diff --git a/modules/bindings/pymod/naccess.py b/modules/bindings/pymod/naccess.py
index 1612c503f9a83e0284e021384b82834aefba166c..df56c2af0944ee603f1467ec61431fa735ed3a47 100644
--- a/modules/bindings/pymod/naccess.py
+++ b/modules/bindings/pymod/naccess.py
@@ -30,16 +30,35 @@ def _GetExecutable(naccess_exe):
"""
return settings.Locate('naccess', explicit_file_name=naccess_exe)
+def _CheckNaccessRoot(naccess_root):
+ """
+ :return: True, if given directory contains "accall" binary and files
+ "vdw.radii" and "standard.data".
+ :param naccess_root: Path to naccess folder to check.
+ """
+ accall_exe = os.path.join(naccess_root, "accall")
+ check = (os.path.exists(accall_exe) and os.access(accall_exe, os.X_OK) \
+ and os.path.exists(os.path.join(naccess_root, "vdw.radii")) \
+ and os.path.exists(os.path.join(naccess_root, "standard.data")))
+ if not check:
+ LogWarning("NACCESS: Could not find required files to launch accall " \
+ "directly in %s." % naccess_root)
+ return check
+
def _SetupFiles(entity, selection, scratch_dir, max_number_of_atoms):
"""
Setup files for naccess calculation in temporary directory
- :param entity: EntityHandle or EntityView to calculate surface
- :param selection: Calculate surface for subset of entity
- :param scratch_dir: Directory for temporary files (NACCESS is sensitive to "." in directory names
- :param max_number_of_atoms: Max Number of atoms in the entity (i.e. is limited in the default NACCESS version to 50 000)
- :returns: array containing temporary directory, input filename for naccess and directory of the input file
- :exception: RuntimeError if selection is not valid
+ :param entity: OST entity to calculate surface
+ :param selection: Calculate surface for subset of entity
+ :param scratch_dir: Scratch directory. A subfolder for temporary files
+ is created in there. If not specified, a default
+ directory is used (see :func:`tempfile.mkdtemp`).
+ :param max_number_of_atoms: Max Number of atoms in the entity (i.e. is limited
+ in the default NACCESS version to 50 000)
+ :returns: Tuple containing temporary directory, input filename for naccess and
+ directory of the input file
+ :exception: RuntimeError if selection is not valid or too many atoms
"""
# create temporary directory
@@ -103,7 +122,8 @@ def _ParseAsaFile(entity, file, asa_atom):
if(a.IsValid()):
a.SetFloatProp(asa_atom, float(asa))
else:
- print chain_id, resNum, atom_name
+ LogWarning("NACCESS: invalid asa entry %s %s %s" \
+ % (chain_id, resNum, atom_name))
def _ParseRsaFile(enti,file, asa_abs, asa_rel):
"""
@@ -161,33 +181,62 @@ def __CleanupFiles(dir_name):
import shutil
shutil.rmtree(dir_name)
+
+def _RunACCALL(command, temp_dir, query):
+ """
+ Fast method to run the Naccess surface calculation.
+
+ This method starts the accall binary directly and pipes in the input provided
+ in *query*. This is faster than calling the "naccess" script since the script
+ has a constant overhead of roughly 1.3s in each call.
+
+ :param command: Command to execute
+ :param temp_dir: Command is executed with this working directory
+ :param query: User input to pipe into *command*
+ :returns: stdout of command
+ :exception: CalledProcessError for non-zero return value
+ """
+ proc = subprocess.Popen(command, stdout=subprocess.PIPE,
+ stderr=subprocess.PIPE, stdin=subprocess.PIPE,
+ cwd=temp_dir)
+ stdout_value, stderr_value = proc.communicate(query)
+
+ # check for successful completion of naccess
+ if proc.returncode != 0:
+ LogWarning("WARNING: naccess error\n%s\n%s" % (stdout_value, stderr_value))
+ raise subprocess.CalledProcessError(proc.returncode, command)
+
+ return stdout_value
+
+
def _RunNACCESS(command, temp_dir):
"""
- Method to run the MSMS surface calculation
+ Method to run the Naccess surface calculation.
- This method starts the external MSMS executable and returns the stdout of MSMS
+ This method starts the external Naccess executable and returns the stdout.
