diff --git a/actions/ost-compare-structures b/actions/ost-compare-structures
index 7ffef2083fb5dc5e3d40e688b79d6410f2e8dd61..4723f573bda777513cd3bb053fddae7055fd0fce 100644
--- a/actions/ost-compare-structures
+++ b/actions/ost-compare-structures
@@ -50,17 +50,19 @@ compare-structures as follows:
# lDDT parameters
#################
--lddt \\
- --structural-checks \\
- --consistency-checks \\
--inclusion-radius 15.0 \\
- --bond-tolerance 15.0 \\
- --angle-tolerance 15.0 \\
- # Molck parameters
- ##################
+ # Molecular check parameters
+ ############################
--molck \\
--remove oxt hyd unk \\
--clean-element-column \\
- --map-nonstandard-residues
+ --map-nonstandard-residues \\
+ # Additional checks
+ ###################
+ --structural-checks \\
+ --bond-tolerance 15.0 \\
+ --angle-tolerance 15.0 \\
+ --consistency-checks
"""
import os
@@ -78,77 +80,51 @@ from ost.conop import CompoundLib
from ost.seq.alg.renumber import Renumber
-class _DefaultStereochemicalParamAction(argparse.Action):
- def __init__(self, default=None, required=False, **kwargs):
- # Try to set default
- cwd = os.path.abspath(os.getcwd())
- parameter_file_path = os.path.join(cwd, "stereo_chemical_props.txt")
- if not os.path.exists(parameter_file_path):
- try:
- parameter_file_path = os.path.join(
- ost.GetSharedDataPath(),
- "stereo_chemical_props.txt")
- default = parameter_file_path
- msg = ""
- except RuntimeError:
- msg = (
- "Could not set default stereochemical parameter file. In "
- "order to use the default one please set $OST_ROOT "
- "environmental variable, run the script with OST binary or"
- " provide a local copy of 'stereo_chemical_props.txt' in "
- "CWD. Alternatively provide the path to the local copy")
- else:
- default = parameter_file_path
- msg = ""
- super(_DefaultStereochemicalParamAction, self).__init__(
- default=default,
- required=required,
- **kwargs)
- if msg:
- self.help += " (WARNING: %s)" % (msg,)
-
- def __call__(self, parser, namespace, values, option_string=None):
- if not os.path.exists(values):
- parser.error(
- "Parameter file %s does not exist." % values)
- setattr(namespace, self.dest, values)
-
-
-class _DefaultCompoundLibraryAction(argparse.Action):
- def __init__(self, default=None, required=False, **kwargs):
- # Try to set default
- cwd = os.path.abspath(os.getcwd())
- compound_library_path = os.path.join(cwd, "compounds.chemlib")
- if not os.path.exists(compound_library_path):
- try:
- compound_library_path = os.path.join(
- ost.GetSharedDataPath(),
- "compounds.chemlib")
- default = compound_library_path
- msg = ""
- except RuntimeError:
- msg = (
- "Could not set default compounds library path. In "
- "order to use the default one please set $OST_ROOT "
- "environmental variable, run the script with OST binary or"
- " provide a local copy of 'compounds.chemlib' in CWD"
- ". Alternatively provide the path to the local copy")
- else:
- default = compound_library_path
- msg = ""
- super(_DefaultCompoundLibraryAction, self).__init__(
- default=default,
- required=required,
- **kwargs)
- if msg:
- self.help += " (WARNING: %s)" % (msg,)
-
- def __call__(self, parser, namespace, values, option_string=None):
- if not os.path.exists(values):
- parser.error(
- "Compounds library file %s does not exist." % values)
- setattr(namespace, self.dest, values)
-
+def _GetDefaultShareFilePath(filename):
+ """Look for filename in working directory and OST shared data path.
+ :return: Path to valid file or None if not found.
+ """
+ # Try current directory
+ cwd = os.path.abspath(os.getcwd())
+ file_path = os.path.join(cwd, filename)
+ if not os.path.isfile(file_path):
+ try:
+ file_path = os.path.join(ost.GetSharedDataPath(), filename)
+ except RuntimeError:
+ # Ignore errors here (caught later together with non-existing file)
+ pass
+ if not os.path.isfile(file_path):
+ file_path = None
+ # Either file_path is valid file path or None
+ return file_path
+
+def _GetDefaultParameterFilePath():
+ # Try to get in default locations
+ parameter_file_path = _GetDefaultShareFilePath("stereo_chemical_props.txt")
+ if parameter_file_path is None:
+ msg = (
+ "Could not set default stereochemical parameter file. In "
+ "order to use the default one please set $OST_ROOT "
+ "environmental variable, run the script with OST binary or"
+ " provide a local copy of 'stereo_chemical_props.txt' in "
+ "CWD. Alternatively provide the path to the local copy.")
