path: root/plip/exchange/report.py

import time
from operator import itemgetter

import lxml.etree as et

from plip.basic import config
from plip.basic.config import __version__
from plip.structure.preparation import PDBComplex


class StructureReport:
    """Creates reports (xml or txt) for one structure/"""

    def __init__(self, mol: PDBComplex, outputprefix: str = "report"):
        self.mol = mol
        self.excluded = self.mol.excluded
        self.xmlreport = self.construct_xml_tree()
        self.txtreport = self.construct_txt_file()
        self.get_bindingsite_data()
        self.outpath = mol.output_path
        self.outputprefix = outputprefix

    def construct_xml_tree(self):
        """Construct the basic XML tree"""
        report = et.Element("report")
        plipversion = et.SubElement(report, "plipversion")
        plipversion.text = __version__
        date_of_creation = et.SubElement(report, "date_of_creation")
        date_of_creation.text = time.strftime("%Y/%m/%d")
        citation_information = et.SubElement(report, "citation_information")
        citation_information.text = (
            "Salentin,S. et al. PLIP: fully automated protein-ligand interaction profiler. "
            "Nucl. Acids Res. (1 July 2015) 43 (W1): W443-W447. doi: 10.1093/nar/gkv315"
        )

        maintainer_information = et.SubElement(report, "maintainer_information")
        maintainer_information.text = config.__maintainer__
        mode = et.SubElement(report, "mode")
        if config.DNARECEPTOR:
            mode.text = "dna_receptor"
        else:
            mode.text = "default"
        pdbid = et.SubElement(report, "pdbid")
        pdbid.text = self.mol.pymol_name.upper()
        filetype = et.SubElement(report, "filetype")
        filetype.text = self.mol.filetype.upper()
        pdbfile = et.SubElement(report, "pdbfile")
        pdbfile.text = self.mol.sourcefiles["pdbcomplex"]
        pdbfixes = et.SubElement(report, "pdbfixes")
        pdbfixes.text = str(self.mol.information["pdbfixes"])
        filename = et.SubElement(report, "filename")
        filename.text = str(self.mol.sourcefiles.get("filename") or None)
        exligs = et.SubElement(report, "excluded_ligands")
        for i, exlig in enumerate(self.excluded):
            e = et.SubElement(exligs, "excluded_ligand", id=str(i + 1))
            e.text = exlig
        covalent = et.SubElement(report, "covlinkages")
        for i, covlinkage in enumerate(self.mol.covalent):
            e = et.SubElement(covalent, "covlinkage", id=str(i + 1))
            f1 = et.SubElement(e, "res1")
            f2 = et.SubElement(e, "res2")
            f1.text = ":".join(
                [covlinkage.id1, covlinkage.chain1, str(covlinkage.pos1)]
            )
            f2.text = ":".join(
                [covlinkage.id2, covlinkage.chain2, str(covlinkage.pos2)]
            )
        return report

    def construct_txt_file(self):
        """Construct the header of the txt file"""
        textlines = [
            "Prediction of noncovalent interactions for PDB structure %s"
            % self.mol.pymol_name.upper(),
        ]
        textlines.append("=" * len(textlines[0]))
        textlines.append(
            "Created on %s using PLIP v%s\n" % (time.strftime("%Y/%m/%d"), __version__)
        )
        textlines.append("If you are using PLIP in your work, please cite:")
        textlines.append(
            "Salentin,S. et al. PLIP: fully automated protein-ligand interaction profiler."
        )
        textlines.append(
            "Nucl. Acids Res. (1 July 2015) 43 (W1): W443-W447. doi: 10.1093/nar/gkv315\n"
        )
        if len(self.excluded) != 0:
            textlines.append(
                "Excluded molecules as ligands: %s\n"
                % ",".join([lig for lig in self.excluded])
            )
        if config.DNARECEPTOR:
            textlines.append("DNA/RNA in structure was chosen as the receptor part.\n")
        return textlines

    def get_bindingsite_data(self):
        """Get the additional data for the binding sites"""
        for i, site in enumerate(sorted(self.mol.interaction_sets)):
            s = self.mol.interaction_sets[site]
            bindingsite = BindingSiteReport(s).generate_xml()
            bindingsite.set("id", str(i + 1))
            bindingsite.set("has_interactions", "False")
            self.xmlreport.insert(i + 1, bindingsite)
            for itype in BindingSiteReport(s).generate_txt():
                self.txtreport.append(itype)
            if not s.no_interactions:
                bindingsite.set("has_interactions", "True")
            else:
                self.txtreport.append("No interactions detected.")