- :param command: Command to execute
- :returns: stdout of MSMS
- :exception: CalledProcessError for non-zero return value
+ :param command: Command to execute
+ :param temp_dir: Command is executed with this working directory
+ :returns: stdout of command
+ :exception: CalledProcessError for non-zero return value
"""
proc = subprocess.Popen(command, shell=True, stdout=subprocess.PIPE,
cwd=temp_dir)
stdout_value, stderr_value = proc.communicate()
# check for successful completion of naccess
- if proc.returncode!=0:
- print "WARNING: naccess error\n", stdout_value
+ if proc.returncode != 0:
+ LogWarning("WARNING: naccess error\n%s" % stdout_value)
raise subprocess.CalledProcessError(proc.returncode, command)
return stdout_value
-
+
def CalculateSurfaceArea(entity, radius=1.4,
include_hydrogens=False, include_hetatm = False,
include_water=False, selection="", naccess_exe=None,
- keep_files=False, asa_abs= "asaAbs", asa_rel="asaRel",
- asa_atom="asaAtom", scratch_dir=None,
+ naccess_root=None, keep_files=False, asa_abs= "asaAbs",
+ asa_rel="asaRel", asa_atom="asaAtom", scratch_dir=None,
max_number_of_atoms=50000):
"""
Calculates analytical the solvent accessible surface area by using the
@@ -206,6 +255,9 @@ def CalculateSurfaceArea(entity, radius=1.4,
:param include_water: Calculate surface including water
:param selection: Calculate surface for subset of entity
:param naccess_exe: naccess executable (full path to executable)
+ :param naccess_root: Path to folder containing "accall" binary and
+ files "vdw.radii" and "standard.data". This is the
+ fastest way to call naccess!
:param keep_files: If True, do not delete temporary files
:param asa_abs: Attaches per residue absolute SASA to specified
FloatProp on residue level
@@ -223,38 +275,70 @@ def CalculateSurfaceArea(entity, radius=1.4,
"""
# check if naccess executable is specified
- naccess_executable=_GetExecutable(naccess_exe)
+ if naccess_root and _CheckNaccessRoot(naccess_root):
+ # use faster, direct call to accall binary
+ fast_mode = True
+ else:
+ # get naccess executable
+ naccess_executable = _GetExecutable(naccess_exe)
+ # see if we can extract naccess_root from there (fallback to old mode)
+ naccess_root = os.path.dirname(naccess_executable)
+ fast_mode = _CheckNaccessRoot(naccess_root)
# setup files for naccess
(naccess_data_dir, naccess_data_file, naccess_data_base) \
= _SetupFiles(entity, selection, scratch_dir, max_number_of_atoms)
- # set command line
- command = "%s %s -p %f " % \
- (naccess_executable, naccess_data_file, radius)
- if include_hydrogens:
- command = "%s -w" % command
- if include_water:
- command = "%s -y" % command
- if include_hetatm:
- command = "%s -h" % command
- # execute naccess
- stdout_value = _RunNACCESS(command, naccess_data_dir)
-
- # parse outout
- new_asa= os.path.join(naccess_data_dir, "%s.asa" % naccess_data_base)
- _ParseAsaFile(entity, new_asa, asa_atom)
+ try:
+ # call naccess
+ if fast_mode:
+ # cook up stdin query (same logic as naccess script)
+ query = "PDBFILE %s\n" \
+ "VDWFILE %s\n" \
+ "STDFILE %s\n" \
+ "PROBE %f\n" \
+ "ZSLICE 0.05\n" \
+ % (naccess_data_file, os.path.join(naccess_root, "vdw.radii"),
+ os.path.join(naccess_root, "standard.data"), radius)
+ if include_hydrogens:
+ query += "HYDROGENS\n"
+ if include_water:
+ query += "WATERS\n"
+ if include_hetatm:
+ query += "HETATOMS\n"
+ # call it
+ command = os.path.join(naccess_root, "accall")
+ _RunACCALL(command, naccess_data_dir, query)
+ else:
+ LogWarning("NACCESS: Falling back to slower call to %s." \
+ % naccess_executable)
+ # set command line
+ command = "%s %s -p %f " % \
+ (naccess_executable, naccess_data_file, radius)
+ if include_hydrogens:
+ command = "%s -w" % command
+ if include_water:
+ command = "%s -y" % command
+ if include_hetatm:
+ command = "%s -h" % command
+ # execute naccess
+ _RunNACCESS(command, naccess_data_dir)
- new_rsa = os.path.join(naccess_data_dir, "%s.rsa" % naccess_data_base)
- _ParseRsaFile(entity, new_rsa, asa_abs, asa_rel)
+ # parse outout
+ new_asa = os.path.join(naccess_data_dir, "%s.asa" % naccess_data_base)
+ _ParseAsaFile(entity, new_asa, asa_atom)
+
+ new_rsa = os.path.join(naccess_data_dir, "%s.rsa" % naccess_data_base)
+ _ParseRsaFile(entity, new_rsa, asa_abs, asa_rel)
+
+ finally:
+ # clean up
+ if not keep_files:
+ __CleanupFiles(naccess_data_dir)
# sum up Asa for all atoms
sasa = 0.0
for a in entity.atoms:
sasa += a.GetFloatProp(asa_atom, 0.0)
-
- # clean up
- if not keep_files:
- __CleanupFiles(naccess_data_dir)
return sasa