import os
import numbers
import coot
import coot_utils

# note to self, debug this file using  python3, not coot

# Dont prejudice (well we do later anyway)
# this could be e.g. "acedrg" or "cprodrg" or "pyrogen" at the moment
global my_favourite_3d_generator
my_favourite_3d_generator=None

cprodrg = "cprodrg"

# if there is a prodrg_xyzin set the current-time to its mtime, else False
#
global prodrg_xyzin
global sbase_to_coot_tlc
prodrg_xyzin      = "coot-lidia.mdl"
sbase_to_coot_tlc = ".sbase-to-coot-comp-id"

def get_file_latest_time(file_name):
    if not os.path.isfile(file_name):
        return False
    else:
        return os.stat(file_name).st_mtime

global mdl_latest_time
global sbase_transfer_latest_time
mdl_latest_time = get_file_latest_time(prodrg_xyzin)
sbase_transfer_latest_time = get_file_latest_time(sbase_to_coot_tlc)


# we cannot use full path as cprodrg is spawning refmac...
#cprodrg = "c:/Programs/CCP4-Packages/ccp4-6.1.13/bin/cprodrg.exe"

# we need $CLIBD to run prodrg (for prodrg.param), so check for it:
if not os.getenv("CLIBD"):
    bin_dir = os.path.dirname(cprodrg)
    base_dir = os.path.dirname(bin_dir)
    clibd = os.path.join(base_dir, "lib", "data")
    prodrg_params = os.path.join(clibd, "prodrg.param")
    if os.path.isfile(prodrg_params):
        os.environ["CLIBD"] = clibd


# this is for BL win machine
# Mmmh. FIXME!!!!
# home = os.getenv("HOME")
# if (not home and coot_utils.is_windows()):
#     home = os.getenv("COOT_HOME")
# if home:
#     prodrg_xyzin      = os.path.join(home, "Projects",
#                                      "build-xp-python", "lbg", "prodrg-in.mdl")
# else:
#     print "BL WARNING:: Problem: home is", home  # FIXME
# sbase_to_coot_tlc = "../../build-xp-python/lbg/.sbase-to-coot-comp-id"


# Need to play with the env variables to make sure acedrg runs in
# (Win)Coot setting since acedrg has a different python
#
def acedrg_env():
    
    import os

    # copy what we have
    my_env = os.environ.copy()
    # then we need:
    # disable python home
    # put ccp4 bin ahead of coot
    dir_name = False
    for ccp4_dir in ["CBIN", "CCP4_BIN"]:
        dir_name = os.environ[ccp4_dir]
        if os.path.isdir(dir_name):
            break
    if dir_name:
        my_env["PATH"] = dir_name + ";" + my_env["PATH"]
    my_env["PYTHONHOME"] = ""
    
    return my_env

def import_from_3d_generator_from_mdl_using_acedrg(mdl_file_name, comp_id):

    pdb_out_file_name = "acedrg-" + comp_id + ".pdb"
    cif_out_file_name = "acedrg-" + comp_id + ".cif"
    stub = "acedrg-" + comp_id

    status = coot_utils.popen_command("acedrg",
                           ["-m", mdl_file_name, "-r", comp_id, "-o", stub],
                           [], "acedrg.log", False, local_env=acedrg_env())
    if status:
        coot.info_dialog("WARNING:: Bad exit status for Acedrg\n - see acedrg.log")
    else:
        coot.handle_read_draw_molecule_and_move_molecule_here(pdb_out_file_name)
        coot.read_cif_dictionary(cif_out_file_name)


def import_from_3d_generator_from_mdl_using_pyrogen(mdl_file_name, comp_id):

