From 1dfd44ba32535bb15e1dfe7f04d4ac576b6129b3 Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Fri, 31 May 2019 15:13:59 +0200
Subject: [PATCH] updated CAD score binding - format of result has changed,
check doc for further details
---
CHANGELOG.txt | 2 +
modules/bindings/pymod/cadscore.py | 261 +++++++++++++++++++++++------
2 files changed, 216 insertions(+), 47 deletions(-)
diff --git a/CHANGELOG.txt b/CHANGELOG.txt
index eb306e7ac..f0f8504a8 100644
--- a/CHANGELOG.txt
+++ b/CHANGELOG.txt
@@ -4,6 +4,8 @@ Changes in Release 1.x.x
* Use system provided SQLite3 library
* C++ wrapper around C++ implementation of TMalign
* Database for efficient in-memory lookup of coordinates and sequences
+ * Updated CAD score binding with change in result format, check documentation
+ for further details
Changes in Release 1.9.0
--------------------------------------------------------------------------------
diff --git a/modules/bindings/pymod/cadscore.py b/modules/bindings/pymod/cadscore.py
index fdaef13a9..8b81c79a9 100644
--- a/modules/bindings/pymod/cadscore.py
+++ b/modules/bindings/pymod/cadscore.py
@@ -28,8 +28,8 @@ Proteins. 2012 Aug 30. [Epub ahead of print]
Authors: Valerio Mariani, Alessandro Barbato
"""
-import subprocess, os, tempfile, platform
-from ost import settings, io
+import subprocess, os, tempfile, platform, re
+from ost import settings, io, mol
def _SetupFiles(model,reference):
# create temporary directory
@@ -37,7 +37,8 @@ def _SetupFiles(model,reference):
dia = 'PDB'
for chain in model.chains:
if chain.name==" ":
- raise RuntimeError("One of the chains in the model has no name. Cannot calculate CAD score")
+ raise RuntimeError("One of the chains in the model has no name. Cannot "
+ "calculate CAD score")
if len(chain.name) > 1:
dia = 'CHARMM'
break;
@@ -49,7 +50,8 @@ def _SetupFiles(model,reference):
dia = 'PDB'
for chain in reference.chains:
if chain.name==" ":
- raise RuntimeError("One of the chains in the reference has no name. Cannot calculate CAD score")
+ raise RuntimeError("One of the chains in the reference has no name. "
+ "Cannot calculate CAD score")
if len(chain.name) > 1:
dia = 'CHARMM'
break;
@@ -64,7 +66,6 @@ def _CleanupFiles(dir_name):
import shutil
shutil.rmtree(dir_name)
-
class CADResult:
"""
Holds the result of running CAD
@@ -77,78 +78,244 @@ class CADResult:
Dictionary containing local CAD's atom-atom (AA) scores.
- :type: dictionary (key: chain.resnum (e.g.: A.24), value: CAD local AA score (see CAD Documentation online)
+ :type: dictionary (key: tuple(chain, resnum) (e.g.:
+ ("A", ost.mol.ResNum(24)), value: CAD local AA score
+ (see CAD Documentation online)
"""
def __init__(self, globalAA, localAA):
self.globalAA=globalAA
self.localAA=localAA
def _ParseCADGlobal(lines):
- interesting_lines=lines[1]
- aa=float(interesting_lines.split()[10])
- return aa
+ header = lines[0].split()
+ aa_idx = header.index("AA")
+ aa_score=float(lines[1].split()[aa_idx])
+ return aa_score
def _ParseCADLocal(lines):
+ local_scores_idx = None
+ for line_idx in range(len(lines)):
+ if "local_scores" in lines[line_idx]:
+ local_scores_idx = line_idx
+ break
+ if local_scores_idx == None:
+ raise RuntimeError("Failed to parse local cadscores")
+ local_aa_dict={}
+ for line_idx in range(local_scores_idx+2, len(lines)):
+ items=lines[line_idx].split()
+ local_aa = float(items[2])
+ if local_aa < 0.0:
+ continue # invalid CAD score
+ key = (items[0], mol.ResNum(int(items[1])))
+ local_aa_dict[key] = local_aa
+
+ return local_aa_dict
+
+def _ParseVoronotaGlobal(lines):
+ return float(lines[0].split()[4])
+
+def _ParseVoronotaLocal(lines):
local_aa_dict={}
- for lin in lines[11:]:
- items=lin.split()
- chain=items[0]
- resnum=int(items[1])
- key=chain+'.'+str(resnum)
- aa=float(items[2])
- local_aa_dict[key]=aa
+ chain_name_regex = r'c\<\D+\>'
+ resnum_regex = r'r\<\d+\>'
+ insertion_code_regex = r'i\<\D\>'
+ for line in lines:
+ local_aa = float(line.split()[-1])
+ if local_aa < 0.0:
+ continue # invalid CAD score
+ chain_data = re.findall(chain_name_regex, line)
+ resnum_data = re.findall(resnum_regex, line)
+ insertion_code_data = re.findall(insertion_code_regex, line)
+ resnum = None
+ if len(insertion_code_data) == 0:
