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actions/ost-compare-ligand-structures
View file @ bf7dbe0b
......@@ -35,10 +35,13 @@ Ligands can be given as path to SDF files containing the ligand for both model
ligands are optionally detected from a structure file if it is given in mmCIF
format. This is based on "non-polymer" _entity.type annotation and the
respective entries must exist in the PDB component dictionary in order to get
connectivity information. For example, receptor structure and ligand(s) are
loaded from the same mmCIF file given as '-m'/'-r'. This does not work for
structures provided in PDB format and an error is raised if ligands are not
explitely given in SDF format.
connectivity information. You can avoid the requirement of the PDB component
dictionary by enabling --allow-heuristic-conn. In this case, connectivity
is established through a distance based heuristic if the ligand is not found in
the component dictionary. Be aware that this might be an issue in ligand
matching.
If you provide structures in PDB format, an error is raised if ligands are not
explicitely given in SDF format.
Ligands undergo gentle processing where hydrogens are removed. Connectivity
is relevant for scoring. It is read directly from SDF input. If ligands are
......@@ -486,6 +489,19 @@ def _ParseArgs():
"specify this mapping with: --trg-seqres-mapping A:1 B:1")
)
parser.add_argument(
"--allow-heuristic-conn",
dest="allow_heuristic_conn",
default=False,
action="store_true",
help=("Default: False - Only relevant if ligands are extracted from "
"ref/mdl in mmCIF format. Connectivity in these cases is based "
"on the chemical component dictionary. If you enable this flag, "
"connectivity can be established by a distance based heuristic "
"if the ligand is not present in the component dictionary. This "
"might cause issues in ligand matching, i.e. graph matching.")
)
args = parser.parse_args()
if args.output is None:
args.output = "out.%s" % args.output_format
......@@ -564,7 +580,8 @@ def _LoadStructureData(receptor_path,
ligand_path,
sformat = None,
bu_id = None,
fault_tolerant = False):
fault_tolerant = False,
allow_heuristic_conn = False):
receptor = None
ligands = None
......@@ -587,7 +604,8 @@ def _LoadStructureData(receptor_path,
receptor, ligands = ligand_scoring_base.MMCIFPrep(receptor_path,
biounit = bu_id,
extract_nonpoly = True,
fault_tolerant = fault_tolerant)
fault_tolerant = fault_tolerant,
allow_heuristic_conn = allow_heuristic_conn)
else:
receptor = ligand_scoring_base.MMCIFPrep(receptor_path,
biounit = bu_id,
......@@ -997,14 +1015,16 @@ def _Main():
args.reference_ligands,
sformat = args.reference_format,
bu_id = args.reference_biounit,
fault_tolerant = args.fault_tolerant)
fault_tolerant = args.fault_tolerant,
allow_heuristic_conn = args.allow_heuristic_conn)
LogInfo("Loading model data")
model, model_ligands = _LoadStructureData(args.model,
args.model_ligands,
sformat = args.model_format,
bu_id = args.model_biounit,
fault_tolerant = args.fault_tolerant)
fault_tolerant = args.fault_tolerant,
allow_heuristic_conn = args.allow_heuristic_conn)
out = _Process(model, model_ligands, reference, reference_ligands, args)
......@@ -1028,6 +1048,7 @@ def _Main():
out["trg_seqres_mapping"] = tmp
else:
out["trg_seqres_mapping"] = None
out["allow_heuristic_conn"] = args.allow_heuristic_conn
# only add lddtpli if actually computed
if args.lddt_pli:
......
modules/doc/actions.rst
View file @ bf7dbe0b
......@@ -543,6 +543,7 @@ Details on the usage (output of ``ost compare-ligand-structures --help``):
[--chem-map-seqid-thresh CHEM_MAP_SEQID_THRESH]
[--seqres SEQRES]
[--trg-seqres-mapping TRG_SEQRES_MAPPING [TRG_SEQRES_MAPPING ...]]
[--allow-heuristic-conn]
Evaluate model with non-polymer/small molecule ligands against reference.
......@@ -580,10 +581,13 @@ Details on the usage (output of ``ost compare-ligand-structures --help``):
ligands are optionally detected from a structure file if it is given in mmCIF
format. This is based on "non-polymer" _entity.type annotation and the
respective entries must exist in the PDB component dictionary in order to get
connectivity information. For example, receptor structure and ligand(s) are
loaded from the same mmCIF file given as '-m'/'-r'. This does not work for
structures provided in PDB format and an error is raised if ligands are not
explitely given in SDF format.
connectivity information. You can avoid the requirement of the PDB component
dictionary by enabling --allow-heuristic-conn. In this case, connectivity
is established through a distance based heuristic if the ligand is not found in
the component dictionary. Be aware that this might be an issue in ligand
matching.
If you provide structures in PDB format, an error is raised if ligands are not
explicitely given in SDF format.
