Structure manipulation: Canonicalization / standardization

Topic Posts Author Date
How can I remove charges from the molecule? 5 User 16a108bed5 10-11-2016 02:30:05
Conversion to Kekule form not working for some molecules 2 User 2235ec4634 08-09-2016 09:27:38
Standarization on whole database 3 User 2235ec4634 16-08-2016 14:11:28
AutoMapper class 3 User 303e8155db 01-08-2016 11:22:50
Cannot execute Standardizer.bat on the DOS level 3 User 773d472e7f 03-07-2016 07:46:17
how does template clean matching work? 2 User 873a9ae9d0 22-06-2016 08:46:16
prevent template layout changes in partial clean 4 User 873a9ae9d0 15-06-2016 06:37:58
user.abbrevgroup file ignored by structure checker 4 User 873a9ae9d0 26-05-2016 17:01:28
standardizer java api-How to get started 4 User 873a9ae9d0 04-05-2016 15:38:56
generate the pictueres of mapped reaction in command line 2 User 230b49d915 08-03-2016 07:54:49
How can I map reaction using changing style in command line 2 User 895d6088ef 25-01-2016 03:33:07
Standardizer freezes Windows 10 64bit 5 User 773d472e7f 08-01-2016 20:35:18
Clean2D (partial) switches double bond stereochemistry 3 User 81a38f9467 15-09-2015 20:40:01
How to arrange molecules in multiple columns 3 User 121285d3c7 01-05-2015 21:18:21
add attached data in bulk 2 User cdc1fd6fff 03-04-2015 13:24:57
Straight alkyl or alkenyl chains with template based clean 3 User 677b9c22ff 27-03-2015 01:23:16
Disconnected structures not reconnecting with Standardizer 7 User 7f33ec9a5c 16-03-2015 19:52:12
how to estimate the quality of jc_standardize clean:full 3 User cf4264f752 17-02-2015 16:34:04
Using several templates as input for jc_standardize 6 User cf4264f752 17-02-2015 14:46:51
How does partial clean works? 5 User cf4264f752 17-02-2015 13:47:52
Replace Atoms 2 User c3397108ba 09-02-2015 11:23:23
Standardizer API function to replicate Marvin Clean in 2D? 5 User f05f6b8c05 19-01-2015 08:32:42
Bug report (14.7.7) 3 User 7910dcb734 16-12-2014 13:15:18
Standardizer command line issue - spaces in file path 3 User a0e3eb3dd1 18-11-2014 10:46:21
Bug Report: Custom IDs are not exported 5 User 38b5a5d7e0 24-10-2014 20:42:12
Standardizer adds additional empty lines to an SDFile 5 User 773d472e7f 02-09-2014 17:15:10
Jchem bases: the problem of standardier molecular structure 20 User 73a1fcfaf4 30-08-2014 12:32:58
the problem about standaradizer molecular structure 3 User 73a1fcfaf4 30-08-2014 12:29:59
Feature Installation insufficiency 2 User 73a1fcfaf4 29-08-2014 03:43:44
Standardizer Stripping Stereochemistry 2 User 535731474a 22-08-2014 16:37:05
Nitro group transformation 1 User a0e3eb3dd1 11-08-2014 10:21:41
ChemAxon standardizer salt stripper bug(?) 3 User 1261fb0e16 22-07-2014 13:16:19
Standardizer exception 4 User 870ab5b546 17-07-2014 19:40:52
Error: Failed to get abbreviations. 5 User 7910dcb734 16-07-2014 15:29:19
overlapping bonds with TBDPS super atom 4 User f05f6b8c05 15-07-2014 00:54:11
GUI to command line 3 User fc80487671 03-07-2014 08:29:54
Mesomerize action fails to produce a canonical structure 2 User 81a38f9467 18-06-2014 23:56:12
fatal standardizer bug in 6.1.7 3 User 21b7e0228c 06-05-2014 09:27:50
Removing Atoms 3 User a9d76a1173 27-01-2014 18:24:38
AutoMapper.guessMappingStyle() alternative 5 User 366e966a35 19-12-2013 12:22:28
problem of standardization 10 User 247a2c5018 17-12-2013 11:47:34
