setup_pyrosetta Namespace Reference

Functions
def	get_profile_fname
def	ask_append_rc

Variables
tuple	parser
	INTERPRETING RESULTS. More...
string	help = "The file to source in order to set the environment. Default is SetPyRosettaEnvironment.sh"
string	default = "SetPyRosettaEnvironment.sh"
tuple	options = parser.parse_args()
	source_environment_fname = options.source
tuple	source_environment_dir = os.path.dirname(os.path.abspath(__file__))
tuple	source_environment_path = os.path.join(source_environment_dir, source_environment_fname)
list	outdir = os.environ["HOME"]
	pyrosetta = source_environment_dir
tuple	outfile_path = os.path.join(outdir, options.outname)
tuple	OUTFILE = open(outfile_path, 'w')
tuple	rc = get_profile_fname()
	Now we figure out the bashrc or equivalent and then see if we already source it. More...
	rc_file_path = options.shell_profile_path
	Append the file. More...
tuple	READ_RCFILE = open(rc_file_path, 'r')
tuple	RCFILE = open(rc_file_path, 'a')
tuple	lines = READ_RCFILE.readlines()
string	source_line = "source "
tuple	append_rc = ask_append_rc()

Function Documentation

def setup_pyrosetta.ask_append_rc

(

)

def setup_pyrosetta.get_profile_fname

(

)

Gets the filename of the profile, which is different depending on operating system and shell.
PLEASE edit this if you have a way to make this more robust.  It feels like the wild west getting this info!
:rtype: str

Variable Documentation

tuple setup_pyrosetta.append_rc = ask_append_rc()

string setup_pyrosetta.default = "SetPyRosettaEnvironment.sh"

string setup_pyrosetta.help = "The file to source in order to set the environment. Default is SetPyRosettaEnvironment.sh"

tuple setup_pyrosetta.lines = READ_RCFILE.readlines()

tuple setup_pyrosetta.options = parser.parse_args()

setup_pyrosetta.outdir = os.environ["HOME"]

tuple setup_pyrosetta.OUTFILE = open(outfile_path, 'w')

tuple setup_pyrosetta.outfile_path = os.path.join(outdir, options.outname)

tuple setup_pyrosetta.parser

Initial value:

= ArgumentParser("This file adds a file to your home directory, "
                            ".pyrosetta_env, "
                            "and by default adds a line to your bash or zsh profile (if not already present) to source this file. "
                            "  After running this script, you will no longer need to run anything before using PyRosetta or add anything to your profile.")

INTERPRETING RESULTS.

COMMANDLINE COMPATIBILITY

Interaction Energy vs. Binding Energy COMMANDLINE COMPATIBILITY

INTERPRETING RESULTS.

INTERPRETING RESULTS COMMANDLINE COMPATIBILITY

setup_pyrosetta.pyrosetta = source_environment_dir

tuple setup_pyrosetta.rc = get_profile_fname()

Now we figure out the bashrc or equivalent and then see if we already source it.

Append it

tuple setup_pyrosetta.rc_file_path = options.shell_profile_path

Append the file.

tuple setup_pyrosetta.RCFILE = open(rc_file_path, 'a')

tuple setup_pyrosetta.READ_RCFILE = open(rc_file_path, 'r')

tuple setup_pyrosetta.source_environment_dir = os.path.dirname(os.path.abspath(__file__))

setup_pyrosetta.source_environment_fname = options.source

tuple setup_pyrosetta.source_environment_path = os.path.join(source_environment_dir, source_environment_fname)

string setup_pyrosetta.source_line = "source "