Structure representation: molecule handling and file formats

Topic Posts Author Date
Returning the title and connection table of a molecule. 2 User 779e37e0e6 22-11-2016 19:49:57
Chemaxon sanity issues with using MolImporter 11 User 45b4c9a16b 21-10-2016 13:51:16
Generic compound explicit in mol file or not 16 User c9ecc1389b 21-10-2016 10:07:47
Unsupported atoms in ChemAxon 3 User c9ecc1389b 20-10-2016 13:40:29
How to fragment CXSMILES with valid extended features? 2 User c5c75876e8 12-09-2016 13:27:49
coordinates change for MOL V3000 MolImporter/MolExporter 4 User c5c75876e8 07-09-2016 15:37:19
How to cast Molecule object to MoleculeGraph? 3 User 873a9ae9d0 21-06-2016 12:18:07
Convert SMILES reaction to xyz with correct atom order 2 User e1170066e6 03-06-2016 19:00:01
InCHI and InCHiKey mobile hydrogens 3 User 677b9c22ff 23-05-2016 18:38:51
NullPointerException on simple reaction transformations 5 User 22cecfe2f7 16-05-2016 22:08:06
Molconvert and generating cas number 2 User c1ce6b3d19 21-04-2016 17:42:18
MolImporter: Problems Creating Molecule From InChi String 4 User bfe5c11485 31-03-2016 18:45:42
Problematic mol file parsing 5 User c9ecc1389b 09-02-2016 11:12:46
problem generating URI for PNG 3 User 870ab5b546 20-01-2016 19:26:07
MolFormatException: Parallel bonds: null 4 User 870ab5b546 19-01-2016 17:34:17
What jar file is chemaxon.util.MolHandler in? 2 User 746708b25a 18-12-2015 21:43:42
PeriodicSystem 22 User 343b63fb52 16-12-2015 09:06:46
molconvert smiles file to image, file not found 3 User 0d64032b61 12-11-2015 05:39:21
Identify ends of asymmetric bonds by Java API 3 User f05f6b8c05 08-11-2015 17:02:13
How to find all the components of a molecule 5 User 779e37e0e6 06-11-2015 16:20:53
RDF to RXN convertion 9 User a0e3eb3dd1 03-11-2015 18:19:52
InChi and InChiKey by Ajax/JSP 7 User 68591793e9 15-10-2015 15:45:35
How to compile java snippet 4 User a0e3eb3dd1 25-09-2015 11:29:56
SD file generated in v3000 format 2 User 23ba1704ca 16-09-2015 05:53:37
Timing out an export to InChI calculation 3 User 0cd5667845 23-07-2015 00:31:45
Determine R or S using getChirality method 6 User 55ffa2f197 17-07-2015 01:44:42
Convert mol V3000 to smiles 2 User 7c177bab3b 15-07-2015 16:55:28
Flip molecule vertically using JChem API 3 User 55ffa2f197 01-07-2015 18:23:41
How to find a Component's parent sgroup that is a Mixture 5 User bc3eb0a599 09-06-2015 21:54:45
MolConvert script/AppleScript for manipulating ~1000 files 3 User 7be2ac490f 08-06-2015 12:50:05
SMILES for classifying compounds in a metabolic network 8 User bef34fe65b 09-05-2015 05:59:15
Molconvert, write additional informations from sdf to SMILE 3 User b54d574d3c 28-04-2015 08:28:09
Convert sdf file to SMILES (at a certain pH) 3 User f8124e7644 14-04-2015 10:01:12
Aromatic nitrogen and explicit hydrogen atoms 2 User 1aed78f6c4 13-04-2015 11:37:22
Molconvert, write additional informations to an sdf 3 User b54d574d3c 30-03-2015 11:42:05
Handling of abnormal charges 2 User 02967e48ce 09-03-2015 15:24:08
Locate framents by id in a fragmented molecule 3 User 55ffa2f197 06-03-2015 15:41:01
