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From: Pascal M. <pas...@gm...> - 2011-08-24 11:36:02
|
Hi, > Hi have tried the following: > alcohol = pybel.Smarts('[OX2H]') > ketone = pybel.Smarts('[#6][CX3](=O)[#6]') > carboxylic_acid = pybel.Smarts('[CX3](=O)[OX2H1]') > Which finds an alcohol a ketone and a carboxylic acid and it should only > find a carboxylic acid. Indeed, [CX3](=O)[OX2H1] is correct and find only carboxylic acid. > If I try the following: > which should not find a alcohol or ketone if they are part of a carboxylic > acid > alcohol = pybel.Smarts('[OX2H];!$[CX3](=O)[OX2H1]') I think that the first atom after the $ sign should be the atom you consider --> O and not C in your exemple. So: [OX2H1;!$(OC=O)] [OX2H1;!$([OX2H1]C=O)] But what about avoiding "!" for more easy to read expression: alcool = pybel.Smarts("[OX2H][CX4,c]") alcoolCH = pybel.Smarts("[OX2H][CX4][H]") Regards, Pascal |
From: Jurgens de B. <deb...@gm...> - 2011-08-24 10:32:46
|
Hi have tried the following: alcohol = pybel.Smarts('[OX2H]') ketone = pybel.Smarts('[#6][CX3](=O)[#6]') carboxylic_acid = pybel.Smarts('[CX3](=O)[OX2H1]') Which finds an alcohol a ketone and a carboxylic acid and it should only find a carboxylic acid. If I try the following: which should not find a alcohol or ketone if they are part of a carboxylic acid alcohol = pybel.Smarts('[OX2H];!$[CX3](=O)[OX2H1]') ketone = pybel.Smarts('[#6][CX3](=O)[#6];!$[CX3](=O)[OX2H1]') I get "Invalid Smart" which is probably my fault. Thanks On 24 August 2011 10:34, Pascal Muller <pas...@gm...> wrote: > Hi, > > > I am searching for a number of active groups in molecules using smarts > and > > it so happens that some of the groups overlap. Thus would it be possible > to > > write a smart stating to find a group but it should not be part of > another > > group. > > smartA = "Some Smart" > > SmartB ='SecondSmart not part of SmartA' > > smartA = C(F)(F)F) > > smartB = A[#6;!$(C(F)(F)F)] > (Aliphatic atom single-bonded to any carbon which isn't a trifluromethyl > carbon) > > http://www.daylight.com/dayhtml_tutorials/languages/smarts/#LOGIC > "!" means "not" - but I guess you already knew that... Doesn't it > match your needs? > > Regards, > Pascal > -- Regards/Groete/Mit freundlichen Grüßen/recuerdos/meilleures salutations/ distinti saluti/siong/duì yú/привет Jurgens de Bruin |
From: Pascal M. <pas...@gm...> - 2011-08-24 08:35:01
|
Hi, > I am searching for a number of active groups in molecules using smarts and > it so happens that some of the groups overlap. Thus would it be possible to > write a smart stating to find a group but it should not be part of another > group. > smartA = "Some Smart" > SmartB ='SecondSmart not part of SmartA' smartA = C(F)(F)F) smartB = A[#6;!$(C(F)(F)F)] (Aliphatic atom single-bonded to any carbon which isn't a trifluromethyl carbon) http://www.daylight.com/dayhtml_tutorials/languages/smarts/#LOGIC "!" means "not" - but I guess you already knew that... Doesn't it match your needs? Regards, Pascal |
From: Jurgens de B. <deb...@gm...> - 2011-08-24 08:19:01
|
Hi, I am searching for a number of active groups in molecules using smarts and it so happens that some of the groups overlap. Thus would it be possible to write a smart stating to find a group but it should not be part of another group. smartA = "Some Smart" SmartB ='SecondSmart not part of SmartA' Thanks -- Regards/Groete/Mit freundlichen Grüßen/recuerdos/meilleures salutations/ distinti saluti/siong/duì yú/привет Jurgens de Bruin |
From: Gonzalo H. <gon...@gm...> - 2011-08-18 17:20:10
|
Hi, I've been working on extracting a SMARTS string from a molecule centered on a given atom and to a given number of shells. So far, I can do it but the possition of the substituents depend on the atoms Idx's. I would like to canonalized the SMARTS in some way so they are the same string when the same environment is extracted from different molecules. Do you have any idea how to do this? Thanks you, Gonzalo. -- --- "For the determined mind, it's not a matter of 'if' it's a matter of 'when'" T. Sanchez |
