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Copy pathExtractAnglesAndInts_Sep5Deg_SepPt1.py
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ExtractAnglesAndInts_Sep5Deg_SepPt1.py
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##########
#Extract Interactions: Spherical Radii at a granularity of 0.1 Angstroms, Anglular Arcs at 5 degree granularity, and Element Occurrance
#Oct 13, 2020
#Latest Author: Jessica Freeze
##########
import numpy as np
import os
import math
####Open input storage file
####Make dictionary
#Variable holding the dictionary for Angular Arcs (AA)
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-40.0,N-F-F-45.0,N-F-F-50.0,N-F-F-55.0,N-F-F-60.0,N-F-F-65.0,N-F-F-70.0,N-F-F-75.0,N-F-F-80.0,N-F-F-85.0,N-F-F-90.0,N-F-F-95.0,N-F-F-100.0,N-F-F-105.0,N-F-F-110.0,N-F-F-115.0,N-F-F-120.0,N-F-F-125.0,N-F-F-130.0,N-F-F-135.0,N-F-F-140.0,N-F-F-145.0,N-F-F-150.0,N-F-F-155.0,N-F-F-160.0,N-F-F-165.0,N-F-F-170.0,N-F-F-175.0,N-F-F-180.0,O-H-O-0.0,O-H-O-5.0,O-H-O-10.0,O-H-O-15.0,O-H-O-20.0,O-H-O-25.0,O-H-O-30.0,O-H-O-35.0,O-H-O-40.0,O-H-O-45.0,O-H-O-50.0,O-H-O-55.0,O-H-O-60.0,O-H-O-65.0,O-H-O-70.0,O-H-O-75.0,O-H-O-80.0,O-H-O-85.0,O-H-O-90.0,O-H-O-95.0,O-H-O-100.0,O-H-O-105.0,O-H-O-110.0,O-H-O-115.0,O-H-O-120.0,O-H-O-125.0,O-H-O-130.0,O-H-O-135.0,O-H-O-140.0,O-H-O-145.0,O-H-O-150.0,O-H-O-155.0,O-H-O-160.0,O-H-O-165.0,O-H-O-170.0,O-H-O-175.0,O-H-O-180.0,O-H-F-0.0,O-H-F-5.0,O-H-F-10.0,O-H-F-15.0,O-H-F-20.0,O-H-F-25.0,O-H-F-30.0,O-H-F-35.0,O-H-F-40.0,O-H-F-45.0,O-H-F-50.0,O-H-F-55.0,O-H-F-60.0,O-H-F-65.0,O-H-F-70.0,O-H-F-75.0,O-H-F-80.0,O-H-F-85.0,O-H-F-90.0,O-H-F-95.0,O-H-F-100.0,O-H-F-105.0,O-H-F-110.0,O-H-F-115.0,O-H-F-120.0,O-H-F-125.0,O-H-F-130.0,O-H-F-135.0,O-H-F-140.0,O-H-F-145.0,O-H-F-150.0,O-H-F-155.0,O-H-F-160.0,O-H-F-165.0,O-H-F-170.0,O-H-F-175.0,O-H-F-180.0,O-C-O-0.0,O-C-O-5.0,O-C-O-10.0,O-C-O-15.0,O-C-O-20.0,O-C-O-25.0,O-C-O-30.0,O-C-O-35.0,O-C-O-40.0,O-C-O-45.0,O-C-O-50.0,O-C-O-55.0,O-C-O-60.0,O-C-O-65.0,O-C-O-70.0,O-C-O-75.0,O-C-O-80.0,O-C-O-85.0,O-C-O-90.0,O-C-O-95.0,O-C-O-100.0,O-C-O-105.0,O-C-O-110.0,O-C-O-115.0,O-C-O-120.0,O-C-O-125.0,O-C-O-130.0,O-C-O-135.0,O-C-O-140.0,O-C-O-145.0,O-C-O-150.0,O-C-O-155.0,O-C-O-160.0,O-C-O-165.0,O-C-O-170.0,O-C-O-175.0,O-C-O-180.0,O-C-F-0.0,O-C-F-5.0,O-C-F-10.0,O-C-F-15.0,O-C-F-20.0,O-C-F-25.0,O-C-F-30.0,O-C-F-35.0,O-C-F-40.0,O-C-F-45.0,O-C-F-50.0,O-C-F-55.0,O-C-F-60.0,O-C-F-65.0,O-C-F-70.0,O-C-F-75.0,O-C-F-80.0,O-C-F-85.0,O-C-F-90.0,O-C-F-95.0,O-C-F-100.0,O-C-F-105.0,O-C-F-110.0,O-C-F-115.0,O-C-F-120.0,O-C-F-125.0,O-C-F-130.0,O-C-F-135.0,O-C-F-140.0,O-C-F-145.0,O-C-F-150.0,O-C-F-