    if not coot_utils.command_in_path_qm("pyrogen"):
        coot.info_dialog("pyrogen not found in path")
    else:
        # happy path, maybe!?
        #  -m for sdf (default) and -c for mmcif
        file_type_flag = "-c" if coot_utils.file_name_extension(mdl_file_name)=="cif" else "-m"
        # depends on if we have mogul as well...
        if coot_utils.command_in_path_qm("mogul"):
            args = [file_type_flag, mdl_file_name, "--residue-type", comp_id]
        else:
            args = ["--no-mogul", file_type_flag, mdl_file_name, "--residue-type", comp_id]
        status = coot_utils.popen_command("pyrogen", args,
                 [], "pyrogen.log", True)
        if status:
            coot.info_dialog("WARNING:: Bad exit status for pyrogen\n - see pyrogen.log")
        else:
            active_res = active_residue()  # what for?
            pdb_out_file_name = comp_id + "-pyrogen.pdb"
            cif_out_file_name = comp_id + "-pyrogen.cif"
            imol_ligand = coot.handle_read_draw_molecule_and_move_molecule_here(pdb_out_file_name)
            if not coot_utils.valid_model_molecule_qm(imol_ligand):
                coot.info_dialog("WARNING:: Something bad happened running pyrogen")
            else:
                coot.read_cif_dictionary(cif_out_file_name)
                return imol_ligand   # should return False otherwise? FIXME

# to be over-ridden by your favourite 3d conformer and restraints generator, if you like...
#
def import_from_3d_generator_from_mdl(mdl_file_name, comp_id):

    global my_favourite_3d_generator
    # if acedrg is in the path use that
    if not my_favourite_3d_generator:
        if coot_utils.command_in_path_qm("acedrg"):
            import_from_3d_generator_from_mdl_using_acedrg(mdl_file_name, comp_id)
        else:
            if coot_utils.command_in_path_qm("pyrogen"):
                import_from_3d_generator_from_mdl_using_pyrogen(mdl_file_name, comp_id)
            else:
                # fallback, to prodrg for now
                import_from_prodrg("mini-no", comp_id)
    else:
        if (my_favourite_3d_generator == "pyrogen"):
            import_from_3d_generator_from_mdl_using_pyrogen(mdl_file_name,
                                                            comp_id)
        else:
            if my_favourite_3d_generator == "cprodrg":
                import_from_prodrg("mini-no", comp_id)
            else:
                print("WARNING:: No 3d generator available")
                coot.info_dialog("WARNING:: No 3d generator available")


def import_ligand_with_overlay(prodrg_xyzout, prodrg_cif):
    
    # OK, so here we read the PRODRG files and
    # manipulate them.  We presume that the active
    # residue is quite like the input ligand from
    # prodrg.
    #
    # Read in the lib and coord output of PRODRG.  Then
    # overalay the new ligand onto the active residue
    # (just so that we can see it approximately
    # oriented). Then match the torsions from the new
    # ligand to the those of the active residue.  Then
    # overlay again so that we have the best match.
    #
    # We want to see just one molecule with the protein
    # and the new ligand.
    # add_ligand_delete_residue_copy_molecule provides
    # that for us.  We just colour it and undisplay the
    # other molecules.
    
    # overlap the imol_ligand residue if there are restraints for the
    # reference residue/ligand.
    #
    # Don't overlap if the reference residue/ligand is not a het-group.
    #
    # return overlapped status
    #
    def overlap_ligands_maybe(imol_ligand, imol_ref, chain_id_ref, res_no_ref):

        # we don't want to overlap-ligands if there is no dictionary
        # for the residue to be matched to.
        res_name = coot.residue_name(imol_ref, chain_id_ref, res_no_ref, "")
        restraints = monomer_restraints(res_name)
        if (not restraints):
            return False
        else:
            if not coot_utils.residue_has_hetatms_qm(imol_ref, chain_id_ref, res_no_ref, ""):
                return False
            else:
                print("----------- overlap-ligands %s %s %s %s ------------" \
                      %(imol_ligand, imol_ref, chain_id_ref, res_no_ref))
                # this can return the rtop operator or False (for fail of course).
                return overlap_ligands(imol_ligand, imol_ref, chain_id_ref, res_no_ref)
            