From: Geoffrey H. <ge...@ge...> - 2011-08-18 17:04:29
|
On Aug 18, 2011, at 5:28 AM, Jurgens de Bruin wrote: > What I would like to know is which atoms belong to the same Ring-Structure. Any help on how to do this would be great. Well, I'd get mol.GetSSSR() and then loop through all the atoms in each OBRing: http://openbabel.org/api/2.3/classOpenBabel_1_1OBRing.shtml Hope that helps, -Geoff |
From: Jurgens de B. <deb...@gm...> - 2011-08-18 10:11:46
|
Thanks On 16 August 2011 18:11, Geoffrey Hutchison <ge...@ge...>wrote: > > I would like to determine if 2 functional groups are within 1 atom from > each other. > > My suggestion would actually be a modified SMARTS using the "*" character > for the one atom. For example: > > [O*O] # matches two oxygens bonded to the same atom > [O**O] # matches two oxygens on neighboring atoms > > Hope that helps, > -Geoff -- Regards/Groete/Mit freundlichen Grüßen/recuerdos/meilleures salutations/ distinti saluti/siong/duì yú/привет Jurgens de Bruin |
From: Jurgens de B. <deb...@gm...> - 2011-08-18 09:28:55
|
Hi all, I have the following SMART : [NX3;H2,H1;!$(NC=O);R] to find intracyclic amines. Given the following SMILES: C1NC(CNC1)C2CNCCN2 I get the following results: [(2,), (5,), (9,), (12,)] What I would like to know is which atoms belong to the same Ring-Structure. Any help on how to do this would be great. -- Regards/Groete/Mit freundlichen Grüßen/recuerdos/meilleures salutations/ distinti saluti/siong/duì yú/привет Jurgens de Bruin |
From: Geoffrey H. <ge...@ge...> - 2011-08-16 16:11:24
|
> I would like to determine if 2 functional groups are within 1 atom from each other. My suggestion would actually be a modified SMARTS using the "*" character for the one atom. For example: [O*O] # matches two oxygens bonded to the same atom [O**O] # matches two oxygens on neighboring atoms Hope that helps, -Geoff |
From: Jurgens de B. <deb...@gm...> - 2011-08-15 12:38:41
|
Hi, I would like to determine if 2 functional groups are within 1 atom from each other. Is their a way I can calculate the distance between two atoms in order to do this or are their any other suggestions? Thanks -- Regards/Groete/Mit freundlichen Grüßen/recuerdos/meilleures salutations/ distinti saluti/siong/duì yú/привет Jurgens de Bruin |
From: Jurgens de B. <deb...@gm...> - 2011-08-15 08:07:38
|
Hi, Would like some help on writing SMARTS: I would like a SMART for urea currently I have the following : [NX3][NX3][CX3]=[OX1] but this does not seem to be able to find urea in a structure. Any help on witting SMARTS would help. Had a loop and the Daylight website but a bit more on designing SMARTS would help. Thanks -- Regards/Groete/Mit freundlichen Grüßen/recuerdos/meilleures salutations/ distinti saluti/siong/duì yú/привет Jurgens de Bruin |
From: Noel O'B. <bao...@gm...> - 2011-07-31 16:29:08
|
What happens when you try that? - Noel On 22 July 2011 20:35, phani ghanakota <gph...@ya...> wrote: > Hi, > > I was following the python openbabel example given on the open babel wiki > below. > > >>> import openbabel>>> conv=openbabel.OBConversion()>>> conv.OpenInAndOutFiles("1200mols.smi","index.fs")True>>> conv.SetInAndOutFormats("smi","fs")True>>> conv.Convert()This will prepare an index of 1200mols.smi and may take some time...It took 6 seconds1192>>> conv.CloseOutFile()>>> conv.OpenInAndOutFiles("index.fs","results.smi")True>>> conv.SetInAndOutFormats("fs","smi")True>>> conv.AddOption("s",conv.GENOPTIONS,"C=CC#N")>>> conv.Convert()10 candidates from fingerprint search