#!/usr/bin/env python

'''Identify the indices of the complementary occupied-virtual pairs (COVPs).

Usage:

qchem_covp_analysis.py [options] <outputfilename>

Options:

--pct_cutoff=CUTOFF Energy percentage cutoff to include an orbital for printing/analysis. [Default: 2]

Set this to 0 to see the entire COVP table.

--plot-separate=XYZFILENAME Generate VMD scripts to plot COVPs within the energy percentage cutoff.

--plot-combined=XYZFILENAME Generate a single VMD script to plot COVPs within the energy percentage cutoff.

--df Dump results to JSON and Excel files using Pandas.

--del If the orbital is below the cutoff, delete its cube file.

--print_args Print the argument block.

'''

from __future__ import print_function

import numpy as np

import os.path

import os

import json

try:

import pandas as pd

except ImportError:

pass

from docopt import docopt

from cclib.io import ccopen

from vmd_templates import pad_left_zeros

from vmd_templates import vmd_covp_write_files

def parse_fragment_block(outputfile, fragment_entries, fragment_idx):

return total

def determine_fragment_indices(fragment_1_to_2, fragment_2_to_1, covpenergies, n_mo, idx_homo):

return fragment_indices

def parse_energy_block(covpenergies, n_occ_t):

return idx_occ_1, idx_occ_2, idx_virt_2_on_1, idx_virt_1_on_2

def get_n_occ_virt_per_fragment(idx_occ_1, idx_occ_2, idx_virt_2, idx_virt_1, n_mo):

return n_occ_1, n_occ_2, n_virt_1, n_virt_2

def dump_vmd_separate(fragment_1_to_2_pairs, fragment_2_to_1_pairs, n_mo, xyzfilename):

vmd_covp_write_files(loadfile, renderfile, xyzfilename, all_pairs, width)

def dump_vmd_combined(fragment_1_to_2_pairs, fragment_2_to_1_pairs, n_mo, xyzfilename):

vmd_covp_write_files(vmdfile, vmdfile, xyzfilename, all_pairs, width)

def dump_pandas(fragment_1_to_2_entries, fragment_2_to_1_entries, prefix):

results_2_to_1_df.to_excel('{}.2_to_1.xls'.format(prefix))

def main(args):

fragment_2_to_1_tot)

if __name__ == '__main__':

args = docopt(__doc__)

main(args)