RenderingStyle 2 User 870ab5b546 24-02-2015 02:18:26
memory leak in MolExporter for svgs 3 User ebc1e6aaea 12-02-2015 05:36:07
How tautomers are defined by JChem 5 User cf4264f752 27-01-2015 15:25:21
Failed to import text file with CAS number into Chemaxon 1 User b993cfcb8f 21-01-2015 16:48:52
Force field conversion errors 4 User 677b9c22ff 18-12-2014 21:55:11
Trouble with BondAngleChecker 6 User f05f6b8c05 18-12-2014 06:27:27
MRectangle point confusion 2 User 870ab5b546 02-12-2014 20:05:13
unneeded stereochemical descriptor 4 User 870ab5b546 23-11-2014 00:42:06
Help please: Convert alias F3^C, F2H^C to MDL without alias 2 User 3898c01b63 18-11-2014 18:42:53
importing n gives N 2 User 870ab5b546 12-11-2014 21:29:00
importing H gives radical 3 User 870ab5b546 06-11-2014 14:40:12
How to convert mol to SMILES? Thanks. 2 User ce2763288e 24-10-2014 16:30:30
fragment stereochemistries in SMILES format 4 User 870ab5b546 21-10-2014 16:01:47
Standard InChI generation 2 User 4e4b708dbd 20-10-2014 13:26:13
shortcut group coordinates after contraction 2 User 870ab5b546 15-10-2014 13:45:07
Ring perception 4 User da8da0ed54 14-10-2014 10:33:33
Conversion of Molecules with HN to SMILES 6 User 3898c01b63 09-10-2014 00:33:09
Merge more inchis 2 User 887fee85a7 04-10-2014 17:33:15
Reference numbers to S-groups does not match number of S-gro 8 User 870ab5b546 30-09-2014 01:12:54
ValenceCheck is supported for atoms in molecules only 20 User 870ab5b546 30-09-2014 00:38:35
Native library is not initialized with MolConvert under Mac 3 User dad335ca51 15-09-2014 09:45:15
Problem with arrangeMolecules() 28 User f05f6b8c05 10-09-2014 04:06:16
unexpected R/S change on atom move 11 User 870ab5b546 08-09-2014 16:40:46
bridged bicyclic compounds and bad stereo depictions 5 User 870ab5b546 08-09-2014 01:15:51
Export to Inchi issues 4 User 0cd5667845 28-08-2014 22:50:14
Bond drawing-order change after call to findFrags() 5 User f05f6b8c05 12-08-2014 11:11:39
Conversion bug in 14.7.7.0 3 User 92a07cc890 01-08-2014 14:13:45
Issue converting Structure to Smile string 6 User 03592810fa 07-07-2014 11:03:42
Br(+) 9 User 870ab5b546 01-07-2014 01:27:30
Colouring with multiple smarts queries 5 User 7c177bab3b 27-06-2014 11:21:08
new exception 2 User 870ab5b546 25-06-2014 20:16:47
Tetrahedral stereocenters in CML and atom ordering issue 4 User 4df9fb85ce 06-06-2014 22:17:00
Tetrahedral centers of symmetric molecules 4 User 050f2b66a2 23-05-2014 13:26:56
Naming multiples files in molconvert -m output 4 User 70fe4ac955 20-05-2014 20:29:45
insertBondInOrder() 3 User 870ab5b546 12-05-2014 16:07:19
AtomProperty.Radical 6 User 870ab5b546 12-05-2014 15:07:16
Method to identify/create Sgroups in structures? 3 User f05f6b8c05 25-04-2014 03:30:35
property calculation with different molecular formats 2 User 8feadbc205 21-04-2014 06:31:03
inchi issues 7 User a827e3e366 10-04-2014 17:51:18
CIF file support 5 User 8688ffe688 10-04-2014 00:46:29
Does MolConverter creates canonical SMILES? 8 User 3d07a7b484 31-03-2014 10:37:25