structurechecker script not passing java options to java 2 User 7c177bab3b 14-10-2013 08:24:23
JPanel for standardizer configuration 3 User 1261fb0e16 11-10-2013 12:59:33
How can I recognize each structure's name in sdf file? 7 User f6549195f0 23-08-2013 12:17:20
Structure Checker and broken SDF files 2 User 677b9c22ff 20-08-2013 02:30:26
How do I output absolute SMILES from jcf.standardize() 2 User 7f33ec9a5c 14-08-2013 18:22:04
Use of SaltStrip standardizing (in cartridge) 6 User 05d9866f9b 29-07-2013 18:27:43
Standardizer use 8 User 1da2e6555b 22-07-2013 05:15:22
Mission Action in List? 4 User fd4af72735 20-06-2013 13:21:51
Structure Checker in PL/SQL with exceptions for abbrevGroup 20 User 05d9866f9b 17-06-2013 16:31:21
How to check and select inaccurate structures in sdf ? 11 User 22c88daf92 30-05-2013 07:15:14
Standardizer: Wedge Clean screws up common amino acids 3 User 81a38f9467 16-05-2013 04:17:16
Structure Checker: Valence Error not detected 2 User 81a38f9467 17-04-2013 19:02:53
array index out of bounds exception 4 User 870ab5b546 17-04-2013 18:53:28
Text Encoding problem in Standardizer 2 User bd14eda7b5 18-03-2013 02:28:43
Remove Explicit Hs removes stereocenters w/ no explicit H's 3 User 81a38f9467 13-03-2013 02:32:31
Standardizer exception 3 User da00f5c453 01-03-2013 19:16:30
Improper mapping values when using Map/Map Reaction 4 User 68341ff45d 01-03-2013 04:21:22
ConcurrentStandardizerProcessor takes Deprecated Standardize 7 User 7910dcb734 27-02-2013 10:55:35
Removing salt from a molecule 8 User 73ad691ca3 21-02-2013 15:53:58
Structure checker 4 User 73ad691ca3 07-02-2013 06:36:03
Getting Exception in Structure Checker command line 2 User 73ad691ca3 06-02-2013 14:14:24
Structure Checker - Infinite Loop? 3 User 7910dcb734 25-01-2013 16:14:17
Removing explicit hydrogrens on large PubChem compounds 3 User 8688ffe688 17-01-2013 17:43:19
separation of counter ions of additional framents 8 User 8bebba65c2 10-01-2013 12:34:38
standardizer problem 2 User 6ce93379c0 20-12-2012 01:54:49
Possible to set timelimit for Standardizer? 4 User 37c69cc8fe 04-12-2012 10:16:19
How to get the information about stripped salt 5 User cdc1fd6fff 16-11-2012 09:12:28
Standartizaion of cyclohexa-2,4-dien-1-one to phenol 3 User 9f43a5a979 09-11-2012 22:38:13
Standardise Problem 2 User fca35de8d7 30-10-2012 17:02:41
jc_standardize best practices. 7 User 7f33ec9a5c 26-10-2012 19:24:12
Change to neutralize behaviour for zwitterions 2 User 7c177bab3b 22-10-2012 11:16:08
How to set create group in standardizer 5 User cdc1fd6fff 17-10-2012 06:21:40
Standardizer java API 2 User 07c4f121e4 10-10-2012 10:34:32
Valence property fixer always reports false (no fix) 10 User 0261d34ad7 04-10-2012 09:09:06
Convert Double Bound 6 User 36e6469614 28-09-2012 07:39:33
ArrayIndexOutOfBoundsException from getParity 4 User 7910dcb734 16-08-2012 10:01:21
Trouble with Standardizer 7 User f05f6b8c05 19-05-2012 22:52:15
clean vrs. clean:full 6 User f05f6b8c05 17-05-2012 10:36:41
Structure Checker 7 User 6d24b35814 26-04-2012 10:38:23
Tautomerize removes some deuterium atoms 2 User 81a38f9467 10-04-2012 01:28:56
How to fuse() with good spacing but no reorientation? 5 User f05f6b8c05 09-04-2012 11:47:57
Issue with Grignard Type molecules and mesomerise 3 User 7b0ee04e66 28-03-2012 07:47:42
