def test_ids(self):
     """Test if the atom IDs are correctly mapped from internal to original PDB."""
     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]
     for contact in s.hydrophobic_contacts:
         if contact.restype == 'ALA' and contact.resnr == 133:
             self.assertEqual(contact.ligatom_orig_idx, 1636)
             self.assertEqual(contact.bsatom_orig_idx, 994)
         if contact.restype == 'ASP' and contact.resnr == 61:
             self.assertEqual(contact.ligatom_orig_idx, 1639)
             self.assertEqual(contact.bsatom_orig_idx, 448)
     for contact in s.hbonds_ldon + s.hbonds_pdon:
         if contact.restype == 'GLN' and contact.resnr == 19:
             self.assertEqual(contact.a_orig_idx, 1649)
             self.assertEqual(contact.d_orig_idx, 153)
         if contact.restype == 'CYS' and contact.resnr == 25:
             self.assertEqual(contact.a_orig_idx, 1649)
             self.assertEqual(contact.d_orig_idx, 183)
         if contact.restype == 'ASN' and contact.resnr == 158:
             self.assertEqual(contact.d_orig_idx, 1629)
             self.assertEqual(contact.a_orig_idx, 1199)
     for contact in s.halogen_bonds:
         if contact.restype == 'TYR' and contact.resnr == 67:
             self.assertEqual(contact.don.x_orig_idx, 1627)
             self.assertEqual(contact.acc.o_orig_idx, 485)
         if contact.restype == 'LEU' and contact.resnr == 157:
             self.assertEqual(contact.don.x_orig_idx, 1628)
             self.assertEqual(contact.acc.o_orig_idx, 1191)
 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))
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    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_1HPX(self):
     """
     HIV-1 Protease complexes with the inhibitor KNI-272
     Reference: Structure of HIV-1 protease with KNI-272, a tight-binding transition-state analog
     containing allophenylnorstatine.
     Note that the residue numbering is different in the publication and the PDB structure.
     For residues in the B chain, the offset is -100 (e.g. Ile 50B in the PDB structure is Ile 150 in the paper).
     """
     tmpmol = PDBComplex()
     tmpmol.load_pdb('./pdb/1hpx.pdb')
     bsid = 'KNI:B:900'
     for ligand in tmpmol.ligands:
         if ':'.join([ligand.hetid, ligand.chain,
                      str(ligand.position)]) == bsid:
             tmpmol.characterize_complex(ligand)
     s = tmpmol.interaction_sets[bsid]
     # Hydrophobic contacts to Val82, Ile84, Ile150 as part of flap (S1, S1' sites)
     hydroph = {
         str(hyd.resnr) + hyd.reschain
         for hyd in s.all_hydrophobic_contacts
     }
     self.assertTrue({'82A', '84A', '50B'}.issubset(hydroph))
     # Hydrogen bonds
     hbonds = {
         str(hbond.resnr) + hbond.reschain
         for hbond in s.hbonds_ldon + s.hbonds_pdon
     }
     # Additional hbond to 25B not detected (low angle?)
     self.assertTrue({'29B', '48B', '27B', '25A'}.issubset(hbonds))
     # Water bridges
     waterbridges = {str(wb.resnr) + wb.reschain for wb in s.water_bridges}
     # Waterbridge with Gly27 is detected instead of Ala28/Asp29
     self.assertTrue({'50A', '50B', '29A'}.issubset(waterbridges))
     print(waterbridges)
 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_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')
     s = tmpmol.interaction_sets['NDP-A-701']
     # 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)
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 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))
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 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))
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 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))
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 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)
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 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))
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 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_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))
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 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_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))