+ else:
+ msg = ""
+ return parameter_file_path, msg
+
+def _GetDefaultCompoundLibraryPath():
+ # Try to get in default locations
+ compound_library_path = _GetDefaultShareFilePath("compounds.chemlib")
+ if compound_library_path is None:
+ msg = (
+ "Could not set default compounds library path. In "
+ "order to use the default one please set $OST_ROOT "
+ "environmental variable, run the script with OST binary or"
+ " provide a local copy of 'compounds.chemlib' in CWD"
+ ". Alternatively provide the path to the local copy.")
+ else:
+ msg = ""
+ return compound_library_path, msg
def _ParseArgs():
"""Parse command-line arguments."""
@@ -227,6 +203,15 @@ def _ParseArgs():
default=False,
action="store_true",
help=("Fault tolerant parsing."))
+ parser.add_argument(
+ "-cl",
+ "--compound-library",
+ dest="compound_library",
+ default=None,
+ help=("Location of the compound library file (compounds.chemlib).\n"
+ "If not provided, the following locations are searched in this\n"
+ "order: 1. Working directory, 2. OpenStructure standard library"
+ "\nlocation."))
#
# QS-scorer options
#
@@ -265,37 +250,6 @@ def _ParseArgs():
default=False,
action="store_true",
help=("Calculate lDDT."))
- parser.add_argument(
- "-sc",
- "--structural-checks",
- dest="structural_checks",
- default=False,
- action="store_true",
- help=("Perform structural checks and filter input data."))
- parser.add_argument(
- "-p",
- "--parameter-file",
- dest="parameter_file",
- action=_DefaultStereochemicalParamAction,
- help=("Location of the stereochemical parameter file\n"
- "(stereo_chemical_props.txt).\n"
- "If not provided, the following locations are searched in this\n"
- "order: 1. Working directory, 2. OpenStructure standard library"
- "\nlocation."))
- parser.add_argument(
- "-bt",
- "--bond-tolerance",
- dest="bond_tolerance",
- type=float,
- default=12.0,
- help=("Tolerance in STD for bonds."))
- parser.add_argument(
- "-at",
- "--angle-tolerance",
- dest="angle_tolerance",
- type=float,
- default=12.0,
- help=("Tolerance in STD for angles."))
parser.add_argument(
"-ir",
"--inclusion-radius",
@@ -312,18 +266,6 @@ def _ParseArgs():
help=("Sequence separation. Only distances between residues whose\n"
"separation is higher than the provided parameter are\n"
"considered when computing the score"))
- parser.add_argument(
- "-cc",
- "--consistency-checks",
- dest="consistency_checks",
- default=False,
- action="store_true",
- help=("Take consistency checks into account. By default residue name\n"
- "consistency between a model-reference pair would be checked\n"
- "but only a warning message will be displayed and the script\n"
- "will continue to calculate scores. If this flag is ON, checks\n"
- "will not be ignored and if the pair does not pass the test\n"
- "all the scores for that pair will be marked as a FAILURE."))
parser.add_argument(
"-spr",
"--save-per-residue-scores",
@@ -332,7 +274,7 @@ def _ParseArgs():
action="store_true",
help=(""))
#
- # Molck parameters
+ # Molecular check parameters
#
parser.add_argument(
"-ml",
@@ -341,15 +283,6 @@ def _ParseArgs():
default=False,
action="store_true",
help=("Run molecular checker to clean up input."))
- parser.add_argument(
- "-cl",
- "--compound-library",
- dest="compound_library",
- action=_DefaultCompoundLibraryAction,
- help=("Location of the compound library file (compounds.chemlib).\n"
- "If not provided, the following locations are searched in this\n"
- "order: 1. Working directory, 2. OpenStructure standard library"
- "\nlocation."))
parser.add_argument(
"-rm",
"--remove",
@@ -380,6 +313,52 @@ def _ParseArgs():
action="store_true",
help=("Map modified residues back to the parent amino acid, for\n"
"example MSE -> MET, SEP -> SER."))
+ #
+ # Options for various checks
+ #
+ parser.add_argument(
+ "-sc",
+ "--structural-checks",
+ dest="structural_checks",
+ default=False,
+ action="store_true",
+ help=("Perform structural checks and filter input data."))
+ parser.add_argument(
+ "-p",
+ "--parameter-file",
+ dest="parameter_file",
+ default=None,
+ help=("Location of the stereochemical parameter file\n"
+ "(stereo_chemical_props.txt).\n"
+ "If not provided, the following locations are searched in this\n"
+ "order: 1. Working directory, 2. OpenStructure standard library"
+ "\nlocation."))