    # return the new molecule number.
    #
    def read_and_regularize(prodrg_xyzout):
        imol = coot.handle_read_draw_molecule_and_move_molecule_here(prodrg_xyzout)
        # speed up the minisation (and then restore setting).
        # No need to put the refinement step stuff in auto accept!?
        s = coot.dragged_refinement_steps_per_frame()
        coot.set_dragged_refinement_steps_per_frame(500)
        with AutoAccept():
            coot.regularize_residues( imol, [["", 1, ""]])
        coot.set_dragged_refinement_steps_per_frame(s)
        return imol

    # return the new molecule number
    # (only works with aa_ins_code of ""), BL:: why? FIXME?
    #
    def read_regularize_and_match_torsions_maybe(prodrg_xyzout, imol_ref,
                                                 chain_id_ref, res_no_ref):
        imol = coot.handle_read_draw_molecule_and_move_molecule_here(prodrg_xyzout)

        if (not have_restraints_for_qm(coot.residue_name(imol_ref, chain_id_ref,
                                                    res_no_ref, ""))):
            return False
        else:
            overlap_status = overlap_ligands_maybe(imol, imol_ref,
                                                   chain_id_ref, res_no_ref)
            
            # speed up the minisation (and then restore setting).
            # No need to put refinement steps in auto accept!?
            s = coot.dragged_refinement_steps_per_frame()
            coot.set_dragged_refinement_steps_per_frame(600)
            with AutoAccept():
                coot.regularize_residues(imol, [["", 1, ""]])
            coot.set_dragged_refinement_steps_per_frame(s)
            if overlap_status:
                coot.match_ligand_torsions(imol, imol_ref, chain_id_ref, res_no_ref)
        return imol

    # return True or False
    #
    def have_restraints_for_qm(res_name):
        restraints = monomer_restraints(res_name)
        return not restraints == False   # twisted but short

    # main line

    coot.read_cif_dictionary(prodrg_cif)

    # we do different things depending on whether or
    # not there is an active residue.  We need to test
    # for having an active residue here (currently we
    # presume that there is).
    # 
    # Similarly, if the aa_ins_code is non-null, let's
    # presume that we do not have an active residue.

    active_atom = active_residue()
    if ((not active_atom) or
        (not active_atom[3] == "")):  # aa_ins_code

        # then there is no active residue to match to
        read_and_regularize(prodrg_xyzout)
        # BL says:: maybe we should merge the ligand into
        # the protein molecule?! But what is the protein?
        # merge_molecules([active_atom[0]], imol)
    else:
        # we have an active residue to match to
        with coot_utils.UsingActiveAtom() as [aa_imol, aa_chain_id, aa_res_no, aa_ins_code,
                                   aa_atom_name, aa_alt_conf]:
            if not coot_utils.residue_is_close_to_screen_centre_qm(
                aa_imol, aa_chain_id, aa_res_no, ""):

                # not close, no overlap
                #
                read_and_regularize(prodrg_xyzout)
            else:
                # try overlap
                imol = read_regularize_and_match_torsions_maybe(prodrg_xyzout,
                                                                aa_imol, aa_chain_id, aa_res_no)

                overlapped_flag = overlap_ligands_maybe(imol, aa_imol,
                                                        aa_chain_id, aa_res_no)

                if overlapped_flag:
                    print("------ overlapped-flag was true!!!!!")
                    coot.set_mol_displayed(aa_imol, 0)
                    coot.set_mol_active(aa_imol, 0)
                    col = coot.get_molecule_bonds_colour_map_rotation(aa_imol)
                    new_col = col + 5 # a tiny amount
                    # new ligand specs, then "reference" ligand (to be deleted)
                    imol_replaced = coot.add_ligand_delete_residue_copy_molecule(
                        imol, "", 1,
                        aa_imol, aa_chain_id, aa_res_no)


                    coot.set_molecule_bonds_colour_map_rotation(imol_replaced, new_col)
                    coot.set_mol_displayed(imol, 0)
                    coot.set_mol_active(imol, 0)
                    coot.graphics_draw()

