New upstream version 1.4.2+dfsg (a390324d) · Commits · Debian Med / plip

CHANGES.txt

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		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

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		@@ -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

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		@@ -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

+19 −19

Original line number	Diff line number	Diff line
		@@ -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

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		@@ -340,7 +340,10 @@ class LigandFinder:

		write_message("Renumerated molecule generated\n", mtype='debug')

		if not config.NOPDBCANMAP:
		atomorder = canonicalize(lig)
		else:
		atomorder = None

		can_to_pdb = {}
		if atomorder is not None: