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From: <nic...@sy...> - 2004-07-06 12:27:43
|
Hi Egon, Hi Joerg,
I have parsed a smile string, C(=N)C(=O)C, into a CDK molecule. All
was ok until I used the convert method to obtains a JOEMol object. This is
the result I found:
-ISIS- 3D
Used JOELib chemistry kernel (expert systems) ID is 715333816
5 4 0 0 0 0 0 0 0 0 1 V2000
0.0000 0.0000 0.0000 Xx 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 Xx 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 Xx 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 Xx 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 Xx 0 0 0 0 0 0 0 0 0 0 0 0
1 2 2 0 0 0 0
1 3 1 0 0 0 0
3 4 2 0 0 0 0
3 5 1 0 0 0 0
M END
$$$$
As you could see, the convert method forget the atoms symbol. On the other
hand, if H atoms are present in the molecule, they are well deferred.
I have a second question concerning the numbering of atoms; if you
asked for the getAtomNumber() method in CDK, it gives you a different number
than the getIdx() method from JOELib. So I have supposed that they were not
correlated. But, If you want to keep in memory the position of one atome in
CDK molecule, how could I retrieved this in my new JOEMol ?
Thanks for your help,
Nico
|
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From: NAJI H. <naj...@ul...> - 2004-07-05 14:01:30
|
HI JOERG=3B Thank very much for your advice =3A sh convert=2Esh yourOriginalFile=2Esm= i = phCorrectedFile=2Esmi=2E Now=2C I can transform my original file to = pHcorrectedfile but in the transformations I don=27t manage to convert C (=3DNH)(-NH2)(-NH-) to C(=3DNH2+)(-NH2)(-NH-) ( a guanidium group found = for example in the arginine ) I have another question =3A Have you got some ideas how I could make in = order to count the total number of hydrogen of a molecule from a smiles = string=2E For example =5BNH3+=5DCC(=5BO-=5D)=3DO (glycine) we have got for this co= mpound 6 = hydrogen=27s because I would like to convert Gibbs energy (pH=3D0) to = Gibbs energy (pH=3D7) with the formula deltaG=270(pH=3D7)=3D deltaG=270(p= H=3D0) =96 = NHRTln10-pH=2C where NH is the hydrogen number of the molecule=2E Kind Regards Naji |
|
From: Joerg K. W. <we...@in...> - 2004-07-02 12:45:35
|
Hi, CVS version has changed again ! Some time ago the performance was discussed: http://sourceforge.net/mailarchive/forum.php?thread_id=4857368&forum_id=26962 I've found another reason for a slower loading process. All molecules uses (since that release) a unique SMILES hash code, which enables uniqueness checkings. This must be calculated at least once, so this requires also runtime. 1. for creating unique renumbering (Morgan), runtime ~O(N^3), because it's a modified breadth first search (BFS). 2. hashing And because the actual up/down auto-detection contained a bug, all hash codes have changed. So, this is an offical warning for users using this code as part of an ID or something else. This should not in general used as primary key in a database, but for uniqueness checking this is a fast possibility, if you store this value. I think i will add a flag, use simple hashing or something else to be available with the next release in JOEMol, which then will avoid the 'unique' hashing method. But then also all auto-assign methods for cis/trans and up/down should use joelib.util.IsomerismDetection which is not the case at the moment (e.g. JOEMol2Smi has it's own method). So i've replaced the actual auto-detection method in the SMILES generator by the auto-detection method in // if the autoAssignFlag is true also up/down flags are assigned IsomerismDetection.isCisTransBond(bond, autoAssignFlag); Kind regards, Joerg -- Dipl. Chem. Joerg K. Wegner Center of Bioinformatics Tuebingen (ZBIT) Department of Computer Architecture Univ. Tuebingen, Sand 1, D-72076 Tuebingen, Germany Phone: (+49/0) 7071 29 78970 Fax: (+49/0) 7071 29 5091 E-Mail: mailto:we...@in... WWW: http://www-ra.informatik.uni-tuebingen.de -- Never mistake motion for action. (E. Hemingway) Never mistake action for meaningful action. (Hugo Kubinyi,2004) |
|
From: Joerg K. W. <we...@in...> - 2004-07-02 11:26:43
|
Hi all, o.k. bug and missing feature. Here are the details: 111. BUG (serious ! Please check the new functionality in CVS !) joelib.smiles.JOEMol2Smi https://sourceforge.net/tracker/?func=detail&atid=425969&aid=983990&group_id=39708 Was caused because the first atom was always detected as recognized. Fixed ! Furthermore i've found interchanged UP/DOWN assignments at the end of this method. So i've changed ALL assignment types. All users should check all kind of import/export methods affecting SMILES and SMARTS matching methods with up/down and cis/trans support heavily. PLEASE ! 222. Up/Down searching functionality in SMARTS was simply not activated Fixed ! I've added the test cases to joelib/src/resources/smartsEvaluation/evaluation.txt Please remember, that the internal auto-detection assign ALWAYS 'up' as preferred case. So cis cases will be always stored as up/up. In trans-cases the match is inverted. I will wait at least two weeks for a new release !!! If anyone of you has time, please check the modified recognition, which affects the SMILES export. ############################### ## cis/trans detection ############################### C\C=C/C a_carbon_in_abcd_with_trans trans-butene#1 C/C=C\C a_carbon_in_abcd_with_trans trans-butene#4 C/C=C/C a_carbon_in_abcd_with_trans trans-butene C\C=C\C a_carbon_in_abcd_with_trans trans-butene C\C=C\C a_carbon_in_abcd_with_cis cis-butene#1#4 # this can not be found for MDL SDF import, because JOELib's auto-assign method assign C\C=C\C !!! C/C=C/C a_carbon_in_abcd_with_cis cis-butene # C/C=C\C a_carbon_in_abcd_with_cis cis-butene C\C=C/C a_carbon_in_abcd_with_cis cis-butene Kind regards, Joerg > Thanks for your quick respose. However, this doesn't seem to change the > results I get for TestSmarts. > > * Joerg K. Wegner <we...@in...> [2004-06-30 10:18 +0200]: > >>Hi all, >> >>As already submitted be Gerd this is a bug in the SMARTS parser. So i >>opened a bug tracking task and will close it today and check in to CVS. >> >> >>>Bugs item #982570, was opened at 2004-06-30 08:09 >>>You can respond by visiting: >>> >> >>https://sourceforge.net/tracker/?func=detail&atid=425969&aid=982570&group_id=39708 >> >>>Initial Comment: >>>The SMARTS encoder writes Stereo-Up as '\' and >>>Stereo-Down as '/' but the specs says it vise versa. >>>---------------------------------------------------------------------- >>>You can respond by visiting: >>> >> >>https://sourceforge.net/tracker/?func=detail&atid=425969&aid=982570&group_id=39708 >> >>If you want a quick fix change line >>-2467- case ('/'): >>with >>-2479- case ('\\'): >> >>Kind regards, Joerg >> >> >>>Hi everyone, I'm new to Joelib and need a little help. >>> >>>I'm having trouble getting the TestSmarts[1] program to recognize >>>stereochemistry. For example, the SMARTS "C\C=C/C" won't match a >>>molecule made with that same SMILES string. I've tried several releases, >>>including the 2004-06-21, on Solaris. SMARTSEvaluationDefault.sh runs >>>with no mismatches. >>> >>>I run: >>> >>> >>>>java joelib.test.TestSmarts butene.trans.sdf C\\C=C/C >>> >>>where butene.trans.sdf is: >>> 4 3 0 0 1 0 999 V2000 >>> 0.8250 0.3572 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 >>> 0.4125 -0.3572 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 >>> -0.4125 -0.3572 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 >>> -0.8250 0.3572 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 >>> 1 2 1 0 0 0 0 >>> 2 3 2 0 0 0 0 >>> 3 4 1 0 0 0 0 >>>M END >>>$$$$ >>> >>>Any suggestions on what I may be doing wrong or what the problem is? >>> >>> 1. >>> http://www-ra.informatik.uni-tuebingen.de/software/joelib/api/joelib/test/TestSmarts.html >> >> >>-- >>Dipl. Chem. Joerg K. Wegner >>Center of Bioinformatics Tuebingen (ZBIT) >>Department of Computer Architecture >>Univ. Tuebingen, Sand 1, D-72076 Tuebingen, Germany >>Phone: (+49/0) 7071 29 78970 >>Fax: (+49/0) 7071 29 5091 >>E-Mail: mailto:we...@in... >>WWW: http://www-ra.informatik.uni-tuebingen.de >>-- >>Never mistake motion for action. >> (E. Hemingway) >> >>Never mistake action for meaningful action. >> (Hugo Kubinyi,2004) >> >> >> >>------------------------------------------------------- >>This SF.Net email sponsored by Black Hat Briefings & Training. >>Attend Black Hat Briefings & Training, Las Vegas July 24-29 - >>digital self defense, top technical experts, no vendor pitches, >>unmatched networking opportunities. Visit www.blackhat.com >>_______________________________________________ >>Joelib-help mailing list >>Joe...@li... >>https://lists.sourceforge.net/lists/listinfo/joelib-help > > -- Dipl. Chem. Joerg K. Wegner Center of Bioinformatics Tuebingen (ZBIT) Department of Computer Architecture Univ. Tuebingen, Sand 1, D-72076 Tuebingen, Germany Phone: (+49/0) 7071 29 78970 Fax: (+49/0) 7071 29 5091 E-Mail: mailto:we...@in... WWW: http://www-ra.informatik.uni-tuebingen.de -- Never mistake motion for action. (E. Hemingway) Never mistake action for meaningful action. (Hugo Kubinyi,2004) |
|
From: Joerg K. W. <we...@in...> - 2004-07-01 09:32:40
|
Hi NAJI, > A question if I use the Smarts in order to transform, for example (In > pH =7), COOH to COO- > HOW COULD I MAKE TO HAVE A SMILES FILE WHERE MOLECULES > ARE REPRESENTED IN PHYSIOLOGICAL PH) without change manually each > smiles of my file. So if i understand this correctly you are interested in: SMILES --> tranform to protonation state at pH=7 --> SMILES. Why do you not simply convert your structures from: sh convert.sh yourOriginalFile.smi phCorrectedFile.smi JOELib applys in the conversion process the pH state defined in joelib/src/joelib/data/plain/phmodel.txt So the only thing you must do is to provide JOElib with the correct protonation transofmation rules given there. So create and check e.g. joelib/src/joelib/data/plain/phmodel_pH7.txt and use in joelib/src/joelib.properties joelib.data.JOEPhModel.resourceFile=joelib/data/plain/phmodel_pH7.txt instead of the default entry. Kind regards, Joerg -- Dipl. Chem. Joerg K. Wegner Center of Bioinformatics Tuebingen (ZBIT) Department of Computer Architecture Univ. Tuebingen, Sand 1, D-72076 Tuebingen, Germany Phone: (+49/0) 7071 29 78970 Fax: (+49/0) 7071 29 5091 E-Mail: mailto:we...@in... WWW: http://www-ra.informatik.uni-tuebingen.de -- Never mistake motion for action. (E. Hemingway) Never mistake action for meaningful action. (Hugo Kubinyi,2004) |
|
From: NAJI H. <naj...@ul...> - 2004-07-01 08:56:32
|
Hi JOERG =2C Tuesday=2C I asked you a question about a Smiles file and you answered = (thank you again) me =3A = =D8 I would like to ask you if we can transform a Smiles file ( = where the = =3E smiles don=27t contain charges ) to a Smiles file where the molecules= = are = =3E charged (compounds and groups must be represented in their common = state = =3E in aqueous solution=2C at pH=3D7) = I think we are talking about SMARTS=2C not SMILES=2E So we are talking on= = regular expression patterns on graphs=2E SMILES is only a subset of = SMARTS=2E In fact =2C from your program joelib/src/joelib/desc/types/LogP and = others programs=2C I can develop a method that estimates Gibbs energy = of small biochemical compounds with a contribution group method=2E From a file Mol (with about 10000 compounds) I obtained a file Smiles=2E = Therefore=2C with the classes that treat =22smiles parser =2C smarts pars= er = =85) I could predict Gibbs energy of small biochemical compounds =2E But the trouble is that I was obliged to transform =22manually=22 each = smiles of my smiles file because in the mol files are not charged and=2C = compounds and groups must be represented in their common state = =3E in aqueous solution=2C at pH=3D7=2EThat=27s why I would like to obtai= n = directly a smiles File where compounds and groups must be represented = in their common state = =3E in aqueous solution=2C at pH=3D7=2E A question if I use the Smarts in order to transform=2C for example (In = pH =3D7)=2C COOH to COO- = and you advice me ( http=3A//www-ra=2Einformatik=2Euni- tuebingen=2Ede/software/joelib/tutorial/functionalities/mol- smarts=2Ehtml ) HOW COULD I MAKE TO HAVE A SMILES FILE WHERE MOLECULES = ARE REPRESENTED IN PHYSIOLOGICAL PH) without change manually each = smiles of my file=2E Kind Regards Naji = |
|
From: Joerg K. W. <we...@in...> - 2004-06-30 14:34:37
|
Hi Nicolas, > -> first, is there a silent mode, to avoid the printing of the descriptors > loading ? All debug, info, error messages can be switched off in the joelib/src/log4j.properties file. So switch all DEBUG and INFO to ERROR and nothing will be printed. > -> second, what is the meaning of the order of the values when for example > you ask for "Atom_in_donor" descriptor and you have as output the following > line: 5<0,0,1,0,0> ? > Is this mean that the atom label 2 is donor ? No, atom starts with 1,2,3, ..., N So atom 3 is a Donor. You can also use the general joelib.molecule.types.AtomProperties interface > -> third, I have asked for Gasteiger-Marsili calculation: a first one is > done without adding Hydrogens, and the second one with adding H in my > molecules. But, at the end the results are different. What does it means ? I > thought that this calculation take always the Hydrogens influence ? Oh, this is a critical question and has no general answer. From the computer science standpoint of view you these are two cases and some descriptors are sensitive to hydrogens, others are not. Why are some descriptors hydrogen independent ? 1. Some use only heavy weight atoms to calculate the descriptors. 2. Some simply remove the hydrogens, before they are calculated. Of course, this is a serious problem, when having the case that one whants all sigma partial charges and on the other side you are interested in one special descriptor using only heavy weight atoms BUT here with the sigma partial charge atom property. So this is and indexing conflict and of course can not be the same. So, if calculating and accessing atom properties you can/should check the hydrogen atom state of the molecule, which is not big deal. I've at least checked these things for the standard descriptor calculation class. The easiest solution is to remove hydrogens, because they are still implicitely available via the JOELib expert system, but on the other hand the user might be interested in protonated molecules assigned by another program, e.g. Corina which is also really good to assign hydrogens. > -> and fourth, how could you explain that, for the same molecule: > "Atom_in_donor" is 5<0,0,1,0,0> > "Atom_in_acceptor" is 5<0,0,0,1,0> > "Atom_in_donor_or_acceptor" is 5<0,0,0,0,0> ? It's only one kind of possible and really huge discrete assignment/label space. So, if you have a look at the used SMARTS pattern in and all literature references given there: joelib.desc.types.AtomInDonAcc joelib.desc.types.AtomInDonor joelib.desc.types.AtomInAcceptor see also joelib.desc.types.HBA1 joelib.desc.types.HBA2 joelib.desc.types.HBD1 joelib.desc.types.HBD2 you can see that they use all different descriptions. And additionally then remind that SMARTS matching is based on the chemical expert systems used, so even if you use the same SMARTS, you will with a high probability get a nice number of mismatches. E.g. i got once a time a complained from a NCI which compared the NCI and JOELib results. YES, that's a problem and i complain every time and in all publications, that we need here an 'chemical expert' system standard which we can test against. http://www-ra.informatik.uni-tuebingen.de/software/joelib/tutorial/atomtyper.html If you do not like them, create your own descriptor. If you want it more dynamic use SMARTS from a text file, but then i recommend to inroduce also an ID as done for the JOELib expert systems. This guarantees you that you will notice if another user changes on single SMARTS entry, which can definitely occur, because we are talking about expert systems. Which are a really evolving type of label assignment (or more general model/hypothesis). See here interfaces: joelib.data.SoftCodedKernel joelib.data.HardCodedKernel Kind regards, Joerg -- Dipl. Chem. Joerg K. Wegner Center of Bioinformatics Tuebingen (ZBIT) Department of Computer Architecture Univ. Tuebingen, Sand 1, D-72076 Tuebingen, Germany Phone: (+49/0) 7071 29 78970 Fax: (+49/0) 7071 29 5091 E-Mail: mailto:we...@in... WWW: http://www-ra.informatik.uni-tuebingen.de -- Never mistake motion for action. (E. Hemingway) Never mistake action for meaningful action. (Hugo Kubinyi,2004) |
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From: <nic...@sy...> - 2004-06-30 14:09:54
|
Hi All, I'm working with JOELib, more specially with descriptors. So, I have several question concerning the use of them; -> first, is there a silent mode, to avoid the printing of the descriptors loading ? -> second, what is the meaning of the order of the values when for example you ask for "Atom_in_donor" descriptor and you have as output the following line: 5<0,0,1,0,0> ? Is this mean that the atom label 2 is donor ? -> third, I have asked for Gasteiger-Marsili calculation: a first one is done without adding Hydrogens, and the second one with adding H in my molecules. But, at the end the results are different. What does it means ? I thought that this calculation take always the Hydrogens influence ? -> and fourth, how could you explain that, for the same molecule: "Atom_in_donor" is 5<0,0,1,0,0> "Atom_in_acceptor" is 5<0,0,0,1,0> "Atom_in_donor_or_acceptor" is 5<0,0,0,0,0> ? Thanks for the responses, regards, nico |
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From: Joerg K. W. <we...@in...> - 2004-06-30 08:53:10
|
Dear developers, dear community, as already mentioned i've less time at the moment and i can only guarantee to maintain JOELib as it should be maintained. I will also submit new functionalities, like maximum common substructure search in 2-3 months, then we have an extensively tested release. Now my help request to all developers and all people which can advertise our projects. Please bear in mind that i've plannded to end my PhD thesis until the middle of 2005, so we need also other people which are able to maintain JOELib, because my spare-time is restricted. But i've no time for refactor-maintenance, which recommended for long term time slides. I'm really interested in a QSAR data mining tool based on Java. http://joelib.sf.net http://qsar.sf.net http://octet.sourceforge.net/ http://cdk.sf.net And as you know JOELib has already some - descriptors and - data mining tools (Weka interface and class structure containing molecules) - basic algorithms, like sub-optimal distance matrix with O(N^3) - Labeling functions for molecular graphs as atom labels (atom properties) - Labeling functions for molecular graphs as bond labels (bond properties) I'm not sure if Rich and Egon have the same opinion, but from