Runtime exception when calling expand atom on MOL 2 User 8d34d3a066 12-03-2012 17:13:56
Array index out of range in Structure Checker 3 User 677b9c22ff 08-03-2012 03:06:54
Tautomerize mangles some cyclic sulfones 2 User 81a38f9467 25-02-2012 01:45:45
Unique representation of molecules 4 User 74c85f9df0 22-02-2012 06:48:22
Standardizer applied tasks are misreported 5 User 0261d34ad7 20-02-2012 14:03:00
jc_standardize with xml configuration 3 User d90f4e1cc8 13-02-2012 09:15:06
Fixing SDF Files Using Marvin API 2 User a9d76a1173 17-12-2011 18:07:16
Adding Hydrogens change molecule coordinates 3 User ed9697d993 16-12-2011 14:12:16
Combining structure checker and standardizer 2 User 0261d34ad7 06-12-2011 16:18:43
could action / rule of standardizer be reported somehow? 7 User 1887159699 23-11-2011 10:21:10
Clean 3D problems 4 User 9b067d2e85 23-11-2011 00:27:29
MESOMER/TAUTOMER 2 User 2c46f693ab 21-11-2011 16:46:14
tautomerism option and mesomers 3 User 2c46f693ab 21-11-2011 15:10:09
How calculate the molecule ?(cxcalc and standardize) 2 User f71f7fbc20 16-11-2011 13:34:02
Structure Checker/fixer API 2 User 9b067d2e85 09-11-2011 23:20:23
Is this expected standardizer behavior? 3 User f05f6b8c05 30-10-2011 06:41:27
Standardizer keep largest on heavy atom count 2 User 7c177bab3b 05-09-2011 10:23:06
molconvert conformer generation 2 User ac20ca0f01 09-08-2011 13:56:57
Tautomerize is 80x slower for some compounds vs. others 9 User 81a38f9467 02-08-2011 00:52:57
Rejecting compounds containing unwanted atom types 2 User a681a7b90d 29-06-2011 16:12:29
mesomerize directive dead in 5.5! 7 User 21b7e0228c 30-05-2011 07:52:08
'Standardizer failed' error message 3 User dc29f3beec 17-05-2011 21:21:43
structure checker 5.5.0 unresponsive doesnt close (substruc) 4 User 677b9c22ff 12-05-2011 20:07:53
Removal of a charge in a sdf->mol2 conversion by molconvert 2 User ed9697d993 11-05-2011 15:51:12
seperated outout in structurecheck 3 User da4de2e985 04-05-2011 17:55:54
Tautomerize introduces valence information 2 User 81a38f9467 31-03-2011 19:16:00
Neutralizing protonated aromatic N 6 User 7c177bab3b 30-03-2011 08:52:21
Tautomerize mangles some cyclic sulfonamides 2 User 81a38f9467 14-03-2011 17:11:31
Saving the other fields of smiles file in Structure Checker 5 User 173254b396 14-03-2011 15:46:03
Mesomerize/Neutralize sequence on iminium ions = reduction 2 User 81a38f9467 14-02-2011 23:00:36
Mesomerize inverts remote stereocenters 2 User 81a38f9467 14-02-2011 22:29:08
Tautomerize migrates double bonds too far 2 User 81a38f9467 14-02-2011 20:49:42
Remove unwanted symbol from group (standardizer) 4 User 8a4ea06b5e 01-02-2011 18:07:07
Molecule.toFormat("smiles:u") depends on input?? 8 User c4e58ee8b2 27-01-2011 22:10:57
Structure Checker: Chiral Flag checking w/ symmetric compds 2 User 81a38f9467 10-12-2010 21:28:48
Structure Checker: Nitrogen Heterocycles w/ covalent salts 4 User 81a38f9467 10-12-2010 21:18:57
Tautomerize introduces wavy bonds 7 User 81a38f9467 09-12-2010 22:06:44
Tautomerize gives aromatic output. Dearomatize fails. 3 User 81a38f9467 02-12-2010 20:56:40
How to expand protein labels in molfile 2 User 73531e86ff 02-12-2010 10:50:21
Tautomerize fails to produce a single canonical tautomer 10 User 81a38f9467 12-11-2010 04:22:31
