[Open Babel] print UFF parameters

2018-05-06 Thread Tang, Dai
Hi, I have a large number database of molecules. In Open-babel (command line version), I can optimize the geometry of molecules separately using UFF. Question: Is there a way to print the UFF parameters for each molecule in database, or even potential formula of each term such as valence, bo

[Open Babel] Problem of installing open-babel locally on Mac

2018-05-08 Thread Tang, Dai
Hi, I'm trying to install Open-babel locally without root access on Mac. However, it fails and shows: [ 87%] Building CXX object test/CMakeFiles/roundtrip.dir/roundtrip.o /bin/sh: -c: line 0: syntax error near unexpected token `(' /bin/sh: -c: line 0: `cd "/Users/macbook/Dropbox (GaTech)/Res

[Open Babel] Question about src/forcefielduff.cpp

2018-05-18 Thread Tang, Dai
Hi, I just want to make sure that I fully understand what a source code src/forcefielduff.cpp is saying. In 'void OBFFAngleCalculationUFF::Compute()', there is no content in case 2 and case 4. Is the energy calculated by using the default form (sp3) for case 2 and case 4, or not calculated a

[Open Babel] Problem with ring detection

2019-01-27 Thread Tang, Dai
Hi, I have a problem with the ring detection using Open Babel 2.4.1. My goal is to know which carbon atoms (or other element) of a molecule belong to a ring structure. So far the method I tried is to grep the label 'TYPE: Car' in .molreport file. Successful case: CC1=CC=CC=C1 The SMILE cod