[med-svn] [plip] 02/09: New upstream version 1.3.5+dfsg
Alex Mestiashvili
malex-guest at moszumanska.debian.org
Fri Dec 1 15:58:11 UTC 2017
This is an automated email from the git hooks/post-receive script.
malex-guest pushed a commit to branch master
in repository plip.
commit efab1b850bd8c70e27726d0c72ffe602b857cd4c
Author: Alexandre Mestiashvili <alex at biotec.tu-dresden.de>
Date: Fri Dec 1 15:11:35 2017 +0100
New upstream version 1.3.5+dfsg
---
CHANGES.txt | 19 +-
DOCUMENTATION.md | 20 ++
LICENSE.txt | 455 ++++++++++++++++++++-------------
TODO.txt | 14 +
plip/__init__.py | 15 +-
plip/modules/__init__.py | 15 +-
plip/modules/chimeraplip.py | 13 -
plip/modules/config.py | 27 +-
plip/modules/detection.py | 153 +++++++----
plip/modules/mp.py | 30 +--
plip/modules/plipremote.py | 13 -
plip/modules/plipxml.py | 22 +-
plip/modules/preparation.py | 183 ++++++++-----
plip/modules/pymolplip.py | 29 ++-
plip/modules/report.py | 59 ++---
plip/modules/supplemental.py | 53 ++--
plip/modules/visualize.py | 32 +--
plip/modules/webservices.py | 22 +-
plip/plipcmd | 43 +---
plip/test/run_all_tests.sh | 1 +
plip/test/test_basic_functions.py | 13 -
plip/test/test_literature_validated.py | 13 -
plip/test/test_metal_coordination.py | 13 -
plip/test/test_remote_services.py | 13 -
plip/test/test_special_cases.py | 15 --
plip/test/test_xml_parser.py | 13 -
setup.py | 19 +-
27 files changed, 678 insertions(+), 639 deletions(-)
diff --git a/CHANGES.txt b/CHANGES.txt
index 121f740..2d53bd6 100644
--- a/CHANGES.txt
+++ b/CHANGES.txt
@@ -1,7 +1,24 @@
Changelog
---------
-# 1.3.3
+### Next version
+-
+
+### 1.3.5
+* Preparation for Python 3: Imports
+* small correction for PDB fixing
+* includes TODO files with user suggestions
+* license adapted to GNU GPLv2
+
+### 1.3.4
+* __DNA/RNA can be selected as receptor with --dnareceptor__
+* __Composite ligands and intra-protein mode: Annotation which part of the ligand interacts with the receptor__
+* Improved handling of NMR structures
+* Filter for extremely large ligands
+* Speed-up for file reading and parallel visualization
+* More debugging messages
+
+### 1.3.3
* __Adds XML Parser module for PLIP XML files__
* Detection of intramolecular interactions with --intra
* improved error correction in PDB files
diff --git a/DOCUMENTATION.md b/DOCUMENTATION.md
index ae28206..ca20f1b 100644
--- a/DOCUMENTATION.md
+++ b/DOCUMENTATION.md
@@ -140,6 +140,12 @@ plip -i 5b2m --intra A -yv
Please note that detection within a chain takes much longer than detection of protein-ligand interactions,
especially for large structures.
+### Interactions of molecules with DNA/RNA (__beta__)
+PLIP can characterize interactions between ligands and DNA/RNA.
+A special mode allows to switch from protein to DNA/RNA as the receptor molecule in the structure.
+To change the receptor mode, start PLIP with the option `--dnareceptor`.
+
+
## Changing detection thresholds
The PLIP algorithm uses a rule-based detection to report non-covalent interaction between proteins and their partners.
The current settings are based on literature values and have been refined based on extensive testing with independent cases from mainly crystallography journals, covering a broad range of structure resolutions.
@@ -480,6 +486,20 @@ Residue type of interacting amino acid
Residue chain of interacting amino acid
+**resnr_ligand**
+
+Residue number of interacting ligand residue
+
+
+**restype_ligand**
+
+Residue type of interacting ligand residue
+
+
+**reschain_ligand**
+
+Residue chain of interacting ligand residue
+
**dist**
diff --git a/LICENSE.txt b/LICENSE.txt
index 92cfcfd..846c036 100644
--- a/LICENSE.txt
+++ b/LICENSE.txt
@@ -1,177 +1,280 @@
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diff --git a/TODO.txt b/TODO.txt
new file mode 100644
index 0000000..93d3639
--- /dev/null
+++ b/TODO.txt
@@ -0,0 +1,14 @@
+Possible future features
+========================
+
+* Python 3 support
+* support special characters in filenames (e.g. spanish accents), currently cause problems in XML report
+* support for mmcif format
+* support presets for hydrogenation
+* detection of steric clashes
+* detection of anion-pi interactions
+* detection of electrostatic repulsion force_string
+* detection of Keesom forces
+* weak hydrogen bonding
+* visualization: show hydrogen atoms in PyMOL for hydrogen bonds and adapt interaction vector accordingly
+* use SMARTS for detection of chemical features (charged groups, etc.)
diff --git a/plip/__init__.py b/plip/__init__.py
index 1ab663b..a1e3ed0 100644
--- a/plip/__init__.py
+++ b/plip/__init__.py
@@ -1,17 +1,4 @@
"""
Protein-Ligand Interaction Profiler - Analyze and visualize protein-ligand interactions in PDB files.
__init__.py - Needed for python modules.
-Copyright 2014-2015 Sebastian Salentin
-
-Licensed under the Apache License, Version 2.0 (the "License");
-you may not use this file except in compliance with the License.
-You may obtain a copy of the License at
-
- http://www.apache.org/licenses/LICENSE-2.0
-
-Unless required by applicable law or agreed to in writing, software
-distributed under the License is distributed on an "AS IS" BASIS,
-WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-See the License for the specific language governing permissions and
-limitations under the License.
-"""
\ No newline at end of file
+"""
diff --git a/plip/modules/__init__.py b/plip/modules/__init__.py
index 1ab663b..a1e3ed0 100644
--- a/plip/modules/__init__.py
+++ b/plip/modules/__init__.py
@@ -1,17 +1,4 @@
"""
Protein-Ligand Interaction Profiler - Analyze and visualize protein-ligand interactions in PDB files.
__init__.py - Needed for python modules.
-Copyright 2014-2015 Sebastian Salentin
-
-Licensed under the Apache License, Version 2.0 (the "License");
-you may not use this file except in compliance with the License.
-You may obtain a copy of the License at
-
- http://www.apache.org/licenses/LICENSE-2.0
-
-Unless required by applicable law or agreed to in writing, software
-distributed under the License is distributed on an "AS IS" BASIS,
-WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-See the License for the specific language governing permissions and
-limitations under the License.
-"""
\ No newline at end of file
+"""
diff --git a/plip/modules/chimeraplip.py b/plip/modules/chimeraplip.py
index 1505a62..96d658d 100644
--- a/plip/modules/chimeraplip.py
+++ b/plip/modules/chimeraplip.py
@@ -1,19 +1,6 @@
"""
Protein-Ligand Interaction Profiler - Analyze and visualize protein-ligand interactions in PDB files.
chimeraplip.py - Visualization class for Chimera.
-Copyright 2014-2015 Sebastian Salentin
-
-Licensed under the Apache License, Version 2.0 (the "License");
-you may not use this file except in compliance with the License.
-You may obtain a copy of the License at
-
- http://www.apache.org/licenses/LICENSE-2.0
-
-Unless required by applicable law or agreed to in writing, software
-distributed under the License is distributed on an "AS IS" BASIS,
-WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-See the License for the specific language governing permissions and
-limitations under the License.
"""
class ChimeraVisualizer():
diff --git a/plip/modules/config.py b/plip/modules/config.py
index 4ae5e4c..4915fb6 100644
--- a/plip/modules/config.py
+++ b/plip/modules/config.py
@@ -1,19 +1,6 @@
"""
Protein-Ligand Interaction Profiler - Analyze and visualize protein-ligand interactions in PDB files.
config.py - Store thresholds used by PLIP.
-Copyright 2014 Sebastian Salentin
-
-Licensed under the Apache License, Version 2.0 (the "License");
-you may not use this file except in compliance with the License.
-You may obtain a copy of the License at
-
- http://www.apache.org/licenses/LICENSE-2.0
-
-Unless required by applicable law or agreed to in writing, software
-distributed under the License is distributed on an "AS IS" BASIS,
-WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-See the License for the specific language governing permissions and
-limitations under the License.
"""
VERBOSE = False # Set verbose mode
@@ -32,6 +19,7 @@ NOFIX = False # Turn off fixing of errors in PDB files
PEPTIDES = [] # Definition which chains should be considered as peptide ligands
INTRA = None
KEEPMOD = False
+DNARECEPTOR = False
# Configuration file for Protein-Ligand Interaction Profiler (PLIP)
# Set thresholds for detection of interactions
@@ -44,7 +32,7 @@ MIN_DIST = 0.5 # Minimum distance for all distance thresholds
HYDROPH_DIST_MAX = 4.0 # Distance cutoff for detection of hydrophobic contacts
HBOND_DIST_MAX = 4.1 # Max. distance between hydrogen bond donor and acceptor (Hubbard & Haider, 2001) + 0.6 A
HBOND_DON_ANGLE_MIN = 100 # Min. angle at the hydrogen bond donor (Hubbard & Haider, 2001) + 10
-PISTACK_DIST_MAX = 7.5 # Max. distance for parallel or offset pistacking (McGaughey, 1998)
+PISTACK_DIST_MAX = 5.5 # Max. distance for parallel or offset pistacking (McGaughey, 1998)
PISTACK_ANG_DEV = 30 # Max. Deviation from parallel or perpendicular orientation (in degrees)
PISTACK_OFFSET_MAX = 2.0 # Maximum offset of the two rings (corresponds to the radius of benzene + 0.5 A)
PICATION_DIST_MAX = 6.0 # Max. distance between charged atom and aromatic ring center (Gallivan and Dougherty, 1999)
@@ -60,6 +48,17 @@ WATER_BRIDGE_OMEGA_MAX = 140 # Max. angle between acceptor, water oxygen and do
WATER_BRIDGE_THETA_MIN = 100 # Min. angle between water oxygen, donor hydrogen and donor atom (Jiang et al., 2005)
METAL_DIST_MAX = 3.0 # Max. distance between metal ion and interacting atom (Harding, 2001)
+# Other thresholds
+MAX_COMPOSITE_LENGTH = 200 # Filter out ligands with more than 200 fragments
+
+#########
+# Names #
+#########
+
+# Names of RNA and DNA residues to be considered (detection by name)
+RNA = ['U', 'A', 'C', 'G']
+DNA = ['DT', 'DA', 'DC', 'DG']
+
#############
# Whitelist #
#############
diff --git a/plip/modules/detection.py b/plip/modules/detection.py
index 6143ea8..61a4f8b 100644
--- a/plip/modules/detection.py
+++ b/plip/modules/detection.py
@@ -1,28 +1,42 @@
"""
Protein-Ligand Interaction Profiler - Analyze and visualize protein-ligand interactions in PDB files.
detection.py - Detect non-covalent interactions.
-Copyright 2014-2015 Sebastian Salentin
-
-Licensed under the Apache License, Version 2.0 (the "License");
-you may not use this file except in compliance with the License.
-You may obtain a copy of the License at
-
- http://www.apache.org/licenses/LICENSE-2.0
-
-Unless required by applicable law or agreed to in writing, software
-distributed under the License is distributed on an "AS IS" BASIS,
-WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-See the License for the specific language governing permissions and
-limitations under the License.
