CHANGES.txt

 Changelog
 ---------
+# Next version
+* Adds information on covalent linkages to XML files
+* __Anaconda package__ (provided by `Ikagami`)
 
 # 1.4.2
 * Adds "--name" option to change name of output files

DOCUMENTATION.md

@@ -44,7 +44,7 @@ and should be executed with Python 2.7.x.
 
 Example command for Ubuntu using apt-get
 ```bash
-sudo apt-get install pymol openbabel python-openbabel imagemagick
+sudo apt-get install pymol openbabel python-openbabel imagemagick swig
 ```
 
 
@@ -67,7 +67,7 @@ You can use any other user directory, but we will use the one given above for th
 The package manager `pip` will create symlinks for you so you can call PLIP using `plip` in the command line. If you cloned from Github, use the following command to do the same:
 
 ```bash
-alias plip='~/pliptool/plip/plipcmd'
+alias plip='python ~/pliptool/plip/plipcmd.py'
 ```
 
 ## Analyze a PDB structure with PLIP

README.md

@@ -18,11 +18,11 @@ git clone https://github.com/ssalentin/plip.git ~/pliptool
 
 ##### As a command line tool
 
-Run the `plipcmd` script inside the PLIP folder to detect, report, and visualize interactions. The following example creates a PYMOL visualization for the interactions
+Run the `plipcmd.py` script inside the PLIP folder to detect, report, and visualize interactions. The following example creates a PYMOL visualization for the interactions
 between the inhibitor NFT and its target protein in the PDB structure 1VSN.
 
 ```bash
-alias plip='~/pliptool/plip/plipcmd'
+alias plip='python ~/pliptool/plip/plipcmd.py'
 mkdir /tmp/1vsn && cd /tmp/1vsn
 plip -i 1vsn -yv
 pymol 1VSN_NFT_A_283.pse
@@ -61,7 +61,7 @@ For a full documentation of running options and output formats, please refear to
 
 ## Versions and Branches
 For production environments, you should use the latest versioned commit from the stable branch.
-Newer commits from the stable and development branch may contains new but untested and not documented features.
+Newer commits from the stable and development branch may contain new but untested and not documented features.
 
 ## Requirements
 Previous to using PLIP, make sure you have the following tools and libraries installed:
@@ -93,3 +93,11 @@ If you are unsure about usage options, don't hesitate to contact me.
 If you are using PLIP in your work, please cite
 > Salentin,S. et al. PLIP: fully automated protein-ligand interaction profiler.
 > Nucl. Acids Res. (1 July 2015) 43 (W1): W443-W447. doi: 10.1093/nar/gkv315
+
+## FAQ
+> I try to run PLIP, but I'm getting an error message saying:
+> ValueError: [...] is not a recognised Open Babel descriptor type
+
+Make sure Open Babel is correctly installed. This error can occur if the installed Python bindings don't match the OpenBabel version on your machine.
+We don't offer technical support for installation of third-party packages.
+For an instruction how to install Open Babel, please refer to their [website](https://openbabel.org/docs/dev/Installation/install.html).

debian/changelog

+plip (1.4.3~b+dfsg-1) unstable; urgency=medium
+
+  * Update Files-Excluded section in d/copyright
+  * New upstream version 1.4.3~b+dfsg
+  * Check for nocheck in DEB_BUILD_OPTIONS for tests, s/plipcmd.py/plipcmd/
+  * Bump Policy to 4.2.1
+
+ -- Alexandre Mestiashvili <mestia@debian.org>  Tue, 25 Sep 2018 09:38:55 +0000
+
 plip (1.4.2+dfsg-1) unstable; urgency=medium
 
   * New upstream version 1.4.2+dfsg

debian/control

@@ -12,7 +12,7 @@ Build-Depends: debhelper (>= 11),
                python-openbabel,
                python-setuptools,
                python-future
-Standards-Version: 4.1.4
+Standards-Version: 4.2.1
 Vcs-Browser: https://salsa.debian.org/med-team/plip
 Vcs-Git: https://salsa.debian.org/med-team/plip.git
 Homepage: https://projects.biotec.tu-dresden.de/plip-web/plip/

debian/copyright

@@ -4,6 +4,8 @@ Source: https://github.com/ssalentin/plip
 Files-Excluded:
   plip/test/pdb/*
   pliplogo*
+  setup_conda.py
+  recipe/*
 
 Files: *
 Copyright: 2016 Sebastian Salentin <sebastian.salentin@biotec.tu-dresden.de>

debian/rules

@@ -12,6 +12,8 @@ PYTHON_DEFAULT_VERSION := $(shell pyversions -d)
 
 override_dh_auto_install:
 	dh_auto_install
+	mv $(CURDIR)/debian/$(PYBUILD_NAME)/usr/bin/plipcmd.py \
+           $(CURDIR)/debian/$(PYBUILD_NAME)/usr/bin/plipcmd
 	mkdir -p $(mandir)
 	export PYTHONPATH=$(CURDIR)/debian/$(PYBUILD_NAME)/usr/lib/$(PYTHON_DEFAULT_VERSION)/dist-packages/:\
 	$(CURDIR)/plip/modules; \
@@ -19,4 +21,6 @@ override_dh_auto_install:
     $(CURDIR)/debian/$(PYBUILD_NAME)/usr/bin/plipcmd > $(mandir)/plipcmd.1
 
 override_dh_auto_test:
+ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
 	debian/tests/special-cases
+endif

plip/modules/detection.py

@@ -17,7 +17,8 @@ def filter_contacts(pairings):
     """Filter interactions by two criteria:
     1. No interactions between the same residue (important for intra mode).
     2. No duplicate interactions (A with B and B with A, also important for intra mode)."""
-    if config.INTRA:
+    if not config.INTRA:
+        return pairings
     filtered1_pairings = [p for p in pairings if (p.resnr, p.reschain) != (p.resnr_l, p.reschain_l)]
     already_considered = []
     filtered2_pairings = []
@@ -30,13 +31,11 @@ def filter_contacts(pairings):
             except AttributeError:
                 dist = 'D{}'.format(round(contact.distance_aw,2))
         res1, res2 = ''.join([str(contact.resnr), contact.reschain]), ''.join([str(contact.resnr_l), contact.reschain_l])
-            data = set([res1, res2, dist])
+        data = {res1, res2, dist}
         if data not in already_considered:
             filtered2_pairings.append(contact)
             already_considered.append(data)
     return filtered2_pairings
-    else:
-        return pairings
 
 
 ##################################################
@@ -54,7 +53,8 @@ def hydrophobic_interactions(atom_set_a, atom_set_b):
         if a.orig_idx == b.orig_idx:
             continue
         e = euclidean3d(a.atom.coords, b.atom.coords)
-        if config.MIN_DIST < e < config.HYDROPH_DIST_MAX:
+        if not config.MIN_DIST < e < config.HYDROPH_DIST_MAX:
+            continue
         restype, resnr, reschain = whichrestype(a.atom), whichresnumber(a.atom), whichchain(a.atom)
         restype_l, resnr_l, reschain_l = whichrestype(b.orig_atom), whichresnumber(b.orig_atom), whichchain(b.orig_atom)
         contact = data(bsatom=a.atom, bsatom_orig_idx=a.orig_idx, ligatom=b.atom, ligatom_orig_idx=b.orig_idx,
@@ -75,13 +75,17 @@ def hbonds(acceptors, donor_pairs, protisdon, typ):
                                'restype reschain resnr_l restype_l reschain_l sidechain atype dtype')
     pairings = []
     for acc, don in itertools.product(acceptors, donor_pairs):
-        if typ == 'strong':  # Regular (strong) hydrogen bonds
+        if not typ == 'strong':
+            continue
+        # Regular (strong) hydrogen bonds
         dist_ah = euclidean3d(acc.a.coords, don.h.coords)
         dist_ad = euclidean3d(acc.a.coords, don.d.coords)
-            if config.MIN_DIST < dist_ad < config.HBOND_DIST_MAX:
+        if not config.MIN_DIST < dist_ad < config.HBOND_DIST_MAX:
+            continue
         vec1, vec2 = vector(don.h.coords, don.d.coords), vector(don.h.coords, acc.a.coords)
         v = vecangle(vec1, vec2)
-                if v > config.HBOND_DON_ANGLE_MIN:
+        if not v > config.HBOND_DON_ANGLE_MIN:
+            continue
         protatom = don.d.OBAtom if protisdon else acc.a.OBAtom
         ligatom = don.d.OBAtom if not protisdon else acc.a.OBAtom
         is_sidechain_hbond = protatom.GetResidue().GetAtomProperty(protatom, 8)  # Check if sidechain atom
@@ -125,7 +129,8 @@ def pistacking(rings_bs, rings_lig):
 
         # SELECTION BY DISTANCE, ANGLE AND OFFSET
         passed = False
-        if config.MIN_DIST < d < config.PISTACK_DIST_MAX:
+        if not config.MIN_DIST < d < config.PISTACK_DIST_MAX:
+            continue
         if 0 < a < config.PISTACK_ANG_DEV and offset < config.PISTACK_OFFSET_MAX:
             ptype = 'P'
             passed = True
@@ -146,7 +151,8 @@ def pication(rings, pos_charged, protcharged):
     """
     data = namedtuple('pication', 'ring charge distance offset type restype resnr reschain restype_l resnr_l reschain_l protcharged')
     pairings = []
-    if not len(rings) == 0 and not len(pos_charged) == 0:
+    if len(rings) == 0 or len(pos_charged) == 0:
+        return pairings
     for ring in rings:
         c = ring.center
         for p in pos_charged:
@@ -154,7 +160,8 @@ def pication(rings, pos_charged, protcharged):
             # Project the center of charge into the ring and measure distance to ring center
             proj = projection(ring.normal, ring.center, p.center)
             offset = euclidean3d(proj, ring.center)
-                if config.MIN_DIST < d < config.PICATION_DIST_MAX and offset < config.PISTACK_OFFSET_MAX:
+            if not config.MIN_DIST < d < config.PICATION_DIST_MAX or not offset < config.PISTACK_OFFSET_MAX:
+                continue
             if type(p).__name__ == 'lcharge' and p.fgroup == 'tertamine':
                 # Special case here if the ligand has a tertiary amine, check an additional angle
                 # Otherwise, we might have have a pi-cation interaction 'through' the ligand
@@ -194,7 +201,8 @@ def saltbridge(poscenter, negcenter, protispos):
     data = namedtuple('saltbridge', 'positive negative distance protispos resnr restype reschain resnr_l restype_l reschain_l')
     pairings = []
     for pc, nc in itertools.product(poscenter, negcenter):
-        if config.MIN_DIST < euclidean3d(pc.center, nc.center) < config.SALTBRIDGE_DIST_MAX:
+        if not config.MIN_DIST < euclidean3d(pc.center, nc.center) < config.SALTBRIDGE_DIST_MAX:
+            continue
         resnr = pc.resnr if protispos else nc.resnr
         resnr_l = whichresnumber(nc.orig_atoms[0]) if protispos else whichresnumber(pc.orig_atoms[0])
         restype = pc.restype if protispos else nc.restype
@@ -215,15 +223,18 @@ def halogen(acceptor, donor):
     pairings = []
     for acc, don in itertools.product(acceptor, donor):
         dist = euclidean3d(acc.o.coords, don.x.coords)
-        if config.MIN_DIST < dist < config.HALOGEN_DIST_MAX:
+        if not config.MIN_DIST < dist < config.HALOGEN_DIST_MAX:
+            continue
         vec1, vec2 = vector(acc.o.coords, acc.y.coords), vector(acc.o.coords, don.x.coords)
         vec3, vec4 = vector(don.x.coords, acc.o.coords), vector(don.x.coords, don.c.coords)
         acc_angle, don_angle = vecangle(vec1, vec2), vecangle(vec3, vec4)
         is_sidechain_hal = acc.o.OBAtom.GetResidue().GetAtomProperty(acc.o.OBAtom, 8)  # Check if sidechain atom
-            if config.HALOGEN_ACC_ANGLE - config.HALOGEN_ANGLE_DEV < acc_angle \
+        if not config.HALOGEN_ACC_ANGLE - config.HALOGEN_ANGLE_DEV < acc_angle \
                 < config.HALOGEN_ACC_ANGLE + config.HALOGEN_ANGLE_DEV:
-                if config.HALOGEN_DON_ANGLE - config.HALOGEN_ANGLE_DEV < don_angle \
+            continue
+        if not config.HALOGEN_DON_ANGLE - config.HALOGEN_ANGLE_DEV < don_angle \
                 < config.HALOGEN_DON_ANGLE + config.HALOGEN_ANGLE_DEV:
+            continue
         restype, reschain, resnr = whichrestype(acc.o), whichchain(acc.o), whichresnumber(acc.o)
         restype_l, reschain_l, resnr_l = whichrestype(don.orig_x), whichchain(don.orig_x), whichresnumber(don.orig_x)
         contact = data(acc=acc, acc_orig_idx=acc.o_orig_idx, don=don, don_orig_idx=don.x_orig_idx,
@@ -269,9 +280,12 @@ def water_bridges(bs_hba, lig_hba, bs_hbd, lig_hbd, water):
     for l, p in itertools.product(lig_aw, prot_hw):
         acc, wl, distance_aw = l
         don, wd, distance_dw, d_angle = p
-        if wl.oxy == wd.oxy:  # Same water molecule and angle within omega
+        if not wl.oxy == wd.oxy:
+            continue
+        # Same water molecule and angle within omega
         w_angle = vecangle(vector(acc.a.coords, wl.oxy.coords), vector(wl.oxy.coords, don.h.coords))
-            if config.WATER_BRIDGE_OMEGA_MIN < w_angle < config.WATER_BRIDGE_OMEGA_MAX:
+        if not config.WATER_BRIDGE_OMEGA_MIN < w_angle < config.WATER_BRIDGE_OMEGA_MAX:
+            continue
         resnr, reschain, restype = whichresnumber(don.d), whichchain(don.d), whichrestype(don.d)
         resnr_l, reschain_l, restype_l = whichresnumber(acc.a_orig_atom), whichchain(acc.a_orig_atom), whichrestype(acc.a_orig_atom)
         contact = data(a=acc.a, a_orig_idx=acc.a_orig_idx, atype=acc.a.type, d=don.d, d_orig_idx=don.d_orig_idx,
@@ -283,9 +297,12 @@ def water_bridges(bs_hba, lig_hba, bs_hbd, lig_hbd, water):
     for p, l in itertools.product(prot_aw, lig_dw):
         acc, wl, distance_aw = p
         don, wd, distance_dw, d_angle = l
-        if wl.oxy == wd.oxy:  # Same water molecule and angle within omega
+        if not wl.oxy == wd.oxy:
+            continue
+        # Same water molecule and angle within omega
         w_angle = vecangle(vector(acc.a.coords, wl.oxy.coords), vector(wl.oxy.coords, don.h.coords))
-            if config.WATER_BRIDGE_OMEGA_MIN < w_angle < config.WATER_BRIDGE_OMEGA_MAX:
+        if not config.WATER_BRIDGE_OMEGA_MIN < w_angle < config.WATER_BRIDGE_OMEGA_MAX:
+            continue
         resnr, reschain, restype = whichresnumber(acc.a), whichchain(acc.a), whichrestype(acc.a)
         resnr_l, reschain_l, restype_l = whichresnumber(don.d_orig_atom), whichchain(don.d_orig_atom), whichrestype(don.d_orig_atom)
         contact = data(a=acc.a, a_orig_idx=acc.a_orig_idx, atype=acc.a.type, d=don.d, d_orig_idx=don.d_orig_idx,
@@ -310,7 +327,8 @@ def metal_complexation(metals, metal_binding_lig, metal_binding_bs):
     metal_to_orig_atom = {}
     for metal, target in itertools.product(metals, metal_binding_lig + metal_binding_bs):
         distance = euclidean3d(metal.m.coords, target.atom.coords)
-        if distance < config.METAL_DIST_MAX:
+        if not distance < config.METAL_DIST_MAX:
+            continue
         if metal.m not in pairings_dict:
             pairings_dict[metal.m] = [(target, distance), ]
             metal_to_id[metal.m] = metal.m_orig_idx

plip/modules/plipxml.py

@@ -22,7 +22,7 @@ class XMLStorage:
     def getdata(self, tree, location, force_string=False):
         """Gets XML data from a specific element and handles types."""