    return True
    # return False otherwise? When? FIXME

    
def import_from_prodrg(minimize_mode, res_name):

    import operator
    global prodrg_xyzin

    # main line of import_from_prodrg
    #
    prodrg_dir = "coot-ccp4"

    coot.make_directory_maybe(prodrg_dir)
    prodrg_xyzout = os.path.join(prodrg_dir, "prodrg-" + res_name + ".pdb")
    prodrg_cif    = os.path.join(prodrg_dir, "prodrg-out.cif")
    prodrg_log    = os.path.join(prodrg_dir, "prodrg.log")

    # FIXME? maybe, we could use 'enum' for mini-no rather than string?!
    # see news_status stuff
    # requires python >= 2.5 (shall we test?)
    mini_mode = "NO" if (minimize_mode == 'mini-no') else "PREP"
    # see if we have cprodrg
    if not (os.path.isfile(cprodrg) or
            coot_utils.command_in_path_qm(cprodrg)):
        coot.info_dialog("BL INFO:: No cprodrg found")
    else:
        status = coot_utils.popen_command(cprodrg,
                               ["XYZIN",  prodrg_xyzin,
                                "XYZOUT", prodrg_xyzout,
                                "LIBOUT", prodrg_cif],
                               ["MINI " + mini_mode, "END"],
                               prodrg_log, True)
        if isinstance(status, int):
            if (status == 0):
                import_ligand_with_overlay(prodrg_xyzout, prodrg_cif)

######################################
##             SMILES               ##
######################################

# Run libcheck to convert from SMILES string
#
def new_molecule_by_smiles_string(tlc_text, smiles_text, force_libcheck=False):

    # generator is "pyrogen" or "acedrg"
    #
    def dict_gen(generator, comp_id, args, working_dir):

        stub = comp_id + "-" + generator
        log_file_name = os.path.join(working_dir, stub + ".log")
        print("::::::::: args", args)
        if generator == "acedrg":
            status = coot_utils.popen_command(generator, args, [], log_file_name, True,
                                   local_env=acedrg_env())
            print("popen_command status:", status)
        else:
            status = coot_utils.popen_command(generator, args, [], log_file_name, True)

        if not status == 0:
            return -1 # bad mol
        else:
            pdb_name = os.path.join(working_dir, stub + ".pdb")
            cif_name = os.path.join(working_dir, stub + ".cif")

            print("************ calling coot.read_pdb()", pdb_name)
            imol = coot.read_pdb(pdb_name)
            print("************ done call coot.read_pdb()", pdb_name)
            coot.read_cif_dictionary(cif_name)
            return imol

    def use_acedrg(three_letter_code):
        working_dir = coot_utils.get_directory("coot-acedrg")
        stub = three_letter_code + "-acedrg"
        smi_file_name = os.path.join(working_dir, stub + "-from-coot.smi")
        coot_utils.save_string_to_file(smiles_text, smi_file_name, True)
        dict_gen("acedrg",
            three_letter_code,
            ["-r", three_letter_code, "-i", smi_file_name, "-o", os.path.join(working_dir, stub)],
            working_dir)


    # keep the legacy...
    def use_libcheck(three_letter_code):

       import shutil

       smiles_file = "coot-" + three_letter_code + ".smi"
       libcheck_data_lines = ["N",
                              "MON " + three_letter_code,
                              "FILE_SMILE " + smiles_file,
                              ""]
       log_file_name = "libcheck-" + three_letter_code + ".log"
       pdb_file_name = "libcheck_" + three_letter_code + ".pdb"
       cif_file_name = "libcheck_" + three_letter_code + ".cif"

       # write the smiles string to a file
       smiles_input = file(smiles_file,'w')
       smiles_input.write(smiles_text)
       smiles_input.close()

       libcheck_exe_file = coot_utils.find_exe(libcheck_exe, "CBIN", "CCP4_BIN", "PATH")

       if (not libcheck_exe_file):
           print(" BL WARNING:: libcheck not found!")
       else:
           status = coot_utils.popen_command(libcheck_exe_file, [], libcheck_data_lines,
                                  log_file_name, True)
           # the output of libcheck goes to libcheck.lib, we want it in
           # (i.e. overwrite the minimal description in cif_file_name
           if coot_utils.isNumber(status):
               if (status == 0):
                   if (os.path.isfile("libcheck.lib")):
                       # copy rather than rename file to avoid accession issues
                       shutil.copy("libcheck.lib", cif_file_name)
                       sc = coot_utils.rotation_centre()
                       imol = coot.handle_read_draw_molecule_with_recentre(pdb_file_name, 0)
                       if (coot.is_valid_model_molecule(imol)):
                           mc = coot_utils.molecule_centre(imol)
                           sc_mc = [sc[i]-mc[i] for i in range(len(mc))]
                           coot.translate_molecule_by(imol, *sc_mc)
                       coot.read_cif_dictionary(cif_file_name)
           else:
               print("OOPs.. libcheck returned exit status", status)




    def use_pyrogen(three_letter_code):

        print("use_pyrogen() -- start ---", three_letter_code)

        # 20230606-PE Hacketty-hack because
        #    NameError: name 'use_mogul' is not defined
        # global use_mogul
        use_mogul = False

        print("use_pyrogen()", three_letter_code, "use_mogul:", use_mogul)

        working_dir = coot_utils.get_directory("coot-pyrogen")
        log_file_name = "pyrogen.log"  # in working_dir

        # Embed a test for mogul

        # needs with_working_directory macro (or such)
        #
        current_dir = os.getcwd()
        os.chdir(working_dir)
        comp_id = tlc_text if tlc_text else "LIG"

        print("use_pyrogen() comp_id:", comp_id)

        if use_mogul:
            args = ["--residue-type", comp_id, smiles_text]
        else:
            if coot_utils.command_in_path_qm("mogul"):
                args = ["--residue-type", comp_id, smiles_text]
            else:
                args = ["--no-mogul", "-M", "--residue-type", comp_id, smiles_text]

        print("use_pyrogen(): args:", args)

        # BL says:: may have to find pyrogen first?! FIXME
        status = coot_utils.popen_command("pyrogen", args, [], log_file_name, True)

        if coot_utils.ok_popen_status_qm(status):
            pdb_file_name = comp_id + "-pyrogen.pdb"
            cif_file_name = comp_id + "-pyrogen.cif"
            sc = coot_utils.rotation_centre()
            imol = coot.handle_read_draw_molecule_with_recentre(pdb_file_name, 0)
            if (coot.is_valid_model_molecule(imol)):
                mc = coot_utils.molecule_centre(imol)
                sc_mc = [sc[i]-mc[i] for i in range(len(mc))]
                coot.translate_molecule_by(imol, *sc_mc)
            coot.read_cif_dictionary(cif_file_name)
        os.chdir(current_dir)

    # main line

    print("********************************************************************************************")
    print("********************************************************************************************")
    print("****************************** new_molecule_by_smiles_string *******************************")
    print("********************************************************************************************")
    print("********************************************************************************************")
    print("****** Path 0 :", smiles_text, ":")
    #
    if len(smiles_text) > 0:

        if ((len(tlc_text) > 0) and (len(tlc_text) < 4)):
            three_letter_code = tlc_text
        elif (len(tlc_text) > 0):
            three_letter_code = tlc_text[0:3]
        else:
            three_letter_code = "XXX"

        print("****** Path Bv")
        rr = False
        print("****** Path Bw")
        try:
            print("****** Path Bx")
            rr = coot.enhanced_ligand_coot_p()
        except KeyError as e:
            print("****** Path By")
            print (e)
        print("****** Path Bz")
        rr = False # use acedrg
        if rr:
            print("****** Path C")
            use_pyrogen(three_letter_code)
        else:
            print("****** Path D")
            use_acedrg(three_letter_code)
        print("****** Path E")

    else:
        # invalid smiles length
        print("WARNING:: no SMILES text found. Bailing out.")
        return False