"""
# Python standard library
+from __future__ import absolute_import
import itertools
from collections import defaultdict
# Own modules
-from supplemental import *
-import config
+from plip.modules.supplemental import *
+import plip.modules.config
+
+
+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:
+ try:
+ dist = 'D{}'.format(round(contact.distance,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
##################################################
@@ -34,18 +48,21 @@ def hydrophobic_interactions(atom_set_a, atom_set_b):
Definition: All pairs of qualified carbon atoms within a distance of HYDROPH_DIST_MAX
"""
data = namedtuple('hydroph_interaction', 'bsatom bsatom_orig_idx ligatom ligatom_orig_idx '
- 'distance restype resnr reschain')
+ 'distance restype resnr reschain restype_l, resnr_l, reschain_l')
pairings = []
for a, b in itertools.product(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=whichrestype(a.atom), resnr=whichresnumber(a.atom),
- reschain=whichchain(a.atom))
+ distance=e, restype=restype, resnr=resnr,
+ reschain=reschain, restype_l=restype_l,
+ resnr_l=resnr_l, reschain_l=reschain_l)
pairings.append(contact)
- return pairings
+ return filter_contacts(pairings)
def hbonds(acceptors, donor_pairs, protisdon, typ):
@@ -55,7 +72,7 @@ def hbonds(acceptors, donor_pairs, protisdon, typ):
and donor angles above HBOND_DON_ANGLE_MIN
"""
data = namedtuple('hbond', 'a a_orig_idx d d_orig_idx h distance_ah distance_ad angle type protisdon resnr '
- 'restype reschain sidechain atype dtype')
+ '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
@@ -65,27 +82,31 @@ def hbonds(acceptors, donor_pairs, protisdon, typ):
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:
- restype = whichrestype(don.d) if protisdon else whichrestype(acc.a)
- reschain = whichchain(don.d) if protisdon else whichchain(acc.a)
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 = 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, sidechain=is_sidechain_hbond,
+ 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 pairings
+ return filter_contacts(pairings)
def pistacking(rings_bs, rings_lig):
"""Return all pi-stackings between the given aromatic ring systems in receptor and ligand."""
- data = namedtuple('pistack', 'proteinring ligandring distance angle offset type restype resnr reschain')
+ data = namedtuple('pistack', 'proteinring ligandring distance angle offset type restype resnr reschain restype_l resnr_l reschain_l')
pairings = []
for r, l in itertools.product(rings_bs, rings_lig):
# DISTANCE AND RING ANGLE CALCULATION
@@ -100,25 +121,30 @@ def pistacking(rings_bs, rings_lig):
# RECEPTOR DATA
resnr, restype, reschain = whichresnumber(r.atoms[0]), whichrestype(r.atoms[0]), whichchain(r.atoms[0])
+ resnr_l, restype_l, reschain_l = whichresnumber(l.orig_atoms[0]), whichrestype(l.orig_atoms[0]), whichchain(l.orig_atoms[0])
# 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:
- contact = data(proteinring=r, ligandring=l, distance=d, angle=a, offset=offset,
- type='P', resnr=resnr, restype=restype, reschain=reschain)
- pairings.append(contact)
+ 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='T', resnr=resnr, restype=restype, reschain=reschain)
+ type=ptype, resnr=resnr, restype=restype, reschain=reschain,
+ resnr_l=resnr_l, restype_l=restype_l, reschain_l=reschain_l)
pairings.append(contact)
- return pairings
+ return filter_contacts(pairings)
def pication(rings, pos_charged, protcharged):
"""Return all pi-Cation interaction between aromatic rings and positively charged groups.
For tertiary and quaternary amines, check also the angle between the ring and the nitrogen.
"""
- data = namedtuple('pication', 'ring charge distance offset type restype resnr reschain 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:
@@ -142,38 +168,50 @@ def pication(rings, pos_charged, protcharged):
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, protcharged=protcharged)
+ 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, protcharged=protcharged)
+ resnr=resnr, reschain=reschain, restype_l=restype_l, resnr_l=resnr_l,
+ reschain_l=reschain_l, protcharged=protcharged)
pairings.append(contact)
- return pairings
+ return filter_contacts(pairings)
def saltbridge(poscenter, negcenter, protispos):
"""Detect all salt bridges (pliprofiler between centers of positive and negative charge)"""
- data = namedtuple('saltbridge', 'positive negative distance protispos resnr restype reschain')
+ 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=resnr, restype=restype, reschain=reschain, resnr_l=resnr_l, restype_l=restype_l,
+ reschain_l=reschain_l)
pairings.append(contact)
- return pairings
+ return filter_contacts(pairings)
def halogen(acceptor, donor):
"""Detect all halogen bonds of the type Y-O...X-C"""
data = namedtuple('halogenbond', 'acc acc_orig_idx don don_orig_idx distance don_angle acc_angle restype '
- 'resnr reschain donortype acctype sidechain')
+ 'resnr reschain restype_l resnr_l reschain_l donortype acctype sidechain')
pairings = []
for acc, don in itertools.product(acceptor, donor):
dist = euclidean3d(acc.o.coords, don.x.coords)
@@ -186,19 +224,22 @@ def halogen(acceptor, donor):
< 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=whichrestype(acc.o), resnr=whichresnumber(acc.o),
- reschain=whichchain(acc.o), donortype=don.x.OBAtom.GetType(), acctype=acc.o.type,
+ 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 pairings
+ return filter_contacts(pairings)
def water_bridges(bs_hba, lig_hba, bs_hbd, lig_hbd, water):
"""Find water-bridged hydrogen bonds between ligand and protein. For now only considers bridged of first degree."""
data = namedtuple('waterbridge', 'a a_orig_idx atype d d_orig_idx dtype h water water_orig_idx distance_aw '
- 'distance_dw d_angle w_angle type resnr restype reschain protisdon')
+ 'distance_dw d_angle w_angle type resnr restype reschain resnr_l restype_l reschain_l protisdon')
pairings = []
# First find all acceptor-water pairs with distance within d
# and all donor-water pairs with distance within d and angle greater theta
@@ -231,11 +272,13 @@ def water_bridges(bs_hba, lig_hba, bs_hbd, lig_hbd, water):
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=whichresnumber(don.d), restype=whichrestype(don.d),
- reschain=whichchain(don.d), protisdon=True)
+ 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
@@ -243,30 +286,35 @@ def water_bridges(bs_hba, lig_hba, bs_hbd, lig_hbd, water):
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=whichresnumber(acc.a),
- restype=whichrestype(acc.a), reschain=whichchain(acc.a), protisdon=False)
+ 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 pairings
+ return filter_contacts(pairings)
def metal_complexation(metals, metal_binding_lig, metal_binding_bs):
"""Find all metal complexes between metals and appropriate groups in both protein and ligand, as well as water"""
data = namedtuple('metal_complex', 'metal metal_orig_idx metal_type target target_orig_idx target_type '
'coordination_num distance resnr restype '
- 'reschain location rms, geometry num_partners complexnum')
+ 'reschain restype_l reschain_l resnr_l location rms, geometry num_partners complexnum')
pairings_dict = {}
pairings = []
# #@todo Refactor
metal_to_id = {}
+ 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))
for cnum, metal in enumerate(pairings_dict):
@@ -391,10 +439,13 @@ def metal_complexation(metals, metal_binding_lig, metal_binding_bs):
for contact_pair in contact_pairs:
target, distance = contact_pair
if target.atom.idx not in excluded:
+ metal_orig_atom = metal_to_orig_atom[metal]
+ restype_l, reschain_l, resnr_l = whichrestype(metal_orig_atom), whichchain(metal_orig_atom), whichresnumber(metal_orig_atom)
contact = data(metal=metal, metal_orig_idx=metal_to_id[metal], metal_type=metal.type,
target=target, target_orig_idx=target.atom_orig_idx, target_type=target.type,
coordination_num=final_coo, distance=distance, resnr=target.resnr,
restype=target.restype, reschain=target.reschain, location=target.location,
- rms=rms, geometry=final_geom, num_partners=num_targets, complexnum=cnum + 1)
+ rms=rms, geometry=final_geom, num_partners=num_targets, complexnum=cnum + 1,
+ resnr_l=resnr_l, restype_l=restype_l, reschain_l=reschain_l)
pairings.append(contact)
- return pairings
+ return filter_contacts(pairings)
diff --git a/plip/modules/mp.py b/plip/modules/mp.py
index ae5a951..ec78f7b 100644
--- a/plip/modules/mp.py
+++ b/plip/modules/mp.py
@@ -1,19 +1,6 @@
"""
Protein-Ligand Interaction Profiler - Analyze and visualize protein-ligand interactions in PDB files.
mp.py - Functions for parallel processing
-Copyright 2014-2015 Sebastian Salentin, Joachim Haupt
-
-Licensed under the Apache License, Version 2.0 (the "License");
-you may not use this file except in compliance with the License.
-You may obtain a copy of the License at
-
- http://www.apache.org/licenses/LICENSE-2.0
-
-Unless required by applicable law or agreed to in writing, software
-distributed under the License is distributed on an "AS IS" BASIS,
-WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-See the License for the specific language governing permissions and
-limitations under the License.
"""
# Python Standard Library
@@ -34,7 +21,7 @@ class SubProcessError(Exception):
def universal_worker(input_pair):
"""This is a wrapper function expecting a tiplet of function, single
argument, dict of keyword arguments. The provided function is called
- with the appropriate arguments."""
+ with the appropriate arguments."""
function, arg, kwargs = input_pair
return function(arg, **kwargs)
@@ -48,22 +35,21 @@ def parallel_fn(f):
"""Simple wrapper function, returning a parallel version of the given function f.
The function f must have one argument and may have an arbitray number of
keyword arguments. """
-
+
def simple_parallel(func, sequence, **args):
""" f takes an element of sequence as input and the keyword args in **args"""
- multiprocessing.freeze_support()
if 'processes' in args:
processes = args.get('processes')
del args['processes']
else:
processes = multiprocessing.cpu_count()
-
- pool = multiprocessing.Pool(processes=processes) # depends on available cores
- result = pool.map(universal_worker, pool_args(func, sequence, args))
- cleaned = [x for x in result if x is not None] # getting results
- cleaned = asarray(cleaned)
+
+ pool = multiprocessing.Pool(processes) # depends on available cores
+
+ result = pool.map_async(universal_worker, pool_args(func, sequence, args))
pool.close()
pool.join()
+ cleaned = [x for x in result.get() if x is not None] # getting results
+ cleaned = asarray(cleaned)
return cleaned
return partial(simple_parallel, f)
-
diff --git a/plip/modules/plipremote.py b/plip/modules/plipremote.py
index e2fd18f..f35cc55 100644
--- a/plip/modules/plipremote.py
+++ b/plip/modules/plipremote.py
@@ -1,19 +1,6 @@
"""
Protein-Ligand Interaction Profiler - Analyze and visualize protein-ligand interactions in PDB files.
plipremote.py - Modules involved in multiprocessing and remote computation.
-Copyright 2014-2015 Sebastian Salentin
-
-Licensed under the Apache License, Version 2.0 (the "License");
-you may not use this file except in compliance with the License.
-You may obtain a copy of the License at
-
- http://www.apache.org/licenses/LICENSE-2.0
-
-Unless required by applicable law or agreed to in writing, software
-distributed under the License is distributed on an "AS IS" BASIS,
-WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-See the License for the specific language governing permissions and
-limitations under the License.
"""
# Python Standard Library
diff --git a/plip/modules/plipxml.py b/plip/modules/plipxml.py
index 96e7f24..a856cac 100644
--- a/plip/modules/plipxml.py
+++ b/plip/modules/plipxml.py
@@ -1,19 +1,6 @@
"""
Protein-Ligand Interaction Profiler - Analyze and visualize protein-ligand interactions in PDB files.
plipxml.py - Read in PLIP XML files for further analysis.
-Copyright 2014-2016 Sebastian Salentin
-
-Licensed under the Apache License, Version 2.0 (the "License");
-you may not use this file except in compliance with the License.
-You may obtain a copy of the License at
-
- http://www.apache.org/licenses/LICENSE-2.0
-
-Unless required by applicable law or agreed to in writing, software
-distributed under the License is distributed on an "AS IS" BASIS,
-WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-See the License for the specific language governing permissions and
-limitations under the License.
"""
# Python standard library
@@ -24,7 +11,6 @@ from itertools import groupby
import sys
import urllib2
-#TODO True/False values for all corresponding attributes
class XMLStorage:
"""Generic class for storing XML data from PLIP XML files."""
@@ -64,7 +50,10 @@ class Interaction(XMLStorage):
self.id = interaction_part.get('id')
self.resnr = self.getdata(interaction_part, 'resnr')
self.restype = self.getdata(interaction_part, 'restype')
- self.reschain = self.getdata(interaction_part, 'reschain')
+ self.reschain = self.getdata(interaction_part, 'reschain', force_string=True)
+ self.resnr_lig = self.getdata(interaction_part, 'resnr_lig')
+ self.restype_lig = self.getdata(interaction_part, 'restype_lig')
+ self.reschain_lig = self.getdata(interaction_part, 'reschain_lig', force_string=True)
self.ligcoo = self.getcoordinates(interaction_part, 'ligcoo')
self.protcoo = self.getcoordinates(interaction_part, 'protcoo')
@@ -267,11 +256,12 @@ class BSite(XMLStorage):
def get_counts(self):
"""counts the interaction types and backbone hydrogen bonding in a binding site"""
- hbondsback = len([hb for hb in self.hbonds if hb.sidechain == 'F'])
+ hbondsback = len([hb for hb in self.hbonds if not hb.sidechain])
counts = {'hydrophobics': len(self.hydrophobics), 'hbonds': len(self.hbonds),
'wbridges': len(self.wbridges), 'sbridges': len(self.sbridges), 'pistacks': len(self.pi_stacks),
'pications': len(self.pi_cations), 'halogens': len(self.halogens), 'metal': len(self.metal_complexes),
'hbond_back': hbondsback, 'hbond_nonback': (len(self.hbonds) - hbondsback)}
+ counts['total'] = counts['hydrophobics'] + counts['hbonds'] + counts['wbridges'] + counts['sbridges'] + counts['pistacks'] + counts['pications'] + counts['halogens'] + counts['metal']
return counts
class PLIPXML(XMLStorage):
diff --git a/plip/modules/preparation.py b/plip/modules/preparation.py
index b839caf..207c474 100644
--- a/plip/modules/preparation.py
+++ b/plip/modules/preparation.py
@@ -1,29 +1,17 @@
"""
Protein-Ligand Interaction Profiler - Analyze and visualize protein-ligand interactions in PDB files.
preparation.py - Prepare PDB input files for processing.
-Copyright 2014-2015 Sebastian Salentin
-
-Licensed under the Apache License, Version 2.0 (the "License");
-you may not use this file except in compliance with the License.
-You may obtain a copy of the License at
-
- http://www.apache.org/licenses/LICENSE-2.0
-
-Unless required by applicable law or agreed to in writing, software
-distributed under the License is distributed on an "AS IS" BASIS,
-WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-See the License for the specific language governing permissions and
-limitations under the License.
"""
# Python Standard Library
+from __future__ import absolute_import
from operator import itemgetter
# Own modules
-from detection import *
-from supplemental import *
-import config
+from plip.modules.detection import *
+from plip.modules.supplemental import *
+import plip.modules.config
################
@@ -38,6 +26,7 @@ class PDBParser:
self.covlinkage = namedtuple("covlinkage", "id1 chain1 pos1 conf1 id2 chain2 pos2 conf2")
self.proteinmap, self.modres, self.covalent, self.altconformations, self.corrected_pdb = self.parse_pdb()
+
def parse_pdb(self):
"""Extracts additional information from PDB files.
I. When reading in a PDB file, OpenBabel numbers ATOMS and HETATOMS continously.
@@ -64,11 +53,20 @@ class PDBParser:
if not config.NOFIX:
if not config.PLUGIN_MODE:
lastnum = 0 # Atom numbering (has to be consecutive)
+ other_models = False
for line in fil:
- corrected_line, newnum = self.fix_pdbline(line, lastnum)
- if corrected_line is not None:
- corrected_lines.append(corrected_line)
- lastnum = newnum
+ if not other_models: # Only consider the first model in an NRM structure
+ corrected_line, newnum = self.fix_pdbline(line, lastnum)
+ if corrected_line is not None:
+ if corrected_line.startswith('MODEL'):
+ try: # Get number of MODEL (1,2,3)
+ model_num = int(corrected_line[10:14])
+ if model_num > 1: # MODEL 2,3,4 etc.
+ other_models = True
+ except ValueError:
+ write_message("Ignoring invalid MODEL entry: %s\n" % corrected_line, mtype='debug')
+ corrected_lines.append(corrected_line)
+ lastnum = newnum
corrected_pdb = ''.join(corrected_lines)
else:
corrected_pdb = self.pdbpath
@@ -156,12 +154,16 @@ class PDBParser:
self.num_fixed_lines += 1
if pdbline.startswith('HETATM'):
newnum = lastnum + 1
- currentnum = int(pdbline[6:11])
+ try:
+ currentnum = int(pdbline[6:11])
+ except ValueError:
+ currentnum = None
+ write_message("Invalid HETATM entry: %s\n" % pdbline, mtype='debug')
if lastnum + 1 != currentnum:
pdbline = pdbline[:6] + (5 - len(str(newnum))) * ' ' + str(newnum) + ' ' + pdbline[12:]
fixed = True
# No chain assigned or number assigned as chain
- if pdbline[21] == ' ' or re.match("[0-9]", pdbline[21]):
+ if pdbline[21] == ' ':
pdbline = pdbline[:21] + 'Z' + pdbline[22:]
fixed = True
# No residue number assigned
@@ -221,7 +223,6 @@ class LigandFinder:
if len(all_from_chain) == 0:
return None
else:
- #TODO Can be done shorter with a split
water = [o for o in all_from_chain if o.GetResidueProperty(9)]
non_water = water = [o for o in all_from_chain if not o.GetResidueProperty(9)]
ligand = self.extract_ligand(non_water)
@@ -250,8 +251,12 @@ class LigandFinder:
res_kmers = self.identify_kmers(all_res_dict)
else:
res_kmers = [[a, ] for a in ligand_residues]
+ write_message("{} ligand kmer(s) detected for closer inspection.\n".format(len(res_kmers)), mtype='debug')
for kmer in res_kmers: # iterate over all ligands and extract molecules + information
- ligands.append(self.extract_ligand(kmer))
+ if len(kmer) > config.MAX_COMPOSITE_LENGTH:
+ write_message("Ligand kmer(s) filtered out with a length of {} fragments ({} allowed).\n".format(len(kmer), config.MAX_COMPOSITE_LENGTH), mtype='debug')
+ else:
+ ligands.append(self.extract_ligand(kmer))
else:
# Extract peptides from given chains
@@ -272,7 +277,7 @@ class LigandFinder:
members = [(res.GetName(), res.GetChain(), int32_to_negative(res.GetNum())) for res in kmer]
members = sort_members_by_importance(members)
rname, rchain, rnum = members[0]
- write_message("Finalizing extraction for ligand %s:%s:%s\n" % (rname, rchain, rnum), mtype='debug')
+ write_message("Finalizing extraction for ligand %s:%s:%s with %i elements\n" % (rname, rchain, rnum, len(kmer)), mtype='debug')
names = [x[0] for x in members]
longname = '-'.join([x[0] for x in members])
@@ -283,6 +288,7 @@ class LigandFinder:
else:
# Classify a ligand by its HETID(s)
ligtype = classify_by_name(names)
+ write_message("Ligand classified as {}\n".format(ligtype), mtype='debug')
hetatoms = set()
for obresidue in kmer:
@@ -295,6 +301,7 @@ class LigandFinder:
if not self.mapper.mapid(atm[0], mtype='protein',
to='internal') in self.altconformations])
hetatoms.update(hetatoms_res)
+ write_message("Hetero atoms determined (n={})\n".format(len(hetatoms)), mtype='debug')
hetatoms = dict(hetatoms) # make it a dict with idx as key and OBAtom as value
lig = pybel.ob.OBMol() # new ligand mol
@@ -305,6 +312,7 @@ class LigandFinder:
# ids of all neighbours of obatom
neighbours[idx] = set([neighbour_atom.GetIdx() for neighbour_atom
in pybel.ob.OBAtomAtomIter(obatom)]) & set(hetatoms.keys())
+ write_message("Atom neighbours mapped\n", mtype='debug')
##############################################################
# map the old atom idx of OBMol to the new idx of the ligand #
@@ -329,6 +337,8 @@ class LigandFinder:
lig.title = ':'.join((rname, rchain, str(rnum)))
self.mapper.ligandmaps[lig.title] = mapold
+ write_message("Renumerated molecule generated\n", mtype='debug')
+
atomorder = canonicalize(lig)
can_to_pdb = {}
@@ -354,7 +364,7 @@ class LigandFinder:
# Only residues with at least one HETATM entry are processed as ligands
het_atoms = []
for atm in pybel.ob.OBResidueAtomIter(obres):
- het_atoms.append(obres.IsHetAtom(atm))
+ het_atoms.append(obres.IsHetAtom(atm))
if True in het_atoms:
return True
return False
@@ -364,6 +374,9 @@ class LigandFinder:
"""Given an OpenBabel Molecule, get all ligands, their names, and water"""
candidates1 = [o for o in pybel.ob.OBResidueIter(self.proteincomplex.OBMol) if not o.GetResidueProperty(9) and self.is_het_residue(o)]
+
+ if config.DNARECEPTOR: # If DNA is the receptor, don't consider DNA as a ligand
+ candidates1 = [res for res in candidates1 if res.GetName() not in config.DNA+config.RNA]
all_lignames = set([a.GetName() for a in candidates1])
water = [o for o in pybel.ob.OBResidueIter(self.proteincomplex.OBMol) if o.GetResidueProperty(9)]
@@ -396,7 +409,8 @@ class LigandFinder:
(link.id2, link.chain2, link.pos2)] for link in
[c for c in self.covalent if c.id1 in self.lignames_kept and c.id2 in self.lignames_kept and
c.conf1 in ['A', ''] and c.conf2 in ['A', '']
- and (c.id1, c.chain1, c.pos1) in residues and (c.id2, c.chain2, c.pos2) in residues]]
+ and (c.id1, c.chain1, c.pos1) in residues
+ and (c.id2, c.chain2, c.pos2) in residues]]
kmers = cluster_doubles(ligdoubles)
if not kmers: # No ligand kmers, just normal independent ligands
return [[residues[res]] for res in residues]
@@ -422,10 +436,11 @@ class Mapper:
def __init__(self):
self.proteinmap = None # Map internal atom IDs of protein residues to original PDB Atom IDs
self.ligandmaps = {} # Map IDs of new ligand molecules to internal IDs (or PDB IDs?)
