#!/usr/bin/env python
# (C) 2024 Cadence Design Systems, Inc. (Cadence) 
# All rights reserved.
# TERMS FOR USE OF SAMPLE CODE The software below ("Sample Code") is
# provided to current licensees or subscribers of Cadence products or
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# subject to these terms. Cadence claims no rights to Customer's
# modifications. Modification of Sample Code is at Customer's sole and
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# THE SAMPLE CODE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
# EXPRESS OR IMPLIED.  OPENEYE DISCLAIMS ALL WARRANTIES, INCLUDING, BUT
# NOT LIMITED TO, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A
# PARTICULAR PURPOSE AND NONINFRINGEMENT. In no event shall Cadence be
# liable for any damages or liability in connection with the Sample Code
# or its use.


import sys
from openeye import oechem
from openeye import oespruce

def main(argv=sys.argv):

    if len(sys.argv) != 4:
        oechem.OEThrow.Usage("%s <FASTA> <ChainIDs> <output>" % sys.argv[0])

    fasta_input = sys.argv[1]
    ifs = oechem.oemolistream()
    ifs.open(fasta_input)

    fastaMol = oechem.OEGraphMol()

    json = oechem.oeout
    if not json.open(sys.argv[3]):
        oechem.OEThrow.Fatal(f'Unable to open {oname} for writing')

    StructMeta = oespruce.OEStructureMetadata()

    SeqMeta = oespruce.OESequenceMetadata()
    seq_list = []
    chainID = ""
    chainIDs = sys.argv[2].split(',')
    i = 0

    while oechem.OEReadFASTAFile(ifs, fastaMol):
        for res in oechem.OEGetResidues(fastaMol):
            seq_list.append(res.GetName()) 

        SeqMeta.SetChainID(chainIDs[i])
        SeqMeta.SetSequence("-".join(seq_list))
        StructMeta.AddSequenceMetadata(SeqMeta)
        i += 1
        if i > len(chainIDs):
            oechem.OEThrow.Fatal('More sequences are in the fasta file than the ChainIDs provided,')

    json.write(oespruce.OEStructureMetadataToJson(StructMeta))


if __name__ == "__main__":
    sys.exit(main(sys.argv))