# coding=utf-8
"""
Protein-Ligand Interaction Profiler - Analyze and visualize protein-ligand interactions in PDB files.
test_literature_validated.py - Unit Tests for literature-validated cases.
Copyright 2014-2015 Sebastian Salentin, Melissa Adasme

Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at

    http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.
"""


import unittest
from plip.modules.preparation import PDBComplex


class LiteratureValidatedTest(unittest.TestCase):
    """Checks predictions against literature-validated interactions"""

    ###############################################
    # Literature-validated cases from publication #
    ###############################################

    def test_1eve(self):
        """Binding of anti-Alzheimer drug E2020 to acetylcholinesterase from Torpedo californica (1eve)
        Reference: Chakrabarti et al. Geometry of nonbonded interactions involving planar groups in proteins. (2007)
        """
        tmpmol = PDBComplex()
        tmpmol.load_pdb('./pdb/1eve.pdb')
        bsid = 'E20:A:2001'
        for ligand in tmpmol.ligands:
            if ':'.join([ligand.hetid, ligand.chain, str(ligand.position)]) == bsid:
                tmpmol.characterize_complex(ligand)
        s = tmpmol.interaction_sets[bsid]
        # Aromatic stacking with Trp84 and Trp279
        pistackres = {pistack.resnr for pistack in s.pistacking}
        self.assertTrue({84, 279}.issubset(pistackres))
        # Pi-Cation interaction of Phe330 with ligand
        pication = {pication.resnr for pication in s.pication_paro}
        self.assertTrue({330}.issubset(pication))

    def test_1h2t(self):
        """Binding of methylated guanosine to heterodimeric nuclear-cap binding complex (1h2t)
        Reference: Chakrabarti et al. Geometry of nonbonded interactions involving planar groups in proteins. (2007)
        """
        tmpmol = PDBComplex()
        tmpmol.load_pdb('./pdb/1h2t.pdb')
        bsid = 'GDP:Z:1151'
        for ligand in tmpmol.ligands:
            if ':'.join([ligand.hetid, ligand.chain, str(ligand.position)]) == bsid:
                tmpmol.characterize_complex(ligand)
        s = tmpmol.interaction_sets[bsid]
        # Sandwiched pi-stacking involving Tyr20 and Tyr43
        pistackres = {pistack.resnr for pistack in s.pistacking}
        self.assertTrue({20, 43}.issubset(pistackres))
        # Hydrogen bond with R112
        hbonds = {hbond.resnr for hbond in s.hbonds_pdon}
        self.assertTrue({112}.issubset(hbonds))
        # Salt bridge with D116
        saltb = {saltbridge.resnr for saltbridge in s.saltbridge_pneg}
        self.assertTrue({116}.issubset(saltb))

    def test_3pxf(self):
        """Binding of ANS to CDK2 (3pxf)
        Reference: Betzi et al. Discovery of a potential allosteric ligand binding site in CDK2 (2012)
        """
        tmpmol = PDBComplex()
        tmpmol.load_pdb('./pdb/3pxf.pdb')
        bsids = ['2AN:A:305', '2AN:A:304']
        for ligand in tmpmol.ligands:
            if ':'.join([ligand.hetid, ligand.chain, str(ligand.position)]) in bsids:
                tmpmol.characterize_complex(ligand)

        s = tmpmol.interaction_sets[bsids[0]]  # 2AN:A:305
        # Hydrogen bonding of Asp145 and Phe146
        hbonds = {hbond.resnr for hbond in s.hbonds_pdon}
        self.assertTrue({145, 146}.issubset(hbonds))
        # Salt bridge by Lys33 to sulfonate group
        saltb = {saltbridge.resnr for saltbridge in s.saltbridge_lneg}
        self.assertTrue({33}.issubset(saltb))
        # Naphtalene positioned between Leu55 and Lys56, indicating hydrophobic interactions
        hydroph = {hydroph.resnr for hydroph in s.hydrophobic_contacts}
        self.assertTrue({55, 56}.issubset(hydroph))

        s = tmpmol.interaction_sets[bsids[1]]  # 2AN:A:304
        # Salt bridges to sulfonate group by Lys56 and His71
        saltb = {saltbridge.resnr for saltbridge in s.saltbridge_lneg}
        self.assertTrue({56, 71}.issubset(saltb))
        # Napthalene with hydrophobic interactions to Ile52 and Leu76
        hydroph = {hydroph.resnr for hydroph in s.hydrophobic_contacts}
        self.assertTrue({52, 76}.issubset(hydroph))

    def test_2reg(self):
        """Binding of choline to ChoX (2reg)
        Reference: Oswald et al. Crystal structures of the choline/acetylcholine substrate-binding protein ChoX
        from Sinorhizobium meliloti in the liganded and unliganded-closed states. (2008)
        """
        tmpmol = PDBComplex()
        tmpmol.load_pdb('./pdb/2reg.pdb')
        bsid = 'CHT:A:1'
        for ligand in tmpmol.ligands:
            if ':'.join([ligand.hetid, ligand.chain, str(ligand.position)]) == bsid:
                tmpmol.characterize_complex(ligand)
        s = tmpmol.interaction_sets[bsid]
        # Cation-pi interactions with Trp43, Trp90, Trp205, and Tyr119
        picat = {pication.resnr for pication in s.pication_paro}
        self.assertEqual({43, 90, 205, 119}, picat)
        # Saltbridge to Asp45
        saltb = {saltbridge.resnr for saltbridge in s.saltbridge_pneg}
        self.assertEqual({45}, saltb)