+ self.original_structure = None
def mapid(self, idx, mtype, bsid=None, to='original'): # Mapping to original IDs is standard for ligands
- # #@todo Check for correct type of idx
- # #@todo Include more safety checks
+ if mtype == 'reversed': # Needed to map internal ID back to original protein ID
+ return self.reversed_proteinmap[idx]
if mtype == 'protein':
return self.proteinmap[idx]
elif mtype == 'ligand':
@@ -434,7 +449,13 @@ class Mapper:
elif to == 'original':
return self.proteinmap[self.ligandmaps[bsid][idx]]
- # #@todo Include chains, resnr and positions here!
+ def id_to_atom(self, idx):
+ """Returns the atom for a given original ligand ID.
+ To do this, the ID is mapped to the protein first and then the atom returned.
+ """
+ mapped_idx = self.mapid(idx, 'reversed')
+ return pybel.Atom(self.original_structure.GetAtom(mapped_idx))
+
class Mol:
@@ -452,47 +473,51 @@ class Mol:
def hydrophobic_atoms(self, all_atoms):
"""Select all carbon atoms which have only carbons and/or hydrogens as direct neighbors."""
atom_set = []
- data = namedtuple('hydrophobic', 'atom orig_idx')
+ data = namedtuple('hydrophobic', 'atom orig_atom orig_idx')
atm = [a for a in all_atoms if a.atomicnum == 6 and set([natom.GetAtomicNum() for natom
in pybel.ob.OBAtomAtomIter(a.OBAtom)]).issubset(
{1, 6})]
for atom in atm:
orig_idx = self.Mapper.mapid(atom.idx, mtype=self.mtype, bsid=self.bsid)
+ orig_atom = self.Mapper.id_to_atom(orig_idx)
if atom.idx not in self.altconf:
- atom_set.append(data(atom=atom, orig_idx=orig_idx))
+ atom_set.append(data(atom=atom, orig_atom=orig_atom, orig_idx=orig_idx))
return atom_set
def find_hba(self, all_atoms):
"""Find all possible hydrogen bond acceptors"""
- data = namedtuple('hbondacceptor', 'a a_orig_idx type')
+ data = namedtuple('hbondacceptor', 'a a_orig_atom a_orig_idx type')
a_set = []
for atom in itertools.ifilter(lambda at: at.OBAtom.IsHbondAcceptor(), all_atoms):
if atom.atomicnum not in [9, 17, 35, 53] and atom.idx not in self.altconf: # Exclude halogen atoms
a_orig_idx = self.Mapper.mapid(atom.idx, mtype=self.mtype, bsid=self.bsid)
- a_set.append(data(a=atom, a_orig_idx=a_orig_idx, type='regular'))
+ a_orig_atom = self.Mapper.id_to_atom(a_orig_idx)
+ a_set.append(data(a=atom, a_orig_atom=a_orig_atom, a_orig_idx=a_orig_idx, type='regular'))
return a_set
def find_hbd(self, all_atoms, hydroph_atoms):
"""Find all possible strong and weak hydrogen bonds donors (all hydrophobic C-H pairings)"""
donor_pairs = []
- data = namedtuple('hbonddonor', 'd d_orig_idx h type')
+ data = namedtuple('hbonddonor', 'd d_orig_atom d_orig_idx h type')
for donor in [a for a in all_atoms if a.OBAtom.IsHbondDonor() and a.idx not in self.altconf]:
in_ring = False
if not in_ring:
for adj_atom in [a for a in pybel.ob.OBAtomAtomIter(donor.OBAtom) if a.IsHbondDonorH()]:
d_orig_idx = self.Mapper.mapid(donor.idx, mtype=self.mtype, bsid=self.bsid)
- donor_pairs.append(data(d=donor, d_orig_idx=d_orig_idx, h=pybel.Atom(adj_atom), type='regular'))
+ d_orig_atom = self.Mapper.id_to_atom(d_orig_idx)
+ donor_pairs.append(data(d=donor, d_orig_atom=d_orig_atom, d_orig_idx=d_orig_idx, h=pybel.Atom(adj_atom), type='regular'))
for carbon in hydroph_atoms:
for adj_atom in [a for a in pybel.ob.OBAtomAtomIter(carbon.atom.OBAtom) if a.GetAtomicNum() == 1]:
d_orig_idx = self.Mapper.mapid(carbon.atom.idx, mtype=self.mtype, bsid=self.bsid)
- donor_pairs.append(data(d=carbon, d_orig_idx=d_orig_idx, h=pybel.Atom(adj_atom), type='weak'))
+ d_orig_atom = self.Mapper.id_to_atom(d_orig_idx)
+ donor_pairs.append(data(d=carbon, d_orig_atom=d_orig_atom, d_orig_idx=d_orig_idx, h=pybel.Atom(adj_atom), type='weak'))
return donor_pairs
def find_rings(self, mol, all_atoms):
"""Find rings and return only aromatic.
Rings have to be sufficiently planar OR be detected by OpenBabel as aromatic."""
- data = namedtuple('aromatic_ring', 'atoms atoms_orig_idx normal obj center type')
+ data = namedtuple('aromatic_ring', 'atoms orig_atoms atoms_orig_idx normal obj center type')
rings = []
aromatic_amino = ['TYR', 'TRP', 'HIS', 'PHE']
ring_candidates = mol.OBMol.GetSSSR()
@@ -511,7 +536,9 @@ class Mol:
ringv1 = vector(ring_atms[0], ring_atms[1])
ringv2 = vector(ring_atms[2], ring_atms[0])
atoms_orig_idx = [self.Mapper.mapid(r_atom.idx, mtype=self.mtype, bsid=self.bsid) for r_atom in r_atoms]
+ orig_atoms = [self.Mapper.id_to_atom(idx) for idx in atoms_orig_idx]
rings.append(data(atoms=r_atoms,
+ orig_atoms=orig_atoms,
atoms_orig_idx=atoms_orig_idx,
normal=normalize_vector(np.cross(ringv1, ringv2)),
obj=ring,
@@ -981,13 +1008,14 @@ class Ligand(Mol):
######
donor_pairs = []
- data = namedtuple('hbonddonor', 'd d_orig_idx h type')
+ data = namedtuple('hbonddonor', 'd d_orig_atom d_orig_idx h type')
for donor in self.all_atoms:
pdbidx = self.Mapper.mapid(donor.idx, mtype='ligand', bsid=self.bsid, to='original')
d = cclass.atoms[self.pdb_to_idx_mapping[pdbidx]]
if d.OBAtom.IsHbondDonor():
for adj_atom in [a for a in pybel.ob.OBAtomAtomIter(d.OBAtom) if a.IsHbondDonorH()]:
- donor_pairs.append(data(d=donor, d_orig_idx=pdbidx, h=pybel.Atom(adj_atom), type='regular'))
+ d_orig_atom = self.Mapper.id_to_atom(pdbidx)
+ donor_pairs.append(data(d=donor, d_orig_atom=d_orig_atom, d_orig_idx=pdbidx, h=pybel.Atom(adj_atom), type='regular'))
self.hbond_don_atom_pairs = donor_pairs
#######
@@ -1009,9 +1037,11 @@ class Ligand(Mol):
self.halogenbond_don = self.find_hal(self.all_atoms)
self.metal_binding = self.find_metal_binding(self.all_atoms, self.water)
self.metals = []
- data = namedtuple('metal', 'm m_orig_idx')
+ data = namedtuple('metal', 'm orig_m m_orig_idx')
for a in [a for a in self.all_atoms if a.type.upper() in config.METAL_IONS]:
- self.metals.append(data(m=a, m_orig_idx=self.Mapper.mapid(a.idx, mtype=self.mtype, bsid=self.bsid)))
+ m_orig_idx = self.Mapper.mapid(a.idx, mtype=self.mtype, bsid=self.bsid)
+ orig_m = self.Mapper.id_to_atom(m_orig_idx)
+ self.metals.append(data(m=a, m_orig_idx=m_orig_idx, orig_m=orig_m))
self.num_hba, self.num_hbd = len(self.hbond_acc_atoms), len(self.hbond_don_atom_pairs)
self.num_hal = len(self.halogenbond_don)
@@ -1064,14 +1094,15 @@ class Ligand(Mol):
def find_hal(self, atoms):
"""Look for halogen bond donors (X-C, with X=F, Cl, Br, I)"""
- data = namedtuple('hal_donor', 'x x_orig_idx c c_orig_idx')
+ data = namedtuple('hal_donor', 'x orig_x x_orig_idx c c_orig_idx')
a_set = []
for a in atoms:
if self.is_functional_group(a, 'halocarbon'):
n_atoms = [na for na in pybel.ob.OBAtomAtomIter(a.OBAtom) if na.GetAtomicNum() == 6]
x_orig_idx = self.Mapper.mapid(a.idx, mtype=self.mtype, bsid=self.bsid)
+ orig_x = self.Mapper.id_to_atom(x_orig_idx)
c_orig_idx = [self.Mapper.mapid(na.GetIdx(), mtype=self.mtype, bsid=self.bsid) for na in n_atoms]
- a_set.append(data(x=a, x_orig_idx=x_orig_idx, c=pybel.Atom(n_atoms[0]), c_orig_idx=c_orig_idx))
+ a_set.append(data(x=a, orig_x=orig_x, x_orig_idx=x_orig_idx, c=pybel.Atom(n_atoms[0]), c_orig_idx=c_orig_idx))
if len(a_set) != 0:
write_message('Ligand contains %i halogen atom(s).\n' % len(a_set), indent=True)
return a_set
@@ -1082,18 +1113,19 @@ class Ligand(Mol):
as mentioned in 'Cation-pi interactions in ligand recognition and catalysis' (Zacharias et al., 2002)).
Identify negatively charged groups in the ligand.