155.0,O-C-F-160.0,O-C-F-165.0,O-C-F-170.0,O-C-F-175.0,O-C-F-180.0,O-N-O-0.0,O-N-O-5.0,O-N-O-10.0,O-N-O-15.0,O-N-O-20.0,O-N-O-25.0,O-N-O-30.0,O-N-O-35.0,O-N-O-40.0,O-N-O-45.0,O-N-O-50.0,O-N-O-55.0,O-N-O-60.0,O-N-O-65.0,O-N-O-70.0,O-N-O-75.0,O-N-O-80.0,O-N-O-85.0,O-N-O-90.0,O-N-O-95.0,O-N-O-100.0,O-N-O-105.0,O-N-O-110.0,O-N-O-115.0,O-N-O-120.0,O-N-O-125.0,O-N-O-130.0,O-N-O-135.0,O-N-O-140.0,O-N-O-145.0,O-N-O-150.0,O-N-O-155.0,O-N-O-160.0,O-N-O-165.0,O-N-O-170.0,O-N-O-175.0,O-N-O-180.0,O-N-F-0.0,O-N-F-5.0,O-N-F-10.0,O-N-F-15.0,O-N-F-20.0,O-N-F-25.0,O-N-F-30.0,O-N-F-35.0,O-N-F-40.0,O-N-F-45.0,O-N-F-50.0,O-N-F-55.0,O-N-F-60.0,O-N-F-65.0,O-N-F-70.0,O-N-F-75.0,O-N-F-80.0,O-N-F-85.0,O-N-F-90.0,O-N-F-95.0,O-N-F-100.0,O-N-F-105.0,O-N-F-110.0,O-N-F-115.0,O-N-F-120.0,O-N-F-125.0,O-N-F-130.0,O-N-F-135.0,O-N-F-140.0,O-N-F-145.0,O-N-F-150.0,O-N-F-155.0,O-N-F-160.0,O-N-F-165.0,O-N-F-170.0,O-N-F-175.0,O-N-F-180.0,O-O-O-0.0,O-O-O-5.0,O-O-O-10.0,O-O-O-15.0,O-O-O-20.0,O-O-O-25.0,O-O-O-30.0,O-O-O-35.0,O-O-O-40.0,O-O-O-45.0,O-O-O-50.0,O-O-O-55.0,O-O-O-60.0,O-O-O-65.0,O-O-O-70.0,O-O-O-75.0,O-O-O-80.0,O-O-O-85.0,O-O-O-90.0,O-O-O-95.0,O-O-O-100.0,O-O-O-105.0,O-O-O-110.0,O-O-O-115.0,O-O-O-120.0,O-O-O-125.0,O-O-O-130.0,O-O-O-135.0,O-O-O-140.0,O-O-O-145.0,O-O-O-150.0,O-O-O-155.0,O-O-O-160.0,O-O-O-165.0,O-O-O-170.0,O-O-O-175.0,O-O-O-180.0,O-O-F-0.0,O-O-F-5.0,O-O-F-10.0,O-O-F-15.0,O-O-F-20.0,O-O-F-25.0,O-O-F-30.0,O-O-F-35.0,O-O-F-40.0,O-O-F-45.0,O-O-F-50.0,O-O-F-55.0,O-O-F-60.0,O-O-F-65.0,O-O-F-70.0,O-O-F-75.0,O-O-F-80.0,O-O-F-85.0,O-O-F-90.0,O-O-F-95.0,O-O-F-100.0,O-O-F-105.0,O-O-F-110.0,O-O-F-115.0,O-O-F-120.0,O-O-F-125.0,O-O-F-130.0,O-O-F-135.0,O-O-F-140.0,O-O-F-145.0,O-O-F-150.0,O-O-F-155.0,O-O-F-160.0,O-O-F-165.0,O-O-F-170.0,O-O-F-175.0,O-O-F-180.0,O-F-O-0.0,O-F-O-5.0,O-F-O-10.0,O-F-O-15.0,O-F-O-20.0,O-F-O-25.0,O-F-O-30.0,O-F-O-35.0,O-F-O-40.0,O-F-O-45.0,O-F-O-50.0,O-F-O-55.0,O-F-O-60.0,O-F-O-65.0,O-F-O-70.0,O-F-O-75.0,O-F-O-80.0,O-F-O-85.0,O-F-O-90.0,O-F-O-95.0,O-F-O-100.0,O-F-O-105.0,O-F-O-110.0,O-F-O-115.0,O-F-O-120.0,O-F-O-125.0,O-F-O-130.0,O-F-O-135.0,O-F-O-140.0,O-F-O-145.0,O-F-O-150.0,O-F-O-155.0,O-F-O-160.0,O-F-O-165.0,O-F-O-170.0,O-F-O-175.0,O-F-O-180.0,O-F-F-0.0,O-F-F-5.0,O-F-F-10.0,O-F-F-15.0,O-F-F-20.0,O-F-F-25.0,O-F-F-30.0,O-F-F-35.0,O-F-F-40.0,O-F-F-45.0,O-F-F-50.0,O-F-F-55.0,O-F-F-60.0,O-F-F-65.0,O-F-F-70.0,O-F-F-75.0,O-F-F-80.0,O-F-F-85.0,O-F-F-90.0,O-F-F-95.0,O-F-F-100.0,O-F-F-105.0,O-F-F-110.0,O-F-F-115.0,O-F-F-120.0,O-F-F-125.0,O-F-F-130.0,O-F-F-135.0,O-F-F-140.0,O-F-F-145.0,O-F-F-150.0,O-F-F-155.0,O-F-F-160.0,O-F-F-165.0,O-F-F-170.0,O-F-F-175.0,O-F-F-180.0,F-H-F-0.0,F-H-F-5.0,F-H-F-10.0,F-H-F-15.0,F-H-F-20.0,F-H-F-25.0,F-H-F-30.0,F-H-F-35.0,F-H-F-40.0,F-H-F-45.0,F-H-F-50.0,F-H-F-55.0,F-H-F-60.0,F-H-F-65.0,F-H-F-70.0,F-H-F-75.0,F-H-F-80.0,F-H-F-85.0,F-H-F-90.0,F-H-F-95.0,F-H-F-100.0,F-H-F-105.0,F-H-F-110.0,F-H-F-115.0,F-H-F-120.0,F-H-F-125.0,F-H-F-130.0,F-H-F-135.0,F-H-F-140.0,F-H-F-145.0,F-H-F-150.0,F-H-F-155.0,F-H-F-160.0,F-H-F-165.0,F-H-F-170.0,F-H-F-175.0,F-H-F-180.0,F-C-F-0.0,F-C-F-5.0,F-C-F-10.0,F-C-F-15.0,F-C-F-20.0,F-C-F-25.0,F-C-F-30.0,F-C-F-35.0,F-C-F-40.0,F-C-F-45.0,F-C-F-50.0,F-C-F-55.0,F-C-F-60.0,F-C-F-65.0,F-C-F-70.0,F-C-F-75.0,F-C-F-80.0,F-C-F-85.0,F-C-F-90.0,F-C-F-95.0,F-C-F-100.0,F-C-F-105.0,F-C-F-110.0,F-C-F-115.0,F-C-F-120.0,F-C-F-125.0,F-C-F-130.0,F-C-F-135.0,F-C-F-140.0,F-C-F-145.0,F-C-F-150.0,F-C-F-155.0,F-C-F-160.0,F-C-F-165.0,F-C-F-170.0,F-C-F-175.0,F-C-F-180.0,F-N-F-0.0,F-N-F-5.0,F-N-F-10.0,F-N-F-15.0,F-N-F-20.0,F-N-F-25.0,F-N-F-30.0,F-N-F-35.0,F-N-F-40.0,F-N-F-45.0,F-N-F-50.0,F-N-F-55.0,F-N-F-60.0,F-N-F-65.0,F-N-F-70.0,F-N-F-75.0,F-N-F-80.0,F-N-F-85.0,F-N-F-90.0,F-N-F-95.0,F-N-F-100.0,F-N-F-105.0,F-N-F-110.0,F-N-F-115.0,F-N-F-120.0,F-N-F-125.0,F-N-F-130.0,F-N-F-135.0,F-N-F-140.0,F-N-F-145.0,F-N-F-150.0,F-N-F-155.0,F-N-F-160.0,F-N-F-165.0,F-N-F-170.0,F-N-F-175.0,F-N-F-180.0,F-O-F-0.0,F-O-F-5.0,F-O-F-10.0,F-O-F-15.0,F-O-F-20.0,F-O-F-25.0,F-O-F-30.0,F-O-F-35.0,F-O-F-40.0,F-O-F-45.0,F-O-F-50.0,F-O-F-55.0,F-O-F-60.0,F-O-F-65.0,F-O-F-70.0,F-O-F-75.0,F-O-F-80.0,F-O-F-85.0,F-O-F-90.0,F-O-F-95.0,F-O-F-100.0,F-O-F-105.0,F-O-F-110.0,F-O-F-115.0,F-O-F-120.0,F-O-F-125.0,F-O-F-130.0,F-O-F-135.0,F-O-F-140.0,F-O-F-145.0,F-O-F-150.0,F-O-F-155.0,F-O-F-160.0,F-O-F-165.0,F-O-F-170.0,F-O-F-175.0,F-O-F-180.0,F-F-F-0.0,F-F-F-5.0,F-F-F-10.0,F-F-F-15.0,F-F-F-20.0,F-F-F-25.0,F-F-F-30.0,F-F-F-35.0,F-F-F-40.0,F-F-F-45.0,F-F-F-50.0,F-F-F-55.0,F-F-F-60.0,F-F-F-65.0,F-F-F-70.0,F-F-F-75.0,F-F-F-80.0,F-F-F-85.0,F-F-F-90.0,F-F-F-95.0,F-F-F-100.0,F-F-F-105.0,F-F-F-110.0,F-F-F-115.0,F-F-F-120.0,F-F-F-125.0,F-F-F-130.0,F-F-F-135.0,F-F-F-140.0,F-F-F-145.0,F-F-F-150.0,F-F-F-155.0,F-F-F-160.0,F-F-F-165.0,F-F-F-170.0,F-F-F-175.0,F-F-F-180.0"
#Turn the AA dictionary string into a list
dictylist=dictylist.split(',')
#Dictionary of elements included in Element Occurrence (EO)
atmlist="H,B,C,N,O,F,Si,S,Cl,Br,I"
#Turn the EO dictionary string into a list
atmlist=atmlist.split(',')
#Make value list for keys in AA dictionary list
dicty = { i :0 for i in dictylist }
#Make value list for keys in EO dictionary list
atms = { i :0 for i in atmlist }
#Range of granularity for angles
rang=np.arange(0.0,185.0,5.0)
#Round to avoid potential errors