    def test_1osn(self):
        """Binding of VZV-tk to BVDU-MP (2reg)
        Reference: Bird et al. Crystal structures of Varicella Zoster Virus Thyrimidine Kinase. (2003)
        """
        tmpmol = PDBComplex()
        tmpmol.load_pdb('./pdb/1osn.pdb')
        bsid = 'BVP:A:500'
        for ligand in tmpmol.ligands:
            if ':'.join([ligand.hetid, ligand.chain, str(ligand.position)]) == bsid:
                tmpmol.characterize_complex(ligand)
        s = tmpmol.interaction_sets[bsid]
        # Sandwiched pi-stacking involving Phe93 and Phe139
        pistackres = {pistack.resnr for pistack in s.pistacking}
        self.assertTrue({93, 139}.issubset(pistackres))
        # Hydrogen bonding of Gln90
        hbonds = {hbond.resnr for hbond in s.hbonds_pdon}
        self.assertTrue({90}.issubset(hbonds))

    def test_2w0s(self):
        """Binding of Vacc-TK to TDP (2w0s)
        Reference: Caillat et al. Crystal structure of poxvirus thymidylate kinase: An unexpected dimerization
        has implications for antiviral therapy (2008)
        """
        tmpmol = PDBComplex()
        tmpmol.load_pdb('./pdb/2w0s.pdb')
        bsid = 'MG:B:1206'  # Complex of BVDU with Magnesium Cofactor
        for ligand in tmpmol.ligands:
            if ':'.join([ligand.hetid, ligand.chain, str(ligand.position)]) == bsid:
                tmpmol.characterize_complex(ligand)
        s = tmpmol.interaction_sets[bsid]
        # Hydrogen bonding of Tyr101 and Arg72
        hbonds = {hbond.resnr for hbond in s.hbonds_pdon}
        self.assertTrue({101, 72}.issubset(hbonds))
        # Halogen Bonding of Asn65
        halogens = {halogen.resnr for halogen in s.halogen_bonds}
        self.assertTrue({65}.issubset(halogens))
        # pi-stacking interaction with Phe68
        pistackres = {pistack.resnr for pistack in s.pistacking}
        self.assertTrue({68}.issubset(pistackres))
        # Saltbridge to Arg41 and Arg93
        saltb = {saltbridge.resnr for saltbridge in s.saltbridge_lneg}
        self.assertTrue({41, 93}.issubset(saltb))

    def test_1vsn(self):
        """Binding of NFT to Cathepsin K (1vsn)
        Reference: Li et al. Identification of a potent and selective non-basic cathepsin K inhibitor. (2006)
        """
        tmpmol = PDBComplex()
        tmpmol.load_pdb('./pdb/1vsn.pdb')
        bsid = 'NFT:A:283'
        for ligand in tmpmol.ligands:
            if ':'.join([ligand.hetid, ligand.chain, str(ligand.position)]) == bsid:
                tmpmol.characterize_complex(ligand)
        s = tmpmol.interaction_sets[bsid]
        # Hydrogen bonding to Gly66
        hbonds = {hbond.resnr for hbond in s.hbonds_pdon}
        self.assertTrue({66}.issubset(hbonds))

    def test_1p5e(self):
        """Binding of TBS to CDK2(1p5e)
        Reference: De Moliner et al. Alternative binding modes of an inhibitor to two different kinases. (2003)
        """
        tmpmol = PDBComplex()
        tmpmol.load_pdb('./pdb/1p5e.pdb')
        bsid = 'TBS:A:301'
        for ligand in tmpmol.ligands:
            if ':'.join([ligand.hetid, ligand.chain, str(ligand.position)]) == bsid:
                tmpmol.characterize_complex(ligand)
        s = tmpmol.interaction_sets[bsid]
        # Halogen Bonding of Ile10 and Leu83
        halogens = {halogen.resnr for halogen in s.halogen_bonds}
        self.assertTrue({10, 83}.issubset(halogens))

    def test_1acj(self):
        """Binding of Tacrine (THA) to active-site gorge of acetylcholinesterase (1acj)
        Reference: Harel et al. Quaternary ligand binding to aromatic residues in the active-site gorge of
        acetylcholinesterase.. (1993)
        """
        tmpmol = PDBComplex()
        tmpmol.load_pdb('./pdb/1acj.pdb')
        bsid = 'THA:A:999'
        for ligand in tmpmol.ligands:
            if ':'.join([ligand.hetid, ligand.chain, str(ligand.position)]) == bsid:
                tmpmol.characterize_complex(ligand)
        s = tmpmol.interaction_sets[bsid]
        # pi-stacking interaction with Phe330 and Trp84
        pistackres = {pistack.resnr for pistack in s.pistacking}
        self.assertTrue({330, 84}.issubset(pistackres))

