[med-svn] [Git][med-team/plip][upstream] New upstream version 1.4.2+dfsg
Alexandre Mestiashvili
gitlab at salsa.debian.org
Fri Jun 8 10:37:51 BST 2018
Alexandre Mestiashvili pushed to branch upstream at Debian Med / plip
Commits:
a390324d by Alexandre Mestiashvili at 2018-06-07T20:04:11+02:00
New upstream version 1.4.2+dfsg
- - - - -
8 changed files:
- CHANGES.txt
- README.md
- plip/modules/config.py
- plip/modules/plipxml.py
- plip/modules/preparation.py
- plip/modules/report.py
- plip/plipcmd
- setup.py
Changes:
=====================================
CHANGES.txt
=====================================
--- a/CHANGES.txt
+++ b/CHANGES.txt
@@ -1,6 +1,11 @@
Changelog
---------
+# 1.4.2
+* Adds "--name" option to change name of output files
+* Adds "--nopdbcanmap" option to skip calculation of canonical->PDB mapping which can lead to segfaults with OpenBabel
+* Improved handling of ligand names
+
# 1.4.1
* Improved import of modules
* Corrections for README and documentation
=====================================
README.md
=====================================
--- a/README.md
+++ b/README.md
@@ -33,7 +33,7 @@ pymol 1VSN_NFT_A_283.pse
In your terminal, add the PLIP repository to your PYTHONPATH variable.
For our example, we also download a PDB file for testing.
```bash
-export PYTHONPATH=~/pliptool/plip:${PYTHONPATH}
+export PYTHONPATH=~/pliptool:${PYTHONPATH}
cd /tmp && wget http://files.rcsb.org/download/1EVE.pdb
python
```
=====================================
plip/modules/config.py
=====================================
--- a/plip/modules/config.py
+++ b/plip/modules/config.py
@@ -23,6 +23,8 @@ PEPTIDES = [] # Definition which chains should be considered as peptide ligands
INTRA = None
KEEPMOD = False
DNARECEPTOR = False
+OUTPUTFILENAME = "report" # Naming for the TXT and XML report files
+NOPDBCANMAP = False # Skip calculation of mapping canonical atom order: PDB atom order
# Configuration file for Protein-Ligand Interaction Profiler (PLIP)
# Set thresholds for detection of interactions
=====================================
plip/modules/plipxml.py
=====================================
--- a/plip/modules/plipxml.py
+++ b/plip/modules/plipxml.py
@@ -53,10 +53,10 @@ class Interaction(XMLStorage):
def __init__(self, interaction_part):
self.id = interaction_part.get('id')
self.resnr = self.getdata(interaction_part, 'resnr')
- self.restype = self.getdata(interaction_part, 'restype')
+ self.restype = self.getdata(interaction_part, 'restype', force_string=True)
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.restype_lig = self.getdata(interaction_part, 'restype_lig', force_string=True)
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')
@@ -87,8 +87,8 @@ class HydrogenBond(Interaction):
self.protisdon = self.getdata(hbond_part, 'protisdon')
self.donoridx = self.getdata(hbond_part, 'donoridx')
self.acceptoridx = self.getdata(hbond_part, 'acceptoridx')
- self.donortype = self.getdata(hbond_part, 'donortype')
- self.acceptortype = self.getdata(hbond_part, 'acceptortype')
+ self.donortype = self.getdata(hbond_part, 'donortype', force_string=True)
+ self.acceptortype = self.getdata(hbond_part, 'acceptortype', force_string=True)
class WaterBridge(Interaction):
@@ -105,8 +105,8 @@ class WaterBridge(Interaction):
self.donor_idx = self.getdata(wbridge_part, 'donor_idx')
self.acceptor_idx = self.getdata(wbridge_part, 'acceptor_idx')
- self.donortype = self.getdata(wbridge_part, 'donortype')
- self.acceptortype = self.getdata(wbridge_part, 'acceptortype')
+ self.donortype = self.getdata(wbridge_part, 'donortype', force_string=True)
+ self.acceptortype = self.getdata(wbridge_part, 'acceptortype', force_string=True)
self.water_idx = self.getdata(wbridge_part, 'water_idx')
self.watercoo = self.getcoordinates(wbridge_part, 'watercoo')
@@ -118,7 +118,7 @@ class SaltBridge(Interaction):
Interaction.__init__(self, sbridge_part)
self.dist = self.getdata(sbridge_part, 'dist')
self.protispos = self.getdata(sbridge_part, 'protispos')
- self.lig_group = self.getdata(sbridge_part, 'lig_group')
+ self.lig_group = self.getdata(sbridge_part, 'lig_group', force_string=True)
self.lig_idx_list = [int(tagpart.text) for tagpart in
sbridge_part.xpath('lig_idx_list/idx')]
@@ -157,8 +157,8 @@ class HalogenBond(Interaction):
self.dist = self.getdata(halogen_part, 'dist')
self.don_angle = self.getdata(halogen_part, 'don_angle')
self.acc_angle = self.getdata(halogen_part, 'acc_angle')
- self.donortype = self.getdata(halogen_part, 'donortype')
- self.acceptortype = self.getdata(halogen_part, 'acceptortype')
+ self.donortype = self.getdata(halogen_part, 'donortype', force_string=True)
+ self.acceptortype = self.getdata(halogen_part, 'acceptortype', force_string=True)
self.don_idx = self.getdata(halogen_part, 'don_idx')
self.acc_idx = self.getdata(halogen_part, 'acc_idx')
self.sidechain = self.getdata(halogen_part, 'sidechain')