rang=np.around(rang,2)
#Variable holding the dictionary for Spherical Radii (SR)
dictylistint="H-H-0.5,H-H-0.6,H-H-0.7,H-H-0.8,H-H-0.9,H-H-1.0,H-H-1.1,H-H-1.2,H-H-1.3,H-H-1.4,H-H-1.5,H-H-1.6,H-H-1.7,H-H-1.8,H-H-1.9,H-H-2.0,H-H-2.1,H-H-2.2,H-H-2.3,H-H-2.4,H-H-2.5,H-H-2.6,H-H-2.7,H-H-2.8,H-H-2.9,H-H-3.0,H-H-3.1,H-H-3.2,H-H-3.3,H-H-3.4,H-H-3.5,H-H-3.6,H-H-3.7,H-H-3.8,H-H-3.9,H-H-4.0,H-H-4.1,H-H-4.2,H-H-4.3,H-H-4.4,H-H-4.5,H-H-4.6,H-H-4.7,H-H-4.8,H-H-4.9,H-H-5.0,H-H-5.1,H-H-5.2,H-H-5.3,H-H-5.4,H-H-5.5,H-H-5.6,H-H-5.7,H-H-5.8,H-H-5.9,H-H-6.0,H-H-6.1,H-H-6.2,H-H-6.3,H-H-6.4,H-H-6.5,H-H-6.6,H-H-6.7,H-H-6.8,H-H-6.9,H-H-7.0,H-H-7.1,H-H-7.2,H-H-7.3,H-H-7.4,H-H-7.5,H-H-7.6,H-H-7.7,H-H-7.8,H-H-7.9,H-H-8.0,H-H-8.1,H-H-8.2,H-H-8.3,H-H-8.4,H-C-0.5,H-C-0.6,H-C-0.7,H-C-0.8,H-C-0.9,H-C-1.0,H-C-1.1,H-C-1.2,H-C-1.3,H-C-1.4,H-C-1.5,H-C-1.6,H-C-1.7,H-C-1.8,H-C-1.9,H-C-2.0,H-C-2.1,H-C-2.2,H-C-2.3,H-C-2.4,H-C-2.5,H-C-2.6,H-C-2.7,H-C-2.8,H-C-2.9,H-C-3.0,H-C-3.1,H-C-3.2,H-C-3.3,H-C-3.4,H-C-3.5,H-C-3.6,H-C-3.7,H-C-3.8,H-C-3.9,H-C-4.0,H-C-4.1,H-C-4.2,H-C-4.3,H-C-4.4,H-C-4.5,H-C-4.6,H-C-4.7,H-C-4.8,H-C-4.9,H-C-5.0,H-C-5.1,H-C-5.2,H-C-5.3,H-C-5.4,H-C-5.5,H-C-5.6,H-C-5.7,H-C-5.8,H-C-5.9,H-C-6.0,H-C-6.1,H-C-6.2,H-C-6.3,H-C-6.4,H-C-6.5,H-C-6.6,H-C-6.7,H-C-6.8,H-C-6.9,H-C-7.0,H-C-7.1,H-C-7.2,H-C-7.3,H-C-7.4,H-C-7.5,H-C-7.6,H-C-7.7,H-C-7.8,H-C-7.9,H-C-8.0,H-C-8.1,H-C-8.2,H-C-8.3,H-C-8.4,H-N-0.5,H-N-0.6,H-N-0.7,H-N-0.8,H-N-0.9,H-N-1.0,H-N-1.1,H-N-1.2,H-N-1.3,H-N-1.4,H-N-1.5,H-N-1.6,H-N-1.7,H-N-1.8,H-N-1.9,H-N-2.0,H-N-2.1,H-N-2.2,H-N-2.3,H-N-2.4,H-N-2.5,H-N-2.6,H-N-2.7,H-N-2.8,H-N-2.9,H-N-3.0,H-N-3.1,H-N-3.2,H-N-3.3,H-N-3.4,H-N-3.5,H-N-3.6,H-N-3.7,H-N-3.8,H-N-3.9,H-N-4.0,H-N-4.1,H-N-4.2,H-N-4.3,H-N-4.4,H-N-4.5,H-N-4.6,H-N-4.7,H-N-4.8,H-N-4.9,H-N-5.0,H-N-5.1,H-N-5.2,H-N-5.3,H-N-5.4,H-N-5.5,H-N-5.6,H-N-5.7,H-N-5.8,H-N-5.9,H-N-6.0,H-N-6.1,H-N-6.2,H-N-6.3,H-N-6.4,H-N-6.5,H-N-6.6,H-N-6.7,H-N-6.8,H-N-6.9,H-N-7.0,H-N-7.1,H-N-7.2,H-N-7.3,H-N-7.4,H-N-7.5,H-N-7.6,H-N-7.7,H-N-7.8,H-N-7.9,H-N-8.0,H-N-8.1,H-N-8.2,H-N-8.3,H-N-8.4,H-O-0.5,H-O-0.6,H-O-0.7,H-O-0.8,H-O-0.9,H-O-1.0,H-O-1.1,H-O-1.2,H-O-1.3,H-O-1.4,H-O-1.5,H-O-1.6,H-O-1.7,H-O-1.8,H-O-1.9,H-O-2.0,H-O-2.1,H-O-2.2,H-O-2.3,H-O-2.4,H-O-2.5,H-O-2.6,H-O-2.7,H-O-2.8,H-O-2.9,H-O-3.0,H-O-3.1,H-O-3.2,H-O-3.3,H-O-3.4,H-O-3.5,H-O-3.6,H-O-3.7,H-O-3.8,H-O-3.9,H-O-4.0,H-O-4.1,H-O-4.2,H-O-4.3,H-O-4.4,H-O-4.5,H-O-4.6,H-O-4.7,H-O-4.8,H-O-4.9,H-O-5.0,H-O-5.1,H-O-5.2,H-O-5.3,H-O-5.4,H-O-5.5,H-O-5.6,H-O-5.7,H-O-5.8,H-O-5.9,H-O-6.0,H-O-6.1,H-O-6.2,H-O-6.3,H-O-6.4,H-O-6.5,H-O-6.6,H-O-6.7,H-O-6.8,H-O-6.9,H-O-7.0,H-O-7.1,H-O-7.2,H-O-7.3,H-O-7.4,H-O-7.5,H-O-7.