    def write_xml(self, as_string=False):
        """Write the XML report"""
        if not as_string:
            et.ElementTree(self.xmlreport).write(
                "{}/{}.xml".format(self.outpath, self.outputprefix),
                pretty_print=True,
                xml_declaration=True,
            )
        else:
            output = et.tostring(self.xmlreport, pretty_print=True)
            print(output.decode("utf8"))

    def write_txt(self, as_string=False):
        """Write the TXT report"""
        if not as_string:
            with open("{}/{}.txt".format(self.outpath, self.outputprefix), "w") as f:
                [f.write(textline + "\n") for textline in self.txtreport]
        else:
            output = "\n".join(self.txtreport)
            print(output)


class BindingSiteReport:
    """Gather report data and generate reports for one binding site in different formats."""

    def __init__(self, plcomplex):

        ################
        # GENERAL DATA #
        ################

        self.complex = plcomplex
        self.ligand = self.complex.ligand
        self.bindingsite = self.complex.bindingsite
        self.output_path = self.complex.output_path
        self.bsid = ":".join(
            [self.ligand.hetid, self.ligand.chain, str(self.ligand.position)]
        )
        self.longname = self.ligand.longname
        self.ligtype = self.ligand.type
        self.bs_res = self.bindingsite.bs_res
        self.min_dist = self.bindingsite.min_dist
        self.bs_res_interacting = self.complex.interacting_res
        self.pdbid = self.complex.pdbid.upper()
        self.lig_members = self.complex.lig_members
        self.interacting_chains = self.complex.interacting_chains

        ############################
        # HYDROPHOBIC INTERACTIONS #
        ############################

        self.hydrophobic_features = (
            "RESNR",
            "RESTYPE",
            "RESCHAIN",
            "RESNR_LIG",
            "RESTYPE_LIG",
            "RESCHAIN_LIG",
            "DIST",
            "LIGCARBONIDX",
            "PROTCARBONIDX",
            "LIGCOO",
            "PROTCOO",
        )
        self.hydrophobic_info = []
        for hydroph in self.complex.hydrophobic_contacts:
            self.hydrophobic_info.append(
                (
                    hydroph.resnr,
                    hydroph.restype,
                    hydroph.reschain,
                    hydroph.resnr_l,
                    hydroph.restype_l,
                    hydroph.reschain_l,
                    "%.2f" % hydroph.distance,
                    hydroph.ligatom_orig_idx,
                    hydroph.bsatom_orig_idx,
                    hydroph.ligatom.coords,
                    hydroph.bsatom.coords,
                )
            )

        ##################
        # HYDROGEN BONDS #
        ##################

        self.hbond_features = (
            "RESNR",
            "RESTYPE",
            "RESCHAIN",
            "RESNR_LIG",
            "RESTYPE_LIG",
            "RESCHAIN_LIG",
            "SIDECHAIN",
            "DIST_H-A",
            "DIST_D-A",
            "DON_ANGLE",
            "PROTISDON",
            "DONORIDX",
            "DONORTYPE",
            "ACCEPTORIDX",
            "ACCEPTORTYPE",
            "LIGCOO",
            "PROTCOO",
        )
        self.hbond_info = []
        for hbond in self.complex.hbonds_pdon + self.complex.hbonds_ldon:
            ligatom, protatom = (
                (hbond.a, hbond.d) if hbond.protisdon else (hbond.d, hbond.a)
            )
            self.hbond_info.append(
                (
                    hbond.resnr,
                    hbond.restype,
                    hbond.reschain,
                    hbond.resnr_l,
                    hbond.restype_l,
                    hbond.reschain_l,
                    hbond.sidechain,
                    "%.2f" % hbond.distance_ah,
                    "%.2f" % hbond.distance_ad,
                    "%.2f" % hbond.angle,
                    hbond.protisdon,
                    hbond.d_orig_idx,
                    hbond.dtype,
                    hbond.a_orig_idx,
                    hbond.atype,
                    ligatom.coords,
                    protatom.coords,
                )
            )

