[med-svn] [Git][med-team/plip][master] 6 commits: Update Files-Excluded section in d/copyright
Alexandre Mestiashvili
gitlab at salsa.debian.org
Tue Sep 25 10:42:41 BST 2018
Alexandre Mestiashvili pushed to branch master at Debian Med / plip
Commits:
57f173a8 by Alexandre Mestiashvili at 2018-09-25T09:36:12Z
Update Files-Excluded section in d/copyright
- - - - -
175430d3 by Alexandre Mestiashvili at 2018-09-25T09:38:16Z
New upstream version 1.4.3~b+dfsg
- - - - -
c480af3e by Alexandre Mestiashvili at 2018-09-25T09:38:16Z
Update upstream source from tag 'upstream/1.4.3_b+dfsg'
Update to upstream version '1.4.3~b+dfsg'
with Debian dir 93fd86deb27d2502735fbc17c609d6d74e3c0b4d
- - - - -
f111ca06 by Alexandre Mestiashvili at 2018-09-25T09:38:35Z
Check for nocheck in DEB_BUILD_OPTIONS for tests, s/plipcmd.py/plipcmd/
- - - - -
70d5820d by Alexandre Mestiashvili at 2018-09-25T09:38:50Z
Bump Policy to 4.2.1
- - - - -
1549568e by Alexandre Mestiashvili at 2018-09-25T09:39:43Z
Update changelog
Gbp-Dch: Ignore
- - - - -
15 changed files:
- CHANGES.txt
- DOCUMENTATION.md
- README.md
- debian/changelog
- debian/control
- debian/copyright
- debian/rules
- plip/modules/detection.py
- plip/modules/plipxml.py
- plip/modules/report.py
- plip/plipcmd → plip/plipcmd.py
- plip/test/test_special_cases.py
- plip/test/test_xml_parser.py
- plip/test/xml/1vsn.report.xml
- setup.py
Changes:
=====================================
CHANGES.txt
=====================================
@@ -1,5 +1,8 @@
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
=====================================
@@ -1,3 +1,12 @@
+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 at 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 at 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
=====================================
@@ -17,26 +17,25 @@ 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:
- filtered1_pairings = [p for p in pairings if (p.resnr, p.reschain) != (p.resnr_l, p.reschain_l)]
- already_considered = []
- filtered2_pairings = []
- for contact in filtered1_pairings:
+ 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 = []
+ for contact in filtered1_pairings:
+ try:
+ dist = 'D{}'.format(round(contact.distance,2))
+ except AttributeError:
try:
- dist = 'D{}'.format(round(contact.distance,2))
+ dist = 'D{}'.format(round(contact.distance_ah,2))
except AttributeError:
- try:
- dist = 'D{}'.format(round(contact.distance_ah,2))
- 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])
- if data not in already_considered:
- filtered2_pairings.append(contact)
- already_considered.append(data)
- return filtered2_pairings
- else:
- return pairings
+ 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 = {res1, res2, dist}
+ if data not in already_considered:
+ filtered2_pairings.append(contact)
+ already_considered.append(data)
+ return filtered2_pairings
##################################################
@@ -54,14 +53,15 @@ 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:
- 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,
- distance=e, restype=restype, resnr=resnr,
- reschain=reschain, restype_l=restype_l,
- resnr_l=resnr_l, reschain_l=reschain_l)
- pairings.append(contact)
+ 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,
+ distance=e, restype=restype, resnr=resnr,
+ reschain=reschain, restype_l=restype_l,
+ resnr_l=resnr_l, reschain_l=reschain_l)
+ pairings.append(contact)
return filter_contacts(pairings)
@@ -75,32 +75,36 @@ 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