+ parser.add_argument(
+ "-bt",
+ "--bond-tolerance",
+ dest="bond_tolerance",
+ type=float,
+ default=12.0,
+ help=("Tolerance in STD for bonds."))
+ parser.add_argument(
+ "-at",
+ "--angle-tolerance",
+ dest="angle_tolerance",
+ type=float,
+ default=12.0,
+ help=("Tolerance in STD for angles."))
+ parser.add_argument(
+ "-cc",
+ "--consistency-checks",
+ dest="consistency_checks",
+ default=False,
+ action="store_true",
+ help=("Take consistency checks into account. By default residue name\n"
+ "consistency between a model-reference pair would be checked\n"
+ "but only a warning message will be displayed and the script\n"
+ "will continue to calculate scores. If this flag is ON, checks\n"
+ "will not be ignored and if the pair does not pass the test\n"
+ "all the scores for that pair will be marked as a FAILURE."))
# Print full help is no arguments provided
if len(sys.argv) == 1:
@@ -395,17 +374,37 @@ def _ParseArgs():
parser.error(
"Cannot parse chain mapping into dictionary. The "
"correct format is: key:value [key2:value2 ...].")
- # Check parameter file if lddt is on
- if opts.lddt and opts.parameter_file is None:
- parser.error(
- "argument -p/--parameter-file is required when --lddt "
- "option is selected.")
-
- # Check parameter file if lddt is on
- if opts.molck and opts.compound_library is None:
- parser.error(
- "argument -cl/--compound-library is required when --molck "
- "option is selected.")
+
+ # Check parameter file if structural checks are on
+ if opts.structural_checks:
+ if opts.parameter_file is None:
+ # try to get default if none provided
+ opts.parameter_file, msg = _GetDefaultParameterFilePath()
+ if msg:
+ parser.error(msg)
+ else:
+ # if provided it must exist
+ if not os.path.isfile(opts.parameter_file):
+ parser.error("Parameter file %s does not exist." \
+ % opts.parameter_file)
+
+ # Check compound library path (always required!)
+ if opts.compound_library is None:
+ # try to get default if none provided
+ opts.compound_library, msg = _GetDefaultCompoundLibraryPath()
+ if msg:
+ parser.error(msg)
+ else:
+ # if provided it must exist
+ if not os.path.isfile(opts.compound_library):
+ parser.error("Compounds library file %s does not exist." \
+ % opts.compound_library)
+
+ # Check model and reference paths
+ if not os.path.isfile(opts.model):
+ parser.error("Model file %s does not exist." % opts.model)
+ if not os.path.isfile(opts.reference):
+ parser.error("Reference file %s does not exist." % opts.reference)
return opts
diff --git a/modules/doc/actions.rst b/modules/doc/actions.rst
index c8502eff4a82e27b1702f57604b364a555b4d66c..779a95ea47b393a7ede6dd395f1f6d650fda576d 100644
--- a/modules/doc/actions.rst
+++ b/modules/doc/actions.rst
@@ -22,13 +22,13 @@ lDDT scores between two complexes from the command line with:
$ ost compare-structures [-h] [-v VERBOSITY] -m MODEL -r REFERENCE
[-o OUTPUT] [-d] [-ds DUMP_SUFFIX]
[-rs REFERENCE_SELECTION] [-ms MODEL_SELECTION]
- [-ca] [-ft] [-qs]
+ [-ca] [-ft] [-cl COMPOUND_LIBRARY] [-qs]
[-c CHAIN_MAPPING [CHAIN_MAPPING ...]] [-rna]
- [-l] [-sc] [-p PARAMETER_FILE]
- [-bt BOND_TOLERANCE] [-at ANGLE_TOLERANCE]
- [-ir INCLUSION_RADIUS] [-ss SEQUENCE_SEPARATION]
- [-cc] [-spr] [-ml] [-cl COMPOUND_LIBRARY]
- [-rm REMOVE [REMOVE ...]] [-ce] [-mn]
+ [-l] [-ir INCLUSION_RADIUS]
+ [-ss SEQUENCE_SEPARATION] [-spr] [-ml]
+ [-rm REMOVE [REMOVE ...]] [-ce] [-mn] [-sc]
+ [-p PARAMETER_FILE] [-bt BOND_TOLERANCE]
+ [-at ANGLE_TOLERANCE] [-cc]
By default the verbosity is set to 3 which will result in the informations
being shown in the console. The result can be (optionally) saved as JSON file