of the atom to which they are added. >Only for the new H atoms, I want to calculate 2D coordinates... That should be straightforward. I'm busy this week but if you look at the 3D H generator I posted to CDK that should be easily tweaked to do 2D - there are fewer options and they should be easier. > > If the new atoms are in a substituent then that could be laid out > > separately and oriented/joined on the current 2D vector. > >Haven't thought of that... just making a new AtomContainer with the new >atoms, and then do a layout... That would be worth doing. > > That would be > > relatively easy though might overlap with current structure. If the new > > atoms alter a ring nucleus then I can't see an alternative to recomputing > > the whole nucleus and probably the whole structure. As a simple example, > > join the 1,6 atoms of cyclodecane with a 1 atom bridge. Do you just want to > > layout the bridge? > >Maybe... a future option I want to add to JCP too, is the relayout of the >selected atoms... and that might involve a situation like to one you gave as >an example... I would restrict it to chains and complete ring nuclei - then it will be fairly simple and robust. It will also be useful if you ever have to expand (say) Bz to a methylene and a benzene ring. P. >Egon |
From: Christoph S. <c.s...@un...> - 2003-07-21 12:29:30
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The StructureDiagramGenerator gradually builds coordinates by first=20 laying out ring systems and then doing chain by chain with decreasing=20 length. There are a couple of methods to do those single tasks and it should be=20 possible already to perform a lot of the layouts for fragments added to=20 an existing system. A writeup on how to do these things would be nice of course and I guess=20 that would be my task. We should start with a couple of explicit problems (start with=20 constitution X with coordinates and added fragment Y and Z, then do the=20 layout). Then we could see how to automate this stuff. Cheers, Chris --=20 Dr. Christoph Steinbeck (e-mail: c.s...@un...) Groupleader Junior Research Group for Applied Bioinformatics Cologne University BioInformatics Center (http://www.cubic.uni-koeln.de) Z=FClpicher Str. 47, 50674 Cologne Tel: +49(0)221-470-7426 Fax: +49 (0) 221-470-7786 What is man but that lofty spirit - that sense of enterprise. ... Kirk, "I, Mudd," stardate 4513.3.. Peter Murray-Rust wrote: > At 18:09 18/07/2003 +0200, E.L. Willighagen (Egon) wrote: >=20 >> > I assume that what you want is to clean up a structure in which an=20 >> author >> > has added or moved some atoms. That doesn't seem to be completely >> > automatic. >> >> Right. What I actually want is this: JCP now has to option to add=20 >> hydrogens, >> and but the now get the 2D coordinates of the atom to which they are=20 >> added. >> Only for the new H atoms, I want to calculate 2D coordinates... >=20 >=20 > That should be straightforward. I'm busy this week but if you look at=20 > the 3D H generator I posted to CDK that should be easily tweaked to do=20 > 2D - there are fewer options and they should be easier. >=20 >> > If the new atoms are in a substituent then that could be laid out >> > separately and oriented/joined on the current 2D vector. >> >> Haven't thought of that... just making a new AtomContainer with the ne= w >> atoms, and then do a layout... >=20 >=20 > That would be worth doing. >=20 >> > That would be >> > relatively easy though might overlap with current structure. If the = new >> > atoms alter a ring nucleus then I can't see an alternative to=20 >> recomputing >> > the whole nucleus and probably the whole structure. As a simple=20 >> example, >> > join the 1,6 atoms of cyclodecane with a 1 atom bridge. Do you just=20 >> want to >> > layout the bridge? >> >> Maybe... a future option I want to add to JCP too, is the relayout of = the >> selected atoms... and that might involve a situation like to one you=20 >> gave as >> an example... >=20 >=20 > I would restrict it to chains and complete ring nuclei - then it will b= e=20 > fairly simple and robust. It will also be useful if you ever have to=20 > expand (say) Bz to a methylene and a benzene ring. |
From: E.L. W. <eg...@sc...> - 2003-07-21 12:35:42
|