- 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:
- 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:
- 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
- resnr = whichresnumber(don.d) if protisdon else whichresnumber(acc.a)
- resnr_l = whichresnumber(acc.a_orig_atom) if protisdon else whichresnumber(don.d_orig_atom)
- restype = whichrestype(don.d) if protisdon else whichrestype(acc.a)
- restype_l = whichrestype(acc.a_orig_atom) if protisdon else whichrestype(don.d_orig_atom)
- reschain = whichchain(don.d) if protisdon else whichchain(acc.a)
- rechain_l = whichchain(acc.a_orig_atom) if protisdon else whichchain(don.d_orig_atom)
- # Next line prevents H-Bonds within amino acids in intermolecular interactions
- if config.INTRA is not None and whichresnumber(don.d) == whichresnumber(acc.a): continue
- # Next line prevents backbone-backbone H-Bonds
- if config.INTRA is not None and protatom.GetResidue().GetAtomProperty(protatom, 8) and ligatom.GetResidue().GetAtomProperty(ligatom, 8): continue
- contact = data(a=acc.a, a_orig_idx=acc.a_orig_idx, d=don.d, d_orig_idx=don.d_orig_idx, h=don.h,
- distance_ah=dist_ah, distance_ad=dist_ad, angle=v, type=typ, protisdon=protisdon,
- resnr=resnr, restype=restype, reschain=reschain, resnr_l=resnr_l,
- restype_l=restype_l, reschain_l=rechain_l, sidechain=is_sidechain_hbond,
- atype=acc.a.type, dtype=don.d.type)
- pairings.append(contact)
+ 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 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 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
+ resnr = whichresnumber(don.d) if protisdon else whichresnumber(acc.a)
+ resnr_l = whichresnumber(acc.a_orig_atom) if protisdon else whichresnumber(don.d_orig_atom)
+ restype = whichrestype(don.d) if protisdon else whichrestype(acc.a)
+ restype_l = whichrestype(acc.a_orig_atom) if protisdon else whichrestype(don.d_orig_atom)
+ reschain = whichchain(don.d) if protisdon else whichchain(acc.a)
+ rechain_l = whichchain(acc.a_orig_atom) if protisdon else whichchain(don.d_orig_atom)
+ # Next line prevents H-Bonds within amino acids in intermolecular interactions
+ if config.INTRA is not None and whichresnumber(don.d) == whichresnumber(acc.a): continue
+ # Next line prevents backbone-backbone H-Bonds
+ if config.INTRA is not None and protatom.GetResidue().GetAtomProperty(protatom, 8) and ligatom.GetResidue().GetAtomProperty(ligatom, 8): continue
+ contact = data(a=acc.a, a_orig_idx=acc.a_orig_idx, d=don.d, d_orig_idx=don.d_orig_idx, h=don.h,
+ distance_ah=dist_ah, distance_ad=dist_ad, angle=v, type=typ, protisdon=protisdon,
+ resnr=resnr, restype=restype, reschain=reschain, resnr_l=resnr_l,
+ restype_l=restype_l, reschain_l=rechain_l, sidechain=is_sidechain_hbond,
+ atype=acc.a.type, dtype=don.d.type)
+ pairings.append(contact)
return filter_contacts(pairings)
@@ -125,18 +129,19 @@ def pistacking(rings_bs, rings_lig):
# SELECTION BY DISTANCE, ANGLE AND OFFSET
passed = False
- if config.MIN_DIST < d < config.PISTACK_DIST_MAX:
- if 0 < a < config.PISTACK_ANG_DEV and offset < config.PISTACK_OFFSET_MAX:
- ptype = 'P'
- passed = True
- if 90 - config.PISTACK_ANG_DEV < a < 90 + config.PISTACK_ANG_DEV and offset < config.PISTACK_OFFSET_MAX:
- ptype = 'T'
- passed = True
- if passed:
- contact = data(proteinring=r, ligandring=l, distance=d, angle=a, offset=offset,
- type=ptype, resnr=resnr, restype=restype, reschain=reschain,
- resnr_l=resnr_l, restype_l=restype_l, reschain_l=reschain_l)
- pairings.append(contact)
