From f6d06f3e2a3de4f91396d4b64f9895f637b53025 Mon Sep 17 00:00:00 2001
From: Rafal Gumienny <r.gumienny@unibas.ch>
Date: Wed, 25 Apr 2018 09:23:11 +0200
Subject: [PATCH] fix: SCHWED-3121 Allow selection for models and references
and use it for all scores
---
actions/ost-compare-structures | 62 +++++++++++++++++++++-------------
1 file changed, 38 insertions(+), 24 deletions(-)
diff --git a/actions/ost-compare-structures b/actions/ost-compare-structures
index 3562b2c6c..c89196433 100644
--- a/actions/ost-compare-structures
+++ b/actions/ost-compare-structures
@@ -198,13 +198,27 @@ def _ParseArgs():
default=".compare.structures.pdb",
help=("Use this suffix to dump structures.\n"
"Defaults to .compare.structures.pdb."))
+ parser.add_argument(
+ "-rs",
+ "--reference-selection",
+ dest="reference_selection",
+ default="",
+ help=("Selection performed on reference structures."))
+ parser.add_argument(
+ "-ms",
+ "--model-selection",
+ dest="model_selection",
+ default="",
+ help=("Selection performed on model structures."))
parser.add_argument(
"-ca",
"--c-alpha-only",
dest="c_alpha_only",
default=False,
action="store_true",
- help=("Use C-alpha atoms only."))
+ help=("Use C-alpha atoms only. Equivalent of calling the action with\n"
+ "'--model-selection=\"aname=CA\" "
+ "--reference-selection=\"aname=CA\"'\noptions."))
parser.add_argument(
"-ft",
"--fault-tolerant",
@@ -250,12 +264,6 @@ def _ParseArgs():
default=False,
action="store_true",
help=("Calculate lDDT."))
- parser.add_argument(
- "-s",
- "--selection",
- dest="selection",
- default="",
- help=("Selection performed on reference."))
parser.add_argument(
"-sc",
"--structural-checks",
@@ -469,7 +477,8 @@ def _GetAlignmentsAsFasta(alignments):
return strings
-def _ReadStructureFile(path, c_alpha_only=False, fault_tolerant=False):
+def _ReadStructureFile(path, c_alpha_only=False, fault_tolerant=False,
+ selection=""):
"""Safely read structure file into OST entity.
The functin can read both PDB and mmCIF files.
@@ -479,7 +488,18 @@ def _ReadStructureFile(path, c_alpha_only=False, fault_tolerant=False):
:returns: Entity
:rtype: :class:`~ost.mol.EntityHandle`
"""
- calpha_messag = "Selecting only C-alpha atoms"
+
+ def _Select(entity):
+ calpha_message = "Selecting only C-alpha atoms"
+ selection_message = "Selecting %s" % selection
+ if c_alpha_only:
+ ost.LogInfo(calpha_message)
+ entity = entity.Select("aname=CA")
+ if selection:
+ ost.LogInfo(selection_message)
+ entity = entity.Select(selection)
+ return entity
+
entities = list()
if not os.path.isfile(path):
raise IOError("%s is not a file" % path)
@@ -488,9 +508,7 @@ def _ReadStructureFile(path, c_alpha_only=False, fault_tolerant=False):
if not entity.IsValid():
raise IOError("Provided file does not contain valid entity.")
entity.SetName(os.path.basename(path))
- if c_alpha_only:
- ost.LogInfo(calpha_messag)
- entity = entity.Select("aname=CA")
+ entity = _Select(entity)
entities.append(entity)
except Exception:
try:
@@ -511,9 +529,7 @@ def _ReadStructureFile(path, c_alpha_only=False, fault_tolerant=False):
entity = tbu.PDBize(tmp_entity, min_polymer_size=0)
entity.SetName(os.path.basename(path) + ".au")
_RevertChainNames(entity)
- if c_alpha_only:
- ost.LogInfo(calpha_messag)
- entity = entity.Select("aname=CA")
+ entity = _Select(entity)
entities.append(entity)
elif len(cif_info.biounits) > 1:
for i, biounit in enumerate(cif_info.biounits, 1):
@@ -523,9 +539,7 @@ def _ReadStructureFile(path, c_alpha_only=False, fault_tolerant=False):
"Provided file does not contain valid entity.")
entity.SetName(os.path.basename(path) + "." + str(i))
_RevertChainNames(entity)
- if c_alpha_only:
- ost.LogInfo(calpha_messag)
- entity = entity.Select("aname=CA")
+ entity = _Select(entity)
entities.append(entity)
else:
biounit = cif_info.biounits[0]
@@ -535,9 +549,7 @@ def _ReadStructureFile(path, c_alpha_only=False, fault_tolerant=False):
"Provided file does not contain valid entity.")
entity.SetName(os.path.basename(path))
_RevertChainNames(entity)
- if c_alpha_only:
- ost.LogInfo(calpha_messag)
- entity = entity.Select("aname=CA")
+ entity = _Select(entity)
entities.append(entity)
except Exception as exc:
@@ -575,12 +587,14 @@ def _Main():
models = _ReadStructureFile(
opts.model,
c_alpha_only=opts.c_alpha_only,
- fault_tolerant=opts.fault_tolerant)
+ fault_tolerant=opts.fault_tolerant,
+ selection=opts.model_selection)
ost.LogInfo(" --> reading reference from %s" % opts.reference)
references = _ReadStructureFile(
opts.reference,
c_alpha_only=opts.c_alpha_only,
- fault_tolerant=opts.fault_tolerant)
+ fault_tolerant=opts.fault_tolerant,
+ selection=opts.reference_selection)
if opts.molck:
ost.LogInfo("#" * 80)
ost.LogInfo("Cleaning up input with Molck")
@@ -731,7 +745,7 @@ def _Main():
angle_tolerance=opts.angle_tolerance,
radius=opts.inclusion_radius,
sequence_separation=opts.sequence_separation,
- sel=opts.selection,
+ sel="",
structural_checks=False, # These are performed elsewhere
consistency_checks=False, # These are performed elsewhere
label="lddt")
--
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