         found = tree.xpath('%s/text()' % location)
-        if found == []:
+        if not found:
             return None
         else:
             data = found[0]
@@ -244,7 +244,7 @@ class BSite(XMLStorage):
         self.halogens = [HalogenBond(x) for x in interactions.xpath('halogen_bonds/halogen_bond')]
         self.metal_complexes = [MetalComplex(x) for x in interactions.xpath('metal_complexes/metal_complex')]
         self.num_contacts = len(self.hydrophobics) + len(self.hbonds) + len(self.wbridges) + len(self.sbridges) + len(self.pi_stacks) + len(self.pi_cations) + len(self.halogens) + len(self.metal_complexes)
-        self.has_interactions = True if self.num_contacts > 0 else False
+        self.has_interactions = self.num_contacts > 0
 
         self.get_atom_mapping()
         self.counts = self.get_counts()
@@ -282,7 +282,7 @@ class PLIPXML(XMLStorage):
         self.filetype = self.getdata(self.doc, '/report/filetype')
         self.fixed = self.getdata(self.doc, '/report/pdbfixes/')
         self.filename = self.getdata(self.doc, '/report/filename')
-        self.excluded = self.getdata(self.doc, '/report/excluded_ligands')
+        self.excluded = self.doc.xpath('/report/excluded_ligands/excluded_ligand/text()')
 
         # Parse binding site information
         self.bsites = {BSite(bs, self.pdbid).bsid: BSite(bs, self.pdbid) for bs in self.doc.xpath('//bindingsite')}

plip/modules/report.py

@@ -19,7 +19,7 @@ from . import config
 # External libraries
 import lxml.etree as et
 
-__version__ = '1.4.2'
+__version__ = '1.4.3'
 
 class StructureReport:
     """Creates reports (xml or txt) for one structure/"""
@@ -61,6 +61,13 @@ class StructureReport:
         for i, exlig in enumerate(self.excluded):
             e = et.SubElement(exligs, 'excluded_ligand', id=str(i + 1))
             e.text = exlig
+        covalent = et.SubElement(report, 'covlinkages')
+        for i, covlinkage in enumerate(self.mol.covalent):
+            e = et.SubElement(covalent, 'covlinkage', id=str(i + 1))
+            f1 = et.SubElement(e, 'res1')
+            f2 = et.SubElement(e, 'res2')
+            f1.text = ":".join([covlinkage.id1, covlinkage.chain1, str(covlinkage.pos1)])
+            f2.text =  ":".join([covlinkage.id2, covlinkage.chain2, str(covlinkage.pos2)])
         return report
 
     def construct_txt_file(self):

plip/plipcmd → plip/plipcmd.py

 #! /usr/bin/env python
 """
 Protein-Ligand Interaction Profiler - Analyze and visualize protein-ligand interactions in PDB files.
-plipcmd - Main script for PLIP command line execution.
+plipcmd.py - Main script for PLIP command line execution.
 """
 
 # Compatibility
@@ -9,12 +9,20 @@ from __future__ import print_function
 from __future__ import absolute_import
 
 # Own modules
+try:
     from plip.modules.preparation import *
     from plip.modules.plipremote import VisualizerData
     from plip.modules.report import StructureReport,__version__
     from plip.modules import config
     from plip.modules.mp import parallel_fn
     from plip.modules.webservices import check_pdb_status, fetch_pdb
+except ImportError:
+    from modules.preparation import *
+    from modules.plipremote import VisualizerData
+    from modules.report import StructureReport,__version__
+    from modules import config
+    from modules.mp import parallel_fn
+    from modules.webservices import check_pdb_status, fetch_pdb
 
 # Python standard library
 import sys
@@ -72,7 +80,10 @@ def process_pdb(pdbfile, outpath, as_string=False, outputprefix='report'):
     ######################################
 
     if config.PYMOL or config.PICS:
+        try:
             from plip.modules.visualize import visualize_in_pymol
+        except ImportError:
+            from modules.visualize import visualize_in_pymol
         complexes = [VisualizerData(mol, site) for site in sorted(mol.interaction_sets)
                      if not len(mol.interaction_sets[site].interacting_res) == 0]
         if config.MAXTHREADS > 1:
@@ -166,12 +177,12 @@ def main(inputstructs, inputpdbids):
         else:
             write_message('\nFinished analysis. Find the result files in %s\n\n' % config.BASEPATH)
 
-if __name__ == '__main__':
 
     ##############################
     # Parse command line arguments
     ##############################
-
+def main_init():
+    """Parse command line arguments and start main script for analysis."""