"""
- data = namedtuple('lcharge', 'atoms atoms_orig_idx type center fgroup')
+ data = namedtuple('lcharge', 'atoms orig_atoms atoms_orig_idx type center fgroup')
a_set = []
for a in all_atoms:
a_orig_idx = self.Mapper.mapid(a.idx, mtype=self.mtype, bsid=self.bsid)
+ a_orig = self.Mapper.id_to_atom(a_orig_idx)
if self.is_functional_group(a, 'quartamine'):
- a_set.append(data(atoms=[a, ], atoms_orig_idx=[a_orig_idx, ], type='positive',
+ a_set.append(data(atoms=[a, ], orig_atoms = [a_orig, ], atoms_orig_idx=[a_orig_idx, ], type='positive',
center=list(a.coords), fgroup='quartamine'))
elif self.is_functional_group(a, 'tertamine'):
- a_set.append(data(atoms=[a, ], atoms_orig_idx=[a_orig_idx, ], type='positive', center=list(a.coords),
+ a_set.append(data(atoms=[a, ], orig_atoms = [a_orig, ], atoms_orig_idx=[a_orig_idx, ], type='positive', center=list(a.coords),
fgroup='tertamine'))
if self.is_functional_group(a, 'sulfonium'):
- a_set.append(data(atoms=[a, ], atoms_orig_idx=[a_orig_idx, ], type='positive', center=list(a.coords),
+ a_set.append(data(atoms=[a, ], orig_atoms = [a_orig, ], atoms_orig_idx=[a_orig_idx, ], type='positive', center=list(a.coords),
fgroup='sulfonium'))
if self.is_functional_group(a, 'phosphate'):
a_contributing = [a, ]
@@ -1101,7 +1133,8 @@ class Ligand(Mol):
[a_contributing.append(pybel.Atom(neighbor)) for neighbor in pybel.ob.OBAtomAtomIter(a.OBAtom)]
[a_contributing_orig_idx.append(self.Mapper.mapid(neighbor.idx, mtype=self.mtype, bsid=self.bsid))
for neighbor in a_contributing]
- a_set.append(data(atoms=a_contributing, atoms_orig_idx=a_contributing_orig_idx, type='negative',
+ orig_contributing = [self.Mapper.id_to_atom(idx) for idx in a_contributing_orig_idx]
+ a_set.append(data(atoms=a_contributing, orig_atoms=orig_contributing, atoms_orig_idx=a_contributing_orig_idx, type='negative',
center=a.coords, fgroup='phosphate'))
if self.is_functional_group(a, 'sulfonicacid'):
a_contributing = [a, ]
@@ -1110,7 +1143,8 @@ class Ligand(Mol):
neighbor.GetAtomicNum() == 8]
[a_contributing_orig_idx.append(self.Mapper.mapid(neighbor.idx, mtype=self.mtype, bsid=self.bsid))
for neighbor in a_contributing]
- a_set.append(data(atoms=a_contributing, atoms_orig_idx=a_contributing_orig_idx, type='negative',
+ orig_contributing = [self.Mapper.id_to_atom(idx) for idx in a_contributing_orig_idx]
+ a_set.append(data(atoms=a_contributing, orig_atoms=orig_contributing, atoms_orig_idx=a_contributing_orig_idx, type='negative',
center=a.coords, fgroup='sulfonicacid'))
elif self.is_functional_group(a, 'sulfate'):
a_contributing = [a, ]
@@ -1118,21 +1152,24 @@ class Ligand(Mol):
[a_contributing_orig_idx.append(self.Mapper.mapid(neighbor.idx, mtype=self.mtype, bsid=self.bsid))
for neighbor in a_contributing]
[a_contributing.append(pybel.Atom(neighbor)) for neighbor in pybel.ob.OBAtomAtomIter(a.OBAtom)]
- a_set.append(data(atoms=a_contributing, atoms_orig_idx=a_contributing_orig_idx, type='negative',
+ orig_contributing = [self.Mapper.id_to_atom(idx) for idx in a_contributing_orig_idx]
+ a_set.append(data(atoms=a_contributing, orig_atoms=orig_contributing, atoms_orig_idx=a_contributing_orig_idx, type='negative',
center=a.coords, fgroup='sulfate'))
if self.is_functional_group(a, 'carboxylate'):
a_contributing = [pybel.Atom(neighbor) for neighbor in pybel.ob.OBAtomAtomIter(a.OBAtom)
if neighbor.GetAtomicNum() == 8]
a_contributing_orig_idx = [self.Mapper.mapid(neighbor.idx, mtype=self.mtype, bsid=self.bsid)
for neighbor in a_contributing]
- a_set.append(data(atoms=a_contributing, atoms_orig_idx=a_contributing_orig_idx, type='negative',
+ orig_contributing = [self.Mapper.id_to_atom(idx) for idx in a_contributing_orig_idx]
+ a_set.append(data(atoms=a_contributing, orig_atoms=orig_contributing, atoms_orig_idx=a_contributing_orig_idx, type='negative',
center=centroid([a.coords for a in a_contributing]), fgroup='carboxylate'))
elif self.is_functional_group(a, 'guanidine'):
a_contributing = [pybel.Atom(neighbor) for neighbor in pybel.ob.OBAtomAtomIter(a.OBAtom)
if neighbor.GetAtomicNum() == 7]
a_contributing_orig_idx = [self.Mapper.mapid(neighbor.idx, mtype=self.mtype, bsid=self.bsid)
for neighbor in a_contributing]
- a_set.append(data(atoms=a_contributing, atoms_orig_idx=a_contributing_orig_idx, type='positive',
+ orig_contributing = [self.Mapper.id_to_atom(idx) for idx in a_contributing_orig_idx]
+ a_set.append(data(atoms=a_contributing, orig_atoms=orig_contributing, atoms_orig_idx=a_contributing_orig_idx, type='positive',
center=a.coords, fgroup='guanidine'))
return a_set
@@ -1142,11 +1179,11 @@ class Ligand(Mol):
nitrogen from imidazole; sulfur from thiolate.
"""
a_set = []
- data = namedtuple('metal_binding', 'atom atom_orig_idx type fgroup restype resnr reschain location')
+ data = namedtuple('metal_binding', 'atom orig_atom atom_orig_idx type fgroup restype resnr reschain location')
for oxygen in water_oxygens:
a_set.append(data(atom=oxygen.oxy, atom_orig_idx=oxygen.oxy_orig_idx, type='O', fgroup='water',
restype=whichrestype(oxygen.oxy), resnr=whichresnumber(oxygen.oxy),
- reschain=whichchain(oxygen.oxy), location='water'))
+ reschain=whichchain(oxygen.oxy), location='water', orig_atom=self.Mapper.id_to_atom(oxygen.oxy_orig_idx)))
# #@todo Refactor code
for a in lig_atoms:
a_orig_idx = self.Mapper.mapid(a.idx, mtype='ligand', bsid=self.bsid)
@@ -1157,11 +1194,11 @@ class Ligand(Mol):
if n_atoms_atomicnum.count('1') == 1 and len(n_atoms_atomicnum) == 2: # Oxygen in alcohol (R-[O]-H)
a_set.append(data(atom=a, atom_orig_idx=a_orig_idx, type='O', fgroup='alcohol',
restype=self.hetid, resnr=self.position, reschain=self.chain,
- location='ligand'))
+ location='ligand', orig_atom=self.Mapper.id_to_atom(a_orig_idx)))
if True in [n.IsAromatic() for n in n_atoms] and not a.OBAtom.IsAromatic(): # Phenolate oxygen
a_set.append(data(atom=a, atom_orig_idx=a_orig_idx, type='O', fgroup='phenolate',
restype=self.hetid, resnr=self.position, reschain=self.chain,
- location='ligand'))
+ location='ligand', orig_atom=self.Mapper.id_to_atom(a_orig_idx)))
if a.atomicnum == 6: # It's a carbon atom
if n_atoms_atomicnum.count(8) == 2 and n_atoms_atomicnum.count(6) == 1: # It's a carboxylate group
for neighbor in [n for n in n_atoms if n.GetAtomicNum() == 8]:
@@ -1170,7 +1207,7 @@ class Ligand(Mol):
fgroup='carboxylate',
restype=self.hetid,
resnr=self.position, reschain=self.chain,
- location='ligand'))
+ location='ligand', orig_atom=self.Mapper.id_to_atom(a_orig_idx)))
if a.atomicnum == 15: # It's a phosphor atom
if n_atoms_atomicnum.count(8) >= 3: # It's a phosphoryl
for neighbor in [n for n in n_atoms if n.GetAtomicNum() == 8]:
@@ -1179,28 +1216,28 @@ class Ligand(Mol):
fgroup='phosphoryl',
restype=self.hetid,
resnr=self.position, reschain=self.chain,
- location='ligand'))
+ location='ligand', orig_atom=self.Mapper.id_to_atom(a_orig_idx)))
if n_atoms_atomicnum.count(8) == 2: # It's another phosphor-containing group #@todo (correct name?)
for neighbor in [n for n in n_atoms if n.GetAtomicNum() == 8]:
neighbor_orig_idx = self.Mapper.mapid(neighbor.GetIdx(), mtype='ligand', bsid=self.bsid)
a_set.append(data(atom=pybel.Atom(neighbor), atom_orig_idx=neighbor_orig_idx, type='O',
fgroup='phosphor.other', restype=self.hetid,
resnr=self.position,
- reschain=self.chain, location='ligand'))
+ reschain=self.chain, location='ligand', orig_atom=self.Mapper.id_to_atom(a_orig_idx)))
if a.atomicnum == 7: # It's a nitrogen atom
if n_atoms_atomicnum.count(6) == 2: # It's imidazole/pyrrole or similar
a_set.append(data(atom=a, atom_orig_idx=a_orig_idx, type='N', fgroup='imidazole/pyrrole',
restype=self.hetid, resnr=self.position, reschain=self.chain,
- location='ligand'))
+ location='ligand', orig_atom=self.Mapper.id_to_atom(a_orig_idx)))
if a.atomicnum == 16: # It's a sulfur atom
if True in [n.IsAromatic() for n in n_atoms] and not a.OBAtom.IsAromatic(): # Thiolate
a_set.append(data(atom=a, atom_orig_idx=a_orig_idx, type='S', fgroup='thiolate',
restype=self.hetid, resnr=self.position, reschain=self.chain,
- location='ligand'))
+ location='ligand', orig_atom=self.Mapper.id_to_atom(a_orig_idx)))
if set(n_atoms_atomicnum) == {26}: # Sulfur in Iron sulfur cluster
a_set.append(data(atom=a, atom_orig_idx=a_orig_idx, type='S', fgroup='iron-sulfur.cluster',
restype=self.hetid, resnr=self.position, reschain=self.chain,
- location='ligand'))
+ location='ligand', orig_atom=self.Mapper.id_to_atom(a_orig_idx)))
return a_set
@@ -1247,6 +1284,7 @@ class PDBComplex:
pdbparser = PDBParser(pdbpath, as_string=as_string) # Parse PDB file to find errors and get additonal data
# #@todo Refactor and rename here
self.Mapper.proteinmap = pdbparser.proteinmap
+ self.Mapper.reversed_proteinmap = inv_map = {v: k for k, v in self.Mapper.proteinmap.iteritems()}
self.modres = pdbparser.modres
self.covalent = pdbparser.covalent
self.altconf = pdbparser.altconformations
@@ -1270,8 +1308,12 @@ class PDBComplex:
else:
self.sourcefiles['filename'] = os.path.basename(self.sourcefiles['pdbcomplex'])
self.protcomplex, self.filetype = read_pdb(self.sourcefiles['pdbcomplex'], as_string=as_string)
+
+ # Update the model in the Mapper class instance
+ self.Mapper.original_structure = self.protcomplex.OBMol
write_message('PDB structure successfully read.\n')
+
# Determine (temporary) PyMOL Name from Filename
self.pymol_name = pdbpath.split('/')[-1].split('.')[0] + '-Protein'
# Replace characters causing problems in PyMOL
@@ -1283,19 +1325,24 @@ class PDBComplex:
self.pymol_name = potential_name
write_message("Pymol Name set as: '%s'\n" % self.pymol_name, mtype='debug')
- self.protcomplex.OBMol.AddPolarHydrogens()
- for atm in self.protcomplex:
- self.atoms[atm.idx] = atm
-
# Extract and prepare ligands
ligandfinder = LigandFinder(self.protcomplex, self.altconf, self.modres, self.covalent, self.Mapper)
self.ligands = ligandfinder.ligands
self.excluded = ligandfinder.excluded
+ # Add polar hydrogens
+ self.protcomplex.OBMol.AddPolarHydrogens()
+ for atm in self.protcomplex:
+ self.atoms[atm.idx] = atm
+ write_message("Assigned polar hydrogens\n", mtype='debug')
+
if len(self.excluded) != 0:
write_message("Excluded molecules as ligands: %s\n" % ','.join([lig for lig in self.excluded]))
- self.resis = [obres for obres in pybel.ob.OBResidueIter(self.protcomplex.OBMol) if obres.GetResidueProperty(0)]
+ if config.DNARECEPTOR:
+ self.resis = [obres for obres in pybel.ob.OBResidueIter(self.protcomplex.OBMol) if obres.GetName() in config.DNA+config.RNA]
+ else:
+ self.resis = [obres for obres in pybel.ob.OBResidueIter(self.protcomplex.OBMol) if obres.GetResidueProperty(0)]
num_ligs = len(self.ligands)
if num_ligs == 1:
diff --git a/plip/modules/pymolplip.py b/plip/modules/pymolplip.py
index 166064f..b654781 100644
--- a/plip/modules/pymolplip.py
+++ b/plip/modules/pymolplip.py
@@ -1,20 +1,8 @@
"""
Protein-Ligand Interaction Profiler - Analyze and visualize protein-ligand interactions in PDB files.
pymolplip.py - Visualization class for PyMOL.