Updating molecule causes hang when saving 10 User 956e0ca334 18-02-2014 17:10:18
Can not reopen Marvin generated files with n-group 6 User 9ca67301a1 11-02-2014 19:51:55
Read error after molecule 0: Reference numbers to S-groups 2 User e3e353e357 05-02-2014 16:34:10
Incorrect stereo label 3 User a11e9761d6 23-01-2014 16:55:50
Question about wedge/hash changes from implicitizing hash Hs 5 User f05f6b8c05 16-01-2014 07:35:53
Validatate a molfile in a single step using Marvin Java API? 3 User e6dac1475d 15-01-2014 14:56:01
How to get the formula of the constant part of a polymer? 3 User e6dac1475d 10-01-2014 15:37:00
Export to SDF doesn't include empty molecule properties 4 User 25a86f2b53 07-01-2014 18:18:25
ChemDraw CDX import prolobem for peptides 3 User 956e0ca334 03-01-2014 12:13:02
CDX import problem Square Brackets 5 User 956e0ca334 03-01-2014 11:31:14
How to combine data with sdf file. 7 User 0b2323d196 09-12-2013 10:11:22
Export problem with multicenter in new version 2 User 761d9eb85b 04-12-2013 10:19:34
MolImporter.importMol() for SDF files issue 2 User 7a902f260f 31-10-2013 14:31:02
null MDocument after importing MOL structure 4 User 870ab5b546 30-10-2013 20:38:20
Convert peptide sequence into 2D structure 7 User 55ffa2f197 18-10-2013 16:58:39
PDF export problem exportToBinFormat 4 User 956e0ca334 15-10-2013 09:32:54
Setting font on png exportToBinFormat 3 User 956e0ca334 14-10-2013 16:35:04
use of skipAtomValues 3 User 6fe3d4c2db 11-10-2013 09:24:11
Problem with Molecule.fuse() 7 User f05f6b8c05 08-10-2013 02:20:53
Converting an imported molecule to smiles 5 User a18e201107 01-10-2013 18:33:01
CXSmiles to PNG - atom labels 5 User 7a95044e7d 26-09-2013 14:46:14
Upgrading to JChem 6.1 6 User 7a902f260f 24-09-2013 14:38:45
how to remove $MolName in the SDF file 3 User cdc1fd6fff 16-09-2013 02:19:30
export error 3 User 870ab5b546 09-09-2013 21:58:50
oeb.gz reader/writer 4 User 2347372188 04-09-2013 04:58:31
Incorrect Chiral Center Counts 9 User 81a38f9467 21-08-2013 18:14:22
SMILE format thow the error. 4 User fec9e52845 13-08-2013 13:13:32
determine tetrhedral charility of C 3 User 55ffa2f197 09-08-2013 18:39:37
breaking mutiple ring bonds 9 User 55ffa2f197 08-08-2013 03:19:22
Break mutiple bonds stepwise, keep the fragments from each 5 User 55ffa2f197 02-08-2013 14:27:04
Problem displaying Salt Multiplicity outside brackets 4 User f3a11790a9 03-07-2013 13:52:03
Get the Parent of the Compound 9 User fec9e52845 28-06-2013 11:07:21
dearomatization of coordinated benzene 10 User 870ab5b546 08-05-2013 21:37:10
shortcut groups with multicenter groups? 5 User 870ab5b546 07-05-2013 15:16:13
Removal of ring labels from imported .mol files. 2 User c279fdedcf 07-05-2013 13:24:32
Extraneous Parity Markers Added to Molecule in "Clean in 3D" 5 User 8c948fd5ba 06-05-2013 20:45:22
MoleculeGraph.fuse() bug with multicenter groups? 6 User 870ab5b546 01-05-2013 20:45:50
explicitizing H with multiatom groups 4 User 870ab5b546 01-05-2013 19:10:35
bug in shortcut ungrouping: geometry problem 21 User 870ab5b546 01-05-2013 16:15:28
