Hi guys, I am using openbabel C++ API to develope a atom mapping program, and I find two problems. And my question is can I customize or create a new element/atom by my own.
*(1) Not chemically interpreted groups* For example, if I have the following .mol file, R cannot be recognized, because I do not have detail information about what R is as a functional group. Can I store R as a new element? How can I do that by C++. $MOL INFOCHEM 2D 1 1.00000 0.00000 0 9 9 0 0 1 0 0 0 0 0999 V2000 -5.0000 0.5016 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.4710 0.3192 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3251 -0.1915 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.7960 -0.1915 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.6136 0.3192 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.0514 0.6476 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.0846 0.5016 0.0000 R 0 0 0 0 0 0 0 0 0 0 0 0 -3.4677 -0.6476 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.6352 -0.6476 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2 1 1 1 0 0 0 2 3 1 0 0 0 0 2 6 1 0 0 0 0 3 4 1 0 0 0 0 3 9 1 6 0 0 0 4 5 1 0 0 0 0 4 8 1 6 0 0 0 5 6 1 0 0 0 0 5 7 1 1 0 0 0 M END *(2) change one atom in a molecular to another atom* In the code, I sometimes need to change one atom to a new one, say I want to change one Carbon (C) to another atom (C1). Can I define a new atom, which is totally different from any atoms I will encounter in this .mol file. I think both problems are about whether openbabel can create a self-defined atom/element and store this information by C++ API. Thanks a lot. -- View this message in context: http://forums.openbabel.org/Custom-a-new-element-atom-tp4657563.html Sent from the General discussion mailing list archive at Nabble.com. ------------------------------------------------------------------------------ Open source business process management suite built on Java and Eclipse Turn processes into business applications with Bonita BPM Community Edition Quickly connect people, data, and systems into organized workflows Winner of BOSSIE, CODIE, OW2 and Gartner awards http://p.sf.net/sfu/Bonitasoft _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