my standpoint of view it is crucial important that this community helps us to implement things. We, the project administrators can assign tasks and help you understand the actual packages, but we can not implement all things we need on our own, as at the moment. So, especially the JOELib project needs more developers and anybody which is willingly to implement the basic Octet-JOELib interface as starting point. Example was already given at: http://www-ra.informatik.uni-tuebingen.de/mitarb/wegner/tmp/octet/ The changes are found in CDKTools 0.2.1, which can be downloaded at: http://sourceforge.net/project/showfiles.php?group_id=96108 Javadoc is at: http://octet.sourceforge.net/api.html What i like to see in the interface is an analogue structure as shown here, especially with respect to the chemical expert systems (chemical kernel) in JOELib: The following ASAP articles were posted to the ACS Web Edition of Journal of Chemical Information and Computer Sciences on June 17, 2004. Title: Some Basic Data Structures and Algorithms for Chemical Generic Programming Authors: Wei Zhang, Tingjun Hou, Xuebin Qiao, and Xiaojie Xu Link: http://dx.doi.org/10.1021/ci049938s Kind regards, Joerg Kurt Wegner -- Dipl. Chem. Joerg K. Wegner Center of Bioinformatics Tuebingen (ZBIT) Department of Computer Architecture Univ. Tuebingen, Sand 1, D-72076 Tuebingen, Germany Phone: (+49/0) 7071 29 78970 Fax: (+49/0) 7071 29 5091 E-Mail: mailto:we...@in... WWW: http://www-ra.informatik.uni-tuebingen.de -- Never mistake motion for action. (E. Hemingway) Never mistake action for meaningful action. (Hugo Kubinyi,2004) |
|
From: Joerg K. W. <we...@in...> - 2004-06-30 08:16:00
|
Hi all, As already submitted be Gerd this is a bug in the SMARTS parser. So i opened a bug tracking task and will close it today and check in to CVS. > Bugs item #982570, was opened at 2004-06-30 08:09 > You can respond by visiting: > https://sourceforge.net/tracker/?func=detail&atid=425969&aid=982570&group_id=39708 > Initial Comment: > The SMARTS encoder writes Stereo-Up as '\' and > Stereo-Down as '/' but the specs says it vise versa. > ---------------------------------------------------------------------- > You can respond by visiting: > https://sourceforge.net/tracker/?func=detail&atid=425969&aid=982570&group_id=39708 If you want a quick fix change line -2467- case ('/'): with -2479- case ('\\'): Kind regards, Joerg > Hi everyone, I'm new to Joelib and need a little help. > > I'm having trouble getting the TestSmarts[1] program to recognize > stereochemistry. For example, the SMARTS "C\C=C/C" won't match a > molecule made with that same SMILES string. I've tried several releases, > including the 2004-06-21, on Solaris. SMARTSEvaluationDefault.sh runs > with no mismatches. > > I run: > >>java joelib.test.TestSmarts butene.trans.sdf C\\C=C/C > > where butene.trans.sdf is: > 4 3 0 0 1 0 999 V2000 > 0.8250 0.3572 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 0.4125 -0.3572 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > -0.4125 -0.3572 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > -0.8250 0.3572 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 1 2 1 0 0 0 0 > 2 3 2 0 0 0 0 > 3 4 1 0 0 0 0 > M END > $$$$ > > Any suggestions on what I may be doing wrong or what the problem is? > > 1. http://www-ra.informatik.uni-tuebingen.de/software/joelib/api/joelib/test/TestSmarts.html -- Dipl. Chem. Joerg K. Wegner Center of Bioinformatics Tuebingen (ZBIT) Department of Computer Architecture Univ. Tuebingen, Sand 1, D-72076 Tuebingen, Germany Phone: (+49/0) 7071 29 78970 Fax: (+49/0) 7071 29 5091 E-Mail: mailto:we...@in... WWW: http://www-ra.informatik.uni-tuebingen.de -- Never mistake motion for action. (E. Hemingway) Never mistake action for meaningful action. (Hugo Kubinyi,2004) |
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From: Joerg K. W. <we...@in...> - 2004-06-29 16:03:55
|
Hi NAJI,
> I would like to ask you if we can transform a Smiles file ( where the
> smiles don't contain charges ) to a Smiles file where the molecules are
> charged (compounds and groups must be represented in their common state
> in aqueous solution, at pH=7)
I think we are talking about SMARTS, not SMILES. So we are talking on
regular expression patterns on graphs. SMILES is only a subset of SMARTS.
Sure you can that's what i expect. If you have time you can also invent
tautomer transfomation rules with the same mechansim.
I would be happy if you will do.
Two possibilities:
1. Modify phmodel.txt and store in myPhModel.txt or what you like
Then change in src/joelib.properties the line
joelib.data.JOEPhModel.resourceFile=joelib/data/plain/phmodel.txt
to
joelib.data.JOEPhModel.resourceFile=joelib/data/plain/myPhModel.txt
2. If you want to use SMARTS transformations in general you can use the
joelib.data.JOEChemTransformation class
see tutorial
http://www-ra.informatik.uni-tuebingen.de/software/joelib/tutorial/functionalities/mol-smarts.html
So for each tranformation you want to apply you need such an instance.
The pH model uses simply a vector of such rules and applys them all.
For N tautomers or biotransformations you can simply call them NxN
times. Then you can try to remove duplicates by using a clever hash code
or whatever. Or you can try to avoid calculating them NxN by assuming a
clever heuristic, ... but's that's another thread, isn't it ? :-)
Kind regards, Joerg
> For example
> CC(N)C(O)=O>> CC([NH3+])C([O-])=O
> In the JOELib I observe source\src\joelib\data\plain/phmodel.txt
> #charged amine
> TRANSFORM [N^3;!$(N~[!#6;!#1]):1] >> [N+:1]
> #carboxylic acid
> TRANSFORM O=C[OQ1-0:1] >> O=C[O-:1]
> Therefore, can I change automatically with a programme in Joelib and
> with a phmodel.txt file a Smiles file file ( where the smiles don't
> contain charges ) to a Smiles file where the molecules are charged
> (compounds and groups must be represented in their common state in
> aqueous solution, at pH=7)
--
Dipl. Chem. Joerg K. Wegner
Center of Bioinformatics Tuebingen (ZBIT)
Department of Computer Architecture
Univ. Tuebingen, Sand 1, D-72076 Tuebingen, Germany
Phone: (+49/0) 7071 29 78970
Fax: (+49/0) 7071 29 5091
E-Mail: mailto:we...@in...
WWW: http://www-ra.informatik.uni-tuebingen.de
--
Never mistake motion for action.
(E. Hemingway)
Never mistake action for meaningful action.
