[med-svn] [Git][med-team/plip][master] 6 commits: New upstream version 2.3.0+dfsg
Alexandre Mestiashvili (@mestia)
gitlab at salsa.debian.org
Mon Sep 4 18:10:39 BST 2023
Alexandre Mestiashvili pushed to branch master at Debian Med / plip
Commits:
3628dbef by Alexandre Mestiashvili at 2023-08-31T17:13:54+02:00
New upstream version 2.3.0+dfsg
- - - - -
c80e84b6 by Alexandre Mestiashvili at 2023-08-31T17:13:54+02:00
Update upstream source from tag 'upstream/2.3.0+dfsg'
Update to upstream version '2.3.0+dfsg'
with Debian dir eda93cc70f7055621a8c1b5e3c4e6d6c08d84523
- - - - -
78c5ae23 by Alexandre Mestiashvili at 2023-09-03T18:26:55+02:00
d/copyright, update Source field
- - - - -
1dbc5a9a by Alexandre Mestiashvili at 2023-09-03T18:27:12+02:00
Add patch reverting update to imagemagick 7
- - - - -
fe88c5a5 by Alexandre Mestiashvili at 2023-09-03T18:29:20+02:00
d/control, bump Policy to 4.6.2
- - - - -
e43d8f6c by Alexandre Mestiashvili at 2023-09-03T18:30:25+02:00
Update changelog
Gbp-Dch: Ignore
- - - - -
12 changed files:
- CHANGES.txt
- README.md
- debian/changelog
- debian/control
- debian/copyright
- + debian/patches/revert_imagemagick_changes.patch
- + debian/patches/series
- plip/basic/config.py
- plip/basic/supplemental.py
- plip/structure/preparation.py
- + plip/test/test_salt_bridges.py
- plip/visualization/pymol.py
Changes:
=====================================
CHANGES.txt
=====================================
@@ -1,5 +1,10 @@
Changelog
---------
+# 2.3.0
+* fixes an issue that caused encoding errors to be thrown
+* salt bridge interaction improved
+* minor bugs fixed
+
# 2.2.2
* fixes an issue that caused encoding errors to be thrown
=====================================
README.md
=====================================
@@ -69,7 +69,7 @@ If you cannot use the containerized bundle or want to use PLIP sources, make sur
- Python >= 3.6.9
- [OpenBabel](#Installing-OpenBabel) >= 3.0.0 with [Python bindings](https://open-babel.readthedocs.io/en/latest/UseTheLibrary/PythonInstall.html)
- PyMOL >= 2.3.0 with Python bindings (optional, for visualization only)
-- ImageMagick >= 6.9 (optional)
+- ImageMagick >= 7.0 (optional)
**Python:** If you are on a system where Python 3 is executed using `python3` instead of just `python`, replace the `python` and `pip` commands in the following steps with `python3` and `pip3` accordingly.
@@ -164,7 +164,7 @@ Using PLIP in your commercial or non-commercial project is generally possible wh
If you are using PLIP in your work, please cite
> Adasme,M. et al. PLIP 2021: expanding the scope of the protein-ligand interaction profiler to DNA and RNA.
> Nucl. Acids Res. (05 May 2021), gkab294. doi: 10.1093/nar/gkab294
-
+
or
> Salentin,S. et al. PLIP: fully automated protein-ligand interaction profiler.