    def test_2zoz(self):
        """Binding of CgmR to ethidium(2z0z)
        Reference: Itou et al. Crystal Structures of the Multidrug Binding Repressor Corynebacterium
        glutamicum CgmR in Complex with Inducers and with an Operator. (2010)
        """
        tmpmol = PDBComplex()
        tmpmol.load_pdb('./pdb/2zoz.pdb')
        bsid = 'ET:B:184'
        for ligand in tmpmol.ligands:
            if ':'.join([ligand.hetid, ligand.chain, str(ligand.position)]) == bsid:
                tmpmol.characterize_complex(ligand)
        s = tmpmol.interaction_sets[bsid]
        # pi-stacking interaction with Trp63 and Phe147
        pistackres = {pistack.resnr for pistack in s.pistacking}
        self.assertTrue({147}.issubset(pistackres))  # Trp 63!!
        # hydrophobic interaction of Leu59, Leu88, Trp63, Trp113, Phe147
        hydrophobics = {hydrophobic.resnr for hydrophobic in s.all_hydrophobic_contacts}
        self.assertTrue({59, 88, 63, 113, 147}.issubset(hydrophobics))
        self.assertTrue({59, 88, 63, 92, 113, 147}.issubset(hydrophobics))

    def test_1xdn(self):
        """Binding of ATP to RNA editing ligase 1 (1xdn)
        Reference: Deng et al. High resolution crystal structure of a key editosome enzyme from Trypanosoma brucei:
        RNA editing ligase 1. (2004)
        """
        tmpmol = PDBComplex()
        tmpmol.load_pdb('./pdb/1xdn.pdb')
        bsid = 'ATP:A:501'
        for ligand in tmpmol.ligands:
            if ':'.join([ligand.hetid, ligand.chain, str(ligand.position)]) == bsid:
                tmpmol.characterize_complex(ligand)
        s = tmpmol.interaction_sets[bsid]
        # Hydrogen bonds to Arg111, Ile61 (backbone), Asn92, Val88, Lys87 and Glu86#
        hbonds = {hbond.resnr for hbond in s.hbonds_pdon}
        self.assertTrue({111, 61, 92, 88, 87}.issubset(hbonds))
        #@todo Publication shows additional waterbridge interacction for Ile59, Glu159
        # Water bridges to Lys307, Arg309 and 111 from phosphate groups
        waterbridges = {wb.resnr for wb in s.water_bridges}
        # Water bridge to 60 not found due to prioritization
        self.assertTrue({307, 309, 111}.issubset(waterbridges))
        # pi-stacking interaction with Phe209
        pistackres = {pistack.resnr for pistack in s.pistacking}
        self.assertTrue({209}.issubset(pistackres))

    def test_1bma(self):
        """Binding of aminimide to porcine pancreatic elastase(1bma)
        Reference: Peisach et al. Interaction of a Peptidomimetic Aminimide Inhibitor with Elastase. (1995)
        """
        tmpmol = PDBComplex()
        tmpmol.load_pdb('./pdb/1bma.pdb')
        bsid = '0QH:A:256'
        for ligand in tmpmol.ligands:
            if ':'.join([ligand.hetid, ligand.chain, str(ligand.position)]) == bsid:
                tmpmol.characterize_complex(ligand)
        s = tmpmol.interaction_sets[bsid]
        # Hydrogen bonds to val224 and Gln200
        hbonds = {hbond.resnr for hbond in s.hbonds_pdon}
        self.assertTrue({224, 200}.issubset(hbonds))
        self.assertTrue({224, 200}.issubset(hbonds))
        # hydrophobic interaction of Phe223 and val103
        hydrophobics = {hydrophobic.resnr for hydrophobic in s.all_hydrophobic_contacts}
        self.assertTrue({223, 103}.issubset(hydrophobics))
        # Water bridges to Ser203 not detected due to prioritization
        waterbridges = {wb.resnr for wb in s.water_bridges}
        self.assertTrue(set().issubset(waterbridges))

    def test_4rao(self):
        """Binding of (4rao)
        Reference: Keough et al. Aza-acyclic Nucleoside Phosphonates Containing a Second Phosphonate Group
        As Inhibitors of the Human, Plasmodium falciparum and vivax 6‑Oxopurine Phosphoribosyltransferases
        and Their Prodrugs As Antimalarial Agents (2004)
        """
        tmpmol = PDBComplex()
        tmpmol.load_pdb('./pdb/4rao.pdb')
        bsid = '3L7:B:301'
        for ligand in tmpmol.ligands:
            if ':'.join([ligand.hetid, ligand.chain, str(ligand.position)]) == bsid:
                tmpmol.characterize_complex(ligand)
        s = tmpmol.interaction_sets[bsid]
        # Hydrogen bonds to Val187, Lys165, Thr141, Lys140, Gly139, Thr138, Asp137
        hbonds = {hbond.resnr for hbond in s.hbonds_pdon}  # res nr 100, 68, 69 and 199 in alternative conformation,
        self.assertTrue({137, 138, 139, 140, 141, 165, 187}.issubset(hbonds))
        # Water bridges to Asp137, Thr141, Met142, Arg199 and Gly139
        # res nr 199 and 142 in alternative conformation
        # Water bridges to 137m 141, 139 not detected due to prioritization
        # pi-stacking interaction with Phe186
        pistackres = {pistack.resnr for pistack in s.pistacking}
        self.assertTrue({186}.issubset(pistackres))