@@ -170,14 +170,14 @@ class MetalComplex(Interaction):
def __init__(self, metalcomplex_part):
Interaction.__init__(self, metalcomplex_part)
self.metal_idx = self.getdata(metalcomplex_part, 'metal_idx')
- self.metal_type = self.getdata(metalcomplex_part, 'metal_type')
+ self.metal_type = self.getdata(metalcomplex_part, 'metal_type', force_string=True)
self.target_idx = self.getdata(metalcomplex_part, 'target_idx')
- self.target_type = self.getdata(metalcomplex_part, 'target_type')
+ self.target_type = self.getdata(metalcomplex_part, 'target_type', force_string=True)
self.coordination = self.getdata(metalcomplex_part, 'coordination')
self.dist = self.getdata(metalcomplex_part, 'dist')
- self.location = self.getdata(metalcomplex_part, 'location')
+ self.location = self.getdata(metalcomplex_part, 'location', force_string=True)
self.rms = self.getdata(metalcomplex_part, 'rms')
- self.geometry = self.getdata(metalcomplex_part, 'geometry')
+ self.geometry = self.getdata(metalcomplex_part, 'geometry', force_string=True)
self.complexnum = self.getdata(metalcomplex_part, 'complexnum')
self.targetcoo = self.getcoordinates(metalcomplex_part, 'targetcoo')
self.metalcoo = self.getcoordinates(metalcomplex_part, 'metalcoo')
@@ -190,13 +190,13 @@ class BSite(XMLStorage):
self.pdbid = pdbid
self.bsid = ":".join(bindingsite.xpath('identifiers/*/text()')[2:5])
self.uniqueid = ":".join([self.pdbid, self.bsid])
- self.hetid = self.getdata(bindingsite, 'identifiers/hetid')
- self.longname = self.getdata(bindingsite, 'identifiers/longname')
- self.ligtype = self.getdata(bindingsite, 'identifiers/ligtype')
- self.smiles = self.getdata(bindingsite, 'identifiers/smiles')
- self.inchikey = self.getdata(bindingsite, 'identifiers/inchikey')
+ self.hetid = self.getdata(bindingsite, 'identifiers/hetid', force_string=True)
+ self.longname = self.getdata(bindingsite, 'identifiers/longname', force_string=True)
+ self.ligtype = self.getdata(bindingsite, 'identifiers/ligtype', force_string=True)
+ self.smiles = self.getdata(bindingsite, 'identifiers/smiles', force_string=True)
+ self.inchikey = self.getdata(bindingsite, 'identifiers/inchikey', force_string=True)
self.position = self.getdata(bindingsite, 'identifiers/position')
- self.chain = self.getdata(bindingsite, 'identifiers/chain')
+ self.chain = self.getdata(bindingsite, 'identifiers/chain', force_string=True)
# Information on binding site members
self.members = []
=====================================
plip/modules/preparation.py
=====================================
--- a/plip/modules/preparation.py
+++ b/plip/modules/preparation.py
@@ -340,7 +340,10 @@ class LigandFinder:
write_message("Renumerated molecule generated\n", mtype='debug')
- atomorder = canonicalize(lig)
+ if not config.NOPDBCANMAP:
+ atomorder = canonicalize(lig)
+ else:
+ atomorder = None
can_to_pdb = {}
if atomorder is not None:
=====================================
plip/modules/report.py
=====================================
--- a/plip/modules/report.py
+++ b/plip/modules/report.py
@@ -19,17 +19,18 @@ from . import config
# External libraries
import lxml.etree as et
-__version__ = '1.4.1'
+__version__ = '1.4.2'
class StructureReport:
"""Creates reports (xml or txt) for one structure/"""
- def __init__(self, mol):
+ def __init__(self, mol, outputprefix='report'):
self.mol = mol
self.excluded = self.mol.excluded
self.xmlreport = self.construct_xml_tree()
self.txtreport = self.construct_txt_file()
self.get_bindingsite_data()
self.outpath = mol.output_path
+ self.outputprefix = outputprefix
def construct_xml_tree(self):
"""Construct the basic XML tree"""
@@ -95,7 +96,7 @@ class StructureReport:
def write_xml(self, as_string=False):
"""Write the XML report"""
if not as_string:
- et.ElementTree(self.xmlreport).write('%s/report.xml' % self.outpath, pretty_print=True, xml_declaration=True)
+ et.ElementTree(self.xmlreport).write('{}/{}.xml'.format(self.outpath, self.outputprefix), pretty_print=True, xml_declaration=True)
else:
output = et.tostring(self.xmlreport, pretty_print=True)
if config.RAWSTRING:
@@ -105,7 +106,7 @@ class StructureReport:
def write_txt(self, as_string=False):
"""Write the TXT report"""
if not as_string:
- with open('%s/report.txt' % self.outpath, 'w') as f:
+ with open('{}/{}.txt'.format(self.outpath, self.outputprefix), 'w') as f:
[f.write(textline + '\n') for textline in self.txtreport]
else:
output = '\n'.join(self.txtreport)
=====================================
plip/plipcmd
=====================================
--- a/plip/plipcmd
+++ b/plip/plipcmd
@@ -44,7 +44,7 @@ def threshold_limiter(aparser, arg):
-def process_pdb(pdbfile, outpath, as_string=False):
+def process_pdb(pdbfile, outpath, as_string=False, outputprefix='report'):
"""Analysis of a single PDB file. Can generate textual reports XML, PyMOL session files and images as output."""