6,H-O-7.7,H-O-7.8,H-O-7.9,H-O-8.0,H-O-8.1,H-O-8.2,H-O-8.3,H-O-8.4,H-F-0.5,H-F-0.6,H-F-0.7,H-F-0.8,H-F-0.9,H-F-1.0,H-F-1.1,H-F-1.2,H-F-1.3,H-F-1.4,H-F-1.5,H-F-1.6,H-F-1.7,H-F-1.8,H-F-1.9,H-F-2.0,H-F-2.1,H-F-2.2,H-F-2.3,H-F-2.4,H-F-2.5,H-F-2.6,H-F-2.7,H-F-2.8,H-F-2.9,H-F-3.0,H-F-3.1,H-F-3.2,H-F-3.3,H-F-3.4,H-F-3.5,H-F-3.6,H-F-3.7,H-F-3.8,H-F-3.9,H-F-4.0,H-F-4.1,H-F-4.2,H-F-4.3,H-F-4.4,H-F-4.5,H-F-4.6,H-F-4.7,H-F-4.8,H-F-4.9,H-F-5.0,H-F-5.1,H-F-5.2,H-F-5.3,H-F-5.4,H-F-5.5,H-F-5.6,H-F-5.7,H-F-5.8,H-F-5.9,H-F-6.0,H-F-6.1,H-F-6.2,H-F-6.3,H-F-6.4,H-F-6.5,H-F-6.6,H-F-6.7,H-F-6.8,H-F-6.9,H-F-7.0,H-F-7.1,H-F-7.2,H-F-7.3,H-F-7.4,H-F-7.5,H-F-7.6,H-F-7.7,H-F-7.8,H-F-7.9,H-F-8.0,H-F-8.1,H-F-8.2,H-F-8.3,H-F-8.4,C-C-0.5,C-C-0.6,C-C-0.7,C-C-0.8,C-C-0.9,C-C-1.0,C-C-1.1,C-C-1.2,C-C-1.3,C-C-1.4,C-C-1.5,C-C-1.6,C-C-1.7,C-C-1.8,C-C-1.9,C-C-2.0,C-C-2.1,C-C-2.2,C-C-2.3,C-C-2.4,C-C-2.5,C-C-2.6,C-C-2.7,C-C-2.8,C-C-2.9,C-C-3.0,C-C-3.1,C-C-3.2,C-C-3.3,C-C-3.4,C-C-3.5,C-C-3.6,C-C-3.7,C-C-3.8,C-C-3.9,C-C-4.0,C-C-4.1,C-C-4.2,C-C-4.3,C-C-4.4,C-C-4.5,C-C-4.6,C-C-4.7,C-C-4.8,C-C-4.9,C-C-5.0,C-C-5.1,C-C-5.2,C-C-5.3,C-C-5.4,C-C-5.5,C-C-5.6,C-C-5.7,C-C-5.8,C-C-5.9,C-C-6.0,C-C-6.1,C-C-6.2,C-C-6.3,C-C-6.4,C-C-6.5,C-C-6.6,C-C-6.7,C-C-6.8,C-C-6.9,C-C-7.0,C-C-7.1,C-C-7.2,C-C-7.3,C-C-7.4,C-C-7.5,C-C-7.6,C-C-7.7,C-C-7.8,C-C-7.9,C-C-8.0,C-C-8.1,C-C-8.2,C-C-8.3,C-C-8.4,C-N-0.5,C-N-0.6,C-N-0.7,C-N-0.8,C-N-0.9,C-N-1.0,C-N-1.1,C-N-1.2,C-N-1.3,C-N-1.4,C-N-1.5,C-N-1.6,C-N-1.7,C-N-1.8,C-N-1.9,C-N-2.0,C-N-2.1,C-N-2.2,C-N-2.3,C-N-2.4,C-N-2.5,C-N-2.6,C-N-2.7,C-N-2.8,C-N-2.9,C-N-3.0,C-N-3.1,C-N-3.2,C-N-3.3,C-N-3.4,C-N-3.5,C-N-3.6,C-N-3.7,C-N-3.8,C-N-3.9,C-N-4.0,C-N-4.1,C-N-4.2,C-N-4.3,C-N-4.4,C-N-4.5,C-N-4.6,C-N-4.7,C-N-4.8,C-N-4.9,C-N-5.0,C-N-5.1,C-N-5.2,C-N-5.3,C-N-5.4,C-N-5.5,C-N-5.6,C-N-5.7,C-N-5.8,C-N-5.9,C-N-6.0,C-N-6.1,C-N-6.2,C-N-6.3,C-N-6.4,C-N-6.5,C-N-6.6,C-N-6.7,C-N-6.8,C-N-6.9,C-N-7.0,C-N-7.1,C-N-7.2,C-N-7.3,C-N-7.4,C-N-7.5,C-N-7.6,C-N-7.7,C-N-7.8,C-N-7.9,C-N-8.0,C-N-8.1,C-N-8.2,C-N-8.3,C-N-8.4,C-O-0.5,C-O-0.6,C-O-0.7,C-O-0.8,C-O-0.9,C-O-1.0,C-O-1.1,C-O-1.2,C-O-1.3,C-O-1.4,C-O-1.5,C-O-1.6,C-O-1.7,C-O-1.8,C-O-1.9,C-O-2.0,C-O-2.1,C-O-2.2,C-O-2.3,C-O-2.4,C-O-2.5,C-O-2.6,C-O-2.7,C-O-2.8,C-O-2.9,C-O-3.0,C-O-3.1,C-O-3.2,C-O-3.3,C-O-3.4,C-O-3.5,C-O-3.6,C-O-3.7,C-O-3.8,C-O-3.9,C-O-4.0,C-O-4.1,C-O-4.2,C-O-4.3,C-O-4.4,C-O-4.5,C-O-4.6,C-O-4.7,C-O-4.8,C-O-4.9,C-O-5.0,C-O-5.1,C-O-5.2,C-O-5.3,C-O-5.4,C-O-5.5,C-O-5.6,C-O-5.7,C-O-5.8,C-O-5.9,C-O-6.0,C-O-6.1,C-O-6.2,C-O-6.3,C-O-6.4,C-O-6.5,C-O-6.6,C-O-6.7,C-O-6.8,C-O-6.9,C-O-7.0,C-O-7.1,C-O-7.2,C-O-7.3,C-O-7.4,C-O-7.5,C-O-7.6,C-O-7.7,C-O-7.8,C-O-7.9,C-O-8.0,C-O-8