# new for ace_drg (not test as BL not running yet), scheme has error...
# stud is a stub until acedrg is running. Scheme code doesnt make sense
# this one currently neither.
def new_molecule_by_smiles_string_by_acedrg(tlc_str, smiles_str):

    smi_file = "acedrg-in.smi"

    # dump the smiles string to a file
    smiles_input = file(smi_file,'w')
    smiles_input.write(smiles_str)
    smiles_input.close()

    stub = "acedrg-" + tlc_str
    pdb_out_file_name = stub + ".pdb"
    cif_out_file_name = stub + ".cif"

    args = ["-i", smi_file, "-r", tlc_str, "-o", stub]
    log_file_name = "acedrg-" + tlc_str + ".log"
    if coot_utils.command_in_path_qm("acedrg"):
        status = coot_utils.popen_command("acedrg", args, [], log_file_name, True,
                               local_env=acedrg_env())
        if (coot_utils.ok_popen_status_qm(status)):
            coot.handle_read_draw_molecule_and_move_molecule_here(pdb_out_file_name)
            coot.read_cif_dictionary(cif_out_file_name)
        else:
            coot.info_dialog("Bad exit status for Acedrg\n - see acedrg log")


def get_file_latest_time(file_name):
    if not os.path.isfile(file_name):
        return False
    else:
        return os.stat(file_name).st_mtime

# FIXME: this is not a proper name
def mdl_update_timeout_func():

    import operator
    global mdl_latest_time
    global sbase_transfer_latest_time
    global prodrg_xyzin
    global sbase_to_coot_tlc
    
    mdl_now_time   = get_file_latest_time(prodrg_xyzin)
    sbase_now_time = get_file_latest_time(sbase_to_coot_tlc)

    # print "sbase_now_time %s    sbase_latest_time %s" %(sbase_now_time, sbase_transfer_latest_time)

    if (isinstance(mdl_now_time, numbers.Number)):
        if isinstance(mdl_latest_time, numbers.Number):
            if (mdl_now_time > mdl_latest_time):
                mdl_latest_time = mdl_now_time
                import_from_prodrg('mini-prep')

    if isinstance(sbase_transfer_latest_time, numbers.Number):
        if isinstance(sbase_now_time, numbers.Number):
            if (sbase_now_time > sbase_transfer_latest_time):
                sbase_transfer_latest_time = sbase_now_time
                try: # sort of check if file exists?
                    fin = open(sbase_to_coot_tlc, 'r')
                    tlc_symbol = fin.readline()  # need to read more? FIXME
                    fin.close()
                    imol = coot.get_ccp4srs_monomer_and_dictionary(tlc_symbol)
                    if not coot_utils.valid_model_molecule_qm(imol):
                        print("failed to get SBase molecule for", tlc_symbol)
                    else:
                        # it was read OK, do an overlap
                        coot_utils.using_active_atom(overlap_ligands, imol,
                                          "aa_imol", "aa_chain_id", "aa_res_no")
                except:
                    print("BL ERROR:: reading sbase file", sbase_to_coot_tlc)
                
    return True # return value, keep running; FIXME:: how to stop?


# This is done internally now, by passing lbg a function that runs
# prodrg after the mdl file has been written.  On demand.  We no
# longer need to have a timeout looking for a new prodrg-in.mdl file.
#
# gobject.timeout_add(500, mdl_update_timeout_func)

# return False (if fail) or a list of: the molecule number of the
# selected residue, the prodrg output mol file_name, the prodrg
# output pdb file_name
#
def prodrg_flat(imol_in, chain_id_in, res_no_in):
    """return False (if fail) or a list of: the molecule number of the
    selected residue, the prodrg output mol file_name, the prodrg
    output pdb file_name