Validate bonds and structures in Standardizer 3 User 677b9c22ff 11-11-2010 01:55:20
Unique smiles which do not tamper with bond orders?? 4 User 21b7e0228c 10-11-2010 14:23:38
Remove ligands 2 ChemAxon 0265132c1a 03-11-2010 16:55:16
java console 2 User 2cd04f3bec 21-10-2010 10:26:45
Converting Wiggly (wavy) bonds to straight bonds 6 User 81a38f9467 14-10-2010 04:26:37
Standardizer exceptions 3 User 870ab5b546 13-10-2010 20:50:21
Standardization error and How to standardize those ? 2 User 3875ae43a1 13-10-2010 09:34:43
Standardizer log output? 8 User f05f6b8c05 24-09-2010 04:57:13
Converting group to pseudo atom in the standardization 12 User a83cdfbe8a 23-09-2010 10:37:58
command-line structure checker? 3 User f05f6b8c05 23-09-2010 01:17:01
Automatically assign stereoisomerical information 13 User e3392a033d 13-07-2010 16:43:34
MRV & SDF Format effect in the standardizer 7 User a83cdfbe8a 05-07-2010 09:52:51
Remove salts and solvents (version problems) 3 User d83653419c 26-05-2010 13:08:41
Saving old coords 3 User 6b2914d174 12-05-2010 10:12:38
How to contract group when standardize the Structures? 6 User a83cdfbe8a 06-05-2010 08:16:33
unable to run the 'Remove Attached Data' in Standardizer 5 User 6ce93379c0 30-04-2010 15:58:47
Mesomerize removes Absolute chiral flag 2 User 81a38f9467 07-04-2010 19:20:06
Tautermization strips stereo information 6 User 8ef5099b33 06-04-2010 18:00:30
Set Abasolute Stereo function does work in standardizer 5.2. 3 User 55ffa2f197 03-03-2010 17:08:00
understanding the addition of implicit hydrogens 13 User a18e201107 14-01-2010 18:11:47
Split a database of molecules into N smaller sets 4 User 2b68687bb8 30-12-2009 10:37:44
about dehydrogenize in standardizer 3 User 941c2467a3 09-11-2009 21:35:44
Mapping error 4 User 761d9eb85b 19-10-2009 08:48:17
Standardization error 2 User da00f5c453 09-10-2009 18:47:18
Customn group transformation 5 User c65f7ade2a 04-08-2009 16:59:10
Neutralizing NH4+ with explicit hydrogens 4 User 331d7f5c0b 03-08-2009 21:03:41
CenTOS Standardizer installation errors 2 User d6d35b90ea 14-07-2009 16:02:24
Exceptions thrown by standardizer 12 User 07c4f121e4 13-07-2009 15:35:50
Are SMILES from GUI Standardizer canonical? 2 User a216001020 10-07-2009 10:48:00
Cleaning Structures using Standardizer 7 User 1efa2c4884 09-07-2009 21:21:25
Exception in thread "main" java.lang.NoSuchMethodE 2 User 75c3bec5c6 10-06-2009 09:41:19
tautomerizer bugs 4 User 568550d85a 25-05-2009 08:57:42
Incorrect Standardizer Configuration Script? 3 User bc9a7e94b9 30-04-2009 21:29:55
Backwards Compatability of Standardizer 2 User bc9a7e94b9 28-04-2009 22:25:45
Problem with CL Standardizer 5 User bc9a7e94b9 26-04-2009 21:55:54
Set valence from coordinates 3 User 538416f930 10-04-2009 01:41:52
Problem using Standardizer to neutralize molecule 9 User 6f58eb8616 26-03-2009 15:11:41
canonical tautomer not working 3 User da00f5c453 06-03-2009 19:23:21
Canonical tautomers 5 User dfbaf76535 17-02-2009 11:27:31
rdf standardization 7 User b91dd8facf 28-01-2009 18:39:23
Transformations with atom lists 2 User 870ab5b546 07-01-2009 23:47:20
chemaxon.reaction.StandardizerException: Error occured 2 User a92fed3a15 19-12-2008 18:32:08
Convert double bonds to wiggly representation 4 User 39a721b0a5 24-11-2008 07:30:40
CoA removal problem 3 User 941c2467a3 23-11-2008 23:42:44