        #################
        # WATER-BRIDGES #
        #################

        self.waterbridge_features = (
            "RESNR",
            "RESTYPE",
            "RESCHAIN",
            "RESNR_LIG",
            "RESTYPE_LIG",
            "RESCHAIN_LIG",
            "DIST_A-W",
            "DIST_D-W",
            "DON_ANGLE",
            "WATER_ANGLE",
            "PROTISDON",
            "DONOR_IDX",
            "DONORTYPE",
            "ACCEPTOR_IDX",
            "ACCEPTORTYPE",
            "WATER_IDX",
            "LIGCOO",
            "PROTCOO",
            "WATERCOO",
        )
        # The coordinate format is an exception here, since the interaction is not only between ligand and protein
        self.waterbridge_info = []
        for wbridge in self.complex.water_bridges:
            lig, prot = (
                (wbridge.a, wbridge.d) if wbridge.protisdon else (wbridge.d, wbridge.a)
            )
            self.waterbridge_info.append(
                (
                    wbridge.resnr,
                    wbridge.restype,
                    wbridge.reschain,
                    wbridge.resnr_l,
                    wbridge.restype_l,
                    wbridge.reschain_l,
                    "%.2f" % wbridge.distance_aw,
                    "%.2f" % wbridge.distance_dw,
                    "%.2f" % wbridge.d_angle,
                    "%.2f" % wbridge.w_angle,
                    wbridge.protisdon,
                    wbridge.d_orig_idx,
                    wbridge.dtype,
                    wbridge.a_orig_idx,
                    wbridge.atype,
                    wbridge.water_orig_idx,
                    lig.coords,
                    prot.coords,
                    wbridge.water.coords,
                )
            )

        ################
        # SALT BRIDGES #
        ################

        self.saltbridge_features = (
            "RESNR",
            "RESTYPE",
            "RESCHAIN",
            "RESNR_LIG",
            "RESTYPE_LIG",
            "RESCHAIN_LIG",
            "DIST",
            "PROTISPOS",
            "LIG_GROUP",
            "LIG_IDX_LIST",
            "LIGCOO",
            "PROTCOO",
        )
        self.saltbridge_info = []
        for sb in self.complex.saltbridge_lneg + self.complex.saltbridge_pneg:
            if sb.protispos:
                group, ids = (
                    sb.negative.fgroup,
                    [str(x) for x in sb.negative.atoms_orig_idx],
                )
                self.saltbridge_info.append(
                    (
                        sb.resnr,
                        sb.restype,
                        sb.reschain,
                        sb.resnr_l,
                        sb.restype_l,
                        sb.reschain_l,
                        "%.2f" % sb.distance,
                        sb.protispos,
                        group.capitalize(),
                        ",".join(ids),
                        tuple(sb.negative.center),
                        tuple(sb.positive.center),
                    )
                )
            else:
                group, ids = (
                    sb.positive.fgroup,
                    [str(x) for x in sb.positive.atoms_orig_idx],
                )
                self.saltbridge_info.append(
                    (
                        sb.resnr,
                        sb.restype,
                        sb.reschain,
                        sb.resnr_l,
                        sb.restype_l,
                        sb.reschain_l,
                        "%.2f" % sb.distance,
                        sb.protispos,
                        group.capitalize(),
                        ",".join(ids),
                        tuple(sb.positive.center),
                        tuple(sb.negative.center),
                    )
                )