-Copyright 2014-2015 Sebastian Salentin
-
-Licensed under the Apache License, Version 2.0 (the "License");
-you may not use this file except in compliance with the License.
-You may obtain a copy of the License at
-
- http://www.apache.org/licenses/LICENSE-2.0
-
-Unless required by applicable law or agreed to in writing, software
-distributed under the License is distributed on an "AS IS" BASIS,
-WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-See the License for the specific language governing permissions and
-limitations under the License.
"""
+
from pymol import cmd
from time import sleep
import sys
@@ -98,6 +86,7 @@ class PyMOLVisualizer:
if not len(hydroph.bs_ids) == 0:
self.select_by_ids('Hydrophobic-P', hydroph.bs_ids, restrict=self.protname)
self.select_by_ids('Hydrophobic-L', hydroph.lig_ids, restrict=self.ligname)
+
for i in hydroph.pairs_ids:
cmd.select('tmp_bs', 'id %i & %s' % (i[0], self.protname))
cmd.select('tmp_lig', 'id %i & %s' % (i[1], self.ligname))
@@ -291,7 +280,11 @@ class PyMOLVisualizer:
selections = cmd.get_names("selections")
for selection in selections:
- if cmd.count_atoms(selection) == 0:
+ try:
+ empty = len(cmd.get_model(selection).atom) == 0
+ except:
+ empty = True
+ if empty:
cmd.delete(selection)
cmd.deselect()
cmd.delete('tmp*')
@@ -401,6 +394,7 @@ class PyMOLVisualizer:
cmd.set('direct', 0)
cmd.set('ray_shadow', 0) # Gives the molecules a flat, modern look
cmd.set('ambient_occlusion_mode', 1)
+ cmd.set('ray_opaque_background', 0) # Transparent background
def adapt_for_peptides(self):
"""Adapt visualization for peptide ligands and interchain contacts"""
@@ -412,6 +406,10 @@ class PyMOLVisualizer:
cmd.remove('%sCartoon and chain %s' % (self.protname, self.plcomplex.chain))
cmd.set('cartoon_side_chain_helper', 0)
+ def adapt_for_intra(self):
+ """Adapt visualization for intra-protein interactions"""
+
+
@@ -456,3 +454,6 @@ class PyMOLVisualizer:
if self.ligandtype in ['PEPTIDE', 'INTRA']:
self.adapt_for_peptides()
+
+ if self.ligandtype == 'INTRA':
+ self.adapt_for_intra()
diff --git a/plip/modules/report.py b/plip/modules/report.py
index b45b998..d622bff 100644
--- a/plip/modules/report.py
+++ b/plip/modules/report.py
@@ -1,19 +1,6 @@
"""
Protein-Ligand Interaction Profiler - Analyze and visualize protein-ligand interactions in PDB files.
report.py - Write PLIP results to output files.
-Copyright 2014-2015 Sebastian Salentin
-
-Licensed under the Apache License, Version 2.0 (the "License");
-you may not use this file except in compliance with the License.
-You may obtain a copy of the License at
-
- http://www.apache.org/licenses/LICENSE-2.0
-
-Unless required by applicable law or agreed to in writing, software
-distributed under the License is distributed on an "AS IS" BASIS,
-WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-See the License for the specific language governing permissions and
-limitations under the License.
"""
@@ -21,12 +8,13 @@ limitations under the License.
import time
from operator import itemgetter
import sys
+import config
# External libraries
import lxml.etree as et
-__version__ = '1.3.3'
+__version__ = '1.3.4'
class StructureReport:
"""Creates reports (xml or txt) for one structure/"""
@@ -48,6 +36,11 @@ class StructureReport:
citation_information = et.SubElement(report, 'citation_information')
citation_information.text = "Salentin,S. et al. PLIP: fully automated protein-ligand interaction profiler. " \
"Nucl. Acids Res. (1 July 2015) 43 (W1): W443-W447. doi: 10.1093/nar/gkv315"
+ mode = et.SubElement(report, 'mode')
+ if config.DNARECEPTOR:
+ mode.text = 'dna_receptor'
+ else:
+ mode.text = 'default'
pdbid = et.SubElement(report, 'pdbid')
pdbid.text = self.mol.pymol_name.upper()
filetype = et.SubElement(report, 'filetype')
@@ -74,6 +67,8 @@ class StructureReport:
textlines.append('Nucl. Acids Res. (1 July 2015) 43 (W1): W443-W447. doi: 10.1093/nar/gkv315\n')
if len(self.excluded) != 0:
textlines.append('Excluded molecules as ligands: %s\n' % ','.join([lig for lig in self.excluded]))
+ if config.DNARECEPTOR:
+ textlines.append('DNA/RNA in structure was chosen as the receptor part.\n')
return textlines
def get_bindingsite_data(self):
@@ -134,11 +129,11 @@ class BindingSiteReport:
# HYDROPHOBIC INTERACTIONS #
############################
- self.hydrophobic_features = ('RESNR', 'RESTYPE', 'RESCHAIN', 'DIST', 'LIGCARBONIDX', 'PROTCARBONIDX', 'LIGCOO',
+ self.hydrophobic_features = ('RESNR', 'RESTYPE', 'RESCHAIN', 'RESNR_LIG', 'RESTYPE_LIG', 'RESCHAIN_LIG', 'DIST', 'LIGCARBONIDX', 'PROTCARBONIDX', 'LIGCOO',
'PROTCOO')
self.hydrophobic_info = []
for hydroph in self.complex.hydrophobic_contacts:
- self.hydrophobic_info.append((hydroph.resnr, hydroph.restype, hydroph.reschain, '%.2f' % hydroph.distance,
+ self.hydrophobic_info.append((hydroph.resnr, hydroph.restype, hydroph.reschain, hydroph.resnr_l, hydroph.restype_l, hydroph.reschain_l, '%.2f' % hydroph.distance,
hydroph.ligatom_orig_idx, hydroph.bsatom_orig_idx, hydroph.ligatom.coords,
hydroph.bsatom.coords))
@@ -146,12 +141,12 @@ class BindingSiteReport:
# HYDROGEN BONDS #
##################
- self.hbond_features = ('RESNR', 'RESTYPE', 'RESCHAIN', 'SIDECHAIN', 'DIST_H-A', 'DIST_D-A', 'DON_ANGLE',
+ self.hbond_features = ('RESNR', 'RESTYPE', 'RESCHAIN', 'RESNR_LIG', 'RESTYPE_LIG', 'RESCHAIN_LIG', 'SIDECHAIN', 'DIST_H-A', 'DIST_D-A', 'DON_ANGLE',
'PROTISDON', 'DONORIDX', 'DONORTYPE', 'ACCEPTORIDX', 'ACCEPTORTYPE', 'LIGCOO', 'PROTCOO')
self.hbond_info = []
for hbond in self.complex.hbonds_pdon + self.complex.hbonds_ldon:
ligatom, protatom = (hbond.a, hbond.d) if hbond.protisdon else (hbond.d, hbond.a)
- self.hbond_info.append((hbond.resnr, hbond.restype, hbond.reschain, hbond.sidechain,
+ self.hbond_info.append((hbond.resnr, hbond.restype, hbond.reschain, hbond.resnr_l, hbond.restype_l, hbond.reschain_l, hbond.sidechain,
'%.2f' % hbond.distance_ah, '%.2f' % hbond.distance_ad, '%.2f' % hbond.angle,
hbond.protisdon, hbond.d_orig_idx, hbond.dtype, hbond.a_orig_idx, hbond.atype,
ligatom.coords, protatom.coords))
@@ -160,14 +155,14 @@ class BindingSiteReport:
# WATER-BRIDGES #
#################
- self.waterbridge_features = ('RESNR', 'RESTYPE', 'RESCHAIN', 'DIST_A-W', 'DIST_D-W', 'DON_ANGLE', 'WATER_ANGLE',
+ self.waterbridge_features = ('RESNR', 'RESTYPE', 'RESCHAIN', 'RESNR_LIG', 'RESTYPE_LIG', 'RESCHAIN_LIG', 'DIST_A-W', 'DIST_D-W', 'DON_ANGLE', 'WATER_ANGLE',
'PROTISDON', 'DONOR_IDX', 'DONORTYPE', 'ACCEPTOR_IDX', 'ACCEPTORTYPE', 'WATER_IDX',
'LIGCOO', 'PROTCOO', 'WATERCOO')
# The coordinate format is an exception here, since the interaction is not only between ligand and protein
self.waterbridge_info = []
for wbridge in self.complex.water_bridges:
lig, prot = (wbridge.a, wbridge.d) if wbridge.protisdon else (wbridge.d, wbridge.a)
- self.waterbridge_info.append((wbridge.resnr, wbridge.restype, wbridge.reschain,
+ self.waterbridge_info.append((wbridge.resnr, wbridge.restype, wbridge.reschain, wbridge.resnr_l, wbridge.restype_l, wbridge.reschain_l,
'%.2f' % wbridge.distance_aw, '%.2f' % wbridge.distance_dw,
'%.2f' % wbridge.d_angle, '%.2f' % wbridge.w_angle, wbridge.protisdon,
wbridge.d_orig_idx, wbridge.dtype, wbridge.a_orig_idx, wbridge.atype,
@@ -177,18 +172,18 @@ class BindingSiteReport:
# SALT BRIDGES #
################
- self.saltbridge_features = ('RESNR', 'RESTYPE', 'RESCHAIN', 'DIST', 'PROTISPOS', 'LIG_GROUP', 'LIG_IDX_LIST',
+ self.saltbridge_features = ('RESNR', 'RESTYPE', 'RESCHAIN', 'RESNR_LIG', 'RESTYPE_LIG', 'RESCHAIN_LIG', 'DIST', 'PROTISPOS', 'LIG_GROUP', 'LIG_IDX_LIST',
'LIGCOO', 'PROTCOO')
self.saltbridge_info = []
for sb in self.complex.saltbridge_lneg + self.complex.saltbridge_pneg:
if sb.protispos:
group, ids = sb.negative.fgroup, [str(x) for x in sb.negative.atoms_orig_idx]
- self.saltbridge_info.append((sb.resnr, sb.restype, sb.reschain, '%.2f' % sb.distance, sb.protispos,
+ self.saltbridge_info.append((sb.resnr, sb.restype, sb.reschain, sb.resnr_l, sb.restype_l, sb.reschain_l, '%.2f' % sb.distance, sb.protispos,
group.capitalize(), ",".join(ids),
tuple(sb.negative.center), tuple(sb.positive.center)))
else:
group, ids = sb.positive.fgroup, [str(x) for x in sb.positive.atoms_orig_idx]
- self.saltbridge_info.append((sb.resnr, sb.restype, sb.reschain, '%.2f' % sb.distance, sb.protispos,
+ self.saltbridge_info.append((sb.resnr, sb.restype, sb.reschain, sb.resnr_l, sb.restype_l, sb.reschain_l, '%.2f' % sb.distance, sb.protispos,
group.capitalize(), ",".join(ids),
tuple(sb.positive.center), tuple(sb.negative.center)))
@@ -196,12 +191,12 @@ class BindingSiteReport:
# PI-STACKING #
###############
- self.pistacking_features = ('RESNR', 'RESTYPE', 'RESCHAIN', 'CENTDIST', 'ANGLE', 'OFFSET', 'TYPE',
+ self.pistacking_features = ('RESNR', 'RESTYPE', 'RESCHAIN', 'RESNR_LIG', 'RESTYPE_LIG', 'RESCHAIN_LIG', 'CENTDIST', 'ANGLE', 'OFFSET', 'TYPE',
'LIG_IDX_LIST', 'LIGCOO', 'PROTCOO')
self.pistacking_info = []