=====================================
debian/changelog
=====================================
@@ -1,3 +1,17 @@
+plip (2.3.0+dfsg-1) unstable; urgency=medium
+
+ [ Nilesh Patra ]
+ * [skip ci] Remove myself from uploaders
+ * [skip ci] Fix mess-ups with automated script
+
+ [ Alexandre Mestiashvili ]
+ * New upstream version 2.3.0+dfsg
+ * d/copyright, update Source field
+ * d/control, bump Policy to 4.6.2
+ * Add patch reverting update to imagemagick 7
+
+ -- Alexandre Mestiashvili <mestia at debian.org> Sun, 03 Sep 2023 18:30:00 +0200
+
plip (2.2.2+dfsg-1) unstable; urgency=medium
* New upstream version 2.2.2+dfsg
=====================================
debian/control
=====================================
@@ -12,7 +12,7 @@ Build-Depends: debhelper-compat (= 13),
python3-numpy,
python3-openbabel,
python3-setuptools
-Standards-Version: 4.5.1
+Standards-Version: 4.6.2
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/
@@ -20,7 +20,9 @@ Rules-Requires-Root: no
Package: plip
Architecture: all
-Depends: python3-openbabel, ${misc:Depends}, ${python3:Depends}
+Depends: python3-openbabel,
+ ${misc:Depends},
+ ${python3:Depends}
Recommends: pymol
Description: fully automated protein-ligand interaction profiler
The Protein-Ligand Interaction Profiler (PLIP) is a tool to analyze
=====================================
debian/copyright
=====================================
@@ -1,6 +1,6 @@
Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Upstream-Name: plip
-Source: https://github.com/ssalentin/plip
+Source: https://github.com/pharmai/plip
Files-Excluded:
plip/test/pdb/*
pliplogo*
=====================================
debian/patches/revert_imagemagick_changes.patch
=====================================
@@ -0,0 +1,43 @@
+Description: keep old imagemagick commands, since Debian doesn't provide
+ imagemagick version 7 for now
+Author: Alex Mestiashvili <mestia at debian.org>
+--- plip.orig/plip/visualization/pymol.py
++++ plip/plip/visualization/pymol.py
+@@ -363,29 +363,21 @@
+ os.rename(originalfile, newfile) # Remove frame number in filename
+
+ # Check if imagemagick is available and crop + resize the images
+- if subprocess.call("magick -version", shell=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE) == 0:
++ if subprocess.call("type convert", shell=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE) == 0:
+ attempts, ecode = 0, 1
+ # Check if file is truncated and wait if that's the case
+ while ecode != 0 and attempts <= 10:
+- ecode = subprocess.call(['magick', newfile, os.devnull], stdout=open(os.devnull, 'w'),
++ ecode = subprocess.call(['convert', newfile, '/dev/null'], stdout=open('/dev/null', 'w'),
+ stderr=subprocess.STDOUT)
+ sleep(0.1)
+ attempts += 1
+- trim = f'magick {newfile} -trim -bordercolor White -border 20x20 {newfile}' # Trim the image
++ trim = 'convert -trim ' + newfile + ' -bordercolor White -border 20x20 ' + newfile + ';' # Trim the image
+ os.system(trim)
+- # Get the width of the new image
+- getwidth = f'magick {newfile} -ping -format "%w" info:'
+- w = int(subprocess.run(getwidth, capture_output=True, text=True).stdout)
+- # Get the hight of the new image
+- getheight = f'magick {newfile} -ping -format "%h" info:'
+- h = int(subprocess.run(getheight, capture_output=True, text=True).stdout)
+- # Set quadratic ratio
+- if w > h:
+- newr= f'{w}x{w}'
+- else:
+- newr= f'{h}x{h}'
+- quadratic = f'magick {newfile} -gravity center -extent {newr} {newfile}' # Fill with whitespace
+- os.system(quadratic)
++ getwidth = 'w=`convert ' + newfile + ' -ping -format "%w" info:`;' # Get the width of the new image
++ getheight = 'h=`convert ' + newfile + ' -ping -format "%h" info:`;' # Get the hight of the new image
++ newres = 'if [ "$w" -gt "$h" ]; then newr="${w%.*}x$w"; else newr="${h%.*}x$h"; fi;' # Set quadratic ratio
++ quadratic = 'convert ' + newfile + ' -gravity center -extent "$newr" ' + newfile # Fill with whitespace
++ os.system(getwidth + getheight + newres + quadratic)
+ else:
+ sys.stderr.write('Imagemagick not available. Images will not be resized or cropped.')
