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Updating ShootPoint arguments #13

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merged 2 commits into from
Sep 25, 2018
Merged

Updating ShootPoint arguments #13

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3880b46
updating arguments to ShootingPoint class instantiation
ldgibson Sep 20, 2018
0fcc978
updated the required arguments for instantiating a ShootingPoint object
ldgibson Sep 25, 2018
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16 changes: 11 additions & 5 deletions aslm/core.py
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Original file line number Diff line number Diff line change
@@ -1,9 +1,9 @@
import os
import os.path as op
import re
import subprocess

import numpy as np
# import pandas as pd

from .utils import log_run

Expand Down Expand Up @@ -58,12 +58,18 @@ def find_and_replace(line, substitutions):


class ShootingPoint:
def __init__(self):
self.name = None # Name of shooting point
def __init__(self, name, input_file, topology_file=None,
md_engine="AMBER"):
self.name = name # Name of shooting point
self.input_file = input_file # Path to input file (e.g., `init.in`)
self.topology_file = topology_file # Path to topology file
self.md_engine = md_engine
self._input_file_dir = op.dirname(op.abspath(self.input_file))
self._input_file_name = op.splitext(op.basename(self.input_file))[0]

self.forward_commit = None # Status of forward simulation
self.reverse_commit = None # Status of reverse simulation
self.result = None # Result of shooting point
self.path = None
self.cv_values = None
return

Expand All @@ -79,7 +85,7 @@ def run_forward(self, inputfile="fwd.in"):
"""
jobname = self.name + "_f"
logfile = self.name + "_f.log"
run_MD(inputfile, jobname, logfile, topology="system.prmtop",
run_MD(self.input_file, jobname, logfile, topology="system.prmtop",
engine="AMBER")
self.forward_commit = self.check_if_committed(logfile)
return
Expand Down
6 changes: 3 additions & 3 deletions aslm/tests/test_core.py
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Original file line number Diff line number Diff line change
Expand Up @@ -10,7 +10,7 @@
def test_read_cv_values():
test_file_loc = op.join(op.dirname(op.abspath(__file__)),
'test_data', 'COLVAR2')
sp = ShootingPoint()
sp = ShootingPoint(name='test', input_file='.')

sp._read_cv_values(test_file_loc)
test_values = sp.cv_values
Expand All @@ -29,7 +29,7 @@ def test_find_and_replace():


def test_check_if_commited():
sp = ShootingPoint()
sp = ShootingPoint(name='test', input_file='.')
test_file_loc = op.join(op.dirname(op.abspath(__file__)),
'test_data', 'commit.log')
test_result = sp.check_if_committed(test_file_loc)
Expand All @@ -43,7 +43,7 @@ def test_check_if_commited():


def test_log():
sp = ShootingPoint()
sp = ShootingPoint(name='test', input_file='.')
sp.name = 'test'
sp.cv_values = [1, 2, 3]
sp.result = 'accepted'
Expand Down