molecule flag for presence of coordinate bond? 2 User 870ab5b546 29-04-2013 15:29:40
Molecule formats changes between 5.6 and 5.12 11 User 7a902f260f 26-04-2013 21:26:31
adding atoms & bonds to SelectionMolecule 6 User 870ab5b546 26-04-2013 13:27:02
request for Sgroup.getBondArray() 4 User 870ab5b546 25-04-2013 20:46:13
Exception when typing invalid control sequnce in group name 2 User 57295192cc 25-04-2013 09:21:45
Problem reading mol files 3 User 25d107bd42 24-04-2013 13:42:37
Backward compatibility of extended SMILES/SMARTS export 2 User 1acfa01768 23-04-2013 14:42:47
chemaxon smiles extension 2 User f28a846261 20-04-2013 00:57:48
NullPointerException after upgrading to JChem 5.12 10 User 7a902f260f 16-04-2013 14:28:09
MulticenterSgroup class? 5 User 870ab5b546 15-04-2013 18:09:47
MolExporter doesn't return standard InChI by default? 9 User 57295192cc 11-04-2013 13:26:25
chemaxon.core.ChemConst 2 User 870ab5b546 08-04-2013 16:21:16
3D generation of both enantiomers from an sd file. 5 User ac9e79dc7d 28-03-2013 18:08:00
Encoding bug in every export 1 ChemAxon 712bc8fcf4 18-03-2013 15:54:01
Convert CML to SMIRKS 7 User 441400200b 14-03-2013 16:20:38
Different results depending on the format 5 User 918876d6ff 13-03-2013 17:23:24
CDX files written with surprising atom charge values. 3 User af3e34cbec 03-03-2013 00:24:26
Aromatic rings 3 User 0742d1ce7b 01-03-2013 06:44:08
molconvert gives unwanted "sorting" of columns 17 User 2ca05a7f4e 28-01-2013 17:29:11
Smiles file with attached data (or other text formate) ? 5 User 2ca05a7f4e 27-01-2013 09:41:56
Change of bond representations by addExplicitHydrogens 3 User f05f6b8c05 16-01-2013 12:41:00
Export of structure as name creates invalid chemical name 4 User 0261d34ad7 07-01-2013 15:48:14
Is this a correct chiral-center count? 14 User f05f6b8c05 10-12-2012 08:33:28
about the standardization of rxn format string 4 User 22c88daf92 06-12-2012 08:34:51
How to create a molecule object by the mol string? 2 User 22c88daf92 03-12-2012 09:21:10
problem running Example script 2 User 4cc64a63fe 27-11-2012 16:51:52
Molconverter class not found 3 User 1f4905a987 26-11-2012 20:51:25
"Position variation bond"-like shadow possible? 4 User 1494e93569 21-11-2012 11:37:08
Using MolConvert to generate images - Need help starting! 14 User cae34764c0 18-11-2012 23:21:09
Problem with convertion from mol2 to sdf 7 User f7c6611bf1 12-11-2012 15:27:21
Change curved arrow attributes? 2 User 9b0b2c1b48 08-11-2012 23:32:31
API method to detect meso compounds? 4 User f05f6b8c05 25-10-2012 10:09:44
Deleting one molecule template from another 3 User da8da0ed54 23-10-2012 08:43:53
Problem with Import Name in 5.11 and 5.11.2 4 User 25d1ad8de8 17-10-2012 09:38:06
Error with handling SGroupData in MDL Molfile 8 User dfeb81947d 10-10-2012 15:11:07
InchiKey and options 8 User dfeb81947d 02-10-2012 14:18:30
Problem Displaying smiles in MarvinSketch 7 User 9b0b2c1b48 01-10-2012 14:54:47
PDF and SVG exports should export text as text. 4 User 49f62f3bcf 26-09-2012 11:52:41