.1,C-O-8.2,C-O-8.3,C-O-8.4,C-F-0.5,C-F-0.6,C-F-0.7,C-F-0.8,C-F-0.9,C-F-1.0,C-F-1.1,C-F-1.2,C-F-1.3,C-F-1.4,C-F-1.5,C-F-1.6,C-F-1.7,C-F-1.8,C-F-1.9,C-F-2.0,C-F-2.1,C-F-2.2,C-F-2.3,C-F-2.4,C-F-2.5,C-F-2.6,C-F-2.7,C-F-2.8,C-F-2.9,C-F-3.0,C-F-3.1,C-F-3.2,C-F-3.3,C-F-3.4,C-F-3.5,C-F-3.6,C-F-3.7,C-F-3.8,C-F-3.9,C-F-4.0,C-F-4.1,C-F-4.2,C-F-4.3,C-F-4.4,C-F-4.5,C-F-4.6,C-F-4.7,C-F-4.8,C-F-4.9,C-F-5.0,C-F-5.1,C-F-5.2,C-F-5.3,C-F-5.4,C-F-5.5,C-F-5.6,C-F-5.7,C-F-5.8,C-F-5.9,C-F-6.0,C-F-6.1,C-F-6.2,C-F-6.3,C-F-6.4,C-F-6.5,C-F-6.6,C-F-6.7,C-F-6.8,C-F-6.9,C-F-7.0,C-F-7.1,C-F-7.2,C-F-7.3,C-F-7.4,C-F-7.5,C-F-7.6,C-F-7.7,C-F-7.8,C-F-7.9,C-F-8.0,C-F-8.1,C-F-8.2,C-F-8.3,C-F-8.4,N-N-0.5,N-N-0.6,N-N-0.7,N-N-0.8,N-N-0.9,N-N-1.0,N-N-1.1,N-N-1.2,N-N-1.3,N-N-1.4,N-N-1.5,N-N-1.6,N-N-1.7,N-N-1.8,N-N-1.9,N-N-2.0,N-N-2.1,N-N-2.2,N-N-2.3,N-N-2.4,N-N-2.5,N-N-2.6,N-N-2.7,N-N-2.8,N-N-2.9,N-N-3.0,N-N-3.1,N-N-3.2,N-N-3.3,N-N-3.4,N-N-3.5,N-N-3.6,N-N-3.7,N-N-3.8,N-N-3.9,N-N-4.0,N-N-4.1,N-N-4.2,N-N-4.3,N-N-4.4,N-N-4.5,N-N-4.6,N-N-4.7,N-N-4.8,N-N-4.9,N-N-5.0,N-N-5.1,N-N-5.2,N-N-5.3,N-N-5.4,N-N-5.5,N-N-5.6,N-N-5.7,N-N-5.8,N-N-5.9,N-N-6.0,N-N-6.1,N-N-6.2,N-N-6.3,N-N-6.4,N-N-6.5,N-N-6.6,N-N-6.7,N-N-6.8,N-N-6.9,N-N-7.0,N-N-7.1,N-N-7.2,N-N-7.3,N-N-7.4,N-N-7.5,N-N-7.6,N-N-7.7,N-N-7.8,N-N-7.9,N-N-8.0,N-N-8.1,N-N-8.2,N-N-8.3,N-N-8.4,N-O-0.5,N-O-0.6,N-O-0.7,N-O-0.8,N-O-0.9,N-O-1.0,N-O-1.1,N-O-1.2,N-O-1.3,N-O-1.4,N-O-1.5,N-O-1.6,N-O-1.7,N-O-1.8,N-O-1.9,N-O-2.0,N-O-2.1,N-O-2.2,N-O-2.3,N-O-2.4,N-O-2.5,N-O-2.6,N-O-2.7,N-O-2.8,N-O-2.9,N-O-3.0,N-O-3.1,N-O-3.2,N-O-3.3,N-O-3.4,N-O-3.5,N-O-3.6,N-O-3.7,N-O-3.8,N-O-3.9,N-O-4.0,N-O-4.1,N-O-4.2,N-O-4.3,N-O-4.4,N-O-4.5,N-O-4.6,N-O-4.7,N-O-4.8,N-O-4.9,N-O-5.0,N-O-5.1,N-O-5.2,N-O-5.3,N-O-5.4,N-O-5.5,N-O-5.6,N-O-5.7,N-O-5.8,N-O-5.9,N-O-6.0,N-O-6.1,N-O-6.2,N-O-6.3,N-O-6.4,N-O-6.5,N-O-6.6,N-O-6.7,N-O-6.8,N-O-6.9,N-O-7.0,N-O-7.1,N-O-7.2,N-O-7.3,N-O-7.4,N-O-7.5,N-O-7.6,N-O-7.7,N-O-7.8,N-O-7.9,N-O-8.0,N-O-8.1,N-O-8.2,N-O-8.3,N-O-8.4,N-F-0.5,N-F-0.6,N-F-0.7,N-F-0.8,N-F-0.9,N-F-1.0,N-F-1.1,N-F-1.2,N-F-1.3,N-F-1.4,N-F-1.5,N-F-1.6,N-F-1.7,N-F-1.8,N-F-1.9,N-F-2.0,N-F-2.1,N-F-2.2,N-F-2.3,N-F-2.4,N-F-2.5,N-F-2.6,N-F-2.7,N-F-2.8,N-F-2.9,N-F-3.0,N-F-3.1,N-F-3.2,N-F-3.3,N-F-3.4,N-F-3.5,N-F-3.6,N-F-3.7,N-F-3.8,N-F-3.9,N-F-4.0,N-F-4.1,N-F-4.2,N-F-4.3,N-F-4.4,N-F-4.5,N-F-4.6,N-F-4.7,N-F-4.8,N-F-4.9,N-F-5.0,N-F-5.1,N-F-5.2,N-F-5.3,N-F-5.4,N-F-5.5,N-F-5.6,N-F-5.7,N-F-5.8,N-F-5.9,N-F-6.0,N-F-6.1,N-F-6.2,N-F-6.3,N-F-6.4,N-F-6.5,N-F-6.6,N-F-6.7,N-F-6.8,N-F-6.9,N-F-7.0,N-F-7.1,N-F-7.2,N-F-7.3,N-F-7.4,N-F-7.5,N-F-7.6,N-F-7.7,N-F-7.8,N-F-7.9,N-F-8.0,N-F-8.1,N-F-8.2,N-F-8.3,N-F-8.4,O-O-0.5,O-O-