        ###############
        # PI-STACKING #
        ###############

        self.pistacking_features = (
            "RESNR",
            "RESTYPE",
            "RESCHAIN",
            "RESNR_LIG",
            "RESTYPE_LIG",
            "RESCHAIN_LIG",
            "CENTDIST",
            "ANGLE",
            "OFFSET",
            "TYPE",
            "LIG_IDX_LIST",
            "LIGCOO",
            "PROTCOO",
        )
        self.pistacking_info = []
        for stack in self.complex.pistacking:
            ids = [str(x) for x in stack.ligandring.atoms_orig_idx]
            self.pistacking_info.append(
                (
                    stack.resnr,
                    stack.restype,
                    stack.reschain,
                    stack.resnr_l,
                    stack.restype_l,
                    stack.reschain_l,
                    "%.2f" % stack.distance,
                    "%.2f" % stack.angle,
                    "%.2f" % stack.offset,
                    stack.type,
                    ",".join(ids),
                    tuple(stack.ligandring.center),
                    tuple(stack.proteinring.center),
                )
            )

        ##########################
        # PI-CATION INTERACTIONS #
        ##########################

        self.pication_features = (
            "RESNR",
            "RESTYPE",
            "RESCHAIN",
            "RESNR_LIG",
            "RESTYPE_LIG",
            "RESCHAIN_LIG",
            "DIST",
            "OFFSET",
            "PROTCHARGED",
            "LIG_GROUP",
            "LIG_IDX_LIST",
            "LIGCOO",
            "PROTCOO",
        )
        self.pication_info = []
        for picat in self.complex.pication_laro + self.complex.pication_paro:
            if picat.protcharged:
                ids = [str(x) for x in picat.ring.atoms_orig_idx]
                group = "Aromatic"
                self.pication_info.append(
                    (
                        picat.resnr,
                        picat.restype,
                        picat.reschain,
                        picat.resnr_l,
                        picat.restype_l,
                        picat.reschain_l,
                        "%.2f" % picat.distance,
                        "%.2f" % picat.offset,
                        picat.protcharged,
                        group,
                        ",".join(ids),
                        tuple(picat.ring.center),
                        tuple(picat.charge.center),
                    )
                )
            else:
                ids = [str(x) for x in picat.charge.atoms_orig_idx]
                group = picat.charge.fgroup
                self.pication_info.append(
                    (
                        picat.resnr,
                        picat.restype,
                        picat.reschain,
                        picat.resnr_l,
                        picat.restype_l,
                        picat.reschain_l,
                        "%.2f" % picat.distance,
                        "%.2f" % picat.offset,
                        picat.protcharged,
                        group,
                        ",".join(ids),
                        tuple(picat.charge.center),
                        tuple(picat.ring.center),
                    )
                )

        #################
        # HALOGEN BONDS #
        #################

        self.halogen_features = (
            "RESNR",
            "RESTYPE",
            "RESCHAIN",
            "RESNR_LIG",
            "RESTYPE_LIG",
            "RESCHAIN_LIG",
            "SIDECHAIN",
            "DIST",
            "DON_ANGLE",
            "ACC_ANGLE",
            "DON_IDX",
            "DONORTYPE",
            "ACC_IDX",
            "ACCEPTORTYPE",
            "LIGCOO",
            "PROTCOO",
        )
        self.halogen_info = []
        for halogen in self.complex.halogen_bonds:
            self.halogen_info.append(
                (
                    halogen.resnr,
                    halogen.restype,
                    halogen.reschain,
                    halogen.resnr_l,
                    halogen.restype_l,
                    halogen.reschain_l,
                    halogen.sidechain,
                    "%.2f" % halogen.distance,
                    "%.2f" % halogen.don_angle,
                    "%.2f" % halogen.acc_angle,
                    halogen.don_orig_idx,
                    halogen.donortype,
                    halogen.acc_orig_idx,
                    halogen.acctype,
                    halogen.acc.o.coords,
                    halogen.don.x.coords,
                )
            )