    Keyword arguments:
    imol_in -- the molecule number
    chain_id_in -- chain id of the molecule
    res_no_in -- residue number ot the molecule
    
    """

    import operator
    import random

    # return a text string, or at least "" if we can't find the prodrg
    # error message output line.
    def get_prodrg_error_message(log_file):
        if not os.path.isfile(log_file):
            return ""
        else:
            fin = open(log_file, 'r')
            lines = fin.readlines()
            fin.close()
            for line in lines:
                if (" PRODRG: " in line):
                    # assuming only one error?!
                    return line
            return ""  # no error

    selection_string = "//" + chain_id_in + "/" + str(res_no_in)
    imol = coot.new_molecule_by_atom_selection(imol_in, selection_string)
    prodrg_input_file_name = os.path.join("coot-ccp4", "tmp-residue-for-prodrg.pdb")
    prodrg_output_mol_file = os.path.join("coot-ccp4", ".coot-to-lbg-mol")
    prodrg_output_pdb_file = os.path.join("coot-ccp4", ".coot-to-lbg-pdb")
    prodrg_output_lib_file = os.path.join("coot-ccp4", ".coot-to-lbg-lib")
    prodrg_log             = os.path.join("coot-ccp4", "tmp-prodrg-flat.log")
    coot.set_mol_displayed(imol, 0)
    set_mol_active   (imol, 0)
    coot.write_pdb_file(imol, prodrg_input_file_name)
    coot.make_directory_maybe("coot-ccp4")
    arg_list = ["XYZIN",  prodrg_input_file_name,
                "MOLOUT", prodrg_output_mol_file,
                "XYZOUT", prodrg_output_pdb_file,
                "LIBOUT", prodrg_output_lib_file]
    print("arg_list", arg_list)
    status = coot_utils.popen_command(cprodrg,
                           arg_list,
                           ["COORDS BOTH", "MINI FLAT", "END"],
                           prodrg_log, True)
    # Does this make sense in python? status being number that is.
    # Maybe rather check for cprodrg exe. FIXME
    if not coot_utils.isNumber(status):
        coot.info_dialog("Ooops: cprodrg not found?")
        return False
    else:
        if not (status == 0):
            # only for python >=2.5
            mess = "Something went wrong running cprodrg\n" + \
                   get_prodrg_error_message(prodrg_log)
            coot.info_dialog(mess)
            return False
        else:
            # normal return value (hopefully)
            return [imol,
                    prodrg_output_mol_file,
                    prodrg_output_pdb_file,
                    prodrg_output_lib_file]


def prodrg_plain(mode, imol_in, chain_id_in, res_no_in):

    selection_string = "//" + chain_id_in + "/" + \
                       str(res_no_in)
    imol = coot.new_molecule_by_atom_selection(imol_in, selection_string)
    stub = os.path.join("coot-ccp4", "prodrg-tmp-" + str(os.getpid()))
    # make the name different as not to be confused with the global
    # prodrg_xyzin.
    prodrg_xyzinX = stub + "-xyzin.pdb"
    prodrg_xyzout = stub + "-xyzout.pdb"
    prodrg_cif    = stub + "-dict.cif"
    prodrg_log    = stub + ".log"

    coot.write_pdb_file(imol, prodrg_xyzinX)
    result = coot_utils.popen_command(cprodrg,
                           ["XYZIN",  prodrg_xyzinX,
                            "XYZOUT", prodrg_xyzout,
                            "LIBOUT", prodrg_cif],
                           ["MINI PREP", "END"],
                           prodrg_log, True)
    coot.close_molecule(imol)
    return [result, prodrg_xyzout, prodrg_cif]