Batch clean molecules from an sd file 5 User 39a721b0a5 31-10-2008 05:24:04
Tautomer NPE 3 User 677b9c22ff 16-08-2008 02:49:31
Standardizer 5.1 NPE 5 User 677b9c22ff 16-08-2008 01:58:28
How to check for valence errors? 3 User 677b9c22ff 06-08-2008 22:58:15
Standardization of Guanidines 7 User 7b0ee04e66 04-07-2008 08:40:07
limit a rule only to the end group 4 User 6e47cbf906 05-06-2008 08:50:49
Standardization Error? 4 User 7b0ee04e66 15-05-2008 07:11:28
Standardization and PubChem Database 3 User 0f28873a29 13-05-2008 00:02:19
Standardizing Queries? 2 User 9d765be2f7 03-04-2008 00:28:05
Standardization rule - enol 2 User 8139ea8dbd 10-03-2008 21:28:10
Standardization of N-Oxide error ? 4 User 7b0ee04e66 10-03-2008 10:05:35
A general xml standardizer 3 User 26c54ae8b9 05-03-2008 10:43:04
Error with Standardizer 4 User 0908c5ccdd 05-02-2008 10:28:37
System() call of standardize in WinXP 2 User b4993d8a3b 11-01-2008 03:42:47
issue (?) whilst trying to fix "covalent salt" for 1 ChemAxon 60ee1f1328 23-10-2007 14:18:11
Aromatization issue 3 User 4e4b708dbd 22-10-2007 09:26:21
Alchemist 3.2.11 error (-2) 5 User 677b9c22ff 19-10-2007 01:24:24
Standardizer 3.2.10 bug? 7 User a54d4c89af 18-10-2007 09:13:12
molecule matching 7 User 031cf6afbd 04-10-2007 14:12:52
Murcko scaffold generation 2 User 2e29183b3d 22-09-2007 18:32:06
Why does this not work? 3 User 4e4b708dbd 14-09-2007 06:42:33
Standardizer error with R-groups 6 User 677b9c22ff 27-08-2007 23:06:59
Mesomerize error using Standardizer 3.2.9 2 User 677b9c22ff 27-08-2007 22:24:29
Alchemist error during tautomerize 3 User 677b9c22ff 27-08-2007 21:31:48
wedge bond removal 7 User 677b9c22ff 27-08-2007 20:51:53
Same input file as ouput file in Standardizer problem 3 User 677b9c22ff 06-08-2007 05:30:40
jc_Standardize and tautomerise option 3 User 7b0ee04e66 16-07-2007 16:47:25
Where can I find *the* large standardizer.xml template? 2 User 677b9c22ff 04-07-2007 07:30:08
Standardization of symmetrical double bonds 7 User c0e481a82c 06-06-2007 08:08:56
Forbidding wedge bonds off of planar (aromatic) atoms 6 User 9d765be2f7 22-05-2007 20:50:20
Option list for jcf_Standardize PL/SQL function 10 User c0e481a82c 22-05-2007 15:02:20
Template based cleaning 6 User 6b0477c86d 23-04-2007 15:32:12
"Either" double bond 13 User 6b0477c86d 20-04-2007 10:16:39
"Standardizer" can't produce only one identical SM 6 User 941c2467a3 02-04-2007 19:49:23
Standardize rule for Ammonium 2 User 9fa69eb201 22-03-2007 08:34:05
Standardizer and Tautomers 3 User 7b0ee04e66 13-03-2007 10:57:05
No valid license key has been found for Standardizer 2 User 6e47cbf906 28-02-2007 11:56:25
tools to check if a drawn structure is correct 11 User 247a2c5018 15-02-2007 09:13:54
standardize / cache question 10 ChemAxon 60ee1f1328 14-02-2007 11:22:28
defining atom type info for aromatic bonds 4 ChemAxon 60ee1f1328 12-02-2007 17:36:08
keepLargest action problem 2 User f09ff22166 01-02-2007 00:22:33
Tuning representation of aromatic cycles 3 User a54d4c89af 31-01-2007 19:03:26
aromatize acts like aromatize/basic for some heterocylics 4 User 39d0b79643 22-01-2007 16:42:13
Standardizer Clear Stereo / Clear Isotope 3 User 7b0ee04e66 22-01-2007 11:26:20
Printing SDF seperately 2 User 9fa69eb201 20-01-2007 02:19:55
Removing salts and neutralizing the molecule 2 User 9fa69eb201 10-01-2007 10:23:01