     parser = ArgumentParser(prog="PLIP", description=descript)
     pdbstructure = parser.add_mutually_exclusive_group(required=True)  # Needs either PDB ID or file
     pdbstructure.add_argument("-f", "--file", dest="input", nargs="+", help="Set input file, '-' reads from stdin") # '-' as file name reads from stdin
@@ -293,3 +304,5 @@ if __name__ == '__main__':
         parser.error("The water bridge omega minimum angle has to be smaller than the water bridge omega maximum angle")
     expanded_path = tilde_expansion(arguments.input) if arguments.input is not None else None
     main(expanded_path, arguments.pdbid)  # Start main script
+if __name__ == '__main__':
+  main_init()

plip/test/test_special_cases.py

@@ -14,20 +14,20 @@ class SpecialCasesTest(unittest.TestCase):
 
     def test_empty_input_file(self):
         """Input file is empty."""
-        exitcode = subprocess.call('../plipcmd -f ./special/empty.pdb -o /tmp', shell=True)
+        exitcode = subprocess.call('python ../plipcmd.py -f ./special/empty.pdb -o /tmp', shell=True)
         self.assertEqual(exitcode, 2)  # Specific exitcode 2
 
     def test_invalid_pdb_id(self):
         """A PDB ID with no valid PDB record is provided."""
-        exitcode = subprocess.call('../plipcmd -i xx1x -o /tmp', shell=True)
+        exitcode = subprocess.call('python ../plipcmd.py -i xx1x -o /tmp', shell=True)
         self.assertEqual(exitcode, 3)  # Specific exitcode 3
 
     def test_invalid_input_file(self):
         """A file is provided which is not a PDB file."""
-        exitcode = subprocess.call('../plipcmd -f ./special/non-pdb.pdb -o /tmp', shell=True)
+        exitcode = subprocess.call('python ../plipcmd.py -f ./special/non-pdb.pdb -o /tmp', shell=True)
         self.assertEqual(exitcode, 4)  # Specific exitcode 4
 
     def test_pdb_format_not_available(self):
         """A valid PDB ID is provided, but there is no entry in PDB format from wwPDB"""
-        exitcode1 = subprocess.call('../plipcmd -i 4v59 -o /tmp', shell=True)
+        exitcode1 = subprocess.call('python ../plipcmd.py -i 4v59 -o /tmp', shell=True)
         self.assertEqual(exitcode1, 5)  # Specific exitcode 5

plip/test/test_xml_parser.py

@@ -15,16 +15,15 @@ class XMLParserTest(unittest.TestCase):
     def setUp(self):
         self.px = PLIPXML('./xml/1vsn.report.xml')
         self.bsite = self.px.bsites['NFT:A:283']
-        self.smiles = 'N=CCNC(=O)[C@H](CC(C)C)N[C@H](C(F)(F)F)c1ccc(cc1)c1ccc(cc1)S(=O)(=O)N'
+        self.smiles = 'CC(C)CC(NC(c1ccc(cc1)c1ccc(cc1)S(N)(=O)=O)C(F)(F)F)C(=O)NCC=N'
 
     def test_general_information(self):
         """Test if general information is correctly parsed."""
-        self.assertEqual(self.px.version, '1.3.2')
+        self.assertEqual(self.px.version, '1.4.2')
         self.assertEqual(self.px.pdbid, '1VSN')
-        self.assertEqual(self.px.filetype, 'PDB')
         self.assertFalse(self.px.fixed)
         self.assertEqual(self.px.filename, '1vsn.pdb')
-        self.assertEqual(self.px.excluded, None)
+        self.assertEqual(self.px.excluded, [])
 
     def test_bsite_information(self):
         """Test if the binding site information is correctly parsed."""
@@ -47,17 +46,17 @@ class XMLParserTest(unittest.TestCase):
         self.assertEqual(self.bsite.unpaired_hal, 1)
         self.assertEqual(self.bsite.rings, 2)
         self.assertEqual(self.bsite.rotatable_bonds, 12)
-        self.assertEqual(self.bsite.molweight, 484.5349896)
-        self.assertEqual(self.bsite.logp, 6.0371)
+        self.assertAlmostEqual(self.bsite.molweight, 484, 0)
+        self.assertAlmostEqual(self.bsite.logp, 6, 0)
 
         # Atom mappings (non-exhaustive test)
         lmap = self.bsite.mappings['pdb_to_smiles']
-        self.assertEqual(lmap[1625], 9)
-        self.assertEqual(lmap[1649], 1)
-        self.assertEqual(lmap[1617], 19)
+        self.assertEqual(lmap[1625], 24)
+        self.assertEqual(lmap[1649], 33)
+        self.assertEqual(lmap[1617], 14)
 
         # Binding site residues
-        self.assertEqual(len(self.bsite.bs_res), 36)
+        self.assertEqual(len(self.bsite.bs_res), 35)
 
         # Interacting chains
         self.assertEqual(self.bsite.interacting_chains, ['A'])
@@ -82,7 +81,7 @@ class XMLParserTest(unittest.TestCase):
 
 
         # Hydrogen Bonds