Loss of double and triple bonds when saving as .pdb 8 User 96b281650a 20-09-2012 10:54:58
Remove a data in Molecule from array of Attached Data 3 User dfeb81947d 19-09-2012 10:30:27
Marvin & AdvancedMolConverter die ungracefully on this 4 User f67d4188b6 17-09-2012 09:30:01
Disconnected Fragments and SGroups 3 User dfeb81947d 13-09-2012 10:02:10
Get the stoichiometry of a fragment 6 User dfeb81947d 11-09-2012 15:23:50
Attachment point handling is not supported for S-groups with 13 User 52a4e280f0 04-09-2012 10:20:26
MolFormatException: Cannot read molecule file 3 User 52a4e280f0 31-08-2012 14:29:30
Inchi format error 3 User 92a07cc890 22-08-2012 09:32:40
Converter Mol para 3D 2 User 7fc1506f44 17-08-2012 15:36:23
Generate 3D molecule 2 User 7fc1506f44 17-08-2012 15:33:15
Problems with non-stereo option in Marvin Sketch 2 User 7fc1506f44 20-07-2012 16:36:11
Export Smiles isomeric without information? 3 User 7fc1506f44 17-07-2012 18:56:36
not all the structure represented in svg 4 User cf4264f752 09-07-2012 10:29:52
R/S bug with short bonds 7 User 870ab5b546 04-07-2012 00:04:27
Get CAS numbers from structure 9 User 96e1912746 29-05-2012 21:16:43
Jchem cartridge cant generate svg from particular molfie 3 User cf4264f752 24-05-2012 09:25:56
Cannot convert smiles to 3D 7 User 96e1912746 23-05-2012 20:31:23
Attached images hidden ? 3 User 25d107bd42 22-05-2012 18:49:37
error with getSSREdges() 5 User 8aa9ad62e8 20-05-2012 15:17:19
valence check problem in JChem 5.9.0 9 User 870ab5b546 15-05-2012 23:58:16
structure to numbering rather than name ? 9 User f93a4318a2 10-05-2012 14:13:47
Compare 3D coordinates 2 User 2b2c2ee399 07-05-2012 08:10:27
InCHI Native Library issue 3 User 9047da8285 03-05-2012 19:17:51
Issues with C-H bond lengths 7 User 25d107bd42 01-05-2012 20:14:26
In which jar is chemaxon.calculations.stereo.*? 3 User f05f6b8c05 27-04-2012 05:02:30
Component grouping not recognized in CDX and SKC imports 9 User 1a8d11549a 25-04-2012 15:33:28
Split a large file into smaller part using molconvert 4 User 2b2c2ee399 18-04-2012 10:28:31
Is it possible to add a label to an Image? 2 User 6adcc60439 18-04-2012 00:44:46
Drawing amino acids and peptide 2 User 729ea99e99 12-04-2012 10:55:25
program dies due to MolFormatException 3 User 55ffa2f197 10-04-2012 01:37:41
i'm beginner please can you help 7 User 8bebba65c2 04-04-2012 10:04:59
RgMolecule -> Molecule ClassCastException 16 User 870ab5b546 02-04-2012 18:10:39
Bridged ring system represented incorrectly 55 User a11e9761d6 31-03-2012 00:05:36
Adding a proton to a given Atom 4 User a9d76a1173 29-03-2012 20:42:04
Invalid "extended" SMILES from chemical in ChemAxon table 3 User 0261d34ad7 24-03-2012 13:14:59
groups: manual flush? 2 User b8fd1c3fa6 04-03-2012 16:16:16
represent two different r groups on one place 3 User cf4264f752 27-02-2012 09:53:15
How to get the centroid of a Molecule 2 ChemAxon fa971619eb 23-02-2012 18:53:32
Resizing an individual molecule 4 User 98ff028321 17-02-2012 06:38:10
Representation of lipid ambiguity 4 User dc11dd6805 15-02-2012 16:52:09