for stack in self.complex.pistacking:
ids = [str(x) for x in stack.ligandring.atoms_orig_idx]
- self.pistacking_info.append((stack.resnr, stack.restype, stack.reschain, '%.2f' % stack.distance,
+ self.pistacking_info.append((stack.resnr, stack.restype, stack.reschain, stack.resnr_l, stack.restype_l, stack.reschain_l, '%.2f' % stack.distance,
'%.2f' % stack.angle, '%.2f' % stack.offset, stack.type, ",".join(ids),
tuple(stack.ligandring.center), tuple(stack.proteinring.center)))
@@ -209,20 +204,20 @@ class BindingSiteReport:
# PI-CATION INTERACTIONS #
##########################
- self.pication_features = ('RESNR', 'RESTYPE', 'RESCHAIN', 'DIST', 'OFFSET', 'PROTCHARGED', 'LIG_GROUP',
+ self.pication_features = ('RESNR', 'RESTYPE', 'RESCHAIN', 'RESNR_LIG', 'RESTYPE_LIG', 'RESCHAIN_LIG', 'DIST', 'OFFSET', 'PROTCHARGED', 'LIG_GROUP',
'LIG_IDX_LIST', 'LIGCOO', 'PROTCOO')
self.pication_info = []
for picat in self.complex.pication_laro + self.complex.pication_paro:
if picat.protcharged:
ids = [str(x) for x in picat.ring.atoms_orig_idx]
group = 'Aromatic'
- self.pication_info.append((picat.resnr, picat.restype, picat.reschain, '%.2f' % picat.distance,
+ self.pication_info.append((picat.resnr, picat.restype, picat.reschain, picat.resnr_l, picat.restype_l, picat.reschain_l, '%.2f' % picat.distance,
'%.2f' % picat.offset, picat.protcharged, group, ",".join(ids),
tuple(picat.ring.center), tuple(picat.charge.center)))
else:
ids = [str(x) for x in picat.charge.atoms_orig_idx]
group = picat.charge.fgroup
- self.pication_info.append((picat.resnr, picat.restype, picat.reschain, '%.2f' % picat.distance,
+ self.pication_info.append((picat.resnr, picat.restype, picat.reschain, picat.resnr_l, picat.restype_l, picat.reschain_l, '%.2f' % picat.distance,
'%.2f' % picat.offset, picat.protcharged, group, ",".join(ids),
tuple(picat.charge.center), tuple(picat.ring.center)))
@@ -230,11 +225,11 @@ class BindingSiteReport:
# HALOGEN BONDS #
#################
- self.halogen_features = ('RESNR', 'RESTYPE', 'RESCHAIN', 'SIDECHAIN', 'DIST', 'DON_ANGLE', 'ACC_ANGLE',
+ self.halogen_features = ('RESNR', 'RESTYPE', 'RESCHAIN', 'RESNR_LIG', 'RESTYPE_LIG', 'RESCHAIN_LIG', 'SIDECHAIN', 'DIST', 'DON_ANGLE', 'ACC_ANGLE',
'DON_IDX', 'DONORTYPE', 'ACC_IDX', 'ACCEPTORTYPE', 'LIGCOO', 'PROTCOO')
self.halogen_info = []
for halogen in self.complex.halogen_bonds:
- self.halogen_info.append((halogen.resnr, halogen.restype, halogen.reschain, halogen.sidechain,
+ self.halogen_info.append((halogen.resnr, halogen.restype, halogen.reschain, halogen.resnr_l, halogen.restype_l, halogen.reschain_l, halogen.sidechain,
'%.2f' % halogen.distance, '%.2f' % halogen.don_angle, '%.2f' % halogen.acc_angle,
halogen.don_orig_idx, halogen.donortype,
halogen.acc_orig_idx, halogen.acctype,
@@ -244,13 +239,13 @@ class BindingSiteReport:
# METAL COMPLEXES #
###################
- self.metal_features = ('RESNR', 'RESTYPE', 'RESCHAIN', 'METAL_IDX', 'METAL_TYPE', 'TARGET_IDX', 'TARGET_TYPE',
+ self.metal_features = ('RESNR', 'RESTYPE', 'RESCHAIN', 'RESNR_LIG', 'RESTYPE_LIG', 'RESCHAIN_LIG', 'METAL_IDX', 'METAL_TYPE', 'TARGET_IDX', 'TARGET_TYPE',
'COORDINATION', 'DIST', 'LOCATION', 'RMS', 'GEOMETRY', 'COMPLEXNUM', 'METALCOO',
'TARGETCOO')
self.metal_info = []
# Coordinate format here is non-standard since the interaction partner can be either ligand or protein
for m in self.complex.metal_complexes:
- self.metal_info.append((m.resnr, m.restype, m.reschain, m.metal_orig_idx, m.metal_type,
+ self.metal_info.append((m.resnr, m.restype, m.reschain, m.resnr_l, m.restype_l, m.reschain_l, m.metal_orig_idx, m.metal_type,
m.target_orig_idx, m.target_type, m.coordination_num, '%.2f' % m.distance,
m.location, '%.2f' % m.rms, m.geometry, str(m.complexnum), m.metal.coords,
m.target.atom.coords))
diff --git a/plip/modules/supplemental.py b/plip/modules/supplemental.py
index be56ccf..a94cfc4 100644
--- a/plip/modules/supplemental.py
+++ b/plip/modules/supplemental.py
@@ -1,26 +1,14 @@
"""
Protein-Ligand Interaction Profiler - Analyze and visualize protein-ligand interactions in PDB files.
supplemental.py - Supplemental functions for PLIP analysis.
-Copyright 2014-2015 Sebastian Salentin, Joachim Haupt
-
-Licensed under the Apache License, Version 2.0 (the "License");
-you may not use this file except in compliance with the License.
-You may obtain a copy of the License at
-
- http://www.apache.org/licenses/LICENSE-2.0
-
-Unless required by applicable law or agreed to in writing, software
-distributed under the License is distributed on an "AS IS" BASIS,
-WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-See the License for the specific language governing permissions and
-limitations under the License.
"""
# Compatibility
from __future__ import print_function
+from __future__ import absolute_import
# PLIP Modules
-import config
+import plip.modules.config as config
# Python standard library
import re
@@ -300,9 +288,9 @@ def ring_is_planar(ring, r_atoms):
def classify_by_name(names):
"""Classify a (composite) ligand by the HETID(s)"""
if len(names) > 3: # Polymer
- if len({'U', 'A', 'C', 'G'}.intersection(set(names))) != 0:
+ if len(set(config.RNA).intersection(set(names))) != 0:
ligtype = 'RNA'
- elif len({'DT', 'DA', 'DC', 'DG'}.intersection(set(names))) != 0:
+ elif len(set(config.DNA).intersection(set(names))) != 0:
ligtype = 'DNA'
else:
ligtype = "POLYMER"
@@ -420,25 +408,30 @@ def read(fil):
def readmol(path, as_string=False):
"""Reads the given molecule file and returns the corresponding Pybel molecule as well as the input file type.
In contrast to the standard Pybel implementation, the file is closed properly."""
- supported_formats = ['pdb', 'pdbqt', 'mmcif']
+ supported_formats = ['pdb', 'mmcif']
obc = pybel.ob.OBConversion()
- if as_string:
- filestr = path
- else:
- with read(path) as f:
- filestr = str(f.read())
for sformat in supported_formats:
obc.SetInFormat(sformat)
+ write_message("Detected {} as format. Now trying to read file with OpenBabel...\n".format(sformat), mtype='debug')
mol = pybel.ob.OBMol()
- obc.ReadString(mol, filestr)
- if not mol.Empty():
- if sformat == 'pdbqt':
- write_message('[EXPERIMENTAL] Input is PDBQT file. Some features (especially visualization) might not '
- 'work as expected. Please consider using PDB format instead.\n')
- if sformat == 'mmcif':
- write_message('[EXPERIMENTAL] Input is mmCIF file. Most features do currently not work with this format.\n')
- return pybel.Molecule(mol), sformat
+
+ # Read molecules with single bond information
+ if as_string:
+ read_file = pybel.readstring(format=sformat, filename=path, opt={"s": None})
+ else:
+ read_file = pybel.readfile(format=sformat, filename=path, opt={"s": None})
+ try:
+ mymol = read_file.next()
+ except StopIteration:
+ sysexit(4, 'File contains no valid molecules.\n')
+
+ write_message("Molecule successfully read.\n", mtype='debug')
+
+ # Assign multiple bonds
+ mymol.OBMol.PerceiveBondOrders()
+ return mymol, sformat
+
sysexit(4, 'No valid file format provided.')
diff --git a/plip/modules/visualize.py b/plip/modules/visualize.py
index 60858d0..640c6d5 100644
--- a/plip/modules/visualize.py
+++ b/plip/modules/visualize.py
@@ -1,27 +1,16 @@
"""
Protein-Ligand Interaction Profiler - Analyze and visualize protein-ligand interactions in PDB files.
visualize.py - Visualization of PLIP results using PyMOL.
-Copyright 2014-2015 Sebastian Salentin
-
-Licensed under the Apache License, Version 2.0 (the "License");
-you may not use this file except in compliance with the License.
-You may obtain a copy of the License at
-
- http://www.apache.org/licenses/LICENSE-2.0
-
-Unless required by applicable law or agreed to in writing, software
-distributed under the License is distributed on an "AS IS" BASIS,
-WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-See the License for the specific language governing permissions and
-limitations under the License.
"""
+# Python standard library
+from __future__ import absolute_import
# Own modules
-from supplemental import initialize_pymol, start_pymol, write_message, colorlog, sysexit
-import config
-from pymolplip import PyMOLVisualizer
-from plipremote import VisualizerData
+from plip.modules.supplemental import initialize_pymol, start_pymol, write_message, colorlog, sysexit
+import plip.modules.config as config
+from plip.modules.pymolplip import PyMOLVisualizer
+from plip.modules.plipremote import VisualizerData
# Python Standard Library
import json
@@ -114,6 +103,7 @@ def visualize_in_pymol(plcomplex):
vis.make_initial_selections()
+
vis.show_hydrophobic() # Hydrophobic Contacts
vis.show_hbonds() # Hydrogen Bonds
vis.show_halogen() # Halogen Bonds
@@ -125,12 +115,18 @@ def visualize_in_pymol(plcomplex):
vis.refinements()
-
vis.zoom_to_ligand()
vis.selections_cleanup()
+
vis.selections_group()
vis.additional_cleanup()
+ if config.DNARECEPTOR:
+ # Rename Cartoon selection to Line selection and change repr.