-        self.assertEqual(len(self.bsite.hbonds), 7)
+        self.assertEqual(len(self.bsite.hbonds), 6)
         hbond1 = self.bsite.hbonds[0]
         self.assertEqual(hbond1.resnr, 19)
         self.assertEqual(hbond1.restype, 'GLN')
@@ -100,7 +99,7 @@ class XMLParserTest(unittest.TestCase):
         self.assertEqual(hbond1.protcoo, (3.976, 15.409, 7.712))
 
         # Water Bridges
-        self.assertEqual(len(self.bsite.wbridges), 2)
+        self.assertEqual(len(self.bsite.wbridges), 1)
         wbridge1 = self.bsite.wbridges[0]
         self.assertEqual(wbridge1.resnr, 159)
         self.assertEqual(wbridge1.restype, 'HIS')

plip/test/xml/1vsn.report.xml

 <?xml version='1.0' encoding='ASCII'?>
 <report>
-  <plipversion>1.3.2</plipversion>
+  <plipversion>1.4.2</plipversion>
   <bindingsite id="1" has_interactions="True">
     <identifiers>
       <longname>NFT</longname>
@@ -12,7 +12,8 @@
       <members>
         <member id="1">NFT:A:283</member>
       </members>
-      <smiles>N=CCNC(=O)[C@H](CC(C)C)N[C@H](C(F)(F)F)c1ccc(cc1)c1ccc(cc1)S(=O)(=O)N</smiles>
+      <smiles>CC(C)CC(NC(c1ccc(cc1)c1ccc(cc1)S(N)(=O)=O)C(F)(F)F)C(=O)NCC=N</smiles>
+      <inchikey>LUFZQYFBEDDLGO-UHFFFAOYSA-N</inchikey>
     </identifiers>
     <lig_properties>
       <num_heavy_atoms>33</num_heavy_atoms>
@@ -24,8 +25,8 @@
       <num_unpaired_hal>1</num_unpaired_hal>
       <num_aromatic_rings>2</num_aromatic_rings>
       <num_rotatable_bonds>12</num_rotatable_bonds>
-      <molweight>484.5349896</molweight>
-      <logp>6.0371</logp>
+      <molweight>483.5270496</molweight>
+      <logp>5.9141</logp>
     </lig_properties>
     <interacting_chains>
       <interacting_chain id="1">A</interacting_chain>
@@ -50,23 +51,22 @@
       <bs_residue aa="PHE" contact="False" id="17" min_dist="7.4">28A</bs_residue>
       <bs_residue aa="LEU" contact="False" id="18" min_dist="4.2">205A</bs_residue>
       <bs_residue aa="THR" contact="False" id="19" min_dist="7.3">69A</bs_residue>
-      <bs_residue aa="TRP" contact="True" id="20" min_dist="5.8">177A</bs_residue>
+      <bs_residue aa="TRP" contact="False" id="20" min_dist="5.8">177A</bs_residue>
       <bs_residue aa="HIS" contact="True" id="21" min_dist="4.0">159A</bs_residue>
       <bs_residue aa="ASN" contact="True" id="22" min_dist="2.9">158A</bs_residue>
       <bs_residue aa="VAL" contact="False" id="23" min_dist="6.9">161A</bs_residue>
       <bs_residue aa="ALA" contact="False" id="24" min_dist="6.8">27A</bs_residue>
       <bs_residue aa="ALA" contact="False" id="25" min_dist="6.8">1156A</bs_residue>
-      <bs_residue aa="CYS" contact="True" id="26" min_dist="1.7">25A</bs_residue>
-      <bs_residue aa="GLY" contact="False" id="27" min_dist="3.4">23A</bs_residue>
-      <bs_residue aa="GLU" contact="False" id="28" min_dist="3.3">59A</bs_residue>
-      <bs_residue aa="GLY" contact="False" id="29" min_dist="5.8">62A</bs_residue>
-      <bs_residue aa="VAL" contact="False" id="30" min_dist="6.0">132A</bs_residue>
-      <bs_residue aa="ASN" contact="False" id="31" min_dist="3.0">60A</bs_residue>
-      <bs_residue aa="ILE" contact="False" id="32" min_dist="5.7">134A</bs_residue>
-      <bs_residue aa="VAL" contact="False" id="33" min_dist="6.3">57A</bs_residue>
-      <bs_residue aa="GLN" contact="True" id="34" min_dist="3.1">19A</bs_residue>
-      <bs_residue aa="ASN" contact="False" id="35" min_dist="5.9">70A</bs_residue>
-      <bs_residue aa="GLY" contact="True" id="36" min_dist="2.9">66A</bs_residue>
+      <bs_residue aa="GLY" contact="False" id="26" min_dist="3.4">23A</bs_residue>
+      <bs_residue aa="GLU" contact="False" id="27" min_dist="3.3">59A</bs_residue>
+      <bs_residue aa="GLY" contact="False" id="28" min_dist="5.8">62A</bs_residue>
+      <bs_residue aa="VAL" contact="False" id="29" min_dist="6.0">132A</bs_residue>
+      <bs_residue aa="ASN" contact="False" id="30" min_dist="3.0">60A</bs_residue>
+      <bs_residue aa="ILE" contact="False" id="31" min_dist="5.7">134A</bs_residue>
+      <bs_residue aa="VAL" contact="False" id="32" min_dist="6.3">57A</bs_residue>
+      <bs_residue aa="GLN" contact="True" id="33" min_dist="3.1">19A</bs_residue>
+      <bs_residue aa="ASN" contact="False" id="34" min_dist="5.9">70A</bs_residue>
+      <bs_residue aa="GLY" contact="True" id="35" min_dist="2.9">66A</bs_residue>