    def test_4qnb(self):
        """Binding of (4qnb)
        Reference:  Bhattacharya et al. Structural basis of HIV-1 capsid recognition by PF74 and CPSF6(2014)
        """
        tmpmol = PDBComplex()
        tmpmol.load_pdb('./pdb/4qnb.pdb')
        bsid = '1B0:A:301'
        for ligand in tmpmol.ligands:
            if ':'.join([ligand.hetid, ligand.chain, str(ligand.position)]) == bsid:
                tmpmol.characterize_complex(ligand)
        s = tmpmol.interaction_sets[bsid]
        # Hydrogen bonds to Asn57 and Lys70
        hbonds = {hbond.resnr for hbond in s.hbonds_pdon}
        self.assertTrue({57, 70}.issubset(hbonds))
        # Cation-pi interactions with Lys70
        picat = {pication.resnr for pication in s.pication_laro}
        self.assertEqual({70}, picat)

    def test_4kya(self):
        """Binding of non-classical TS inhibitor 3 with Toxoplasma gondii TS-DHFR(4kya)
        Reference:  Zaware et al. Structural basis of HIV-1 capsid recognition by PF74 and CPSF6(2014)
        """
        tmpmol = PDBComplex()
        tmpmol.load_pdb('./pdb/4kya.pdb')
        bsid = '1UG:E:702'
        for ligand in tmpmol.ligands:
            if ':'.join([ligand.hetid, ligand.chain, str(ligand.position)]) == bsid:
                tmpmol.characterize_complex(ligand)
        s = tmpmol.interaction_sets[bsid]
        # Hydrogen bonds to Ala609
        hbonds = {hbond.resnr for hbond in s.hbonds_pdon}
        self.assertTrue({609}.issubset(hbonds))
        # Saltbridge to Asp513
        saltb = {saltbridge.resnr for saltbridge in s.saltbridge_pneg}
        self.assertTrue({513}.issubset(saltb))
        # hydrophobic interaction of Ile402, Leu516, Phe520 and Met608
        hydrophobics = {hydrophobic.resnr for hydrophobic in s.all_hydrophobic_contacts}
        self.assertTrue({402, 516, 520, 608}.issubset(hydrophobics))
        # pi-stacking interaction with Trp403 and Phe520
        pistackres = {pistack.resnr for pistack in s.pistacking}
        self.assertTrue({403, 520}.issubset(pistackres))

    def test_1n7g(self):
        """Binding of NADPH to MURI from Arabidopsis thaliana (1n7g)
        Reference:  Mulichak et al. Structure of the MUR1 GDP-mannose 4, 6-dehydratase from Arabidopsis thaliana:
        implications for ligand binding and specificity(2002)
        """
        tmpmol = PDBComplex()
        tmpmol.load_pdb('./pdb/1n7g.pdb')
        bsid = 'NDP:A:701'
        for ligand in tmpmol.ligands:
            if ':'.join([ligand.hetid, ligand.chain, str(ligand.position)]) == bsid:
                tmpmol.characterize_complex(ligand)
        s = tmpmol.interaction_sets[bsid]
        # Hydrogen bonds to Thr37, Gly38, Gln39, Asp40,  Arg60, Leu92, Asp91, Ser63, Leu92, Ala115, Ser117,
        # Tyr128, Tyr185, Lys189, His215 and Arg220
        # Publication give the Prediction for Asp91 as hydrogen bond, when this contains two acceptor atoms.
        hbonds = {hbond.resnr for hbond in s.hbonds_pdon}
        # #@todo Hbond to 128 not detected
        self.assertTrue({37, 38, 39, 40, 92, 63, 92, 115, 117, 185, 189, 215, 220}.issubset(hbonds))
        # Water bridges to Gly35, Thr37, Gly38, Asp40, Arg60, Arg61, Ser63, Asn66, Ser117, Tyr128, Lys189, Arg220
        waterbridges = {wb.resnr for wb in s.water_bridges}
        # Hydrogen bonds to 35, 37, 38, 40, 63, 117, 128, 189, 220 not detected due to prioritization
        self.assertTrue({60, 66, 61}.issubset(waterbridges))
        # Saltbridge to arg60, Arg61, Arg69 and Arg220
        saltb = {saltbridge.resnr for saltbridge in s.saltbridge_lneg}
        # #@todo Additional saltbridges report to 69 and 200 (with large distances)
        self.assertTrue({60, 61}.issubset(saltb))
        # Cation-pi interactions with Arg60
        picat = {pication.resnr for pication in s.pication_laro}
        self.assertEqual({60}, picat)