Salt stripping 1 ChemAxon 43e6884a7a 07-12-2006 10:34:05
Standardizer GUI - How to add own commands? 5 User 677b9c22ff 22-11-2006 01:35:26
Standardization error 2 User 7b0ee04e66 10-11-2006 11:50:31
tautomerization module and certain charged moeties 2 User d83ec9d6e4 30-10-2006 20:04:41
MDL Enhanced Stereo Representation 3 User 70dc09049e 09-10-2006 13:02:29
Does standardizer always keep atoms sequence? 9 User a216001020 02-10-2006 12:02:45
how to know molecule configuration? 5 User 86810cf9fa 25-09-2006 19:00:30
How to get the largest ring system of a molecule 2 ChemAxon d76e6e95eb 19-09-2006 08:49:41
JChemManager Import with Dearomatize standardization rule 8 User 70dc09049e 05-09-2006 15:31:06
NoClassDefFoundError : org/jaxen/JaxenException 3 User a52f97d128 18-08-2006 15:22:33
using standardizer action "keepone" 5 ChemAxon 60ee1f1328 17-07-2006 08:42:08
Standardizer order 3 User 7b0ee04e66 03-07-2006 12:29:40
Standardizer GUI 7 User 7b0ee04e66 12-06-2006 08:20:01
Merging 2 documents DOM4J please help I'm getting lost 3 User 35bef27df0 02-05-2006 18:00:47
Merging 2 documents 2 User 35bef27df0 02-05-2006 17:54:15
Dearomtizing 2 User ceb580837f 20-04-2006 16:09:03
error in java : cannot access org.dom4j.Element 3 User 247a2c5018 07-04-2006 12:38:53
...and find the lowest energy conformer 5 User 717c2fe15b 17-02-2006 09:10:00
creation of 3D structure using action strings 3 User 717c2fe15b 17-02-2006 09:05:45
tautomer canonicalization 6 User 538416f930 16-02-2006 21:38:15
Errors regenerating table with custom standardization 4 User 818520b6b8 02-01-2006 15:23:34
Problem regenerating structure table with custom standard 3 User 818520b6b8 15-12-2005 07:31:47
Help to standardize 5 User dfeb81947d 14-12-2005 15:50:25
About Template base clean 6 User 8fb8115204 10-12-2005 15:46:37
getting indexes of chiral atoms-no configuration specified 3 User a52f97d128 27-10-2005 16:37:20
Full Clean didn't get the atom coordinates 2 User 7c5047cd7b 25-10-2005 10:26:01
About T (Tritium), D (Deuterium) 7 User 7c5047cd7b 24-10-2005 03:12:45
Problem with the clean option in Standardizer 6 User e47fc0b649 20-10-2005 16:05:44
Template Based Clean 3 19-10-2005 12:50:30
About one standardizer's rule 6 User 7c5047cd7b 15-10-2005 09:51:18
Unvoluntary 3D conversion in Standardizer? 3 User e47fc0b649 13-10-2005 13:32:54
generating all tautomers for given SMILES 17 ChemAxon 60ee1f1328 12-10-2005 12:50:08
command line vs. class differences 5 User b7aa615db3 10-10-2005 18:02:38
Problem with the action "Aromatize" on a pyrrol gr 9 User e47fc0b649 10-10-2005 07:57:54
Question about V3000 mol 5 User 7c5047cd7b 05-10-2005 08:54:19
<implH> in standardizer 4 User 7c5047cd7b 15-09-2005 05:56:46
About Aromatize of Standardizer (urgent) 4 User 7c5047cd7b 15-09-2005 02:28:06
Could you help me correct the standardizer's rule? 5 User 7c5047cd7b 14-09-2005 13:10:50
Standardizer action for converting 3D to 2D? 4 ChemAxon fa971619eb 10-05-2005 16:07:32
The Error, while I test Standardize 8 User 8fb8115204 09-10-2004 09:00:35
Now the single bond thing ... below was another problem ;-) 2 ChemAxon 587f88acea 23-09-2004 14:27:06
Standardizer output with "mysterious" single bonds 4 ChemAxon 587f88acea 23-09-2004 14:14:47
MolImporter having problems on importing SMILES with "[ 6 ChemAxon 587f88acea 23-09-2004 13:24:07