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 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))
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 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))
Exemple #18
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 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))
Exemple #19
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 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 = 'BVP:B:1207'  # 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_ids(self):
     """Test if the atom IDs are correctly mapped from internal to original PDB."""
     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]
     for contact in s.hydrophobic_contacts:
         if contact.restype == 'ALA' and contact.resnr == 133:
             self.assertEqual(contact.ligatom_orig_idx, 1636)
             self.assertEqual(contact.bsatom_orig_idx, 994)
         if contact.restype == 'ASP' and contact.resnr == 61:
             self.assertEqual(contact.ligatom_orig_idx, 1639)
             self.assertEqual(contact.bsatom_orig_idx, 448)
     for contact in s.hbonds_ldon + s.hbonds_pdon:
         if contact.restype == 'GLN' and contact.resnr == 19:
             self.assertEqual(contact.a_orig_idx, 1649)
             self.assertEqual(contact.d_orig_idx, 153)
         if contact.restype == 'CYS' and contact.resnr == 25:
             self.assertEqual(contact.a_orig_idx, 1649)
             self.assertEqual(contact.d_orig_idx, 183)
         if contact.restype == 'ASN' and contact.resnr == 158:
             self.assertEqual(contact.d_orig_idx, 1629)
             self.assertEqual(contact.a_orig_idx, 1199)
     for contact in s.halogen_bonds:
         if contact.restype == 'TYR' and contact.resnr == 67:
             self.assertEqual(contact.don.x_orig_idx, 1627)
             self.assertEqual(contact.acc.o_orig_idx, 485)
         if contact.restype == 'LEU' and contact.resnr == 157:
             self.assertEqual(contact.don.x_orig_idx, 1628)
             self.assertEqual(contact.acc.o_orig_idx, 1191)
Exemple #21
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 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_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_1HPX(self):
     """
     HIV-1 Protease complexes with the inhibitor KNI-272
     Reference: Structure of HIV-1 protease with KNI-272, a tight-binding transition-state analog
     containing allophenylnorstatine.
     Note that the residue numbering is different in the publication and the PDB structure.
     For residues in the B chain, the offset is -100 (e.g. Ile 50B in the PDB structure is Ile 150 in the paper).
     """
     tmpmol = PDBComplex()
     tmpmol.load_pdb('./pdb/1hpx.pdb')
     bsid = 'KNI:B:900'
     for ligand in tmpmol.ligands:
         if ':'.join([ligand.hetid, ligand.chain, str(ligand.position)]) == bsid:
             tmpmol.characterize_complex(ligand)
     s = tmpmol.interaction_sets[bsid]
     # Hydrophobic contacts to Val82, Ile84, Ile150 as part of flap (S1, S1' sites)
     hydroph = {str(hyd.resnr)+hyd.reschain for hyd in s.all_hydrophobic_contacts}
     self.assertTrue({'82A', '84A', '50B'}.issubset(hydroph))
     # Hydrogen bonds
     hbonds = {str(hbond.resnr)+hbond.reschain for hbond in s.hbonds_ldon+s.hbonds_pdon}
     # Additional hbond to 25B not detected (low angle?)
     self.assertTrue({'29B', '48B', '27B', '25A'}.issubset(hbonds))
     # Water bridges
     waterbridges = {str(wb.resnr)+wb.reschain for wb in s.water_bridges}
     # Waterbridge with Gly27 is detected instead of Ala28/Asp29
     self.assertTrue({'50A', '50B', '29A'}.issubset(waterbridges))
     print(waterbridges)
Exemple #24
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 def run(self):
     stream = self._patch_molecule()
     pdbcomplex = PDBComplex()
     pdbcomplex.load_pdb(stream.getvalue(), as_string=True)
     pdbcomplex.analyze()
     pdbcomplex.sourcefiles['filename'] = '/dev/null'
     stream.close()
     self.complex = pdbcomplex
Exemple #25
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def plip_read_pdb_complex(path):
    mol = PDBComplex()
    mol.load_pdb(path)
    mol.analyze()