    def test_4alw(self):
        """Binding of benzofuropyrimidinones compound 3 to PIM-1 (4alw)
        Reference:  Tsuhako et al. The design, synthesis, and biological evaluation of PIM kinase inhibitors.(2012)
        """
        tmpmol = PDBComplex()
        tmpmol.load_pdb('./pdb/4alw.pdb')
        bsid = 'HY7:A:1308'
        for ligand in tmpmol.ligands:
            if ':'.join([ligand.hetid, ligand.chain, str(ligand.position)]) == bsid:
                tmpmol.characterize_complex(ligand)
        s = tmpmol.interaction_sets[bsid]
        # Hydrogen bonds to Asp186
        hbonds = {hbond.resnr for hbond in s.hbonds_pdon}
        self.assertTrue({186}.issubset(hbonds))
        # Saltbridge to A186 and Glu171
        saltb = {saltbridge.resnr for saltbridge in s.saltbridge_pneg}
        self.assertTrue({186, 171}.issubset(saltb))

    def test_3o1h(self):
        """Binding of TMAO to TorT-TorS system(3o1h)
        Reference:  Hendrickson et al. An Asymmetry-to-Symmetry Switch in Signal Transmission by the Histidine Kinase Receptor
        for TMAO.(2013)
        """
        tmpmol = PDBComplex()
        tmpmol.load_pdb('./pdb/3o1h.pdb')
        bsid = 'TMO:B:1'
        for ligand in tmpmol.ligands:
            if ':'.join([ligand.hetid, ligand.chain, str(ligand.position)]) == bsid:
                tmpmol.characterize_complex(ligand)
        s = tmpmol.interaction_sets[bsid]
        # Hydrogen bonds to Trp45
        hbonds = {hbond.resnr for hbond in s.hbonds_pdon}
        self.assertTrue({45}.issubset(hbonds))
        # Water bridges to Trp45 not detected due to priorization of hydrogen bonds
        # Cation-pi interactions with Tyr44
        picat = {pication.resnr for pication in s.pication_paro}
        self.assertEqual({44}, picat)

    def test_3thy(self):
        """Binding of ADP tp MutS(3thy)
        Reference:  Shikha et al. Mechanism of mismatch recognition revealed by human MutSβ bound to unpaired DNA loops.(2012)
        """
        tmpmol = PDBComplex()
        tmpmol.load_pdb('./pdb/3thy.pdb')
        bsid = 'ADP:A:935'
        for ligand in tmpmol.ligands:
            if ':'.join([ligand.hetid, ligand.chain, str(ligand.position)]) == bsid:
                tmpmol.characterize_complex(ligand)
        s = tmpmol.interaction_sets[bsid]
        # Saltbridge to His295 and Lys675
        saltb = {saltbridge.resnr for saltbridge in s.saltbridge_lneg}
        self.assertTrue({675}.issubset(saltb))
        # pi-stacking interaction with Tyr815
        pistackres = {pistack.resnr for pistack in s.pistacking}
        self.assertTrue({815}.issubset(pistackres))

    def test_3tah(self):
        """Binding of BGO to an an N11A mutant of the G-protein domain of FeoB.(3tah)
        Reference:  Ash et al. The structure of an N11A mutant of the G-protein domain of FeoB.(2011)
        """
        tmpmol = PDBComplex()
        tmpmol.load_pdb('./pdb/3tah.pdb')
        bsid = 'BGO:A:300'
        for ligand in tmpmol.ligands:
            if ':'.join([ligand.hetid, ligand.chain, str(ligand.position)]) == bsid:
                tmpmol.characterize_complex(ligand)
        s = tmpmol.interaction_sets[bsid]
        # Hydrogen bonds to Ala11, Lys14, Thr15, Ser16, Asp113, Met114, Ala143 and Asp113
        hbonds = {hbond.resnr for hbond in s.hbonds_pdon}
        self.assertTrue({11, 13, 14, 15, 16, 113, 114, 143, 113}.issubset(hbonds))
        # Water bridges to Ala11 not detected due to prioritization of hydrogen bonds
        # Saltbridge to Asp116
        saltb = {saltbridge.resnr for saltbridge in s.saltbridge_pneg}
        self.assertTrue({116}.issubset(saltb))

    def test_3r0t(self):
        """Binding of protein kinase CK2 alpha subunit in with the inhibitor CX-5279 (3r0t)
        Reference:  Battistutta et al. Unprecedented selectivity and structural determinants of a new class of protein
        kinase CK2 inhibitors in clinical trials for the treatment of cancer..(2011)
        """
        tmpmol = PDBComplex()
        tmpmol.load_pdb('./pdb/3r0t.pdb')
        bsid = 'FU9:A:338'
        for ligand in tmpmol.ligands:
            if ':'.join([ligand.hetid, ligand.chain, str(ligand.position)]) == bsid:
                tmpmol.characterize_complex(ligand)
        s = tmpmol.interaction_sets[bsid]
        # Hydrogen bonds to Val116
        hbonds = {hbond.resnr for hbond in s.hbonds_pdon}
        self.assertTrue({116}.issubset(hbonds))
        # Water bridges to Lys68 and Trp176
        waterbridges = {wb.resnr for wb in s.water_bridges}
        self.assertTrue({68, 176}.issubset(waterbridges))
        # Saltbridge to Ly68
        saltb = {saltbridge.resnr for saltbridge in s.saltbridge_lneg}
        self.assertTrue({68}.issubset(saltb))
        # hydrophobic interaction of Val66, Phe113 and Ile174
        hydrophobics = {hydrophobic.resnr for hydrophobic in s.all_hydrophobic_contacts}
        self.assertTrue({66, 113, 174}.issubset(hydrophobics))
        # pi-stacking interaction with His160
        pistackres = {pistack.resnr for pistack in s.pistacking}
        self.assertTrue({160}.issubset(pistackres))