        ###################
        # METAL COMPLEXES #
        ###################

        self.metal_features = (
            "RESNR",
            "RESTYPE",
            "RESCHAIN",
            "RESNR_LIG",
            "RESTYPE_LIG",
            "RESCHAIN_LIG",
            "METAL_IDX",
            "METAL_TYPE",
            "TARGET_IDX",
            "TARGET_TYPE",
            "COORDINATION",
            "DIST",
            "LOCATION",
            "RMS",
            "GEOMETRY",
            "COMPLEXNUM",
            "METALCOO",
            "TARGETCOO",
        )
        self.metal_info = []
        # Coordinate format here is non-standard since the interaction partner can be either ligand or protein
        for m in self.complex.metal_complexes:
            self.metal_info.append(
                (
                    m.resnr,
                    m.restype,
                    m.reschain,
                    m.resnr_l,
                    m.restype_l,
                    m.reschain_l,
                    m.metal_orig_idx,
                    m.metal_type,
                    m.target_orig_idx,
                    m.target_type,
                    m.coordination_num,
                    "%.2f" % m.distance,
                    m.location,
                    "%.2f" % m.rms,
                    m.geometry,
                    str(m.complexnum),
                    m.metal.coords,
                    m.target.atom.coords,
                )
            )

    def write_section(self, name, features, info, f):
        """Provides formatting for one section (e.g. hydrogen bonds)"""
        if not len(info) == 0:
            f.write("\n\n### %s ###\n" % name)
            f.write("%s\n" % "\t".join(features))
            for line in info:
                f.write("%s\n" % "\t".join(map(str, line)))

    def rst_table(self, array):
        """Given an array, the function formats and returns and table in rST format."""
        # Determine cell width for each column
        cell_dict = {}
        for i, row in enumerate(array):
            for j, val in enumerate(row):
                if j not in cell_dict:
                    cell_dict[j] = []
                cell_dict[j].append(val)
        for item in cell_dict:
            cell_dict[item] = (
                max([len(x) for x in cell_dict[item]]) + 1
            )  # Contains adapted width for each column

        # Format top line
        num_cols = len(array[0])
        form = "+"
        for col in range(num_cols):
            form += (cell_dict[col] + 1) * "-"
            form += "+"
        form += "\n"

        # Format values
        for i, row in enumerate(array):
            form += "| "
            for j, val in enumerate(row):
                cell_width = cell_dict[j]
                form += str(val) + (cell_width - len(val)) * " " + "| "
            form.rstrip()
            form += "\n"

            # Seperation lines
            form += "+"
            if i == 0:
                sign = "="
            else:
                sign = "-"
            for col in range(num_cols):
                form += (cell_dict[col] + 1) * sign
                form += "+"
            form += "\n"
        return form

    def generate_txt(self):
        """Generates an flat text report for a single binding site"""

        txt = []
        titletext = "%s (%s) - %s" % (self.bsid, self.longname, self.ligtype)
        txt.append(titletext)
        for i, member in enumerate(self.lig_members[1:]):
            txt.append("  + %s" % ":".join(str(element) for element in member))
        txt.append("-" * len(titletext))
        txt.append(
            "Interacting chain(s): %s\n"
            % ",".join([chain for chain in self.interacting_chains])
        )
        for section in [
            [
                "Hydrophobic Interactions",
                self.hydrophobic_features,
                self.hydrophobic_info,
            ],
            ["Hydrogen Bonds", self.hbond_features, self.hbond_info],
            ["Water Bridges", self.waterbridge_features, self.waterbridge_info],
            ["Salt Bridges", self.saltbridge_features, self.saltbridge_info],
            ["pi-Stacking", self.pistacking_features, self.pistacking_info],
            ["pi-Cation Interactions", self.pication_features, self.pication_info],
            ["Halogen Bonds", self.halogen_features, self.halogen_info],
            ["Metal Complexes", self.metal_features, self.metal_info],
        ]:
            iname, features, interaction_information = section
            # Sort results first by res number, then by distance and finally ligand coordinates to get a unique order
            interaction_information = sorted(
                interaction_information, key=itemgetter(0, 2, -2)
            )
            if not len(interaction_information) == 0:

                txt.append("\n**%s**" % iname)
                table = [
                    features,
                ]
                for single_contact in interaction_information:
                    values = []
                    for x in single_contact:
                        if type(x) == str:
                            values.append(x)
                        elif type(x) == tuple and len(x) == 3:  # Coordinates
                            values.append("%.3f, %.3f, %.3f" % x)
                        else:
                            values.append(str(x))
                    table.append(values)
                txt.append(self.rst_table(table))
        txt.append("\n")
        return txt

    def generate_xml(self):
        """Generates an XML-formatted report for a single binding site"""
        report = et.Element("bindingsite")
        identifiers = et.SubElement(report, "identifiers")
        longname = et.SubElement(identifiers, "longname")
        ligtype = et.SubElement(identifiers, "ligtype")
        hetid = et.SubElement(identifiers, "hetid")
        chain = et.SubElement(identifiers, "chain")
        position = et.SubElement(identifiers, "position")
        composite = et.SubElement(identifiers, "composite")
        members = et.SubElement(identifiers, "members")
        smiles = et.SubElement(identifiers, "smiles")
        inchikey = et.SubElement(identifiers, "inchikey")

        # Ligand properties. Number of (unpaired) functional atoms and rings.
        lig_properties = et.SubElement(report, "lig_properties")
        num_heavy_atoms = et.SubElement(lig_properties, "num_heavy_atoms")
        num_hbd = et.SubElement(lig_properties, "num_hbd")
        num_hbd.text = str(self.ligand.num_hbd)
        num_unpaired_hbd = et.SubElement(lig_properties, "num_unpaired_hbd")
        num_unpaired_hbd.text = str(self.complex.num_unpaired_hbd)
        num_hba = et.SubElement(lig_properties, "num_hba")
        num_hba.text = str(self.ligand.num_hba)
        num_unpaired_hba = et.SubElement(lig_properties, "num_unpaired_hba")
        num_unpaired_hba.text = str(self.complex.num_unpaired_hba)
        num_hal = et.SubElement(lig_properties, "num_hal")
        num_hal.text = str(self.ligand.num_hal)
        num_unpaired_hal = et.SubElement(lig_properties, "num_unpaired_hal")
        num_unpaired_hal.text = str(self.complex.num_unpaired_hal)
        num_aromatic_rings = et.SubElement(lig_properties, "num_aromatic_rings")
        num_aromatic_rings.text = str(self.ligand.num_rings)
        num_rot_bonds = et.SubElement(lig_properties, "num_rotatable_bonds")
        num_rot_bonds.text = str(self.ligand.num_rot_bonds)
        molweight = et.SubElement(lig_properties, "molweight")
        molweight.text = str(self.ligand.molweight)
        logp = et.SubElement(lig_properties, "logp")
        logp.text = str(self.ligand.logp)

        ichains = et.SubElement(report, "interacting_chains")
        bsresidues = et.SubElement(report, "bs_residues")
        for i, ichain in enumerate(self.interacting_chains):
            c = et.SubElement(ichains, "interacting_chain", id=str(i + 1))
            c.text = ichain
        for i, bsres in enumerate(self.bs_res):
            contact = "True" if bsres in self.bs_res_interacting else "False"
            distance = "%.1f" % self.min_dist[bsres][0]
            aatype = self.min_dist[bsres][1]
            c = et.SubElement(
                bsresidues,
                "bs_residue",
                id=str(i + 1),
                contact=contact,
                min_dist=distance,
                aa=aatype,
            )
            c.text = bsres
        hetid.text, chain.text, position.text = (
            self.ligand.hetid,
            self.ligand.chain,
            str(self.ligand.position),
        )
        composite.text = "True" if len(self.lig_members) > 1 else "False"
        longname.text = self.longname
        ligtype.text = self.ligtype
        smiles.text = self.ligand.smiles
        inchikey.text = self.ligand.inchikey
        num_heavy_atoms.text = str(
            self.ligand.heavy_atoms
        )  # Number of heavy atoms in ligand
        for i, member in enumerate(self.lig_members):
            bsid = ":".join(str(element) for element in member)
            m = et.SubElement(members, "member", id=str(i + 1))
            m.text = bsid
        interactions = et.SubElement(report, "interactions")