How to get the field Value from SDF file? 2 User a83cdfbe8a 15-02-2012 11:49:15
convert smile format molecules into individual .pdb files 21 User 53b9950b3b 05-02-2012 23:45:41
Set starting atom when generating SMILES 3 User 22337819af 01-02-2012 15:08:31
The smile format from MARVIN is not consistent with MetaCyc. 4 User 276147625b 28-01-2012 17:28:19
Canonical/unique smiles 4 User da00f5c453 24-01-2012 22:33:30
molconvert misaligns functional groups exported to png 3 User bc1ce546aa 22-01-2012 06:20:43
Marvin Fails to Generate SMILES 2 User a9d76a1173 20-01-2012 15:39:33
2D clean and stereochemistry 3 User 80c35730b2 17-01-2012 19:41:57
Expanding Abbreviated Amino Acids 3 User a9d76a1173 17-01-2012 19:02:12
Double C/T or Unspec bond type in MarvinSketch 6 User 9ef27c545f 16-01-2012 12:03:24
How do I mix molecules as if in a bottle? 2 User d1576ddecb 13-01-2012 11:30:27
MDL mol file format web pages no more existent 3 User 25d107bd42 10-01-2012 18:58:38
Support for .sk2 files in MolConverter possible? 2 User f9b647ae98 06-01-2012 13:05:51
Files in tomcat/temp directory 3 User 276402c609 28-12-2011 14:35:16
Generating smiles 2 User ece72b21c8 21-12-2011 07:41:06
Reading and Writing to SDF 13 User a9d76a1173 16-12-2011 20:31:54
Molecule symmetry 12 User 9b067d2e85 16-12-2011 19:44:09
How to make absolute stereochemistry the default in MSketch? 14 User a11e9761d6 16-12-2011 00:25:47
Problem displaying protonated amine groups/ammonium ions 3 User e281a05693 13-12-2011 18:56:44
Macromolecule object and Mol2 format 2 User 6b2914d174 05-12-2011 16:58:19
InChI error messages using Protonation plugin 4 User 8961c1b53b 30-11-2011 06:59:28
IUPAC naming issue 17 User cf4264f752 23-11-2011 14:35:36
Insert failed: "Some features .. cannot be converted to..." 13 User a7faa21887 22-11-2011 15:48:39
adding R/S labels to graphics from molconvert 3 User f93a4318a2 21-11-2011 15:33:59
Problems saving as *.mol file 8 User 25d107bd42 20-11-2011 11:26:07
converting in mol with the right bond topology 6 User 779e37e0e6 10-11-2011 18:47:50
Conversion of IUPAC name into 2D structure 2 User cf163fb4ae 07-11-2011 10:41:18
Molecule.toFormat() 6 User cdd15e6bb1 31-10-2011 15:47:17
another problem with standardizer 8 User cf4264f752 28-10-2011 13:06:12
Prevent "InChiKey=" in exported InChiKey? 3 User 0261d34ad7 28-10-2011 10:15:38
Library problem with InChi String conversion 17 User b0f6d33590 27-10-2011 11:15:39
how to turn off AuxInfo when generating InChI 6 User cf4264f752 26-10-2011 13:56:01
Cannot generate SVG with "cannot expand invisible group" err 9 User a7faa21887 23-10-2011 15:29:12
Old topics in structure representation 1 ChemAxon 25dcd765a3 14-10-2011 12:59:31
valence error failures 10 User 870ab5b546 11-10-2011 14:51:37
SVG does not have symbols but source MOL have it 10 User a7faa21887 05-10-2011 11:09:57
Lose of Sulfur and Phosphorus mol2 types using standardize 5 User ed9697d993 22-03-2011 12:54:46
Incorrect interpetation of CML bondstereo 19 User bd69837856 16-06-2010 15:08:59
Mechanism arrows 35 User 5efe442094 30-07-2004 11:25:05