phase1202>>> f=open("results.smi")>>> f.read()'OC(=O)C(=Cc1ccccc1)C#N\t298\nN#CC(=Cc1ccccc1)C#N\t490\nO=N(=O)c1cc(ccc1)C=C(C#N)C#N\t491\nClc1ccc(cc1)C=C(C#N)C#N\t492\nClc1ccc(c(c1)Cl)C=C(C#N)C#N\t493\nClc1ccc(cc1Cl)C=C(C#N)C#N\t494\nBrc1ccc(cc1)C=C(C#N)C#N\t532\nClc1ccccc1C=C(C#N)C#N\t542\nN#CC(=CC=Cc1occc1)C#N\t548\nCCOC(=O)C(C#N)=C(C)C\t1074\n' > > > If I wanted to change the fingerprint from the default FP2 to MACCS > what would be the command that I would have to use. > > I am guessing it might be > > conv.AddOption("f",conv.OUTOPTIONS,"MACCS") > > could you confirm if this is right? > > Thanks, > Phani. > > > > ------------------------------------------------------------------------------ > 10 Tips for Better Web Security > Learn 10 ways to better secure your business today. Topics covered include: > Web security, SSL, hacker attacks & Denial of Service (DoS), private keys, > security Microsoft Exchange, secure Instant Messaging, and much more. > http://www.accelacomm.com/jaw/sfnl/114/51426210/ > _______________________________________________ > OpenBabel-scripting mailing list > Ope...@li... > https://lists.sourceforge.net/lists/listinfo/openbabel-scripting > > |
From: Noel O'B. <bao...@gm...> - 2011-07-26 08:22:40
|
The Python bindings require OB to be compiled with Eigen2. See the install instructions at http://openbabel.org/docs/2.3.0/Installation/install.html - Noel On 26 July 2011 03:53, Daniel Sindhikara <sin...@gm...> wrote: > Hi, > I downloaded "openbabel-2.3.0.tar.gz" > When I run that command, I get: > otool -L > /Users/sindhikara/Tools/openbabel-install/lib/python2.7/site-packages/_openbabel.so > /Users/sindhikara/Tools/openbabel-install/lib/python2.7/site-packages/_openbabel.so: > /Users/sindhikara/Downloads/openbabel-2.3.0/lib/libopenbabel.4.dylib > (compatibility version 4.0.0, current version 4.0.0) > /usr/lib/libstdc++.6.dylib (compatibility version 7.0.0, current version > 7.9.0) > /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version > 125.2.11) > > Thanks! > > > > On Mon, Jul 25, 2011 at 11:49 PM, Geoffrey Hutchison > <ge...@ge...> wrote: >> >> > I am running Mac OSX 10.6.8. When I e-mailed you originally I had >> > installed "iBabel" the mac version. Since then tried installing the linux >> > version and I suppose it installed correctly, but I still cannot import it: >> >> What "linux version" did you install? >> >> Can you run "otool -L >> /Users/sindhikara/Tools/openbabel-install/lib/python2.7/site-packages/_openbabel.so" >> for me? >> >> Thanks, >> -Geoff > > > -- > Dr. Daniel J. Sindhikara > Institute for Molecular Science > E-mail: sin...@gm... > Website: http://sites.google.com/site/dansindhikara/ > -- > > ------------------------------------------------------------------------------ > Magic Quadrant for Content-Aware Data Loss Prevention > Research study explores the data loss prevention market. Includes in-depth > analysis on the changes within the DLP market, and the criteria used to > evaluate the strengths and weaknesses of these DLP solutions. > http://www.accelacomm.com/jaw/sfnl/114/51385063/ > _______________________________________________ > OpenBabel-scripting mailing list > Ope...@li... > https://lists.sourceforge.net/lists/listinfo/openbabel-scripting > > |
From: Daniel S. <sin...@gm...> - 2011-07-26 02:54:04
|
Hi, I downloaded "openbabel-2.3.0.tar.gz" When I run that command, I get: otool -L /Users/sindhikara/Tools/openbabel-install/lib/python2.7/site-packages/_openbabel.so /Users/sindhikara/Tools/openbabel-install/lib/python2.7/site-packages/_openbabel.so: /Users/sindhikara/Downloads/openbabel-2.3.0/lib/libopenbabel.4.dylib (compatibility version 4.0.0, current version 4.0.0) /usr/lib/libstdc++.6.dylib (compatibility version 7.0.0, current version 7.9.0) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 125.2.11) Thanks! On Mon, Jul 25, 2011 at 11:49 PM, Geoffrey Hutchison < ge...@ge...> wrote: > > I am running Mac OSX 10.6.8. When I e-mailed you originally I had > installed "iBabel" the mac version. Since then tried installing the linux > version and I suppose it installed correctly, but I still cannot import it: > > What "linux version" did you install? > > Can you run "otool -L > /Users/sindhikara/Tools/openbabel-install/lib/python2.7/site-packages/_openbabel.so" > for me? > > Thanks, > -Geoff -- Dr. Daniel J. Sindhikara Institute for Molecular Science E-mail: sin...@gm... Website: http://sites.google.com/site/dansindhikara/ -- |
