Bugs item #3526866, was opened at 2012-05-15 01:18 Message generated for change (Tracker Item Submitted) made by jvoorhees You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=428740&aid=3526866&group_id=40728
Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: Library Functions Group: 2.3.x Status: Open Resolution: None Priority: 5 Private: No Submitted By: Giorgio (jvoorhees) Assigned to: Nobody/Anonymous (nobody) Summary: Incorrect reading number of bonds from V2000 MOL/SDF Initial Comment: File format: SDF/MOL file with V2000 Connection Table Situation If both number of atoms and number of bonds are greater than 99 (thus both have 3 digits) the function OBConversion::Read() fails to read properly the molecule. Comment The standard Counts Line (in CTAB V2000) must have the following format: "aaabbblllfffcccsssxxxrrrpppiiimmmvvvvvv " where "aaa" is the number of atoms and "bbb" is the number of bonds, but if both have 3 digits as in the following example "102107 0 0 0 0 0 0 0 0 1 V2000" the function OBConversion::Read() does not read the molecule and return the error *** Open Babel Warning in ReadMolecule WARNING: Problems reading a MDL file Invalid bond specification, atom numbers or bond order are wrong. Example In the attachment file there is a molecule with 102 atoms and 107 bonds that the function can not read, with two different forms of Counts Line. In the first the counts line is: "102 107 0 0 0 0 0 0 0 0 1 V2000", with the number of atoms and bonds separated by a space; in this case the function reads a molecule with 102 atoms but 10 bonds, and returns the error: *** Open Babel Warning in ReadMolecule Either the file contains Atom Lists, which are not currently supported and are ignored or the atom or bond count is >999, which is not allowed in V2000 MDL files. In the second the counts line is: "102107 0 0 0 0 0 0 0 0 1 V2000" and the molecule is not read, with the error *** Open Babel Warning in ReadMolecule WARNING: Problems reading a MDL file Invalid bond specification, atom numbers or bond order are wrong. OpenBabel Version: 2.3.1 System: Linux Thanks, Giorgio. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=428740&aid=3526866&group_id=40728 ------------------------------------------------------------------------------ Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ _______________________________________________ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