     </bs_residues>
     <interactions>
       <hydrophobic_interactions>
@@ -74,6 +74,9 @@
           <resnr>61</resnr>
           <restype>ASP</restype>
           <reschain>A</reschain>
+          <resnr_lig>283</resnr_lig>
+          <restype_lig>NFT</restype_lig>
+          <reschain_lig>A</reschain_lig>
           <dist>3.67</dist>
           <ligcarbonidx>1639</ligcarbonidx>
           <protcarbonidx>448</protcarbonidx>
@@ -92,6 +95,9 @@
           <resnr>67</resnr>
           <restype>TYR</restype>
           <reschain>A</reschain>
+          <resnr_lig>283</resnr_lig>
+          <restype_lig>NFT</restype_lig>
+          <reschain_lig>A</reschain_lig>
           <dist>3.73</dist>
           <ligcarbonidx>1622</ligcarbonidx>
           <protcarbonidx>482</protcarbonidx>
@@ -110,6 +116,9 @@
           <resnr>67</resnr>
           <restype>TYR</restype>
           <reschain>A</reschain>
+          <resnr_lig>283</resnr_lig>
+          <restype_lig>NFT</restype_lig>
+          <reschain_lig>A</reschain_lig>
           <dist>3.84</dist>
           <ligcarbonidx>1636</ligcarbonidx>
           <protcarbonidx>481</protcarbonidx>
@@ -128,6 +137,9 @@
           <resnr>133</resnr>
           <restype>ALA</restype>
           <reschain>A</reschain>
+          <resnr_lig>283</resnr_lig>
+          <restype_lig>NFT</restype_lig>
+          <reschain_lig>A</reschain_lig>
           <dist>3.97</dist>
           <ligcarbonidx>1636</ligcarbonidx>
           <protcarbonidx>994</protcarbonidx>
@@ -148,6 +160,9 @@
           <resnr>19</resnr>
           <restype>GLN</restype>
           <reschain>A</reschain>
+          <resnr_lig>283</resnr_lig>
+          <restype_lig>NFT</restype_lig>
+          <reschain_lig>A</reschain_lig>
           <sidechain>True</sidechain>
           <dist_h-a>2.16</dist_h-a>
           <dist_d-a>3.11</dist_d-a>
@@ -169,33 +184,12 @@
           </protcoo>
         </hydrogen_bond>
         <hydrogen_bond id="2">
-          <resnr>25</resnr>
-          <restype>CYS</restype>
-          <reschain>A</reschain>
-          <sidechain>False</sidechain>
-          <dist_h-a>2.21</dist_h-a>
-          <dist_d-a>3.09</dist_d-a>
-          <don_angle>146.90</don_angle>
-          <protisdon>True</protisdon>
-          <donoridx>183</donoridx>
-          <donortype>Nam</donortype>
-          <acceptoridx>1649</acceptoridx>
-          <acceptortype>N2</acceptortype>
-          <ligcoo>
-            <x>2.820</x>
-            <y>18.145</y>
-            <z>6.806</z>
-          </ligcoo>
-          <protcoo>
-            <x>3.306</x>
-            <y>18.620</y>
-            <z>9.817</z>
-          </protcoo>
-        </hydrogen_bond>
-        <hydrogen_bond id="3">
           <resnr>61</resnr>
           <restype>ASP</restype>
           <reschain>A</reschain>
+          <resnr_lig>283</resnr_lig>
+          <restype_lig>NFT</restype_lig>
+          <reschain_lig>A</reschain_lig>
           <sidechain>True</sidechain>
           <dist_h-a>2.26</dist_h-a>
           <dist_d-a>2.99</dist_d-a>
@@ -216,10 +210,13 @@
             <z>9.223</z>
           </protcoo>
         </hydrogen_bond>
-        <hydrogen_bond id="4">
+        <hydrogen_bond id="3">
           <resnr>61</resnr>
           <restype>ASP</restype>
           <reschain>A</reschain>
+          <resnr_lig>283</resnr_lig>
+          <restype_lig>NFT</restype_lig>
+          <reschain_lig>A</reschain_lig>
           <sidechain>True</sidechain>
           <dist_h-a>1.98</dist_h-a>
           <dist_d-a>2.99</dist_d-a>
@@ -240,10 +237,13 @@
             <z>9.223</z>
           </protcoo>
         </hydrogen_bond>
-        <hydrogen_bond id="5">
+        <hydrogen_bond id="4">
           <resnr>66</resnr>
           <restype>GLY</restype>
           <reschain>A</reschain>
+          <resnr_lig>283</resnr_lig>
+          <restype_lig>NFT</restype_lig>
+          <reschain_lig>A</reschain_lig>
           <sidechain>False</sidechain>
           <dist_h-a>2.33</dist_h-a>
           <dist_d-a>3.18</dist_d-a>
@@ -264,10 +264,13 @@
             <z>8.576</z>
           </protcoo>
         </hydrogen_bond>
-        <hydrogen_bond id="6">
+        <hydrogen_bond id="5">
           <resnr>66</resnr>
           <restype>GLY</restype>
           <reschain>A</reschain>
+          <resnr_lig>283</resnr_lig>