From: Geoffrey H. <ge...@ge...> - 2011-07-25 15:30:07
|
> I am running Mac OSX 10.6.8. When I e-mailed you originally I had installed "iBabel" the mac version. Since then tried installing the linux version and I suppose it installed correctly, but I still cannot import it: What "linux version" did you install? Can you run "otool -L /Users/sindhikara/Tools/openbabel-install/lib/python2.7/site-packages/_openbabel.so" for me? Thanks, -Geoff |
From: Daniel S. <sin...@gm...> - 2011-07-25 09:20:50
|
---------- Forwarded message ---------- From: Daniel Sindhikara <sin...@gm...> Date: Mon, Jul 25, 2011 at 4:29 PM Subject: Re: [OpenBabel-scripting] importing pybel To: Noel O'Boyle <bao...@gm...> I am running Mac OSX 10.6.8. When I e-mailed you originally I had installed "iBabel" the mac version. Since then tried installing the linux version and I suppose it installed correctly, but I still cannot import it: 16:25:32 [danpc: ~]$ python2.7 Python 2.7.2 (default, Jun 21 2011, 13:19:45) [GCC 4.2.1 (Apple Inc. build 5666) (dot 3)] on darwin Type "help", "copyright", "credits" or "license" for more information. >>> import pybel Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/Users/sindhikara/Tools/openbabel-install/lib/python2.7/site-packages/pybel.py", line 16, in <module> import openbabel as ob File "/Users/sindhikara/Tools/openbabel-install/lib/python2.7/site-packages/openbabel.py", line 70, in <module> _openbabel = swig_import_helper() File "/Users/sindhikara/Tools/openbabel-install/lib/python2.7/site-packages/openbabel.py", line 66, in swig_import_helper _mod = imp.load_module('_openbabel', fp, pathname, description) ImportError: dlopen(/Users/sindhikara/Tools/openbabel-install/lib/python2.7/site-packages/_openbabel.so, 2): Symbol not found: __ZTVN9OpenBabel20OBRMSDConformerScoreE Referenced from: /Users/sindhikara/Tools/openbabel-install/lib/python2.7/site-packages/_openbabel.so Expected in: flat namespace in /Users/sindhikara/Tools/openbabel-install/lib/python2.7/site-packages/_openbabel.so On Wed, Jul 13, 2011 at 10:19 PM, Noel O'Boyle <bao...@gm...> wrote: > Hi Dan, > > What operating system? How did you install Open Babel? > > - Noel > > On 11 July 2011 12:28, Daniel Sindhikara <sin...@gm...> wrote: > > Hello, > > I'm somewhat new to python but would like to use pybel. I have > openbabel > > installed, but I'm not sure exactly how to get pybel working. Do I need > to > > install pybel separately? Is it included in some package? I can't find a > > download link for it. Of course if I try "import pybel" I get: Traceback > > (most recent call last): > > File "<pyshell#0>", line 1, in <module> > > import pybel > > ImportError: No module named pybel > > > > Thanks for any help! > > --Dan > > > > > > > ------------------------------------------------------------------------------ > > AppSumo Presents a FREE Video for the SourceForge Community by Eric > > Ries, the creator of the Lean Startup Methodology on "Lean Startup > > Secrets Revealed." This video shows you how to validate your ideas, > > optimize your ideas and identify your business strategy. > > http://p.sf.net/sfu/appsumosfdev2dev > > _______________________________________________ > > OpenBabel-scripting mailing list > > Ope...@li... > > https://lists.sourceforge.net/lists/listinfo/openbabel-scripting > > > > > -- Dr. Daniel J. Sindhikara Institute for Molecular Science E-mail: sin...@gm... Website: http://sites.google.com/site/dansindhikara/ -- -- Dr. Daniel J. Sindhikara Institute for Molecular Science E-mail: sin...@gm... Website: http://sites.google.com/site/dansindhikara/ -- |
