Program to generate different conformations of a molecule. Can input a file containing a molecule (currently only XYZ files), assign bonds (given uniform bond length), and then perform rotations about bonds.
Compile as gcc main.c -lm -o conf -O3, and run as either ./conf script.r (to run a script) or ./conf to open interactive mode.
The following commands are available
- open FILENAME Opens xyz file at FILENAME
- bond BL Generates bonds between atoms where distance < BL (angstroms)
- rotate A B THETA Rotates atoms connected to B about the A-B axis an amount theta (radians)
- output FILENAME Writes output as xyz file to FILENAME.
- open FILENAME opens xyz file FILENAME
- bond BL sets up bonds between all atoms with distance < BL angstroms
- graph N prints out graph starting at atom N
- print prints out entire system
- rotate A B THETA applies a rotation to atoms connected to B about the A-B axis an amount theta radians.
- output FILENAME outputs as XYZ file into FILENAME
- run SCRIPT runs script in SCRIPT.
- exit exits program
obabel -:"<smiles>" -oxyz -O<filename.xyz> --gen3d
Can be used to generate xyz files to test this with.