    def test_1aku(self):
        """Binding of Flavin mononucleotido with D.Vulgaris(1aku)
        Reference:  McCarthy et al. Crystallographic Investigation of the Role of Aspartate 95 in the Modulation of the
        Redox Potentials of DesulfoVibrio Vulgaris Flavodoxin.(2002)
        """
        tmpmol = PDBComplex()
        tmpmol.load_pdb('./pdb/1aku.pdb')
        bsid = 'FMN:A:150'
        for ligand in tmpmol.ligands:
            if ':'.join([ligand.hetid, ligand.chain, str(ligand.position)]) == bsid:
                tmpmol.characterize_complex(ligand)
        s = tmpmol.interaction_sets[bsid]
        # Hydrogen bonds to Tht59 and Trp60
        hbonds = {hbond.resnr for hbond in s.hbonds_pdon}
        self.assertTrue({59, 60}.issubset(hbonds))
        # Water bridges to Asp63 and Tyr100
        waterbridges = {wb.resnr for wb in s.water_bridges}
        # Water bridge to Tyr100 not detected due to prioritization
        self.assertTrue({63}.issubset(waterbridges))
        # hydrophobic interaction of Trp60
        hydrophobics = {hydrophobic.resnr for hydrophobic in s.all_hydrophobic_contacts}
        self.assertTrue({60}.issubset(hydrophobics))
        # pi-stacking interaction with Tyr98
        pistackres = {pistack.resnr for pistack in s.pistacking}
        self.assertTrue({98}.issubset(pistackres))

    def test_4pjt(self):
        """Binding of BMN 673 to catPARP1(4pj7)
        Reference:  Aoyagi-Scharber et al. Structural basis for the inhibition of poly(ADP-ribose) polymerases 1 and 2 by BMN
        673, a potent inhibitor derived from dihydropyridophthalazinone.(2014)
        """
        tmpmol = PDBComplex()
        tmpmol.load_pdb('./pdb/4pjt.pdb')
        bsid = '2YQ:D:1104'
        for ligand in tmpmol.ligands:
            if ':'.join([ligand.hetid, ligand.chain, str(ligand.position)]) == bsid:
                tmpmol.characterize_complex(ligand)
        s = tmpmol.interaction_sets[bsid]
        # Hydrogen bonds to Gly863
        hbonds = {hbond.resnr for hbond in s.hbonds_pdon}
        self.assertTrue({863}.issubset(hbonds))
        # pi-stacking interaction with Tyr889 and Tyr907
        pistackres = {pistack.resnr for pistack in s.pistacking}
        self.assertTrue({889, 907}.issubset(pistackres))

    def test_1bju(self):
        """Binding of ACPU to bovine tripsin(1bju)
        Reference:  Presnell et al. Oxyanion-Mediated Inhibition of Serine Proteases.(1998)
        """
        tmpmol = PDBComplex()
        tmpmol.load_pdb('./pdb/1bju.pdb')
        bsid = 'GP6:A:910'
        for ligand in tmpmol.ligands:
            if ':'.join([ligand.hetid, ligand.chain, str(ligand.position)]) == bsid:
                tmpmol.characterize_complex(ligand)
        s = tmpmol.interaction_sets[bsid]
        #@todo Publication show hydrogen bond interactions for Gly219
        # Hydrogen bonds to Ser190, Ser195, Gly219 and Asp189
        hbonds = {hbond.resnr for hbond in s.hbonds_pdon+s.hbonds_ldon}
        self.assertTrue({189, 190, 195}.issubset(hbonds))
        # Water bridges to Ser190 and Val227
        # Water bridge to 190 not detected due to prioritization
        waterbridges = {wb.resnr for wb in s.water_bridges}
        self.assertTrue({227}.issubset(waterbridges))
        # hydrophobic interaction of Leu99
        hydrophobics = {hydrophobic.resnr for hydrophobic in s.all_hydrophobic_contacts}
        self.assertTrue({99}.issubset(hydrophobics))
        # pi-stacking interaction with His57
        pistackres = {pistack.resnr for pistack in s.pistacking}
        self.assertTrue({57}.issubset(pistackres))

    def test_4agl(self):
        """Binding of P53 to PhiKan784(4agl)
        Reference:  Wilcken et al. Halogen-Enriched Fragment Libraries as Leads for Drug Rescue of Mutant p53.(2012)
        """
        tmpmol = PDBComplex()
        tmpmol.load_pdb('./pdb/4agl.pdb')
        bsid = 'P84:A:400'
        for ligand in tmpmol.ligands:
            if ':'.join([ligand.hetid, ligand.chain, str(ligand.position)]) == bsid:
                tmpmol.characterize_complex(ligand)
        s = tmpmol.interaction_sets[bsid]
        # Water bridges to Val147
        waterbridges = {wb.resnr for wb in s.water_bridges}
        self.assertTrue({147}.issubset(waterbridges))
        # hydrophobic interaction of Thr150
        hydrophobics = {hydrophobic.resnr for hydrophobic in s.all_hydrophobic_contacts}
        self.assertTrue({150}.issubset(hydrophobics))
        # Halogen Bonding of Leu145
        halogens = {halogen.resnr for halogen in s.halogen_bonds}
        self.assertTrue({145}.issubset(halogens))