From: phani g. <gph...@ya...> - 2011-07-22 19:35:31
|
Hi, I was following the python openbabel example given on the open babel wiki below. >>> import openbabel >>> conv=openbabel.OBConversion() >>> conv.OpenInAndOutFiles("1200mols.smi","index.fs") True >>> conv.SetInAndOutFormats("smi","fs") True >>> conv.Convert() This will prepare an index of 1200mols.smi and may take some time... It took 6 seconds 1192 >>> conv.CloseOutFile() >>> conv.OpenInAndOutFiles("index.fs","results.smi") True >>> conv.SetInAndOutFormats("fs","smi") True >>> conv.AddOption("s",conv.GENOPTIONS,"C=CC#N") >>> conv.Convert() 10 candidates from fingerprint search phase 1202 >>> f=open("results.smi") >>> f.read() 'OC(=O)C(=Cc1ccccc1)C#N\t298\nN#CC(=Cc1ccccc1)C#N\t490\nO=N(=O)c1cc(ccc1)C=C(C#N )C#N\t491\nClc1ccc(cc1)C=C(C#N)C#N\t492\nClc1ccc(c(c1)Cl)C=C(C#N)C#N\t493\nClc1c cc(cc1Cl)C=C(C#N)C#N\t494\nBrc1ccc(cc1)C=C(C#N)C#N\t532\nClc1ccccc1C=C(C#N)C#N\t 542\nN#CC(=CC=Cc1occc1)C#N\t548\nCCOC(=O)C(C#N)=C(C)C\t1074\n' If I wanted to change the fingerprint from the default FP2 to MACCS what would be the command that I would have to use. I am guessing it might be conv.AddOption("f",conv.OUTOPTIONS,"MACCS") could you confirm if this is right? Thanks, Phani. |
From: Noel O'B. <bao...@gm...> - 2011-07-13 13:20:04
|
Hi Dan, What operating system? How did you install Open Babel? - Noel On 11 July 2011 12:28, Daniel Sindhikara <sin...@gm...> wrote: > Hello, > I'm somewhat new to python but would like to use pybel. I have openbabel > installed, but I'm not sure exactly how to get pybel working. Do I need to > install pybel separately? Is it included in some package? I can't find a > download link for it. Of course if I try "import pybel" I get: Traceback > (most recent call last): > File "<pyshell#0>", line 1, in <module> > import pybel > ImportError: No module named pybel > > Thanks for any help! > --Dan > > > ------------------------------------------------------------------------------ > AppSumo Presents a FREE Video for the SourceForge Community by Eric > Ries, the creator of the Lean Startup Methodology on "Lean Startup > Secrets Revealed." This video shows you how to validate your ideas, > optimize your ideas and identify your business strategy. > http://p.sf.net/sfu/appsumosfdev2dev > _______________________________________________ > OpenBabel-scripting mailing list > Ope...@li... > https://lists.sourceforge.net/lists/listinfo/openbabel-scripting > > |
From: Daniel S. <sin...@gm...> - 2011-07-11 11:29:01
|
Hello, I'm somewhat new to python but would like to use pybel. I have openbabel installed, but I'm not sure exactly how to get pybel working. Do I need to install pybel separately? Is it included in some package? I can't find a download link for it. Of course if I try "import pybel" I get: Traceback (most recent call last): File "<pyshell#0>", line 1, in <module> import pybel ImportError: No module named pybel Thanks for any help! --Dan |
From: Andrew F. <fa...@mo...> - 2011-07-07 18:54:54
|
and, as an aside, it doesn't help that to access the base openbabel methods from a pybel mol object you use Pybel.Mol.OBMol, but to access the openbabel smarts methods, you need to use Pybel.Smarts.obsmarts. :-) On Jul 7, 2011, at 2:39 PM, Geoffrey Hutchison wrote: >> Is there an easy way to generate a printable representation of a SMARTS query object from the object? I guess I could carry the string representation that the query was generated from around with the query in a tuple, but I'm hoping to find something a little cleaner. > > Use the GetSMARTS() method? > > http://openbabel.org/api/2.3/classOpenBabel_1_1OBSmartsPattern.shtml#a52d9a732c39944ff60d06aeacb96617c > > Hope that helps, > -Geoff |