+ 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
+ if 90 - config.PISTACK_ANG_DEV < a < 90 + config.PISTACK_ANG_DEV and offset < config.PISTACK_OFFSET_MAX:
+ ptype = 'T'
+ passed = True
+ if passed:
+ contact = data(proteinring=r, ligandring=l, distance=d, angle=a, offset=offset,
+ type=ptype, resnr=resnr, restype=restype, reschain=reschain,
+ resnr_l=resnr_l, restype_l=restype_l, reschain_l=reschain_l)
+ pairings.append(contact)
return filter_contacts(pairings)
@@ -146,46 +151,48 @@ 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:
- for ring in rings:
- c = ring.center
- for p in pos_charged:
- d = euclidean3d(c, p.center)
- # 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 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
- n_atoms = [a_neighbor for a_neighbor in OBAtomAtomIter(p.atoms[0].OBAtom)]
- n_atoms_coords = [(a.x(), a.y(), a.z()) for a in n_atoms]
- amine_normal = np.cross(vector(n_atoms_coords[0], n_atoms_coords[1]),
- vector(n_atoms_coords[2], n_atoms_coords[0]))
- b = vecangle(ring.normal, amine_normal)
- # Smallest of two angles, depending on direction of normal
- a = min(b, 180 - b if not 180 - b < 0 else b)
- if not a > 30.0:
- resnr, restype = whichresnumber(ring.atoms[0]), whichrestype(ring.atoms[0])
- reschain = whichchain(ring.atoms[0])
- resnr_l, restype_l = whichresnumber(p.orig_atoms[0]), whichrestype(p.orig_atoms[0])
- reschain_l = whichchain(p.orig_atoms[0])
- contact = data(ring=ring, charge=p, distance=d, offset=offset, type='regular',
- restype=restype, resnr=resnr, reschain=reschain,
- restype_l=restype_l, resnr_l=resnr_l, reschain_l=reschain_l,
- protcharged=protcharged)
- pairings.append(contact)
- break
- resnr = whichresnumber(p.atoms[0]) if protcharged else whichresnumber(ring.atoms[0])
- resnr_l = whichresnumber(ring.orig_atoms[0]) if protcharged else whichresnumber(p.orig_atoms[0])
- restype = whichrestype(p.atoms[0]) if protcharged else whichrestype(ring.atoms[0])
- restype_l = whichrestype(ring.orig_atoms[0]) if protcharged else whichrestype(p.orig_atoms[0])
- reschain = whichchain(p.atoms[0]) if protcharged else whichchain(ring.atoms[0])
- reschain_l = whichchain(ring.orig_atoms[0]) if protcharged else whichchain(p.orig_atoms[0])
- contact = data(ring=ring, charge=p, distance=d, offset=offset, type='regular', restype=restype,
- resnr=resnr, reschain=reschain, restype_l=restype_l, resnr_l=resnr_l,
- reschain_l=reschain_l, protcharged=protcharged)
+ if len(rings) == 0 or len(pos_charged) == 0:
+ return pairings
+ for ring in rings:
+ c = ring.center
+ for p in pos_charged:
+ d = euclidean3d(c, p.center)
+ # 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 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
+ n_atoms = [a_neighbor for a_neighbor in OBAtomAtomIter(p.atoms[0].OBAtom)]
+ n_atoms_coords = [(a.x(), a.y(), a.z()) for a in n_atoms]
+ amine_normal = np.cross(vector(n_atoms_coords[0], n_atoms_coords[1]),
+ vector(n_atoms_coords[2], n_atoms_coords[0]))
+ b = vecangle(ring.normal, amine_normal)
+ # Smallest of two angles, depending on direction of normal
+ a = min(b, 180 - b if not 180 - b < 0 else b)
+ if not a > 30.0:
+ resnr, restype = whichresnumber(ring.atoms[0]), whichrestype(ring.atoms[0])
+ reschain = whichchain(ring.atoms[0])
+ resnr_l, restype_l = whichresnumber(p.orig_atoms[0]), whichrestype(p.orig_atoms[0])
+ reschain_l = whichchain(p.orig_atoms[0])
+ contact = data(ring=ring, charge=p, distance=d, offset=offset, type='regular',
+ restype=restype, resnr=resnr, reschain=reschain,