    def test_2efj(self):
        """Binding of teobromine to 1,7 dimethylxanthine methyltransferase(2efj)
        Reference:  McCarthy et al. The Structure of Two N-Methyltransferases from the Caffeine Biosynthetic
        Pathway.(2007)
        """
        tmpmol = PDBComplex()
        tmpmol.load_pdb('./pdb/2efj.pdb')
        bsid = '37T:A:502'
        for ligand in tmpmol.ligands:
            if ':'.join([ligand.hetid, ligand.chain, str(ligand.position)]) == bsid:
                tmpmol.characterize_complex(ligand)
        s = tmpmol.interaction_sets[bsid]
        # Hydrogen bonds to Trp161, Ser237
        hbonds = {hbond.resnr for hbond in s.hbonds_pdon}
        self.assertTrue({161, 237}.issubset(hbonds))
        # pi-stacking interaction with Tyr157
        pistackres = {pistack.resnr for pistack in s.pistacking}
        self.assertTrue({157}.issubset(pistackres))

    def test_2iuz(self):
        """Binding of C2-dicaffeine to Aspergilius fumigates(2iuz)
        Reference:  Schüttelkopf et al. Screening-based discovery and structural dissection of a novel family 18 chitinase
        inhibitor.(2006)
        """
        tmpmol = PDBComplex()
        tmpmol.load_pdb('./pdb/2iuz.pdb')
        bsid = 'D1H:A:1440'
        for ligand in tmpmol.ligands:
            if ':'.join([ligand.hetid, ligand.chain, str(ligand.position)]) == bsid:
                tmpmol.characterize_complex(ligand)
        s = tmpmol.interaction_sets[bsid]
        # Hydrogen bonds to Trp137, Trp184
        hbonds = {hbond.resnr for hbond in s.hbonds_pdon}  # res nr 52 mentioned in alternative conformation, not considered
        self.assertTrue({137, 384}.issubset(hbonds))
        # Water bridges to Trp137
        waterbridges = {wb.resnr for wb in s.water_bridges}  # res nr 52 mentioned in alternative conformation not considered
        self.assertTrue({137}.issubset(waterbridges))
        # pi-stacking interaction with Trp384, Trp137 and Trp52
        pistackres = {pistack.resnr for pistack in s.pistacking}
        self.assertTrue({52, 137, 384}.issubset(pistackres))

    def test_3shy(self):
        """Binding of 5FO to PDE5A1 catalytic domain(3shy)
        Reference:  Xu et al. Utilization of halogen bond in lead optimization: A case study of rational design of potent
        phosphodiesterase type 5 (PDE5) inhibitors.(2011)
        """
        tmpmol = PDBComplex()
        tmpmol.load_pdb('./pdb/3shy.pdb')
        bsid = '5FO:A:1'
        for ligand in tmpmol.ligands:
            if ':'.join([ligand.hetid, ligand.chain, str(ligand.position)]) == bsid:
                tmpmol.characterize_complex(ligand)
        s = tmpmol.interaction_sets[bsid]
        # Hydrogen bonds to Gln817
        hbonds = {hbond.resnr for hbond in s.hbonds_pdon}
        self.assertTrue({817}.issubset(hbonds))
        # hydrophobic interaction of Tyr612
        hydrophobics = {hydrophobic.resnr for hydrophobic in s.all_hydrophobic_contacts}
        self.assertTrue({612}.issubset(hydrophobics))
        # pi-stacking interaction with Phe820
        pistackres = {pistack.resnr for pistack in s.pistacking}
        self.assertTrue({820}.issubset(pistackres))
        # Halogen Bonding of Tyr612
        halogens = {halogen.resnr for halogen in s.halogen_bonds}
        self.assertTrue({612}.issubset(halogens))

    def test_1ay8(self):
        """Binding of PLP to aromatic amino acid aminotransferase(1ay8)
        Reference:  Okamoto et al. Crystal structures of Paracoccus denitrificans aromatic amino acid aminotransferase: a
        substrate recognition site constructed by rearrangement of hydrogen bond network..(1998)
        """
        tmpmol = PDBComplex()
        tmpmol.load_pdb('./pdb/1ay8.pdb')
        bsid = 'PLP:A:413'
        for ligand in tmpmol.ligands:
            if ':'.join([ligand.hetid, ligand.chain, str(ligand.position)]) == bsid:
                tmpmol.characterize_complex(ligand)
        s = tmpmol.interaction_sets[bsid]
        # Hydrogen bonds to Gly108, Thr109, Asn194 and Ser257
        hbonds = {hbond.resnr for hbond in s.hbonds_pdon}
        self.assertTrue({108, 109, 194, 257}.issubset(hbonds))
        # Saltbridge to Ly258 and Arg266
        saltb = {saltbridge.resnr for saltbridge in s.saltbridge_lneg}
        self.assertTrue({258, 266}.issubset(saltb))
        # pi-stacking interaction with Trp140
        pistackres = {pistack.resnr for pistack in s.pistacking}
        self.assertTrue({140}.issubset(pistackres))