From: Andrew F. <fa...@mo...> - 2011-07-07 18:44:32
|
Thanks, Geoff. (if you can't tell by the questions I ask, my C++ is basically non-existant and I get very lost, very quickly when I try to dig into the API documentation) On Jul 7, 2011, at 2:39 PM, Geoffrey Hutchison wrote: >> Is there an easy way to generate a printable representation of a SMARTS query object from the object? I guess I could carry the string representation that the query was generated from around with the query in a tuple, but I'm hoping to find something a little cleaner. > > Use the GetSMARTS() method? > > http://openbabel.org/api/2.3/classOpenBabel_1_1OBSmartsPattern.shtml#a52d9a732c39944ff60d06aeacb96617c > > Hope that helps, > -Geoff |
From: Geoffrey H. <ge...@ge...> - 2011-07-07 18:40:03
|
> Is there an easy way to generate a printable representation of a SMARTS query object from the object? I guess I could carry the string representation that the query was generated from around with the query in a tuple, but I'm hoping to find something a little cleaner. Use the GetSMARTS() method? http://openbabel.org/api/2.3/classOpenBabel_1_1OBSmartsPattern.shtml#a52d9a732c39944ff60d06aeacb96617c Hope that helps, -Geoff |
From: Andrew F. <fa...@mo...> - 2011-07-07 18:30:38
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Is there an easy way to generate a printable representation of a SMARTS query object from the object? I guess I could carry the string representation that the query was generated from around with the query in a tuple, but I'm hoping to find something a little cleaner. Thanks, Andy |
From: Noel O'B. <bao...@gm...> - 2011-07-05 08:19:10
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(ccing to the list) I use the standard Python from Python.org. I haven't tested that the bindings are compatible with enthought, but AFAIK everything that works with one will work with the other. The installer just copies three files to site-packages, pybel.py, openbabel.py and _openbabel.pyd. These can be uninstalled from "add or remove programs" or else manually. - Noel On 4 July 2011 23:46, Andrew Fant <fa...@mo...> wrote: > Thanks, Noel. > > Looking through the openbabel documentation, I see that whoever wrote the windows documentation was using enthought python. Are the binary distributions for openbabel on sourceforge compatible with enthought? I'd try it myself, but cleaning up after bad installs on windows is such a pain that I thought I would ask an expert first. > > Thanks again, > Andy |
From: Noel O'B. <bao...@gm...> - 2011-07-04 08:24:47
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Convert to smiles and search for "." or else call Molecule.OBMol.Separate and look at the number of components. - Noel On 4 July 2011 02:04, Andrew Fant <fa...@mo...> wrote: > Is there a simple way to determine if there are multiple unlinked fragments in a molecule from pybel? I'm trying to clean out a bunch of old compound lists that I inherited, and since I have to do it once, I might as well try to avoid doing it a second time. > > Thanks, > Andy > > > ------------------------------------------------------------------------------ > All of the data generated in your IT infrastructure is seriously valuable. > Why? It contains a definitive record of application performance, security > threats, fraudulent activity, and more. Splunk takes this data and makes > sense of it. IT sense. And common sense. > http://p.sf.net/sfu/splunk-d2d-c2 > _______________________________________________ > OpenBabel-scripting mailing list > Ope...@li... > https://lists.sourceforge.net/lists/listinfo/openbabel-scripting > |