On Monday 21 July 2003 14:29, Christoph Steinbeck wrote: > The StructureDiagramGenerator gradually builds coordinates by first > laying out ring systems and then doing chain by chain with decreasing > length. > There are a couple of methods to do those single tasks and it should be > possible already to perform a lot of the layouts for fragments added to > an existing system. > A writeup on how to do these things would be nice of course and I guess > that would be my task. > We should start with a couple of explicit problems (start with > constitution X with coordinates and added fragment Y and Z, then do the > layout). Then we could see how to automate this stuff. A nice example, which I would appreciate very much, is the following: JCP can at this moment add hydrogens, but it does not create 2D coordinates for them yet, it just copies them from the atom to which the are attached... It would be nice if the example would show how coordinates for the hydrogens are calculated when added to a methane carbon, while keeping the C coords fixed... Egon |
From: Christoph S. <c.s...@un...> - 2003-07-22 07:42:48
|
E.L. Willighagen wrote: > On Monday 21 July 2003 14:29, Christoph Steinbeck wrote: >=20 >>The StructureDiagramGenerator gradually builds coordinates by first >>laying out ring systems and then doing chain by chain with decreasing >>length. >>There are a couple of methods to do those single tasks and it should be >>possible already to perform a lot of the layouts for fragments added to >>an existing system. >>A writeup on how to do these things would be nice of course and I guess >>that would be my task. >>We should start with a couple of explicit problems (start with >>constitution X with coordinates and added fragment Y and Z, then do the >>layout). Then we could see how to automate this stuff. >=20 >=20 > A nice example, which I would appreciate very much, is the following: >=20 > JCP can at this moment add hydrogens, but it does not create 2D coordin= ates=20 > for them yet, it just copies them from the atom to which the are attach= ed... > It would be nice if the example would show how coordinates for the hydr= ogens > are calculated when added to a methane carbon, while keeping the C coor= ds > fixed... Isn't that exactly what Peter was working on - indendently from what I=20 in the SDG module? Cheers, Chris --=20 Dr. Christoph Steinbeck (e-mail: c.s...@un...) Groupleader Junior Research Group for Applied Bioinformatics Cologne University BioInformatics Center (http://www.cubic.uni-koeln.de) Z=FClpicher Str. 47, 50674 Cologne Tel: +49(0)221-470-7426 Fax: +49 (0) 221-470-7786 What is man but that lofty spirit - that sense of enterprise. ... Kirk, "I, Mudd," stardate 4513.3.. |
From: E.L. W. <eg...@sc...> - 2003-07-22 09:31:46
|
On Tuesday 22 July 2003 09:42, Christoph Steinbeck wrote: > E.L. Willighagen wrote: > > A nice example, which I would appreciate very much, is the following: > > > > JCP can at this moment add hydrogens, but it does not create 2D > > coordinates for them yet, it just copies them from the atom to which the > > are attached... It would be nice if the example would show how > > coordinates for the hydrogens are calculated when added to a methane > > carbon, while keeping the C coords fixed... > > Isn't that exactly what Peter was working on - indendently from what I > in the SDG module? That was for 3D... Egon |
From: Peter Murray-R. <pm...@ca...> - 2003-07-26 09:40:23
|
At 11:31 22/07/2003 +0200, E.L. Willighagen wrote: >On Tuesday 22 July 2003 09:42, Christoph Steinbeck wrote: > > E.L. Willighagen wrote: > > > A nice example, which I would appreciate very much, is the following: > > > > > > JCP can at this moment add hydrogens, but it does not create 2D > > > coordinates for them yet, it just copies them from the atom to which the > > > are attached... It would be nice if the example would show how > > > coordinates for the hydrogens are calculated when added to a methane > > > carbon, while keeping the C coords fixed... > > > > Isn't that exactly what Peter was working on - indendently from what I > > in the SDG module? > >That was for 3D... Yes, but I said it would be fairly easy to convert to 2D. I was leaving that till Egon came over in August. The actual generation of H coordinates is easy - probably less than a mornings work - but there is the problem of overlap and that would take longer. I don't know whether CDK/JCP has a layout tweaker that minimises overlap. P. >Egon > > >------------------------------------------------------- >This SF.net email is sponsored by: VM Ware >With VMware you can run multiple operating systems on a single machine. >WITHOUT REBOOTING! Mix Linux / Windows / Novell virtual machines at the >same time. Free trial click here: http://www.vmware.com/wl/offer/345/0 >_______________________________________________ >Cdk-devel mailing list >Cdk...@li... >https://lists.sourceforge.net/lists/listinfo/cdk-devel |