0.6,O-O-0.7,O-O-0.8,O-O-0.9,O-O-1.0,O-O-1.1,O-O-1.2,O-O-1.3,O-O-1.4,O-O-1.5,O-O-1.6,O-O-1.7,O-O-1.8,O-O-1.9,O-O-2.0,O-O-2.1,O-O-2.2,O-O-2.3,O-O-2.4,O-O-2.5,O-O-2.6,O-O-2.7,O-O-2.8,O-O-2.9,O-O-3.0,O-O-3.1,O-O-3.2,O-O-3.3,O-O-3.4,O-O-3.5,O-O-3.6,O-O-3.7,O-O-3.8,O-O-3.9,O-O-4.0,O-O-4.1,O-O-4.2,O-O-4.3,O-O-4.4,O-O-4.5,O-O-4.6,O-O-4.7,O-O-4.8,O-O-4.9,O-O-5.0,O-O-5.1,O-O-5.2,O-O-5.3,O-O-5.4,O-O-5.5,O-O-5.6,O-O-5.7,O-O-5.8,O-O-5.9,O-O-6.0,O-O-6.1,O-O-6.2,O-O-6.3,O-O-6.4,O-O-6.5,O-O-6.6,O-O-6.7,O-O-6.8,O-O-6.9,O-O-7.0,O-O-7.1,O-O-7.2,O-O-7.3,O-O-7.4,O-O-7.5,O-O-7.6,O-O-7.7,O-O-7.8,O-O-7.9,O-O-8.0,O-O-8.1,O-O-8.2,O-O-8.3,O-O-8.4,O-F-0.5,O-F-0.6,O-F-0.7,O-F-0.8,O-F-0.9,O-F-1.0,O-F-1.1,O-F-1.2,O-F-1.3,O-F-1.4,O-F-1.5,O-F-1.6,O-F-1.7,O-F-1.8,O-F-1.9,O-F-2.0,O-F-2.1,O-F-2.2,O-F-2.3,O-F-2.4,O-F-2.5,O-F-2.6,O-F-2.7,O-F-2.8,O-F-2.9,O-F-3.0,O-F-3.1,O-F-3.2,O-F-3.3,O-F-3.4,O-F-3.5,O-F-3.6,O-F-3.7,O-F-3.8,O-F-3.9,O-F-4.0,O-F-4.1,O-F-4.2,O-F-4.3,O-F-4.4,O-F-4.5,O-F-4.6,O-F-4.7,O-F-4.8,O-F-4.9,O-F-5.0,O-F-5.1,O-F-5.2,O-F-5.3,O-F-5.4,O-F-5.5,O-F-5.6,O-F-5.7,O-F-5.8,O-F-5.9,O-F-6.0,O-F-6.1,O-F-6.2,O-F-6.3,O-F-6.4,O-F-6.5,O-F-6.6,O-F-6.7,O-F-6.8,O-F-6.9,O-F-7.0,O-F-7.1,O-F-7.2,O-F-7.3,O-F-7.4,O-F-7.5,O-F-7.6,O-F-7.7,O-F-7.8,O-F-7.9,O-F-8.0,O-F-8.1,O-F-8.2,O-F-8.3,O-F-8.4,F-F-0.5,F-F-0.6,F-F-0.7,F-F-0.8,F-F-0.9,F-F-1.0,F-F-1.1,F-F-1.2,F-F-1.3,F-F-1.4,F-F-1.5,F-F-1.6,F-F-1.7,F-F-1.8,F-F-1.9,F-F-2.0,F-F-2.1,F-F-2.2,F-F-2.3,F-F-2.4,F-F-2.5,F-F-2.6,F-F-2.7,F-F-2.8,F-F-2.9,F-F-3.0,F-F-3.1,F-F-3.2,F-F-3.3,F-F-3.4,F-F-3.5,F-F-3.6,F-F-3.7,F-F-3.8,F-F-3.9,F-F-4.0,F-F-4.1,F-F-4.2,F-F-4.3,F-F-4.4,F-F-4.5,F-F-4.6,F-F-4.7,F-F-4.8,F-F-4.9,F-F-5.0,F-F-5.1,F-F-5.2,F-F-5.3,F-F-5.4,F-F-5.5,F-F-5.6,F-F-5.7,F-F-5.8,F-F-5.9,F-F-6.0,F-F-6.1,F-F-6.2,F-F-6.3,F-F-6.4,F-F-6.5,F-F-6.6,F-F-6.7,F-F-6.8,F-F-6.9,F-F-7.0,F-F-7.1,F-F-7.2,F-F-7.3,F-F-7.4,F-F-7.5,F-F-7.6,F-F-7.7,F-F-7.8,F-F-7.9,F-F-8.0,F-F-8.1,F-F-8.2,F-F-8.3,F-F-8.4"
dictylistint=dictylistint.split(',')
#Make value list for keys in SA dictionary list
dictyint = { i : 0 for i in dictylistint }
#Range of granularity for radii
rangint=np.arange(0.5,8.5,0.1)
#Round to avoid potential errors
rangint=np.around(rangint,2)
###For each file in directory
allfile=[fle for fle in os.listdir('.') if os.path.isfile(fle)]
#Collect user input
savename=input("What name would you like for the filename of your generated dataset input file? (.csv extension): ")
extension=input("What are the extensions of input Gaussian files you would like extracted interactions from? (ex: .gjf)")
IDnumber=input("What index of the filename should be used as the file identifier?")
#Open the file we wish to save the dataset input to
w = open(savename,"a+")
#Iterate over every file
for file in allfile:
####Grab the input files
if file.endswith(extension):
#Open a Gaussian input file
f = open(file,'r+')
#Print the filename as a progress note
print(file)
#Get the file identifier and remove the extension
fileid=(file.split("_")[int(IDnumber)])[:-4]
###Read in all lines and then remove the route card, comment, and charge/multiplicity
data = f.readlines()
atmcrd=data[5:]
#Remove the newlines and generate a list of the atoms
atmcrd = [x for x in atmcrd if ((x != '\n'))]
#Iterate over each atom in the coordinate list
for i in atmcrd:
#Make a list of all atoms that aren't the atom we currently have set by the iterator i
othratms = [x for x in atmcrd if ((x != '\n') and (x != i))]
#Split the coordinate line i in to a list on whitespace
atm1=i.split()
#Make the list into a numpy array
atm1=np.array(atm1)
#Get the element indentfier
atmkey=atm1[0]
#Iterate over each atom in the coordinate list not including i
for j in othratms:
#Split the coordinate line j in to a list on whitespace
atm2=j.split()
#Make the list into a numpy array
atm2=np.array(atm2)
#Calculate the distance between the i and j atoms
dist=math.sqrt((float(atm1[1])-float(atm2[1]))**2 + (float(atm1[2])-float(atm2[2]))**2 + (float(atm1[3])-float(atm2[3]))**2)
#If the distance is less than 2 angstroms
if dist < 2.0:
#Make a list of all atoms that aren't the atom we currently have set by the iterator j
thrdatm = [x for x in othratms if ((x != '\n') and (x != j))]
#Iterate over each atom in the coordinate list not including j
for l in thrdatm:
#Check value for if it has already been added to the AA dictionary value list
chk=0
#Split the coordinate line l in to a list on whitespace
atm3=l.split()
#Make the list into a numpy array
atm3=np.array(atm3)
#Calculate the distance between the i and l atoms
dist2=math.sqrt((float(atm1[1])-float(atm3[1]))**2 + (float(atm1[2])-float(atm3[2]))**2 + (float(atm1[3])-float(atm3[3]))**2)
#If the distance is less than 3 angstroms
if dist2 < 3.0:
###Calculate the angle
#Make arrays for interim distances
onetwo=np.array([0.0,0.0,0.0])
twothree=np.array([0.0,0.0,0.0])
#Iterate over each cartesian coordinate
for y in range(1,4):
#Subtract the coordinates between two of the three atoms.
onetwo[y-1] = float(atm1[y])-float(atm2[y])
twothree[y-1] = float(atm3[y])-float(atm2[y])
#Calculate the cosine of the angle
cosine_angle = np.dot(onetwo, twothree) / (np.linalg.norm(onetwo) * np.linalg.norm(twothree))
#Calculate the angle between the three atoms
angle = np.arccos(cosine_angle)
#For each angle granularity
for k in rang:
#If angle is less than current granularity and nothing has been added to the value array for this atom triple yet
if (np.degrees(angle) <= k) and chk==0:
#Update the chk for addition to the value array
chk=1
#Make the dictionary key first attempt
dictkey = atm1[0]+"-"+atm2[0]+"-"+atm3[0]+"-"+str(k)
#Check if the attempted key is in the AA dictionary keys
if dictkey in dicty.keys():
#If yes, add a +1 to that key's value
dicty[dictkey]=dicty[dictkey]+1
else:
#If no generate the opposite key permutation
dictkey = atm3[0]+"-"+atm2[0]+"-"+atm1[0]+"-"+str(k)
#If no, add a +1 to the newly generated key's value
dicty[dictkey]=dicty[dictkey]+1
#Check value for if it has already been added to the SR dictionary value list
chkint=0
#For each SR granularity
for p in rangint:
#If SR is less than current granularity and nothing has been added to the value array for this atom double yet
if (dist < p) and chkint==0:
#Update the chk for addition to the value array
chkint=1
#Make the dictionary key first attempt
dictkeyint = atm1[0]+"-"+atm2[0]+"-"+str(p)
#Check if the attempted key is in the SR dictionary keys
if dictkeyint in dictyint.keys():
#If yes, add a +1 to that key's value
dictyint[dictkeyint]=dictyint[dictkeyint]+1
else:
#If no generate the opposite key permutation
dictkeyint = atm2[0]+"-"+atm1[0]+"-"+str(p)
#If no, add a +1 to the newly generated key's value
dictyint[dictkeyint]=dictyint[dictkeyint]+1
#Check if the element is in the EO keys
if atmkey in atms.keys():
#If yes, add one to that key's value
atms[atmkey]=atms[atmkey]+1
#Write the EO and SR and AA to file
w.write(fileid+","+str(list(dictyint.values()))[1:-1]+","+str(list(dicty.values()))[1:-1]+","+str(list(atms.values()))[1:-1]+"\n")
#Reset the value arrays to 0
dicty = { i : 0 for i in dictylist }
dictyint = { i : 0 for i in dictylistint }
atms = { i : 0 for i in atmlist }
#Close File
w.close()