+          <restype_lig>NFT</restype_lig>
+          <reschain_lig>A</reschain_lig>
           <sidechain>False</sidechain>
           <dist_h-a>2.05</dist_h-a>
           <dist_d-a>2.95</dist_d-a>
@@ -288,10 +291,13 @@
             <z>8.621</z>
           </protcoo>
         </hydrogen_bond>
-        <hydrogen_bond id="7">
+        <hydrogen_bond id="6">
           <resnr>158</resnr>
           <restype>ASN</restype>
           <reschain>A</reschain>
+          <resnr_lig>283</resnr_lig>
+          <restype_lig>NFT</restype_lig>
+          <reschain_lig>A</reschain_lig>
           <sidechain>False</sidechain>
           <dist_h-a>1.95</dist_h-a>
           <dist_d-a>2.92</dist_d-a>
@@ -318,6 +324,9 @@
           <resnr>159</resnr>
           <restype>HIS</restype>
           <reschain>A</reschain>
+          <resnr_lig>283</resnr_lig>
+          <restype_lig>NFT</restype_lig>
+          <reschain_lig>A</reschain_lig>
           <dist_a-w>3.67</dist_a-w>
           <dist_d-w>3.13</dist_d-w>
           <don_angle>126.73</don_angle>
@@ -344,36 +353,6 @@
             <z>3.309</z>
           </watercoo>
         </water_bridge>
-        <water_bridge id="2">
-          <resnr>177</resnr>
-          <restype>TRP</restype>
-          <reschain>A</reschain>
-          <dist_a-w>3.96</dist_a-w>
-          <dist_d-w>3.04</dist_d-w>
-          <don_angle>125.14</don_angle>
-          <water_angle>84.15</water_angle>
-          <protisdon>True</protisdon>
-          <donor_idx>1380</donor_idx>
-          <donortype>Nar</donortype>
-          <acceptor_idx>1649</acceptor_idx>
-          <acceptortype>N2</acceptortype>
-          <water_idx>1735</water_idx>
-          <ligcoo>
-            <x>2.820</x>
-            <y>18.145</y>
-            <z>6.806</z>
-          </ligcoo>
-          <protcoo>
-            <x>7.577</x>
-            <y>15.116</y>
-            <z>5.463</z>
-          </protcoo>
-          <watercoo>
-            <x>4.665</x>
-            <y>15.397</y>
-            <z>4.635</z>
-          </watercoo>
-        </water_bridge>
       </water_bridges>
       <salt_bridges/>
       <pi_stacks/>
@@ -383,6 +362,9 @@
           <resnr>67</resnr>
           <restype>TYR</restype>
           <reschain>A</reschain>
+          <resnr_lig>283</resnr_lig>
+          <restype_lig>NFT</restype_lig>
+          <reschain_lig>A</reschain_lig>
           <sidechain>True</sidechain>
           <dist>3.37</dist>
           <don_angle>156.70</don_angle>
@@ -406,6 +388,9 @@
           <resnr>157</resnr>
           <restype>LEU</restype>
           <reschain>A</reschain>
+          <resnr_lig>283</resnr_lig>
+          <restype_lig>NFT</restype_lig>
+          <reschain_lig>A</reschain_lig>
           <sidechain>False</sidechain>
           <dist>3.24</dist>
           <don_angle>141.32</don_angle>
@@ -429,12 +414,14 @@
       <metal_complexes/>
     </interactions>
     <mappings>
-      <smiles_to_pdb>1:1649,2:1648,3:1630,4:1629,5:1637,6:1632,7:1631,8:1624,9:1625,10:1626,11:1627,12:1628,13:1623,14:1621,15:1620,16:1619,17:1618,18:1622,19:1617,20:1639,21:1640,22:1641,23:1642,24:1643,25:1644,26:1645,27:1646,28:1647,29:1633,30:1634,31:1635,32:1636,33:1638</smiles_to_pdb>
+      <smiles_to_pdb>1:1636,2:1634,3:1635,4:1633,5:1632,6:1631,7:1624,8:1623,9:1621,10:1620,11:1619,12:1618,13:1622,14:1617,15:1639,16:1640,17:1641,18:1642,19:1643,20:1644,21:1645,22:1646,23:1647,24:1625,25:1626,26:1627,27:1628,28:1637,29:1638,30:1629,31:1630,32:1648,33:1649</smiles_to_pdb>
     </mappings>
   </bindingsite>
+  <date_of_creation>2018/08/07</date_of_creation>
+  <citation_information>Salentin,S. et al. PLIP: fully automated protein-ligand interaction profiler. Nucl. Acids Res. (1 July 2015) 43 (W1): W443-W447. doi: 10.1093/nar/gkv315</citation_information>
+  <mode>default</mode>
   <pdbid>1VSN</pdbid>
-  <filetype>PDB</filetype>
-  <pdbfile>1vsn.pdb</pdbfile>
+  <pdbfile>./1vsn.pdb</pdbfile>
   <pdbfixes>False</pdbfixes>
   <filename>1vsn.pdb</filename>
   <excluded_ligands/>

setup.py

@@ -22,7 +22,7 @@ setup(name='plip',
       author_email='sebastian.salentin@tu-dresden.de',
       license='GPLv2',
       packages=['plip', 'plip/modules'],
-      scripts=['plip/plipcmd'],
+      scripts=['plip/plipcmd.py'],
       install_requires=[
           'openbabel',
           'numpy',