        def format_interactions(element_name, features, interaction_information):
            """Returns a formatted element with interaction information."""
            interaction = et.Element(element_name)
            # Sort results first by res number, then by distance and finally ligand coordinates to get a unique order
            interaction_information = sorted(
                interaction_information, key=itemgetter(0, 2, -2)
            )
            for j, single_contact in enumerate(interaction_information):
                if not element_name == "metal_complexes":
                    new_contact = et.SubElement(
                        interaction, element_name[:-1], id=str(j + 1)
                    )
                else:  # Metal Complex[es]
                    new_contact = et.SubElement(
                        interaction, element_name[:-2], id=str(j + 1)
                    )
                for i, feature in enumerate(single_contact):
                    # Just assign the value unless it's an atom list, use subelements in this case
                    if features[i] == "LIG_IDX_LIST":
                        feat = et.SubElement(new_contact, features[i].lower())
                        for k, atm_idx in enumerate(feature.split(",")):
                            idx = et.SubElement(feat, "idx", id=str(k + 1))
                            idx.text = str(atm_idx)
                    elif features[i].endswith("COO"):
                        feat = et.SubElement(new_contact, features[i].lower())
                        xc, yc, zc = feature
                        xcoo = et.SubElement(feat, "x")
                        xcoo.text = "%.3f" % xc
                        ycoo = et.SubElement(feat, "y")
                        ycoo.text = "%.3f" % yc
                        zcoo = et.SubElement(feat, "z")
                        zcoo.text = "%.3f" % zc
                    else:
                        feat = et.SubElement(new_contact, features[i].lower())
                        feat.text = str(feature)
            return interaction

        interactions.append(
            format_interactions(
                "hydrophobic_interactions",
                self.hydrophobic_features,
                self.hydrophobic_info,
            )
        )
        interactions.append(
            format_interactions("hydrogen_bonds", self.hbond_features, self.hbond_info)
        )
        interactions.append(
            format_interactions(
                "water_bridges", self.waterbridge_features, self.waterbridge_info
            )
        )
        interactions.append(
            format_interactions(
                "salt_bridges", self.saltbridge_features, self.saltbridge_info
            )
        )
        interactions.append(
            format_interactions(
                "pi_stacks", self.pistacking_features, self.pistacking_info
            )
        )
        interactions.append(
            format_interactions(
                "pi_cation_interactions", self.pication_features, self.pication_info
            )
        )
        interactions.append(
            format_interactions(
                "halogen_bonds", self.halogen_features, self.halogen_info
            )
        )
        interactions.append(
            format_interactions("metal_complexes", self.metal_features, self.metal_info)
        )

        # Mappings
        mappings = et.SubElement(report, "mappings")
        smiles_to_pdb = et.SubElement(
            mappings, "smiles_to_pdb"
        )  # SMILES numbering to PDB file numbering (atoms)
        bsid = ":".join(
            [self.ligand.hetid, self.ligand.chain, str(self.ligand.position)]
        )
        if self.ligand.atomorder is not None:
            smiles_to_pdb_map = [
                (
                    key,
                    self.ligand.Mapper.mapid(
                        self.ligand.can_to_pdb[key], mtype="protein", bsid=bsid
                    ),
                )
                for key in self.ligand.can_to_pdb
            ]
            smiles_to_pdb.text = ",".join(
                [
                    str(mapping[0]) + ":" + str(mapping[1])
                    for mapping in smiles_to_pdb_map
                ]
            )
        else:
            smiles_to_pdb.text = ""

        return report