+
=====================================
debian/patches/series
=====================================
@@ -0,0 +1 @@
+revert_imagemagick_changes.patch
=====================================
plip/basic/config.py
=====================================
@@ -1,4 +1,4 @@
-__version__ = '2.2.2'
+__version__ = '2.3.0'
__maintainer__ = 'PharmAI GmbH (2020-2021) - www.pharm.ai - hello at pharm.ai'
__citation_information__ = "Adasme,M. et al. PLIP 2021: expanding the scope of the protein-ligand interaction profiler to DNA and RNA. " \
"Nucl. Acids Res. (05 May 2021), gkab294. doi: 10.1093/nar/gkab294"
=====================================
plip/basic/supplemental.py
=====================================
@@ -298,7 +298,6 @@ def sort_members_by_importance(members):
main = [x for x in members if x[0] not in config.METAL_IONS]
ion = [x for x in members if x[0] in config.METAL_IONS]
sorted_main = sorted(main, key=lambda x: (x[1], x[2]))
- sorted_main = sorted(main, key=lambda x: (x[1], x[2]))
sorted_ion = sorted(ion, key=lambda x: (x[1], x[2]))
return sorted_main + sorted_ion
=====================================
plip/structure/preparation.py
=====================================
@@ -51,14 +51,16 @@ class PDBParser:
alt = []
previous_ter = False
- model_dict = {1: list()}
+ model_dict = {0: list()}
# Standard without fixing
if not config.NOFIX:
if not config.PLUGIN_MODE:
lastnum = 0 # Atom numbering (has to be consecutive)
other_models = False
- current_model = 1
+ # Model 0 stores header and similar additional data
+ # or the full file if no MODEL entries exist in the file
+ current_model = 0
for line in fil:
corrected_line, newnum = self.fix_pdbline(line, lastnum)
if corrected_line is not None:
@@ -81,8 +83,11 @@ class PDBParser:
try:
if other_models:
logger.info(f'selecting model {config.MODEL} for analysis')
- corrected_pdb = ''.join(model_dict[config.MODEL])
- corrected_lines = model_dict[config.MODEL]
+ corrected_pdb = ''.join(model_dict[0])
+ corrected_lines = model_dict[0]
+ if current_model > 0:
+ corrected_pdb += ''.join(model_dict[config.MODEL])
+ corrected_lines += model_dict[config.MODEL]
except KeyError:
corrected_pdb = ''.join(model_dict[1])
corrected_lines = model_dict[1]
@@ -924,6 +929,7 @@ class BindingSite(Mol):
def find_charged(self, mol):
"""Looks for positive charges in arginine, histidine or lysine, for negative in aspartic and glutamic acid."""
+ """If nucleic acids are part of the receptor, looks for negative charges in phosphate backbone"""
data = namedtuple('pcharge', 'atoms atoms_orig_idx type center restype resnr reschain')
a_set = []
# Iterate through all residue, exclude those in chains defined as peptides
@@ -961,6 +967,17 @@ class BindingSite(Mol):
restype=res.GetName(),
resnr=res.GetNum(),
reschain=res.GetChain()))
+ if res.GetName() in config.DNA + config.RNA and config.DNARECEPTOR: # nucleic acids have negative charge in sugar phosphate
+ for a in pybel.ob.OBResidueAtomIter(res):
+ if a.GetType().startswith('P') and res.GetAtomProperty(a, 9) \
+ and not self.Mapper.mapid(a.GetIdx(), mtype='protein') in self.altconf:
+ a_contributing.append(pybel.Atom(a))
+ a_contributing_orig_idx.append(self.Mapper.mapid(a.GetIdx(), mtype='protein'))
+ if not len(a_contributing) == 0:
+ a_set.append(data(atoms=a_contributing,atoms_orig_idx=a_contributing_orig_idx, type='negative',
+ center=centroid([ac.coords for ac in a_contributing]), restype=res.GetName(),
+ resnr=res.GetNum(),
+ reschain=res.GetChain()))
return a_set
def find_metal_binding(self, mol):
@@ -1365,7 +1382,7 @@ class PDBComplex:
if not as_string:
self.sourcefiles['filename'] = os.path.basename(self.sourcefiles['pdbcomplex'])
- self.protcomplex, self.filetype = read_pdb(self.corrected_pdb, as_string=True)
