Merge pull request #309 from UCL-CCS/ties_md_update

make md changes

ties/md.py

@@ -1,34 +1,62 @@
 import os
 
-from TIES_MD import TIES, cli
-from TIES_MD.ties_analysis import ties_analysis
+from TIES_MD import TIES
+from TIES_MD import ties_analysis
+from openmm import unit
+import json
 
 class MD():
-    def __init__(self, sim_dir, sim_name='complex', fast=False):
+    '''
+    Class a wrapper around TIES_MD API that exposes a simplified interface.
 
-        self.sim_dir = sim_dir
-        cfg_file = os.path.join(self.sim_dir, 'TIES.cfg')
-        md_config = cli.read_config(cfg_file)
-        self.md = TIES.TIES(cwd=self.sim_dir, exp_name=sim_name, **md_config)
+    :param sim_dir: str, points to where the simulation is running i.e where the TIES.cfg file is.
+    :param sim_name: str, the prefix to the input param and topo file i.e complex for complex.pdb/prmtop.
+    :param fast: boolean, if True the setting is TIES.cfg will be overwritten with minimal TIES protocol.
+    '''
+    def __init__(self, sim_dir, sim_name='complex', fast=False):
+        cwd = os.getcwd()
+        self.sim_dir = os.path.join(cwd, sim_dir)
+        self.analysis_dir = os.path.join(self.sim_dir, '..', '..', '..')
+        #This is the main TIES MD object we call it options as the user interacts with this object to change options
+        self.options = TIES(cwd=self.sim_dir, exp_name=sim_name)
 
         if fast:
             #modify md to cut as many corners as possible i.e. reps, windows, sim length
-            self.md.reps_per_exec = 1
-            self.md.total_reps = 3
-            self.md.global_lambdas = [0.00, 0.05, 0.1, 0.3, 0.5, 0.7, 0.9, 0.95, 1.00]
-            self.md.sampling_per_window = self.md.sampling_per_window*0.5
-            self.md.update_cfg()
+            self.options.total_reps = 3
+            self.options.global_lambdas = [0.00, 0.05, 0.1, 0.3, 0.5, 0.7, 0.9, 0.95, 1.00]
+            self.options.sampling_per_window = 2*unit.nanoseconds()
+
+        self.options.setup()
 
     def run(self):
-        self.md.run()
+        '''
+        Wrapper for TIES_MD.TIES.run()
+
+        :return: None
+        '''
+        self.options.run()
+
+    def analysis(self, legs, analysis_cfg='./analysis.cfg'):
+        '''
+        Wrapper for TIES_MD.ties_analysis()
+
+        :param legs: list of strings, these are the thermodynamic legs of the simulation i.e. ['lig', 'com'].
+        :param analysis_cfg: str, for what the analysis config file is called.
+
+        :return: None
+        '''
+        os.chdir(self.analysis_dir)
+        if not os.path.exists('exp.dat'):
+            ties_analysis.make_exp(verbose=False)
 
-    def setup(self):
-        self.md.setup()
+        #read the experimental data
+        with open('exp.dat') as f:
+            data = f.read()
+        exp_js = json.loads(data)
 
-    def analysis(self, exp_data, legs, analysis_cfg='./analysis.cfg'):
         ana_cfg = ties_analysis.Config(analysis_cfg)
         ana_cfg.simulation_legs = legs
-        ana_cfg.exp_data = exp_data
+        ana_cfg.exp_data = exp_js
         ana = ties_analysis.Analysis(ana_cfg)
         ana.run()