+ cmd.set_name('%sCartoon' % plcomplex.pdbid, '%sLines' % plcomplex.pdbid)
+ cmd.hide('cartoon', '%sLines' % plcomplex.pdbid)
+ cmd.show('lines', '%sLines' % plcomplex.pdbid)
+
if config.PEPTIDES != []:
filename = "%s_PeptideChain%s" % (pdbid.upper(), plcomplex.chain)
if config.PYMOL:
diff --git a/plip/modules/webservices.py b/plip/modules/webservices.py
index c1f283f..b790dc6 100644
--- a/plip/modules/webservices.py
+++ b/plip/modules/webservices.py
@@ -1,27 +1,15 @@
"""
Protein-Ligand Interaction Profiler - Analyze and visualize protein-ligand interactions in PDB files.
webservices.py - Connect to various webservices to retrieve data
-Copyright 2014-2016 Sebastian Salentin
-
-Licensed under the Apache License, Version 2.0 (the "License");
-you may not use this file except in compliance with the License.
-You may obtain a copy of the License at
-
- http://www.apache.org/licenses/LICENSE-2.0
-
-Unless required by applicable law or agreed to in writing, software
-distributed under the License is distributed on an "AS IS" BASIS,
-WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-See the License for the specific language governing permissions and
-limitations under the License.
"""
-# Own modules
-from supplemental import write_message, sysexit
-
-# Python standard libary
+# Python standard library
+from __future__ import absolute_import
import urllib2
+# Own modules
+from plip.modules.supplemental import write_message, sysexit
+
# External libraries
import lxml.etree as et
diff --git a/plip/plipcmd b/plip/plipcmd
index 3bfd0f7..406ddc9 100755
--- a/plip/plipcmd
+++ b/plip/plipcmd
@@ -2,41 +2,20 @@
"""
Protein-Ligand Interaction Profiler - Analyze and visualize protein-ligand interactions in PDB files.
plipcmd - Main script for PLIP command line execution.
-Copyright 2014-2015 Sebastian Salentin
-
-Licensed under the Apache License, Version 2.0 (the "License");
-you may not use this file except in compliance with the License.
-You may obtain a copy of the License at
-
- http://www.apache.org/licenses/LICENSE-2.0
-
-Unless required by applicable law or agreed to in writing, software
-distributed under the License is distributed on an "AS IS" BASIS,
-WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-See the License for the specific language governing permissions and
-limitations under the License.
"""
# Compatibility
from __future__ import print_function
+from __future__ import absolute_import
# Own modules
-try:
- from plip.modules.preparation import *
- from plip.modules.visualize import visualize_in_pymol
- 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.visualize import visualize_in_pymol
- 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
+from plip.modules.preparation import *
+from plip.modules.visualize import visualize_in_pymol
+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
# Python standard library
import sys
@@ -152,7 +131,7 @@ def main(inputstructs, inputpdbids):
if os.path.getsize(inputstruct) == 0:
sysexit(2, 'Empty PDB file\n') # Exit if input file is empty
if num_structures > 1:
- basename = inputstruct.split('.')[0].split('/')[-1]
+ basename = inputstruct.split('.')[-2].split('/')[-1]
config.OUTPATH = '/'.join([config.BASEPATH, basename])
process_pdb(inputstruct, config.OUTPATH)
else: # Try to fetch the current PDB structure(s) directly from the RCBS server
@@ -206,6 +185,9 @@ if __name__ == '__main__':
parser.add_argument("--nofix", dest="nofix", default=False,
help="Turns off fixing of PDB files.",
action="store_true")
+ parser.add_argument("--dnareceptor", dest="dnareceptor", default=False,
+ help="Uses the DNA instead of the protein as a receptor for interactions.",
+ action="store_true")
ligandtype = parser.add_mutually_exclusive_group() # Either peptide/inter or intra mode
ligandtype.add_argument("--peptides", "--inter", dest="peptides", default=[],
help="Allows to define one or multiple chains as peptide ligands or to detect inter-chain contacts",
@@ -248,6 +230,7 @@ if __name__ == '__main__':
config.INTRA = arguments.intra
config.NOFIX = arguments.nofix
config.KEEPMOD = arguments.keepmod
+ config.DNARECEPTOR = arguments.dnareceptor
# Assign values to global thresholds
for t in thresholds:
tvalue = getattr(arguments, t.name)
diff --git a/plip/test/run_all_tests.sh b/plip/test/run_all_tests.sh
new file mode 100755
index 0000000..99c0fc0
--- /dev/null
+++ b/plip/test/run_all_tests.sh
@@ -0,0 +1 @@
+python -m unittest discover -s . -p 'test_*.py'
diff --git a/plip/test/test_basic_functions.py b/plip/test/test_basic_functions.py
index 79ffd51..6e3437d 100644
--- a/plip/test/test_basic_functions.py
+++ b/plip/test/test_basic_functions.py
@@ -2,19 +2,6 @@
"""
Protein-Ligand Interaction Profiler - Analyze and visualize protein-ligand interactions in PDB files.
test_basic_functions.py - Unit Tests for basic functionality.
-Copyright 2014-2015 Sebastian Salentin
-
-Licensed under the Apache License, Version 2.0 (the "License");
-you may not use this file except in compliance with the License.
-You may obtain a copy of the License at
-
- http://www.apache.org/licenses/LICENSE-2.0
-
-Unless required by applicable law or agreed to in writing, software
-distributed under the License is distributed on an "AS IS" BASIS,
-WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-See the License for the specific language governing permissions and
-limitations under the License.
"""
# Python Standard Library
diff --git a/plip/test/test_literature_validated.py b/plip/test/test_literature_validated.py
index 31c56a7..7fe2502 100644
--- a/plip/test/test_literature_validated.py
+++ b/plip/test/test_literature_validated.py
@@ -2,19 +2,6 @@
"""
Protein-Ligand Interaction Profiler - Analyze and visualize protein-ligand interactions in PDB files.
test_literature_validated.py - Unit Tests for literature-validated cases.
-Copyright 2014-2015 Sebastian Salentin, Melissa Adasme
-
-Licensed under the Apache License, Version 2.0 (the "License");
-you may not use this file except in compliance with the License.
-You may obtain a copy of the License at
-
- http://www.apache.org/licenses/LICENSE-2.0
-
-Unless required by applicable law or agreed to in writing, software
-distributed under the License is distributed on an "AS IS" BASIS,
-WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-See the License for the specific language governing permissions and
-limitations under the License.
"""
diff --git a/plip/test/test_metal_coordination.py b/plip/test/test_metal_coordination.py
index 8073ec5..16dd4a8 100644
--- a/plip/test/test_metal_coordination.py
+++ b/plip/test/test_metal_coordination.py
@@ -2,19 +2,6 @@
"""
Protein-Ligand Interaction Profiler - Analyze and visualize protein-ligand interactions in PDB files.
test_metal_coordination.py - Unit Tests for Metal Coordination.
-Copyright 2014-2015 Sebastian Salentin
-
-Licensed under the Apache License, Version 2.0 (the "License");
-you may not use this file except in compliance with the License.
-You may obtain a copy of the License at
-
- http://www.apache.org/licenses/LICENSE-2.0
-
-Unless required by applicable law or agreed to in writing, software
-distributed under the License is distributed on an "AS IS" BASIS,
-WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-See the License for the specific language governing permissions and
-limitations under the License.
"""
diff --git a/plip/test/test_remote_services.py b/plip/test/test_remote_services.py
index c8ecde8..fb61d34 100644
--- a/plip/test/test_remote_services.py
+++ b/plip/test/test_remote_services.py
@@ -2,19 +2,6 @@
"""
Protein-Ligand Interaction Profiler - Analyze and visualize protein-ligand interactions in PDB files.
test_remote_services.py - Unit Tests for remote services.
-Copyright 2014-2016 Sebastian Salentin
-
-Licensed under the Apache License, Version 2.0 (the "License");
-you may not use this file except in compliance with the License.
-You may obtain a copy of the License at
-
- http://www.apache.org/licenses/LICENSE-2.0
-
-Unless required by applicable law or agreed to in writing, software
-distributed under the License is distributed on an "AS IS" BASIS,
-WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-See the License for the specific language governing permissions and
-limitations under the License.
"""
diff --git a/plip/test/test_special_cases.py b/plip/test/test_special_cases.py
index 440d68e..d2791c5 100644
--- a/plip/test/test_special_cases.py
+++ b/plip/test/test_special_cases.py
@@ -2,19 +2,6 @@
"""
Protein-Ligand Interaction Profiler - Analyze and visualize protein-ligand interactions in PDB files.
test_special_cases.py - Unit Tests for special cases.
-Copyright 2014-2015 Sebastian Salentin
-
-Licensed under the Apache License, Version 2.0 (the "License");
-you may not use this file except in compliance with the License.
-You may obtain a copy of the License at
-
- http://www.apache.org/licenses/LICENSE-2.0
-
-Unless required by applicable law or agreed to in writing, software
-distributed under the License is distributed on an "AS IS" BASIS,
-WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-See the License for the specific language governing permissions and
-limitations under the License.
"""
@@ -44,5 +31,3 @@ class SpecialCasesTest(unittest.TestCase):
"""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)
self.assertEqual(exitcode1, 5) # Specific exitcode 5
-
-
diff --git a/plip/test/test_xml_parser.py b/plip/test/test_xml_parser.py
index 64bed55..53f65ac 100644
--- a/plip/test/test_xml_parser.py
+++ b/plip/test/test_xml_parser.py
@@ -2,19 +2,6 @@
"""
Protein-Ligand Interaction Profiler - Analyze and visualize protein-ligand interactions in PDB files.
test_xml_parser.py - Unit Tests for XML Parser.
-Copyright 2014-2016 Sebastian Salentin
-
-Licensed under the Apache License, Version 2.0 (the "License");
-you may not use this file except in compliance with the License.
-You may obtain a copy of the License at
-
- http://www.apache.org/licenses/LICENSE-2.0
-
-Unless required by applicable law or agreed to in writing, software
-distributed under the License is distributed on an "AS IS" BASIS,
-WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-See the License for the specific language governing permissions and
-limitations under the License.
"""
diff --git a/setup.py b/setup.py
index 6d068b6..b5580cb 100644
--- a/setup.py
+++ b/setup.py
@@ -1,38 +1,25 @@
"""
Protein-Ligand Interaction Profiler - Analyze and visualize protein-ligand interactions in PDB files.
setup.py - Setup configuration file for pip, etc.
-Copyright 2014 Sebastian Salentin
-
-Licensed under the Apache License, Version 2.0 (the "License");
-you may not use this file except in compliance with the License.
-You may obtain a copy of the License at
-
- http://www.apache.org/licenses/LICENSE-2.0
-
-Unless required by applicable law or agreed to in writing, software
-distributed under the License is distributed on an "AS IS" BASIS,
-WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-See the License for the specific language governing permissions and
-limitations under the License.
"""
from setuptools import setup
setup(name='plip',
- version='1.3.3',
+ version='1.3.5',
description='PLIP - Fully automated protein-ligand interaction profiler',
classifiers=[
'Development Status :: 5 - Production/Stable',
'Intended Audience :: Science/Research',
'Natural Language :: English',
- 'License :: OSI Approved :: Apache Software License',
+ 'License :: OSI Approved :: GNU General Public License v2 (GPLv2)',
'Programming Language :: Python :: 2.7',
'Topic :: Scientific/Engineering :: Bio-Informatics'
],
url='https://github.com/ssalentin/plip',
author='Sebastian Salentin',
author_email='sebastian.salentin at biotec.tu-dresden.de',
- license='Apache',
+ license='GPLv2',
packages=['plip', 'plip/modules'],
scripts=['plip/plipcmd'],
install_requires=[
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