if not as_string:
startmessage = '\nStarting analysis of %s\n' % pdbfile.split('/')[-1]
@@ -62,7 +62,7 @@ def process_pdb(pdbfile, outpath, as_string=False):
create_folder_if_not_exists(outpath)
# Generate the report files
- streport = StructureReport(mol)
+ streport = StructureReport(mol, outputprefix=outputprefix)
config.MAXTHREADS = min(config.MAXTHREADS, len(mol.interaction_sets))
@@ -127,6 +127,7 @@ def main(inputstructs, inputpdbids):
write_message('\n' + '*' * len(title) + '\n')
write_message(title)
write_message('\n' + '*' * len(title) + '\n\n')
+ outputprefix = config.OUTPUTFILENAME
if inputstructs is not None: # Process PDB file(s)
num_structures = len(inputstructs)
@@ -147,7 +148,8 @@ def main(inputstructs, inputpdbids):
if num_structures > 1:
basename = inputstruct.split('.')[-2].split('/')[-1]
config.OUTPATH = '/'.join([config.BASEPATH, basename])
- process_pdb(inputstruct, config.OUTPATH, as_string=read_from_stdin)
+ outputprefix = 'report'
+ process_pdb(inputstruct, config.OUTPATH, as_string=read_from_stdin, outputprefix=outputprefix)
else: # Try to fetch the current PDB structure(s) directly from the RCBS server
num_pdbids = len(inputpdbids)
inputpdbids =remove_duplicates(inputpdbids)
@@ -155,7 +157,8 @@ def main(inputstructs, inputpdbids):
pdbpath, pdbid = download_structure(inputpdbid)
if num_pdbids > 1:
config.OUTPATH = '/'.join([config.BASEPATH, pdbid[1:3].upper(), pdbid.upper()])
- process_pdb(pdbpath, config.OUTPATH)
+ outputprefix = 'report'
+ process_pdb(pdbpath, config.OUTPATH, outputprefix=outputprefix)
if (pdbid is not None or inputstructs is not None) and config.BASEPATH is not None:
if config.BASEPATH in ['.', './']:
@@ -204,9 +207,14 @@ if __name__ == '__main__':
parser.add_argument("--nofixfile", dest="nofixfile", default=False,
help="Turns off writing files for fixed PDB files.",
action="store_true")
+ parser.add_argument("--nopdbcanmap", dest="nopdbcanmap", default=False,
+ help="Turns off calculation of mapping between canonical and PDB atom order for ligands.",
+ 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")
+ parser.add_argument("--name", dest="outputfilename", default="report",
+ help="Set a filename for the report TXT and XML files. Will only work when processing single structures.")
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",
@@ -251,8 +259,10 @@ if __name__ == '__main__':
config.INTRA = arguments.intra
config.NOFIX = arguments.nofix
config.NOFIXFILE = arguments.nofixfile
+ config.NOPDBCANMAP = arguments.nopdbcanmap
config.KEEPMOD = arguments.keepmod
config.DNARECEPTOR = arguments.dnareceptor
+ config.OUTPUTFILENAME = arguments.outputfilename
# Make sure we have pymol with --pics and --pymol
if config.PICS or config.PYMOL:
try:
=====================================
setup.py
=====================================
--- a/setup.py
+++ b/setup.py
@@ -6,7 +6,7 @@ setup.py - Setup configuration file for pip, etc.
from setuptools import setup
setup(name='plip',
- version='1.4.1',
+ version='1.4.2',
description='PLIP - Fully automated protein-ligand interaction profiler',
classifiers=[
'Development Status :: 5 - Production/Stable',
View it on GitLab: https://salsa.debian.org/med-team/plip/commit/a390324dd12ca8dccd970ab27aa8d7ecadcf1acc
--
View it on GitLab: https://salsa.debian.org/med-team/plip/commit/a390324dd12ca8dccd970ab27aa8d7ecadcf1acc
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