    assert (len(mol.interaction_sets) == 1)
    inter = mol.interaction_sets.values()[0]
    return inter
 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')
     s = tmpmol.interaction_sets['NFT-A-283']
     # Hydrogen bonding to Gly66
     hbonds = {hbond.resnr for hbond in s.hbonds_pdon}
     self.assertTrue({66}.issubset(hbonds))
 def test_dna_rna(self):
     """Test if DNA and RNA is correctly processed as ligands"""
     tmpmol = PDBComplex()
     tmpmol.load_pdb('./pdb/1tf6.pdb')
     # DNA ligand four times consisting of 31 parts (composite)
     self.assertEqual([len(ligand.members) for ligand in tmpmol.ligands].count(31), 4)
     for ligset in [set((x[0] for x in ligand.members)) for ligand in tmpmol.ligands]:
         if len(ligset) == 4:
             # DNA only contains four bases
             self.assertEqual(ligset, set(['DG', 'DC', 'DA', 'DT']))
 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')
     s = tmpmol.interaction_sets['TBS-A-301']
     # Halogen Bonding of Ile10 and Leu83
     halogens = {halogen.resnr for halogen in s.halogen_bonds}
     self.assertTrue({10, 83}.issubset(halogens))
 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')
     s = tmpmol.interaction_sets['NFT-A-283']
     # 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')
     s = tmpmol.interaction_sets['TBS-A-301']
     # Halogen Bonding of Ile10 and Leu83
     halogens = {halogen.resnr for halogen in s.halogen_bonds}
     self.assertTrue({10, 83}.issubset(halogens))
Exemple #31
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def load_complex_from_string(pdb_string, lig_id):
    complex = PDBComplex()  # plip molecule
    complex.load_pdb(pdb_string, as_string=True)
    lig_pdb_string = []
    for line in pdb_string.split('\n'):
        if line[17:20] == lig_id or line[:6] == 'CONECT':
            lig_pdb_string.append(line)
    lig_pdb_string = '\n'.join(lig_pdb_string)
    lig = pybel.readstring('pdb', lig_pdb_string)  # openbabel molecule
    # lig = Chem.MolFromPDBBlock(lig_pdb_string, removeHs=False)  # rdkit molecule
    return complex, lig
 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')
     s = tmpmol.interaction_sets['032-A-1']
     # Hydrogen bonds
     hbonds = {str(hbond.resnr)+hbond.reschain for hbond in s.hbonds_pdon+s.hbonds_ldon}
     self.assertTrue({'594A', '530A'}.issubset(hbonds))
 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')
     s = tmpmol.interaction_sets['THA-A-999']
     # pi-stacking interaction with Phe330 and Trp84
     pistackres = {pistack.resnr for pistack in s.pistacking}
     self.assertTrue({330, 84}.issubset(pistackres))
 def test_dna_rna(self):
     """Test if DNA and RNA is correctly processed as ligands"""
     tmpmol = PDBComplex()
     tmpmol.load_pdb('./pdb/1tf6.pdb')
     bsid = 'DA:B:1'
     # DNA ligand four times consisting of 31 parts (composite)
     self.assertEqual([len(ligand.members) for ligand in tmpmol.ligands].count(31), 4)
     for ligset in [set((x[0] for x in ligand.members)) for ligand in tmpmol.ligands]:
         if len(ligset) == 4:
             # DNA only contains four bases
             self.assertEqual(ligset, set(['DG', 'DC', 'DA', 'DT']))
 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')
     s = tmpmol.interaction_sets['THA-A-999']
     # pi-stacking interaction with Phe330 and Trp84
     pistackres = {pistack.resnr for pistack in s.pistacking}
     self.assertTrue({330, 84}.issubset(pistackres))
Exemple #36
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def plip_analysis(pdbpath, pdb_id):
    ''' run PLIP analysis for pdb file '''

