The bondobj example program
Bondobj is a small but functional program that demonstrates using the OTF for application creation. Bondobj takes as input a PDB file and produces a representation of the molecule's bonds in MidasPlus graphics object format (described briefly in the README file). Bondobj can also optionally handle the hydrogen bonds and salt bridges delineated in the PDB file if given the '-h' or '-s' flags (respectively).
The files in the bondobj example directory are:
- README
- Contains brief description of the subset of MidasPlus graphics object format used by bondobj as well as some miscellaneous information.
- Makefile
- The default make target will compile bondobj by first running genlib with Mol.genlib as input (genlib -n Mol Mol.genlib), creating Mol/libMol.a which contains the classes Molecule, Atom, Bond, etc. Then bondobj.cc is compiled and linked with the library to produce bondobj. The Makefile also has a clean target which will return the directory to its initial state.
- Mol.genlib
- The input file for genlib. It is only two lines long!
- bondobj.cc
- The main program that makes use of the generated class library. It reads command line arguments, reads the PDB file, and processes the resulting bond list to output the bonds in graphics object format. You may want to refer to the OTF component documentation while perusing bondobj.cc.