# Why do we pass imol etc and then use active atom?
def fle_view(imol, chain_id, res_no, ins_code):

    import operator
    global have_mingw
    
    # not using active atom, but make property list
    r_flat  = prodrg_flat (imol, chain_id, res_no)
    r_plain = prodrg_plain('mini-no', imol, chain_id, res_no)
    if (r_flat and (r_plain[0] == 0 )):
        imol_ligand_fragment = r_flat[0]
        prodrg_output_flat_mol_file_name = r_flat[1]
        prodrg_output_flat_pdb_file_name = r_flat[2]
        prodrg_output_cif_file_name      = r_flat[3]
        prodrg_output_3d_pdb_file_name   = r_plain[1]
        # 'using_active_atom'
        active_atom = active_residue()
        aa_imol     = active_atom[0]
        aa_chain_id = active_atom[1]
        aa_res_no   = active_atom[2]
        coot.fle_view_internal(aa_imol, aa_chain_id, aa_res_no, "",  # should be from active_atom!!     coot_utils.using_active_atom([[]])
                          imol_ligand_fragment,
                          prodrg_output_flat_mol_file_name,
                          prodrg_output_flat_pdb_file_name,
                          prodrg_output_3d_pdb_file_name,
                          prodrg_output_cif_file_name)
        # touch on Windows!?
        # either distribute touch.exe or use DOS:
        # for non existing file use:
        # copy NUL YourFile.txt
        # for existing:
        # copy /b filename.ext +,,
        #
        # all not neede any more...
        # BL says:: just keep in case I need to touch anything again!!!
        #
        #if (coot_utils.is_windows()):
        #    import subprocess
        #    lbg_ready = os.path.abspath(os.path.join("coot-ccp4",
        #                                              ".coot-to-lbg-mol-ready"))
        #    print "BL DEBUG:: lbg_ready is", lbg_ready
        #    if os.path.isfile(lbg_ready):
        #        subprocess.call("copy /b /y " + lbg_ready + " +,, " + lbg_ready
        #                        , shell=True)
        #    else:
        #        subprocess.call("copy NUL " + lbg_ready, shell=True)
        #else:
        #    coot_utils.popen_command("touch",
        #                  [os.path.join("coot-ccp4",
        #                                ".coot-to-lbg-mol-ready")],
        #                  [],
        #                  "/dev/null", False)

# using cprodrg
# again, why passing imol etc? FIXME
#
def fle_view_to_png(imol, chain_id, res_no, ins_code, neighb_radius,
                    png_file_name):

    # not using active atom, but make property list
    # 'using_active_atom'
    active_atom = active_residue()
    imol     = active_atom[0]
    chain_id = active_atom[1]
    res_no   = active_atom[2]
    
    r_flat  = prodrg_flat (imol, chain_id, res_no)
    r_plain = prodrg_plain('mini-no', imol, chain_id, res_no)
    
    if (r_flat and (r_plain[0] == 0 )):
        imol_ligand_fragment = r_flat[0]
        prodrg_output_flat_mol_file_name = r_flat[1]
        prodrg_output_flat_pdb_file_name = r_flat[2]
        prodrg_output_cif_file_name      = r_flat[3]
        prodrg_output_3d_pdb_file_name   = r_plain[1]
        coot.fle_view_internal_to_png(imol, chain_id, res_no, "",  # should be from active_atom!!     coot_utils.using_active_atom([[]])
                                 imol_ligand_fragment,
                                 prodrg_output_flat_mol_file_name,
                                 prodrg_output_flat_pdb_file_name,
                                 prodrg_output_3d_pdb_file_name,
                                 prodrg_output_cif_file_name, 1,
                                 png_file_name)
                

# import from SRS, callback using sbase_import_function
# BL says:: not tested; FIXME
#
def get_ccp4srs_monomer_and_overlay(comp_id):

    """
    import from SBASE, callback using sbase_import_function
    """

    if (active_residue()):
        with coot_utils.UsingActiveAtom() as [aa_imol, aa_chain_id, aa_res_no,
                                   aa_ins_code, aa_atom_name, aa_alt_conf]:
            imol = coot.get_ccp4srs_monomer_and_dictionary(comp_id)
            overlap_ligands(imol, aa_imol, aa_chain_id, aa_res_no)
    else:
        coot.get_ccp4srs_monomer_and_dictionary(comp_id)