Thought about this as a small patch while working on a separate project. Can be named anything; this is the simplest way to expose the conversion function without a heavy refactor. Other commands can be added, but it looks like this is pretty much the only file that a user would access directly.
This automatically adds the command intermol-convert to the user's $PATH if locally installed with pip; having it automagically work in a conda install can be done if/when there's another release.
(openff-dev) [InterMol] python -m pip install -e .
Obtaining file:///Users/mwt/software/InterMol
Requirement already satisfied: numpy in /Users/mwt/miniconda3/envs/openff-dev/lib/python3.7/site-packages (from intermol==0.1.0) (1.19.4)
Requirement already satisfied: parmed in /Users/mwt/miniconda3/envs/openff-dev/lib/python3.7/site-packages (from intermol==0.1.0) (at20RC5-54.g5702a232fe.dirty)
Requirement already satisfied: six in /Users/mwt/miniconda3/envs/openff-dev/lib/python3.7/site-packages (from intermol==0.1.0) (1.15.0)
Installing collected packages: intermol
Attempting uninstall: intermol
Found existing installation: intermol 0.1.0
Uninstalling intermol-0.1.0:
Successfully uninstalled intermol-0.1.0
Running setup.py develop for intermol
Successfully installed intermol
(openff-dev) [InterMol] intermol-convert --help # same output as python intermol/convert.py --help
usage: intermol-convert [-h] [--des_in file] [--gro_in file file]
[--lmp_in file] [--amb_in file file] [--crm_in file]
[--desmond] [--gromacs] [--lammps] [--amber]
[--charmm] [--odir directory] [--oname prefix] [-e]
[--inefile INEFILE] [-dp path] [-ds settings]
[-gp path] [-gs settings] [-lp path] [-ls settings]
[-ap path] [-as settings] [-cp path] [-cs settings]
[-f] [-v] [-n]
Perform a file conversion
optional arguments:
-h, --help show this help message and exit
Choose input conversion format:
--des_in file .cms file for conversion from DESMOND file format
--gro_in file file .gro and .top file for conversion from GROMACS file
format
--lmp_in file input file for conversion from LAMMPS file format
(expects data file in same directory and a read_data
call)
--amb_in file file input files (.prmtop) and (.crd or equivalent) for
conversion from AMBER file format
--crm_in file input file for conversion from CHARMM file format
Choose output conversion format(s):
--desmond convert to DESMOND
--gromacs convert to GROMACS
--lammps convert to LAMMPS
--amber convert to AMBER
--charmm convert to CHARMM
Other optional arguments:
--odir directory specification of output directory (default: ./)
--oname prefix specification of prefix for output filenames (default:
inputprefix_converted)
-e, --energy evaluate energy of input and output files for
comparison
--inefile INEFILE optional run settings file for input energy evaluation
(e.g. .cfg, .mdp, .input)
-dp path, --despath path
path for DESMOND binary, needed for energy evaluation
-ds settings, --desmondsettings settings
Desmond .cfg settings file used for energy evaluation
-gp path, --gropath path
path for GROMACS binary, needed for energy evaluation
-gs settings, --gromacssettings settings
Gromacs .mdp settings file used for energy evaluation
-lp path, --lmppath path
path for LAMMPS binary, needed for energy evaluation
-ls settings, --lammpssettings settings
pair_style string to use in the output file. Default
is a periodic Ewald simulation
-ap path, --amberpath path
path for AMBER binary, needed for energy evaluation
-as settings, --ambersettings settings
AMBER .in file used for energy evaluation
-cp path, --charmmpath path
path for CHARMM binary, needed for energy evaluation
-cs settings, --charmmsettings settings
CHARMM .in settings used for energy evaluation.
Because of the unified input file, settings lines
rather than a file are part
-f, --force ignore warnings (NOTE: may lead to partially correct
topologies)
-v, --verbose high verbosity, includes DEBUG level output
-n, --noncanonical print the 'noncanonical' enery terms, the ones that
only occur in 1 or 2 programs
mattwthompson
commented
3 years ago
Thought about this as a small patch while working on a separate project. Can be named anything; this is the simplest way to expose the conversion function without a heavy refactor. Other commands can be added, but it looks like this is pretty much the only file that a user would access directly.
This automatically adds the command
intermol-convertto the user's $PATH if locally installed with pip; having it automagically work in a conda install can be done if/when there's another release.