+ restype_l=restype_l, resnr_l=resnr_l, reschain_l=reschain_l,
+ protcharged=protcharged)
pairings.append(contact)
+ break
+ resnr = whichresnumber(p.atoms[0]) if protcharged else whichresnumber(ring.atoms[0])
+ resnr_l = whichresnumber(ring.orig_atoms[0]) if protcharged else whichresnumber(p.orig_atoms[0])
+ restype = whichrestype(p.atoms[0]) if protcharged else whichrestype(ring.atoms[0])
+ restype_l = whichrestype(ring.orig_atoms[0]) if protcharged else whichrestype(p.orig_atoms[0])
+ reschain = whichchain(p.atoms[0]) if protcharged else whichchain(ring.atoms[0])
+ reschain_l = whichchain(ring.orig_atoms[0]) if protcharged else whichchain(p.orig_atoms[0])
+ contact = data(ring=ring, charge=p, distance=d, offset=offset, type='regular', restype=restype,
+ resnr=resnr, reschain=reschain, restype_l=restype_l, resnr_l=resnr_l,
+ reschain_l=reschain_l, protcharged=protcharged)
+ pairings.append(contact)
return filter_contacts(pairings)
@@ -194,17 +201,18 @@ 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:
- 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
- restype_l = whichrestype(nc.orig_atoms[0]) if protispos else whichrestype(pc.orig_atoms[0])
- reschain = pc.reschain if protispos else nc.reschain
- reschain_l = whichchain(nc.orig_atoms[0]) if protispos else whichchain(pc.orig_atoms[0])
- contact = data(positive=pc, negative=nc, distance=euclidean3d(pc.center, nc.center), protispos=protispos,
- resnr=resnr, restype=restype, reschain=reschain, resnr_l=resnr_l, restype_l=restype_l,
- reschain_l=reschain_l)
- pairings.append(contact)
+ 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
+ restype_l = whichrestype(nc.orig_atoms[0]) if protispos else whichrestype(pc.orig_atoms[0])
+ reschain = pc.reschain if protispos else nc.reschain
+ reschain_l = whichchain(nc.orig_atoms[0]) if protispos else whichchain(pc.orig_atoms[0])
+ contact = data(positive=pc, negative=nc, distance=euclidean3d(pc.center, nc.center), protispos=protispos,
+ resnr=resnr, restype=restype, reschain=reschain, resnr_l=resnr_l, restype_l=restype_l,
+ reschain_l=reschain_l)
+ pairings.append(contact)
return filter_contacts(pairings)
@@ -215,24 +223,27 @@ 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:
- 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 \
- < config.HALOGEN_ACC_ANGLE + config.HALOGEN_ANGLE_DEV:
- if config.HALOGEN_DON_ANGLE - config.HALOGEN_ANGLE_DEV < don_angle \
- < config.HALOGEN_DON_ANGLE + config.HALOGEN_ANGLE_DEV:
- 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,
- distance=dist, don_angle=don_angle, acc_angle=acc_angle,
- restype=restype, resnr=resnr,
- reschain=reschain, restype_l=restype_l,
- reschain_l=reschain_l, resnr_l=resnr_l, donortype=don.x.OBAtom.GetType(), acctype=acc.o.type,
- sidechain=is_sidechain_hal)
- pairings.append(contact)
+ 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 not config.HALOGEN_ACC_ANGLE - config.HALOGEN_ANGLE_DEV < acc_angle \
+ < config.HALOGEN_ACC_ANGLE + config.HALOGEN_ANGLE_DEV:
+ 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,
+ distance=dist, don_angle=don_angle, acc_angle=acc_angle,
+ restype=restype, resnr=resnr,
+ reschain=reschain, restype_l=restype_l,
+ reschain_l=reschain_l, resnr_l=resnr_l, donortype=don.x.OBAtom.GetType(), acctype=acc.o.type,
+ sidechain=is_sidechain_hal)
+ pairings.append(contact)
return filter_contacts(pairings)
@@ -269,32 +280,38 @@ 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
- 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:
- 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,