(Hugo Kubinyi,2004)
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From: NAJI H. <naj...@ul...> - 2004-06-29 14:00:41
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Hi all, I would like to ask you if we can transform a Smiles file ( where the smiles don't contain charges ) to a Smiles file where the molecules are charged (compounds and groups must be represented in their common state in aqueous solution, at pH=7) For example CC(N)C(O)=O>> CC([NH3+])C([O-])=O In the JOELib I observe source\src\joelib\data\plain/phmodel.txt #charged amine TRANSFORM [N^3;!$(N~[!#6;!#1]):1] >> [N+:1] #carboxylic acid TRANSFORM O=C[OQ1-0:1] >> O=C[O-:1] Therefore, can I change automatically with a programme in Joelib and with a phmodel.txt file a Smiles file file ( where the smiles don't contain charges ) to a Smiles file where the molecules are charged (compounds and groups must be represented in their common state in aqueous solution, at pH=7) If I can Could you tell me What classes I could use. Kind Regards Naji |
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From: Joerg K. W. <we...@in...> - 2004-06-21 15:50:39
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Minor feature enhancement release: https://sourceforge.net/forum/forum.php?forum_id=385130 -- Dipl. Chem. Joerg K. Wegner Center of Bioinformatics Tuebingen (ZBIT) Department of Computer Architecture Univ. Tuebingen, Sand 1, D-72076 Tuebingen, Germany Phone: (+49/0) 7071 29 78970 Fax: (+49/0) 7071 29 5091 E-Mail: mailto:we...@in... WWW: http://www-ra.informatik.uni-tuebingen.de -- Never mistake motion for action. (E. Hemingway) Never mistake action for meaningful action. (Hugo Kubinyi,2004) |
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From: Joerg K. W. <we...@in...> - 2004-06-15 15:54:44
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Hi JOElib members, this is a cross-post from the developer mailing list, because i think some of you might be also interested in a SMARTS pattern discussion. For previous mails, see developer mailing list. Kind regards, Joerg -- Dipl. Chem. Joerg K. Wegner Center of Bioinformatics Tuebingen (ZBIT) Department of Computer Architecture Univ. Tuebingen, Sand 1, D-72076 Tuebingen, Germany Phone: (+49/0) 7071 29 78970 Fax: (+49/0) 7071 29 5091 E-Mail: mailto:we...@in... WWW: http://www-ra.informatik.uni-tuebingen.de -- Never mistake motion for action. (E. Hemingway) Never mistake action for meaningful action. (Hugo Kubinyi,2004) |
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From: Joerg K. W. <we...@in...> - 2004-06-15 15:49:31
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Hi naji, i will forward this also to the mailing list. Hope you don't mind. I=20 think this is a general question and also interesting for other=20 users/developers. > 1) >NH(participating in a ring ) > [#7;r;H1;$(*-*);$(*-*)] it matches NH in C1CNC=3DCC=3DC1 but > it doesn't match a NH of a heteroaromatic ring for example : cytosine = ( how could I do?) So as said aromatic, means aromatic bonds (:) and not aliphatic bonds (-)= . So use $(:) or try another representation, e.g. nitrogen in ring with=20 two heavy weight neighbours, implicite+explicite number of hydrogens is=20 still one. [#7;r;H1;Q2] > 2) [c+0X3&H0](:n)(:a) with this pattern I wanted to match 2*(ring> C=3D= ) (participating in two fused non-benzene rings) > in the adenosine (heteroaromatic ring) The number of participating rings to an atom is [R] The ring size is [r] So what's with [c;R2](:n) I think (:a) will match always if you use [c], so i will skip this. Aromatic [c,n] or nonaromatic [C,N] ? I think i've still not completely=20 understood your pattern request. > [c+0X3&H0](:n)(A) with this pattern I wanted to match 1*(ring> C=3D) = (two single bonds participating in a non- benzene ring) in the cytosine > there is a problem when I run the program (the same program that joelib= /src/joelib/desc/types/logP).Although *(ring> C=3D)(adenosine) and *(ri= ng> C=3D) (cytosine) are different ( in regard to contribution group) I d= on't manage to differ them how could I make?). In fact , I would like to = estimate standard Gibbs energy changes of biochemical compounds and I try= to convert from a table the different groups (nitrogen,oxygen,etc..)of t= he contribution group to smarts pattern.For small molecules there is not = very difficult but for the rings (benzene ,heteroaromatic rings=85) I enc= ounter some problems to differ the different molecular fragments of those= rings. =20 I recommend to use the added SMARTS matching code in the CVS, so you can=20 proceed much faster to generate and test different SMARTS patterns. Just add the single molecule file MDL-SD with .mol extension to=20 joelib/src/resource/smartsEvaluation/*.mol and add your test patterns to joelib/src/resource/smartsEvaluation/evaluation.txt So you can try different things and you can also see the internal=20 representation of these patterns in the result file. So you can work in=20 a kind of 'debugging mode'. > 3)> C=3D (participating in two fused non-benzene rings) > [r;!a]~[#6]~[r;!a] two non-aromatic rings connected via=20 > aliphatic/aromatic via any bonds but how could I find the smarts patte= rn if I have adenosine as molecule. Is the adenine part really non-aromatic ? If you want only exclude aromatic six rings i would use. [r6;!a]~[#6]~[r6;!a] But i'm not sure if this will match, because the 5-ring looks really=20 imidazol like :-) > 4) > C=3D (the formal double bond and a formal single bond participatin= g in a non-benzene ring) > difference to -CH=3D ? for example,in the cytosine, there are 1 fragme= nt of > C=3D (the formal double bond and a formal single bond participati= ng in=20 > a non-benzene ring) and an other fragment t -CH=3D (participating in a= non benzene ring) Definitely aromatic in cytosine, because Keto-Enol-Tautomerism ! So, i would say n:c:n > 5) how could I differ(with smarts pattern) cH aromatic of the benzene =96= CH=3D (participating in a benzene ring) and cH aromatic of the tyrosine (= cH of the phenol fragment).The contribution of those fragments is difeere= nt. From the SMARTS standpoint of view there does not exists -CH=3D in=20 benzene. Because the 'atom typer' expert systems (chemical kernel) in=20 JOELib assigns 'c:c' to all carbon atoms connected with aromatic bonds. So the only difference to the phenol part of tyrosine is 'c-OH' the=20 aliphatic bond to the hydroxyl group. Again, please use the matching module submitted to CVS, so you can try=20 the different options. Furthermore you can have a look at http://www-ra.informatik.uni-tuebingen.de/software/joelib/tutorial/atomty= per.html and you can see that the aromaticity is the first step of the atom=20 typing process, followed by the hybridization and the implicite valence. The SMARTS matching and also the real 'atom typer' works on the=20 previously assigned 'expert systems' of the chemical kernel. Kind regards, Joerg --=20 Dipl. Chem. Joerg K. Wegner Center of Bioinformatics Tuebingen (ZBIT) Department of Computer Architecture Univ. Tuebingen, Sand 1, D-72076 Tuebingen, Germany Phone: (+49/0) 7071 29 78970 Fax: (+49/0) 7071 29 5091 E-Mail: mailto:we...@in... WWW: http://www-ra.informatik.uni-tuebingen.de -- Never mistake motion for action. (E. Hemingway) Never mistake action for meaningful action. (Hugo Kubinyi,2004) |