Ligands undergo gentle processing where hydrogens are removed. Connectivity
is relevant for scoring. It is read directly from SDF input. If ligands are
......@@ -613,10 +617,10 @@ Details on the usage (output of ``ost compare-ligand-structures --help``):
in chain mapping. That is 1) pass the same size threshold as for chem_groups
2) can be aligned to any of the chem groups with a sequence identity
threshold that can be controlled by --chem-map-seqid-thresh.
* "mdl_chains_without_chem_mapping": Model chains that could be considered in chain mapping,
i.e. are long enough, but could not be mapped to any chem group.
Depends on --chem-map-seqid-thresh. A mapping for each model chain can be
enforced by setting it to 0.
* "mdl_chains_without_chem_mapping": Model chains that could be considered in
chain mapping, i.e. are long enough, but could not be mapped to any chem
group. Depends on --chem-map-seqid-thresh. A mapping for each model chain can
be enforced by setting it to 0.
* "status": SUCCESS if everything ran through. In case of failure, the only
content of the JSON output will be "status" set to FAILURE and an
additional key: "traceback".
......@@ -691,7 +695,7 @@ Details on the usage (output of ``ost compare-ligand-structures --help``):
Path to model ligand files.
-r REFERENCE, --ref REFERENCE, --reference REFERENCE
Path to reference file.
-rl [REFERENCE_LIGANDS ...], --ref-ligands [REFERENCE_LIGANDS ...], --reference-ligands [ REFERENCE_LIGANDS ...]
-rl [REFERENCE_LIGANDS ...], --ref-ligands [REFERENCE_LIGANDS ...], --reference-ligands [REFERENCE_LIGANDS ...]
Path to reference ligand files.
-o OUTPUT, --out OUTPUT, --output OUTPUT
Output file name. Default depends on format: out.json
......@@ -810,4 +814,14 @@ Details on the usage (output of ``ost compare-ligand-structures --help``):
which you provide a seqres file containing one
sequence with name "1". You can specify this mapping
with: --trg-seqres-mapping A:1 B:1
--allow-heuristic-conn
Default: False - Only relevant if ligands are
extracted from ref/mdl in mmCIF format. Connectivity
in these cases is based on the chemical component
dictionary. If you enable this flag, connectivity can
be established by a distance based heuristic if the
ligand is not present in the component dictionary.
This might cause issues in ligand matching, i.e. graph
matching.
modules/mol/alg/pymod/ligand_scoring_base.py
View file @ bf7dbe0b
......@@ -77,7 +77,7 @@ def CleanHydrogens(ent, clib):
def MMCIFPrep(mmcif_path, biounit=None, extract_nonpoly=False,
fault_tolerant=False):
fault_tolerant=False, allow_heuristic_conn=False):
""" Ligand scoring helper - Prepares :class:`LigandScorer` input from mmCIF
Only performs gentle cleanup of hydrogen atoms. Further cleanup is delegated
......@@ -95,6 +95,15 @@ def MMCIFPrep(mmcif_path, biounit=None, extract_nonpoly=False,
:type extract_nonpoly: :class:`bool`
:param fault_tolerant: Passed as parameter to :func:`ost.io.LoadMMCIF`
:type fault_tolerant: :class:`bool`
:param allow_heuristic_conn: Only relevant if extract_nonpoly is True.
The chemical component dictionary is relevant
for connectivity information. By default, we
enforce the presence of each non-polymer in
the dictionary to ensure correct connectity.
If you enable this flag, you allow the use
of a distance based heuristic as fallback.
With all its consequences in ligand matching.
:type allow_heuristic_conn: :class:`bool`
:returns: :class:`ost.mol.EntityHandle` which only contains polymer
entities representing the receptor structure. If *extract_nonpoly*
is True, a tuple is returned which additionally contains a
......@@ -175,12 +184,13 @@ def MMCIFPrep(mmcif_path, biounit=None, extract_nonpoly=False,
f"{mmcif_path} to contain exactly 1 "
f"residue. Got {ch.GetResidueCount()} "
f"in chain {ch.name}")
compound = clib.FindCompound(view.residues[0].name)
if compound is None:
raise RuntimeError(f"Can only extract non-polymer entities if "
f"respective residues are available in PDB "
f"component dictionary. Can't find "
f"\"{view.residues[0].name}\"")
if not allow_heuristic_conn:
compound = clib.FindCompound(view.residues[0].name)
if compound is None:
raise RuntimeError(f"Can only extract non-polymer entities if "
f"respective residues are available in PDB "
f"component dictionary. Can't find "
f"\"{view.residues[0].name}\"")
non_poly_entities.append(mol.CreateEntityFromView(view, True))
......
modules/mol/alg/pymod/ligand_scoring_lddtpli.py
View file @ bf7dbe0b
......@@ -451,6 +451,11 @@ class LDDTPLIScorer(ligand_scoring_base.LigandScorer):
already_mapped = set()
for mdl_ch in mdl_chains:
if mdl_ch not in lddt_chain_mapping:
if mdl_ch in self._mdl_chains_without_chem_mapping:
# this mdl chain does not map to any trg chain
continue
# check which chain in trg is closest
chem_grp_idx = None
for i, m in enumerate(self._chem_mapping):
......