    def test_4rdl(self):
        """Binding of Norovirus Boxer P domain with Lewis y tetrasaccharide(4rdl)
        Reference:  Hao et al. Crystal structures of GI.8 Boxer virus P dimers in complex with HBGAs, a novel
        evolutionary path selected by the Lewis epitope..(2014)
        """
        tmpmol = PDBComplex()
        tmpmol.load_pdb('./pdb/4rdl.pdb')
        bsid = 'FUC:A:601'
        for ligand in tmpmol.ligands:
            if ':'.join([ligand.hetid, ligand.chain, str(ligand.position)]) == bsid:
                tmpmol.characterize_complex(ligand)
        s = tmpmol.interaction_sets[bsid]  # Instead of FUC-A-604 (sugar representative)
        # Water bridges to Asn395
        waterbridges = {wb.resnr for wb in s.water_bridges}
        self.assertTrue({395}.issubset(waterbridges))
        # Hydrogen bonds to Thr347, Gly348 and Asn395
        hbonds = {hbond.resnr for hbond in s.hbonds_pdon}
        self.assertTrue({347, 348, 395}.issubset(hbonds))
        # hydrophobic interaction of Trp392
        hydrophobics = {hydrophobic.resnr for hydrophobic in s.all_hydrophobic_contacts}
        self.assertTrue({392}.issubset(hydrophobics))

    #########################################
    # Additional literature-validated cases #
    #########################################

    def test_1hii(self):
        """HIV-2 protease in complex with novel inhibitor CGP 53820 (1hii)
        Reference:  Comparative analysis of the X-ray structures of HIV-1 and HIV-2 proteases in complex
        with CGP 53820, a novel pseudosymmetric inhibitor (1995)
        """
        tmpmol = PDBComplex()
        tmpmol.load_pdb('./pdb/1hii.pdb')
        bsid = 'C20:B:101'
        for ligand in tmpmol.ligands:
            if ':'.join([ligand.hetid, ligand.chain, str(ligand.position)]) == bsid:
                tmpmol.characterize_complex(ligand)
        s = tmpmol.interaction_sets[bsid]
        # Water bridges
        waterbridges = {str(wb.resnr)+wb.reschain for wb in s.water_bridges}
        self.assertTrue({'50A', '50B'}.issubset(waterbridges))  # Bridging Ile-B50 and Ile-A50 with ligand
        # Hydrogen bonds
        hbonds = {str(hbond.resnr)+hbond.reschain for hbond in s.hbonds_pdon+s.hbonds_ldon}
        self.assertTrue({'27A', '27B', '29A', '48A', '48B'}.issubset(hbonds))
        # #@todo Publication mentions additional possible hydrogen bond with Asp28B
        # Hydrogen bonds with Asp-A25 are reported as a salt bridge as both partners have (potential) charges

    def test_1hvi(self):
        """HIV-1 protease in complex with Diol inhibitor (1hvi)
        Reference: Influence of Stereochemistry on Activity and Binding Modes for C2 Symmetry-Based
         Diol Inhibitors of HIV-1 Protease (1994)
        """
        tmpmol = PDBComplex()
        tmpmol.load_pdb('./pdb/1hvi.pdb')
        bsid = 'A77:A:800'
        for ligand in tmpmol.ligands:
            if ':'.join([ligand.hetid, ligand.chain, str(ligand.position)]) == bsid:
                tmpmol.characterize_complex(ligand)
        s = tmpmol.interaction_sets[bsid]
        # Water bridges
        waterbridges = {str(wb.resnr)+wb.reschain for wb in s.water_bridges}
        # #@todo Water bridge with 50B not detected
        self.assertTrue({'50A'}.issubset(waterbridges))  # Bridging Ile-B50 and Ile-A50 with ligand
        # pi-cation Interactions
        picat = {pication.resnr for pication in s.pication_laro}
        self.assertEqual({8}, picat)  # Described as weakly polar contact/stacking in paper
        # Hydrogen bonds
        hbonds = {str(hbond.resnr)+hbond.reschain for hbond in s.hbonds_pdon+s.hbonds_ldon}
        self.assertTrue({'25B', '27A', '27B', '48A', '48B'}.issubset(hbonds))
        # #@todo Paper describes additional hydrogen bond with Asp25A

    def test_3OG7(self):
        """Inhibitor PLX4032 binding to B-RAF(V600E) (3og7)
        Reference: Clinical efficacy of a RAF inhibitor needs broad target blockade in BRAF-mutant
        melanoma (2010)
        """
        tmpmol = PDBComplex()
        tmpmol.load_pdb('./pdb/3og7.pdb')
        bsid = '032:A:1'
        for ligand in tmpmol.ligands:
            if ':'.join([ligand.hetid, ligand.chain, str(ligand.position)]) == bsid:
                tmpmol.characterize_complex(ligand)
        s = tmpmol.interaction_sets[bsid]
        # Hydrogen bonds
        hbonds = {str(hbond.resnr)+hbond.reschain for hbond in s.hbonds_pdon+s.hbonds_ldon}
        self.assertTrue({'594A', '530A'}.issubset(hbonds))