+ resnum = mol.ResNum(int(resnum_data[0][1:].strip('><')))
+ else:
+ resnum = mol.ResNum(int(resnum_data[0][1:].strip('><')),
+ insertion_code_data[0][1:].strip('><'))
+ key = (chain_data[0][1:].strip('><'), resnum)
+ local_aa_dict[key] = local_aa
return local_aa_dict
-def _RunCAD(max_iter, tmp_dir):
+def _RunCAD(tmp_dir, mode, cad_bin_path, old_regime):
+
model_filename=os.path.join(tmp_dir, 'model.pdb')
reference_filename=os.path.join(tmp_dir, 'reference.pdb')
+ globalAA = None
+ localAA = None
+
if platform.system() == "Windows":
raise RuntimeError('CAD score not available on Windows')
+
+ if mode == "classic":
+ cad_calc_path = None
+ cad_read_g_path = None
+ cad_read_l_path = None
+ if cad_bin_path:
+ cad_calc_path = settings.Locate('CADscore_calc.bash',
+ search_paths=[cad_bin_path],
+ search_system_paths=False)
+ cad_read_g_path = settings.Locate('CADscore_read_global_scores.bash',
+ search_paths=[cad_bin_path],
+ search_system_paths=False)
+ cad_read_l_path=settings.Locate('CADscore_read_local_scores.bash',
+ search_paths=[cad_bin_path],
+ search_system_paths=False)
+ # also try to locate the actual executable that is called from the
+ # bash scripts
+ executable_path = settings.Locate('voroprot2',
+ search_paths=[cad_bin_path],
+ search_system_paths=False)
+ else:
+ cad_calc_path = settings.Locate('CADscore_calc.bash')
+ cad_read_g_path = settings.Locate('CADscore_read_global_scores.bash')
+ cad_read_l_path = settings.Locate('CADscore_read_local_scores.bash')
+ # also try to locate the actual executable that is called from the
+ # bash scripts
+ executable_path = settings.Locate('voroprot2')
+ command1="\"%s\" -m \"%s\" -t \"%s\" -D \"%s\"" %(cad_calc_path,
+ model_filename,
+ reference_filename,
+ os.path.join(tmp_dir,
+ "cadtemp"))
+ command2="\"%s\" -D \"%s\"" %(cad_read_g_path, os.path.join(tmp_dir,
+ "cadtemp"))
+ command3="\"%s\" -m \"%s\" -t \"%s\" -D \"%s\" -c AA" %(cad_read_l_path,
+ model_filename,
+ reference_filename,
+ os.path.join(tmp_dir,
+ "cadtemp"))
+
+ ps1=subprocess.Popen(command1, shell=True, stdout=subprocess.PIPE)
+ ps1.wait()
+ ps2=subprocess.Popen(command2, shell=True, stdout=subprocess.PIPE)
+ ps2.wait()
+ lines=ps2.stdout.readlines()
+ try:
+ globalAA=_ParseCADGlobal(lines)
+ except:
+ raise RuntimeError("CAD calculation failed")
+ ps3=subprocess.Popen(command3, shell=True, stdout=subprocess.PIPE)
+ ps3.wait()
+ lines=ps3.stdout.readlines()
+ try:
+ localAA=_ParseCADLocal(lines)
+ except:
+ raise RuntimeError("CAD calculation failed")
+
+ elif mode == "voronota":
+ local_score_filename = os.path.join(tmp_dir, "local_scores.txt")
+ voronota_cadscore_path = None
+ if cad_bin_path:
+ voronota_cadscore_path = settings.Locate("voronota-cadscore",
+ search_paths=[cad_bin_path],
+ search_system_paths=False)
+ # also try to locate the actual executable that is called from the
+ # bash script
+ executable_path = settings.Locate("voronota",
+ search_paths=[cad_bin_path],
+ search_system_paths=False)
+ else:
+ voronota_cadscore_path = settings.Locate("voronota-cadscore")
+ # also try to locate the actual executable that is called from the
+ # bash script
+ executable_path = settings.Locate("voronota")
+ cmd = [voronota_cadscore_path, '-m', model_filename, '-t',
+ reference_filename, '--contacts-query-by-code AA',
+ '--output-residue-scores', local_score_filename]
+ if old_regime:
+ cmd.append("--old-regime")
+ cmd = ' '.join(cmd)
+ ps = subprocess.Popen(cmd, shell=True, stdout=subprocess.PIPE)
+ ps.wait()
+ try:
+ globalAA = _ParseVoronotaGlobal(ps.stdout.readlines())
+ except:
+ raise RuntimeError("CAD calculation failed")
+ try:
+ localAA = _ParseVoronotaLocal(open(local_score_filename).readlines())
+ except:
+ raise RuntimeError("CAD calculation failed")
+
else:
- cad_calc_path=settings.Locate('CADscore_calc.bash')
- cad_read_g_path=settings.Locate('CADscore_read_global_scores.bash')
- cad_read_l_path=settings.Locate('CADscore_read_local_scores.bash')
- command1="\"%s\" -o %i -m \"%s\" -t \"%s\" -D \"%s\"" %(cad_calc_path, max_iter, model_filename, reference_filename, os.path.join(tmp_dir,"cadtemp"))
- command2="\"%s\" -D \"%s\"" %(cad_read_g_path, os.path.join(tmp_dir,"cadtemp"))