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From: Joerg K. W. <we...@in...> - 2004-06-15 12:46:10
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Hi all, 1. SMARTS matching test class to check cross-dependencies for the atom typer or simple testing purpose. So, this is the first step to be able to formulate a classification problem for the atom type assignment process. So let me know if you are interested to discuss the details for this idea. I think this can be published, also. 2. I'm preparing a new updated CVS version and i've added the SMARTS testing class joelib/src/joelib/smarts/test/SMARTSEvaluation.java and the examples defined in joelib/src/resource/smartsEvaluation/evaluation.txt and all the corresponding molecule files joelib/src/resource/smartsEvaluation/*.mol to the CVS of JOELib. Please remember that the CVS checkout process has changed: http://sourceforge.net/cvs/?group_id=39708 The included default batch testing can be started with: SMARTSEvaluationDefault.sh The result is stored in: evaluationResult.txt and should look like the following lines, if no error occured. If mismatches occured they will be printed first ! ====================================================== Checking 73 SMARTS patterns. ---------------------------------------------- Correct matches: 315 Mismatches: 0 ---------------------------------------------- Parsed SMARTS patterns: [#8][#1] hydroxy_group_explicit_h LEAF(ELEM,8) vb: 0 OR(SINGLE,AROM) with grow: true src: 0 dst: 1 LEAF(ELEM,1) vb: 0 ---------------------------------------------- [#8;H1] hydroxy_group ANDLO(LEAF(ELEM,8),LEAF(HCOUNT,1)) vb: 0 ---------------------------------------------- [*;!#6;r3] heteroatoms_in_3-ring ANDLO(ANDLO(LEAF(CONST,1),NOT(LEAF(ELEM,6))),LEAF(SIZE,3)) vb: 0 Kind regards, Joerg -- Dipl. Chem. Joerg K. Wegner Center of Bioinformatics Tuebingen (ZBIT) Department of Computer Architecture Univ. Tuebingen, Sand 1, D-72076 Tuebingen, Germany Phone: (+49/0) 7071 29 78970 Fax: (+49/0) 7071 29 5091 E-Mail: mailto:we...@in... WWW: http://www-ra.informatik.uni-tuebingen.de -- Never mistake motion for action. (E. Hemingway) Never mistake action for meaningful action. (Hugo Kubinyi,2004) |
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From: Joerg K. W. <we...@in...> - 2004-06-15 09:46:29
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And again,
see also:
joelib.desc.types.SSKey3DS in method getFingerprintPatterns()
see also:
joelib/data/plain/*.contributions for MR, PSA, LogP SMARTS contribution
patterns.
They contain no $(...) environments, which is the most powerfull tool in
SMARTS expression searching, so i recommend to use it heavily, although
it is also time consuming.
Here are three more examples:
patty.addRule("[$([NH2]-c),ND1H3,ND2H2,ND3H1,ND2H1,$(Cl-[C,c]),$(Br-[C,c]),$(I-[C,c])]",
"donor");
patty.addRule("[$(N#C-[C,c]),OD1X1,OD2X2,ND3X3,ND2X2]",
"acceptor");
patty.addRule("[$([NH2]-C),$([OH]-C),$([OH]-c)]", "donoracceptor");
So, now you've nearly all public examples in JOELib collected in these
mails.
I've also a SMARTS testing environment with side effect testing when
changing the atom typer. Very usefull, for changing the expert system.
I've used it also to resolve the aromaticity typer problems without
loosing generalization ability.
So i will publish these classes and all molecular structures with the
next release, so please be patient. Once a time if already submitted
these classes to the JOELib/OpenBabel mailing list, but i will it make
more official and write some documentation for this pretty piece of code.
Kind, regards, Joerg
> Hi,
>
> sorry, replace all
> ,=or statement
> ;=and statement
>
>> Hi naji,
>>
>> so here are my guesses, no gurantee that the SMART patterns work. So
>> please resend the tested/working patterns.
>>
>>>> C= (participating in two fused benzene rings)
>>
>>
>> c~[#6]~c two benzene rings connected via aliphatic/aromatic via any bonds
>> or general aromatic rings ?
>> [r;a]~[#6]~[r;a]
>>
>>>> C= (participating in two fused non-benzene rings)
>>
>>
>> [r;!a]~[#6]~[r;!a] two non-aromatic rings connected via
>> aliphatic/aromatic via any bonds
>>
>>>> C= (participating in two fused rings: one benzene ring and one
>>>> non-benzene ring)
>>
>>
>> [r;!a]~[#6]~[r;a]
>>
>>> -CH=( participating in a benzene ring)
>>>
>>>> C= (the formal double bond and a formal single bond participating in
>>>> a benzene ring)
>>
>>
>> [#6,a,Q2,$(*-*),$(*=*)] so two heavy weight neighbors and neighbour
>> environments with $(...), here general aromatic ring.
>> You can also work with hybridisation states using ^2, see
>> joelib/data/plain/*.txt for examples
>>
>>>> C= (two single bonds participating in a non- benzene ring)
>>
>>
>> with or without implicite hydrogens, so X or D or Q
>> http://www-ra.informatik.uni-tuebingen.de/software/joelib/tutorial/functionalities/mol-smarts.html
>>
>> and reference and link to daylight tutorial.
>> [#6,!a,r,Q2,$(*-*),$(*-*)] so two heavy weight neighbours, here
>> general non-aromatic ring
>>
>>> -CH=( participating in a non- benzene ring)
>>
>>
>> [#6,!a,r,Q2,$(*-*),$(*=*)]
>>
>>>> C= (the formal double bond and a formal single bond participating in
>>>> a non-benzene ring)
>>
>>
>> difference to -CH= ?
>>
>>> =N- (participating in a ring )
>>
>>
>> [#7,r,Q2,$(*-*),$(*-*)] so assuming any ring, or only aliphatic ones ?
>>
>>>> NH(participating in a ring )
>>
>>
>> [#7,r,H1,$(*-*),$(*-*)]
>>
>>> -N< (participating in a ring )
>>> -N< (participating in two fused rings )
>>
>>
>> analogue to C, more or less.
>>
>>> Any suggestions?
>>
>>
>> Yes :-)
>>
>>> Thanks
>>
>>
>> Was me a pleasure.
>>
>> Kind regards, Joerg
>
>
>
--
Dipl. Chem. Joerg K. Wegner
Center of Bioinformatics Tuebingen (ZBIT)
Department of Computer Architecture
Univ. Tuebingen, Sand 1, D-72076 Tuebingen, Germany
Phone: (+49/0) 7071 29 78970
Fax: (+49/0) 7071 29 5091
E-Mail: mailto:we...@in...
WWW: http://www-ra.informatik.uni-tuebingen.de
--
Never mistake motion for action.
(E. Hemingway)
Never mistake action for meaningful action.
(Hugo Kubinyi,2004)
|
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From: Joerg K. W. <we...@in...> - 2004-06-15 09:29:48
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Hi, sorry, replace all ,=or statement ;=and statement > Hi naji, > > so here are my guesses, no gurantee that the SMART patterns work. So > please resend the tested/working patterns. > >>> C= (participating in two fused benzene rings) > > c~[#6]~c two benzene rings connected via aliphatic/aromatic via any bonds > or general aromatic rings ? > [r;a]~[#6]~[r;a] > >>> C= (participating in two fused non-benzene rings) > > [r;!a]~[#6]~[r;!a] two non-aromatic rings connected via > aliphatic/aromatic via any bonds > >>> C= (participating in two fused rings: one benzene ring and one >>> non-benzene ring) > > [r;!a]~[#6]~[r;a] > >> -CH=( participating in a benzene ring) >> >>> C= (the formal double bond and a formal single bond participating in >>> a benzene ring) > > [#6,a,Q2,$(*-*),$(*=*)] so two heavy weight neighbors and neighbour > environments with $(...), here general aromatic ring. > You can also work with hybridisation states using ^2, see > joelib/data/plain/*.txt for examples > >>> C= (two single bonds participating in a non- benzene ring) > > with or without implicite hydrogens, so X or D or Q > http://www-ra.informatik.uni-tuebingen.de/software/joelib/tutorial/functionalities/mol-smarts.html > > and reference and link to daylight tutorial. > [#6,!a,r,Q2,$(*-*),$(*-*)] so two heavy weight neighbours, here general > non-aromatic ring > >> -CH=( participating in a non- benzene ring) > > [#6,!a,r,Q2,$(*-*),$(*=*)] > >>> C= (the formal double bond and a formal single bond participating in >>> a non-benzene ring) > > difference to -CH= ? > >> =N- (participating in a ring ) > > [#7,r,Q2,$(*-*),$(*-*)] so assuming any ring, or only aliphatic ones ? > >>> NH(participating in a ring ) > > [#7,r,H1,$(*-*),$(*-*)] > >> -N< (participating in a ring ) >> -N< (participating in two fused rings ) > > analogue to C, more or less. > >> Any suggestions? > > Yes :-) > >> Thanks > > Was me a pleasure. > > Kind regards, Joerg -- Dipl. Chem. Joerg K. Wegner Center of Bioinformatics Tuebingen (ZBIT) Department of Computer Architecture Univ. Tuebingen, Sand 1, D-72076 Tuebingen, Germany Phone: (+49/0) 7071 29 78970 Fax: (+49/0) 7071 29 5091 E-Mail: mailto:we...@in... WWW: http://www-ra.informatik.uni-tuebingen.de -- Never mistake motion for action. (E. Hemingway) Never mistake action for meaningful action. (Hugo Kubinyi,2004) |
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From: Joerg K. W. <we...@in...> - 2004-06-15 09:25:58
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Hi naji, so here are my guesses, no gurantee that the SMART patterns work. So please resend the tested/working patterns. >>C= (participating in two fused benzene rings) c~[#6]~c two benzene rings connected via aliphatic/aromatic via any bonds or general aromatic rings ? [r;a]~[#6]~[r;a] >>C= (participating in two fused non-benzene rings) [r;!a]~[#6]~[r;!a] two non-aromatic rings connected via aliphatic/aromatic via any bonds >>C= (participating in two fused rings: one benzene ring and one non-benzene ring) [r;!a]~[#6]~[r;a] > -CH=( participating in a benzene ring) > >>C= (the formal double bond and a formal single bond participating in a benzene ring) [#6,a,Q2,$(*-*),$(*=*)] so two heavy weight neighbors and neighbour environments with $(...), here general aromatic ring. You can also work with hybridisation states using ^2, see joelib/data/plain/*.txt for examples >>C= (two single bonds participating in a non- benzene ring) with or without implicite hydrogens, so X or D or Q http://www-ra.informatik.uni-tuebingen.de/software/joelib/tutorial/functionalities/mol-smarts.html and reference and link to daylight tutorial. [#6,!a,r,Q2,$(*-*),$(*-*)] so two heavy weight neighbours, here general non-aromatic ring > -CH=( participating in a non- benzene ring) [#6,!a,r,Q2,$(*-*),$(*=*)] >>C= (the formal double bond and a formal single bond participating in a non-benzene ring) difference to -CH= ? > =N- (participating in a ring ) [#7,r,Q2,$(*-*),$(*-*)] so assuming any ring, or only aliphatic ones ? >>NH(participating in a ring ) [#7,r,H1,$(*-*),$(*-*)] > -N< (participating in a ring ) > -N< (participating in two fused rings ) analogue to C, more or less. > Any suggestions? Yes :-) > Thanks Was me a pleasure. Kind regards, Joerg -- Dipl. Chem. Joerg K. Wegner Center of Bioinformatics Tuebingen (ZBIT) Department of Computer Architecture Univ. Tuebingen, Sand 1, D-72076 Tuebingen, Germany Phone: (+49/0) 7071 29 78970 Fax: (+49/0) 7071 29 5091 E-Mail: mailto:we...@in... WWW: http://www-ra.informatik.uni-tuebingen.de -- Never mistake motion for action. (E. Hemingway) Never mistake action for meaningful action. (Hugo Kubinyi,2004) |
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From: naji h. <sun...@or...> - 2004-06-15 09:00:42
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HI all, By using Smarts patterns I don't manage to differ some molecu= lar fragments (see below). It's a problem because each group has a diff= erent contribution in order to calculate a property. For example: I do= n't know how I could make (with Smarts patterns) to differ those groups.=0D = >C=3D (participating in two fused benzene rings) >C=3D (participating in= two fused non-benzene rings) >C=3D (participating in two fused rings: = one benzene ring and one non-benzene ring) -CH=3D( participating in a be= nzene ring) >C=3D (the formal double bond and a formal single bond parti= cipating in a benzene ring) >C=3D (two single bonds participating in a n= on- benzene ring) -CH=3D( participating in a non- benzene ring) >C=3D (= the formal double bond and a formal single bond participating in a non-be= nzene ring) =3DN- (participating in a ring ) >NH(participating in a rin= g ) -N< (participating in a ring ) -N< (participating in two fused ring= s ) Any suggestions? Thanks Naji |