    mol = PDBComplex()
    mol.load_pdb(pdbpath)
    chain_id = pdb_id.split('_')[-1]
    ligand_interactions_dict = {}

    # invastigate only proteins with following ligands
    ligand_whitelist = set([
        'NAD', 'FAD', 'NDP', 'NAP', 'NAI', 'ADP', 'AMP', 'ATP', 'FMN', 'GTP',
        'ADN', 'SAH', 'GDP', '5GP', 'ADX', 'LSS', '1ZZ', 'COA', 'ACO', '01A',
        'HMG', 'SAI', 'GRA', 'ST9', 'MCA', 'SAM', 'HEM', 'CLA', 'BCB', 'BCL',
        'HEA', 'HEC', 'HEB', 'HAS'
    ])

    # plip analysis
    ligand_list_from_mol = [x.hetid for x in mol.ligands]
    print('=> ' + str(len(ligand_list_from_mol)) + ' ligands to process')

    # if any ligand of interest present
    #     if not ligand_whitelist.intersection(set(ligand_list_from_mol)):
    #         print('=> No ligands of interest found')
    #         #print(ligand_list_from_mol)
    #         return ligand_interactions_dict

    mol.analyze()
    full_data_mol[pdb_id] = mol

    for bsid in [
            ":".join([x.hetid, x.chain, str(x.position)]) for x in mol.ligands
    ]:
        # for every ligand encountered in pdb
        print bsid
        #print '|',

        interactions = mol.interaction_sets[
            bsid]  # Contains all interaction data
        print interactions.interacting_res
        interacting_residues = [
            int(res[:-1]) for res in interactions.interacting_res
            if res[-1] == chain_id
        ]

        if interacting_residues:
            ligand_interactions_dict[bsid] = interacting_residues
    print '=> ' + str(
        len(ligand_interactions_dict
            )) + ' ligands interacting with chain ' + chain_id + ' found'
    print

    return ligand_interactions_dict
 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')
     s = tmpmol.interaction_sets['BVP-A-500']
     # 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_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')
     s = tmpmol.interaction_sets['1B0-A-301']
     # 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_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')
     s = tmpmol.interaction_sets['HY7-A-1308']
     # 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_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')
     s = tmpmol.interaction_sets['E20-A-2001']
     # 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_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')
     s = tmpmol.interaction_sets['BVP-A-500']
     # 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_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')
     s = tmpmol.interaction_sets['ADP-A-935']
     # 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_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')
     s = tmpmol.interaction_sets['HY7-A-1308']
     # 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_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')
     s = tmpmol.interaction_sets['E20-A-2001']
     # 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_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')
     s = tmpmol.interaction_sets['1B0-A-301']
     # 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_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')
     s = tmpmol.interaction_sets['ADP-A-935']
     # 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_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))
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 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_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')
     s = tmpmol.interaction_sets['C20-B-101']
     # 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))
 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_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')
     s = tmpmol.interaction_sets['2YQ-D-1104']
     # 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_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')
     s = tmpmol.interaction_sets['CHT-A-1']
     # 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)
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 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_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')
     s = tmpmol.interaction_sets['BGO-A-300']
     # 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_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')
     s = tmpmol.interaction_sets['37T-A-502']
     # 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_2pvb(self):
        """Pike parvalbumin binding calcium (2pvb)
        Reference: Harding. The architecture of metal coordination groups in proteins. (2004), Fig. 6
        """

        tmpmol = PDBComplex()
        tmpmol.load_pdb('./pdb/2pvb.pdb')
        bsid = 'CA:A:110'
        for ligand in tmpmol.ligands:
            if ':'.join([ligand.hetid, ligand.chain, str(ligand.position)]) == bsid:
                tmpmol.characterize_complex(ligand)
        s = tmpmol.interaction_sets[bsid]
        # Ca atom with square pyramidal geometry (coordination number 5)
        self.assertEqual(s.metal_complexes[0].coordination_num, 5)
        self.assertEqual(s.metal_complexes[0].geometry, 'square.pyramidal')
 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')
     s = tmpmol.interaction_sets['TMO-B-1']
     # 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_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_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))
 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')
     s = tmpmol.interaction_sets['7MG-Z-1152']
     # 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))