- dtype=don.d.type, h=don.h, water=wl.oxy, water_orig_idx=wl.oxy_orig_idx,
- distance_aw=distance_aw, distance_dw=distance_dw, d_angle=d_angle, w_angle=w_angle,
- type='first_deg', resnr=resnr, restype=restype,
- reschain=reschain, restype_l=restype_l, resnr_l=resnr_l, reschain_l=reschain_l, protisdon=True)
- pairings.append(contact)
+ 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 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,
+ dtype=don.d.type, h=don.h, water=wl.oxy, water_orig_idx=wl.oxy_orig_idx,
+ distance_aw=distance_aw, distance_dw=distance_dw, d_angle=d_angle, w_angle=w_angle,
+ type='first_deg', resnr=resnr, restype=restype,
+ reschain=reschain, restype_l=restype_l, resnr_l=resnr_l, reschain_l=reschain_l, protisdon=True)
+ pairings.append(contact)
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
- 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:
- 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,
- dtype=don.d.type, h=don.h, water=wl.oxy, water_orig_idx=wl.oxy_orig_idx,
- distance_aw=distance_aw, distance_dw=distance_dw,
- d_angle=d_angle, w_angle=w_angle, type='first_deg', resnr=resnr,
- restype=restype, reschain=reschain,
- restype_l=restype_l, reschain_l=reschain_l, resnr_l=resnr_l, protisdon=False)
- pairings.append(contact)
+ 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 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,
+ dtype=don.d.type, h=don.h, water=wl.oxy, water_orig_idx=wl.oxy_orig_idx,
+ distance_aw=distance_aw, distance_dw=distance_dw,
+ d_angle=d_angle, w_angle=w_angle, type='first_deg', resnr=resnr,
+ restype=restype, reschain=reschain,
+ restype_l=restype_l, reschain_l=reschain_l, resnr_l=resnr_l, protisdon=False)
+ pairings.append(contact)
return filter_contacts(pairings)
@@ -310,13 +327,14 @@ 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 metal.m not in pairings_dict:
- pairings_dict[metal.m] = [(target, distance), ]
- metal_to_id[metal.m] = metal.m_orig_idx
- metal_to_orig_atom[metal.m] = metal.orig_m
- else:
- pairings_dict[metal.m].append((target, distance))
+ 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
+ metal_to_orig_atom[metal.m] = metal.orig_m
+ else:
+ pairings_dict[metal.m].append((target, distance))
for cnum, metal in enumerate(pairings_dict):
rms = 0.0
excluded = []
=====================================
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
=====================================
@@ -1,7 +1,7 @@
#! /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
-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
+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:
- from plip.modules.visualize import visualize_in_pymol
+ 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 at H](CC(C)C)N[C at 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
=====================================
@@ -1,6 +1,6 @@
<?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 at H](CC(C)C)N[C at 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 at tu-dresden.de',
license='GPLv2',
packages=['plip', 'plip/modules'],
- scripts=['plip/plipcmd'],
+ scripts=['plip/plipcmd.py'],
install_requires=[
'openbabel',
'numpy',
View it on GitLab: https://salsa.debian.org/med-team/plip/compare/5b8735d8202fdf271d2e6ac7693c538d3f072871...1549568ef24d351577628567a87eaa5c72bd3c96
--
View it on GitLab: https://salsa.debian.org/med-team/plip/compare/5b8735d8202fdf271d2e6ac7693c538d3f072871...1549568ef24d351577628567a87eaa5c72bd3c96
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