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From: Joerg K. W. <we...@in...> - 2004-06-11 08:50:52
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Hi, was added to support request with a very low priority. If anyone has time this is not that difficult, if you are having a closer look at: joelib/src/joelib/io/types/MDLSD.java joelib/src/joelib/smiles/JOESmilesParser.java Only 'Rnumber' entries should be parsed and stored in 'RgroupDescriptors ' as done by MDLSD.java Then you can use e.g. the joelib/src/joelib/molecule/generation/MolGenerationHelper.java to attach Rgroups to this scaffold. Support Requests item #970983, was opened at 2004-06-11 08:44 Message generated for change (Tracker Item Submitted) made by Item Submitter You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=425970&aid=970983&group_id=39708 Category: SMARTS/SMILES Group: None Status: Open Priority: 1 Submitted By: Joerg Kurt Wegner (wegner) Assigned to: Joerg Kurt Wegner (wegner) Summary: Allow Rgroup 'Rnumber' entry in SMILES pattern Kind regards, Joerg -- Dipl. Chem. Joerg K. Wegner Center of Bioinformatics Tuebingen (ZBIT) Department of Computer Architecture Univ. Tuebingen, Sand 1, D-72076 Tuebingen, Germany Phone: (+49/0) 7071 29 78970 Fax: (+49/0) 7071 29 5091 E-Mail: mailto:we...@in... WWW: http://www-ra.informatik.uni-tuebingen.de -- Never mistake motion for action. (E. Hemingway) Never mistake action for meaningful action. (Hugo Kubinyi,2004) |
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From: <nic...@sy...> - 2004-06-09 13:38:11
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Hi Joerg, I think we could associate R as an R.group, indeed. Where we can use the R symbol is for an attachement point in a fragment or substituent in order to respect valency. CDK currently use this notation in the SmilesParser and SmilesGenerator methods(). But for calculation, the R notation doesn't have any chemical sens. Regards, Nico |
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From: Joerg K. W. <we...@in...> - 2004-06-09 13:17:47
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Hi Nicolas, 1. CDK->JOELib Egon, can you have a look or are you busy? 2. R in SMILES Is not allowed at the moment! What expresses R in real life ? Is this analogue to the rGroup, which is allowed in SDF ? Kind regards, Joerg -- Dipl. Chem. Joerg K. Wegner Center of Bioinformatics Tuebingen (ZBIT) Department of Computer Architecture Univ. Tuebingen, Sand 1, D-72076 Tuebingen, Germany Phone: (+49/0) 7071 29 78970 Fax: (+49/0) 7071 29 5091 E-Mail: mailto:we...@in... WWW: http://www-ra.informatik.uni-tuebingen.de -- Never mistake motion for action. (E. Hemingway) Never mistake action for meaningful action. (Hugo Kubinyi,2004) |
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From: <nic...@sy...> - 2004-06-09 13:10:41
|
Hi all,
I have two questions concerning the convert() method in JOELib in
order to transform a CDK molecule in a JOEMol molecule:
Convertor conv = new Convertor();
JOEMol joemol = conv.convert(CDKmolecule);
When I try to do this, my resulting molecule contains bonds but not the
atoms:
-ISIS- 3D
Used JOELib chemistry kernel (expert systems) ID is 715333816
3 2 0 0 0 0 0 0 0 0 1 V2000
0.0000 0.0000 0.0000 Xx 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 Xx 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 Xx 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
2 3 1 0 0 0 0
M END
$$$$
instead of:
-ISIS- 3D
Used JOELib chemistry kernel (expert systems) ID is 715333816
3 2 0 0 0 0 0 0 0 0 1 V2000
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
2 3 1 0 0 0 0
M END
$$$$
This second output result from a CDKmolecule to smile conversion first, and
then, a smile To JOEmol conversion.
An other problem is about the pseudoAtom R: When I try to parse this smile:
[*]CO, I have the following error:
[*]CO
14:03:55 [ERROR] joelib.molecule.JOEMol - _mod is negative - EndModify()
called too many times
SMILES entry "[*]CO" could not be loaded.
Thanks,
best regards,
Nico
|
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From: Joerg W. <we...@in...> - 2004-06-04 15:21:51
|
Hi again, JCAMP is definitely not available from the command line. It is more ahidden feature in JOELib, so has the user used it's own developer interface ? If yes, details would be helpfull to find the problems. Kind regards, Joerg On Thu, 3 Jun 2004, Stefan Kuhn wrote: > Hi everybody, > I have a question about the jcamp parser: Which Versions of jcamp data = can be=20 > read? Because one of our users says: "I have tried V 5.0, 5.01 and 6.0,= but=20 > none of the files, which have been generated by our NMR-software works.= "=20 > Could you shed some light on this? > Thanks > Stefan > --=20 > Stefan Kuhn M. A. > Cologne University BioInformatics Center (http://www.cubic.uni-koeln.de= ) > Z=C3=BClpicher Str. 47, 50674 Cologne > Tel: +49(0)221-470-7428 Fax: +49 (0) 221-470-7786 > My public PGP key is available at http://pgp.mit.edu >=20 >=20 >=20 > ------------------------------------------------------- > This SF.Net email is sponsored by the new InstallShield X. > >From Windows to Linux, servers to mobile, InstallShield X is the one > installation-authoring solution that does it all. Learn more and > evaluate today! http://www.installshield.com/Dev2Dev/0504 > _______________________________________________ > Joelib-devel mailing list > Joe...@li... > https://lists.sourceforge.net/lists/listinfo/joelib-devel >=20 Dipl. Chem. Joerg K. Wegner Center of Bioinformatics Tuebingen (ZBIT) Department of Computer Architecture Univ. Tuebingen, Sand 1, D-72076 Tuebingen, Germany Phone: (+49/0) 7071 29 78970 Fax: (+49/0) 7071 29 5091 E-Mail: mailto:we...@in... WWW: http://www-ra.informatik.uni-tuebingen.de -- Never mistake motion for action. (E. Hemingway) =20 Never mistake action for meaningful action. (Hugo Kubinyi,2004) = =20 |
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