- command3="\"%s\" -m \"%s\" -t \"%s\" -D \"%s\" -c AA" %(cad_read_l_path, model_filename, reference_filename,os.path.join(tmp_dir,"cadtemp"))
- ps1=subprocess.Popen(command1, shell=True, stdout=subprocess.PIPE)
- ps1.wait()
- ps2=subprocess.Popen(command2, shell=True, stdout=subprocess.PIPE)
- ps2.wait()
- lines=ps2.stdout.readlines()
- try:
- globalAA=_ParseCADGlobal(lines)
- except:
- raise RuntimeError("CAD calculation failed")
- ps3=subprocess.Popen(command3, shell=True, stdout=subprocess.PIPE)
- ps3.wait()
- lines=ps3.stdout.readlines()
- try:
- localAA=_ParseCADLocal(lines)
- except:
- raise RuntimeError("CAD calculation failed")
+ raise RuntimeError("Invalid CAD mode! Allowed are: "
+ "[\"classic\", \"voronota\"]")
+
return CADResult(globalAA,localAA)
+def _HasInsertionCodes(model, reference):
+ for r in model.residues:
+ if r.GetNumber().GetInsCode() != "\0":
+ print r
+ return True
+ for r in reference.residues:
+ if r.GetNumber().GetInsCode() != "\0":
+ print r
+ return True
+ return False
-def CADScore(model, reference, max_iter=300):
+def _MapLabels(model, cad_results, label):
+ for k,v in cad_results.localAA.iteritems():
+ r = model.FindResidue(k[0], k[1])
+ if not r.IsValid():
+ raise RuntimeError("Failed to map cadscore on residues: " +
+ "CAD score estimated for residue in chain \"" +
+ k[0] + "\" with ResNum " + str(k[1]) + ". Residue " +
+ "could not be found in model.")
+ r.SetFloatProp(label, v)
+
+def CADScore(model, reference, mode = "classic", label = "localcad",
+ old_regime = False, cad_bin_path = None):
"""
- Calculates global and local atom-atom (AA) CAD Scores
-
+ Calculates global and local atom-atom (AA) CAD Scores.
+
+ You can either access the original implementation available from
+ https://bitbucket.org/kliment/cadscore/downloads/
+ or the new implementation which is part of the Voronota package
+ available from https://bitbucket.org/kliment/voronota/downloads/.
+
+ The scores of the two implementations differ but strongly correlate
+ as the contacts between atoms are estimated differently. When using
+ the "voronota" *mode* you can minimize those discrepancies by
+ setting the *old_regime* flag to True.
+
+ Furthermore, the "voronota" *mode* generates per-residue scores that
+ are inverted when compared to the classical implementation
+ (0.0: bad, 1.0 good).
:param model: The model structure.
:type model: :class:`~ost.mol.EntityView` or :class:`~ost.mol.EntityHandle`
:param reference: The reference structure
- :type model2: :class:`~ost.mol.EntityView` or :class:`~ost.mol.EntityHandle`
- :param max_iter: Optional. The maximum number of iteration for the tessellation algorithm before giving up. By default 300
+ :type reference: :class:`~ost.mol.EntityView` or
+ :class:`~ost.mol.EntityHandle`
+ :param mode: What CAD score implementation to use, must be one in
+ ["classic", "voronota"]
+ :param label: Local CAD scores will be mapped on residues of model as
+ float property with this name
+ :type label: :class:`str`
+ :param old_regime: Only has an effect if *mode* is "voronota". If set to true,
+ the discrepancies between the two modes is minimized but
+ the behaviour of inverted scores persists.
+ :type old_regime: :class:`bool`
+ :param cad_bin_path: Path to search for the required executables
+ (["CADscore_calc.bash",
+ "CADscore_read_global_scores.bash",
+ "CADscore_read_local_scores.bash"] for "classic" *mode*
+ or ["voronota-cadscore"] for "voronota" *mode*). If not
+ set, the env path is searched.
+ :type cad_bin_path: :class:`str`
:returns: The result of the CAD score calculation
:rtype: :class:`CADResult`
- :raises: :class:`~ost.settings.FileNotFound` if any of the CAD score exacutables could not be located.
+ :raises: :class:`~ost.settings.FileNotFound` if any of the CAD score
+ executables could not be located.
:raises: :class:`RuntimeError` if the calculation failed
"""
+ if mode == "classic" and _HasInsertionCodes(model, reference):
+ raise RuntimeError("The classic CAD score implementation does not support "
+ "insertion codes in residues")
tmp_dir_name=_SetupFiles(model, reference)
- result=_RunCAD(max_iter, tmp_dir_name)
+ result=_RunCAD(tmp_dir_name, mode, cad_bin_path, old_regime)
_CleanupFiles(tmp_dir_name)
+ _MapLabels(model, result, label)
return result
-
--
GitLab