#!/usr/bin/env python
# (C) 2022 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
# SaaS offerings (each a "Customer").
# Customer is hereby permitted to use, copy, and modify the Sample Code,
# subject to these terms. Cadence claims no rights to Customer's
# modifications. Modification of Sample Code is at Customer's sole and
# exclusive risk. Sample Code may require Customer to have a then
# current license or subscription to the applicable Cadence offering.
# 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 oebioisostere

class BroodOptions(oechem.OEOptions):
    def __init__(self):
        oechem.OEOptions.__init__(self, "BroodOptions")
        self._genOpts = oebioisostere.ToGeneralOptions(self.AddOption(oebioisostere.OEBroodGeneralOptions()))
        self._scoreOpts = oebioisostere.ToScoreOptions(self.AddOption(oebioisostere.OEBroodScoreOptions()))
        self._buildOpts = oebioisostere.ToBuildOptions(self.AddOption(oebioisostere.OEBroodBuildOptions()))
        pass

    def CreateCopy(self):
        return self

    def GetGenOpts(self):
        return self._genOpts

    def GetScoreOpts(self):
        return self._scoreOpts

    def GetBuildOpts(self):
        return self._buildOpts


def main(argv=[__name__]):
    broodOpts = BroodOptions()
    opts = oechem.OERefInputAppOptions(broodOpts, "ReplaceFragment", oechem.OEFileStringType_Mol3D,
                                     oechem.OEFileStringType_Mol3D, oechem.OEFileStringType_Mol3D, "-query")
    if oechem.OEConfigureOpts(opts, argv, False) == oechem.OEOptsConfigureStatus_Help:
        return 0
    broodOpts.UpdateValues(opts)

    ifs = oechem.oemolistream()
    if not ifs.open(opts.GetInFile()):
        oechem.OEThrow.Fatal("Unable to open %s for reading" % opts.GetInFile())

    rfs = oechem.oemolistream()
    if not rfs.open(opts.GetRefFile()):
        oechem.OEThrow.Fatal("Unable to open %s for reading" % opts.GetRefFile())

    ofs = oechem.oemolostream()
    if not ofs.open(opts.GetOutFile()):
        oechem.OEThrow.Fatal("Unable to open %s for writing" % opts.GetOutFile())

    query = oebioisostere.OEBroodQuery()
    retCode = oebioisostere.OEReadBroodQuery(rfs, query)
    if retCode != oebioisostere.OEBroodStatusCode_Success:
        oechem.OEThrow.Fatal("Failed: %s" % oebioisostere.OEGetBroodStatus(retCode))

    prep = oebioisostere.OEBroodFragPrep()
    overlay = oebioisostere.OEBroodOverlay(broodOpts.GetGenOpts(), broodOpts.GetScoreOpts())
    overlay.SetupRef(query);
    builder = oebioisostere.OEBroodMolBuilder(query, broodOpts.GetGenOpts(), broodOpts.GetBuildOpts())

    for frag in ifs.GetOEMols():
        print("Replacement fragment %s" % frag.GetTitle())
        prep.Prep(frag)
        score = oebioisostere.OEBroodScore()
        ret_code = overlay.Overlay(frag, score)
        if ret_code == oebioisostere.OEBroodStatusCode_Success:
            comboScore = score.GetComboScore()
            if broodOpts.GetGenOpts().GetScoreType() == oebioisostere.OEBroodScoreType_ET:
                comboScore = score.GetETComboScore()
            print("Fragment: %s Combo Score: %2f" % (frag.GetTitle(), comboScore))
            hit = oebioisostere.OEBroodHit()
            if builder.Build(score, hit) == oebioisostere.OEBroodStatusCode_Success:
                oechem.OEWriteMolecule(ofs, hit.GetMol())
        else:
            errMsg = oebioisostere.OEGetBroodStatus(ret_code)
            print("%s: %s" % (frag.GetTitle(), errMsg))
    return 0


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