#!/opt/opt/bin/python
import sys
import numpy as np
from msmbuilder import Project, Conformation, Serializer
#import DihedralTools
import RefactoredDihedralTools

print("""USAGE:  GetProjectTorsions.py RamaFilename OutputFilename

Input: 
This will calculate a pairwise distance matrix based on backbone torsion angles.
Notes:

1.  Assumes ProjectInfo.h5 is located in current directory, per MSMBuilder convention.

""")

ProjectFile="./ProjectInfo.h5"
P1=Project.Project.LoadFromHDF(ProjectFile)

RamaFilename=sys.argv[1]
Rama=Serializer.LoadData(RamaFilename)

OutputFilename=sys.argv[2]

PairwiseTorsions=RefactoredDihedralTools.CalculatePairwiseTorsionMatrix(P1,Rama).astype('float32')

Serializer.SaveData(OutputFilename,PairwiseTorsions)