+ self.protcomplex, self.filetype = read_pdb(self.corrected_pdb, as_string= (self.corrected_pdb != pdbpath)) # self.corrected_pdb may fallback to pdbpath
# Update the model in the Mapper class instance
self.Mapper.original_structure = self.protcomplex.OBMol
=====================================
plip/test/test_salt_bridges.py
=====================================
@@ -0,0 +1,23 @@
+import unittest
+
+from plip.basic import config
+from plip.structure.preparation import PDBComplex, PLInteraction
+
+
+def characterize_complex(pdb_file: str, binding_site_id: str) -> PLInteraction:
+ pdb_complex = PDBComplex()
+ pdb_complex.load_pdb(pdb_file)
+ for ligand in pdb_complex.ligands:
+ if ':'.join([ligand.hetid, ligand.chain, str(ligand.position)]) == binding_site_id:
+ pdb_complex.characterize_complex(ligand)
+ return pdb_complex.interaction_sets[binding_site_id]
+
+class SaltBridgeTest(unittest.TestCase):
+
+ def test_4yb0(self):
+ '''test salt bridge detection for nucleic acids as part of the receptor'''
+
+ config.DNARECEPTOR = True
+ interactions = characterize_complex('./pdb/4yb0.pdb', 'C2E:R:102')
+ salt_bridges = interactions.saltbridge_lneg + interactions.saltbridge_pneg
+ self.assertTrue(len(salt_bridges) == 1)
\ No newline at end of file
=====================================
plip/visualization/pymol.py
=====================================
@@ -363,21 +363,29 @@ class PyMOLVisualizer:
os.rename(originalfile, newfile) # Remove frame number in filename
# Check if imagemagick is available and crop + resize the images
- if subprocess.call("type convert", shell=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE) == 0:
+ if subprocess.call("magick -version", shell=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE) == 0:
attempts, ecode = 0, 1
# Check if file is truncated and wait if that's the case
while ecode != 0 and attempts <= 10:
- ecode = subprocess.call(['convert', newfile, '/dev/null'], stdout=open('/dev/null', 'w'),
+ ecode = subprocess.call(['magick', newfile, os.devnull], stdout=open(os.devnull, 'w'),
stderr=subprocess.STDOUT)
sleep(0.1)
attempts += 1
- trim = 'convert -trim ' + newfile + ' -bordercolor White -border 20x20 ' + newfile + ';' # Trim the image
+ trim = f'magick {newfile} -trim -bordercolor White -border 20x20 {newfile}' # Trim the image
os.system(trim)
- getwidth = 'w=`convert ' + newfile + ' -ping -format "%w" info:`;' # Get the width of the new image
- getheight = 'h=`convert ' + newfile + ' -ping -format "%h" info:`;' # Get the hight of the new image
- newres = 'if [ "$w" -gt "$h" ]; then newr="${w%.*}x$w"; else newr="${h%.*}x$h"; fi;' # Set quadratic ratio
- quadratic = 'convert ' + newfile + ' -gravity center -extent "$newr" ' + newfile # Fill with whitespace
- os.system(getwidth + getheight + newres + quadratic)
+ # Get the width of the new image
+ getwidth = f'magick {newfile} -ping -format "%w" info:'
+ w = int(subprocess.run(getwidth, capture_output=True, text=True).stdout)
+ # Get the hight of the new image
+ getheight = f'magick {newfile} -ping -format "%h" info:'
+ h = int(subprocess.run(getheight, capture_output=True, text=True).stdout)
+ # Set quadratic ratio
+ if w > h:
+ newr= f'{w}x{w}'
+ else:
+ newr= f'{h}x{h}'
+ quadratic = f'magick {newfile} -gravity center -extent {newr} {newfile}' # Fill with whitespace
+ os.system(quadratic)
else:
sys.stderr.write('Imagemagick not available. Images will not be resized or cropped.')
View it on GitLab: https://salsa.debian.org/med-team/plip/-/compare/a43e46690df606a04be8a0d89d0b092440e7640a...e43d8f6c342df40629ee2ae1472376b6503ce783
--
View it on GitLab: https://salsa.debian.org/med-team/plip/-/compare/a43e46690df606a04be8a0d89d0b092440e7640a...e43d8f6c342df40629ee2ae1472376b6503ce783
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