From d7b28f120bb8a5fdfb18d1e84d7504724ead30fe Mon Sep 17 00:00:00 2001
From: Josh <jsmith07@uw.edu>
Date: Mon, 2 Apr 2018 15:04:47 -0700
Subject: [PATCH] Add input bias parser to core functions.

---
 plumitas/core.py         | 47 ++++++++++++++++++++++++++++++++++++++++
 plumitas/data/plumed.dat | 37 +++++++++++++++++++++++++++++++
 2 files changed, 84 insertions(+)
 create mode 100644 plumitas/data/plumed.dat

diff --git a/plumitas/core.py b/plumitas/core.py
index b5817e4..5fa9124 100644
--- a/plumitas/core.py
+++ b/plumitas/core.py
@@ -1,4 +1,5 @@
 import os
+import re
 
 import pandas as pd
 
@@ -68,3 +69,49 @@ def read_hills(filename='HILLS'):
         CVs and bias as columns, time as index.
     """
     return read_colvar(filename)
+
+
+def parse_bias(filename='plumed.dat', method=None):
+    """
+    Function that takes experimental data and gives us the
+    dependent/independent variables for analysis.
+
+    Parameters
+    ----------
+    filename : string
+        Name of the plumed input file used for enhanced sampling run.
+    method : string
+        Name of bias method used during
+    Returns
+    -------
+    bias_args : dict
+        Dictionary of key: value pairs from the plumed.dat file. Will
+        facilitate automatic reading of parameter reading once
+        core.SamplingProject class is implemented.
+    """
+    if not method:
+        print('Parser requires method to identify biased CVs. '
+              'Please retry with valid method arg.')
+        return
+
+    # read input file into string
+    full_path = os.path.abspath(filename)
+    input_string = ''
+    with open(full_path) as input_file:
+        for line in input_file:
+            input_string += line
+
+    # isolate bias section
+    method = method.upper()
+    bias_string = input_string.split(method)[1].lower()
+
+    # use regex to create dictionary of arguments
+    arguments = (re.findall(r'\w+=".+?"', bias_string)
+                 + re.findall(r'\w+=[\S.]+', bias_string))
+
+    # partition each match at '='
+    arguments = [(m.split('=')[0], m.split('=')[1].split(','))
+                 for m in arguments]
+    bias_args = dict(arguments)
+
+    return bias_args
diff --git a/plumitas/data/plumed.dat b/plumitas/data/plumed.dat
new file mode 100644
index 0000000..5f047f4
--- /dev/null
+++ b/plumitas/data/plumed.dat
@@ -0,0 +1,37 @@
+RESTART
+MOLINFO MOLTYPE=protein STRUCTURE=reference.pdb
+WHOLEMOLECULES ENTITY0=1-55
+
+CENTER ATOMS=20-28   LABEL=pos0
+CENTER ATOMS=45-47   LABEL=neg0
+dp0n0: DISTANCE ATOMS=pos0,neg0
+
+#### DIHEDRALS ####
+#phiA0:  TORSION ATOMS=@phi-A2
+psiA0:  TORSION ATOMS=@psi-2
+phiA1:  TORSION ATOMS=@phi-3
+psiA1:  TORSION ATOMS=@psi-3
+phiA2:  TORSION ATOMS=@phi-4
+#psiA2:  TORSION ATOMS=@psi-A4
+
+#### Water COORDINATION ####
+GROUP ATOMS=21,24,25,27,28 LABEL=pos_H
+GROUP ATOMS=46,47 LABEL=neg_O
+GROUP ATOMS=56-4118:3 LABEL=sol_O
+
+coord_H: COORDINATION GROUPA=pos_H GROUPB=sol_O D_0=0.19 R_0=0.03
+coord_O: COORDINATION GROUPA=neg_O GROUPB=sol_O D_0=0.27 R_0=0.03
+
+PBMETAD ...
+ARG=dp0n0,psiA0,phiA1,psiA1,phiA2,coord_H,coord_O
+PACE=500 BIASFACTOR=10.0 HEIGHT=2.0 TEMP=300.0
+SIGMA=0.02,0.25,0.25,0.25,0.25,0.25,0.25
+FILE=HILLS_MTD0,HILLS_psiA0,HILLS_phiA1,HILLS_psiA1,HILLS_phiA2,HILLS_coord_H,HILLS_coord_O
+GRID_MIN=0,-pi,-pi,-pi,-pi,-2,-2
+GRID_MAX=3.0,pi,pi,pi,pi,20,20
+LABEL=pb
+WALKERS_MPI
+... PBMETAD
+
+#make STRIDE = to your exchange attempt frequency!!!
+PRINT FILE=COLVAR ARG=* STRIDE=500