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Versioning alignments
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@ConorFWild
ConorFWild committed Apr 17, 2024
1 parent 0665ce2 commit 25bf276
Showing 1 changed file with 71 additions and 65 deletions.
136 changes: 71 additions & 65 deletions src/xchemalign/aligner.py
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Original file line number Diff line number Diff line change
Expand Up @@ -344,6 +344,9 @@ def _perform_alignments(self, meta):
assemblies = _load_assemblies(fs_model.xtalforms, self.assemblies_file)
self.logger.info(f"Got {len(assemblies)} assemblies")

# # Derive alignment heirarchy
# alignment_heirarchy = _derive_alignment_heirarchy(assemblies)

# # Get xtalforms
if source_fs_model:
xtalforms: dict[str, dt.XtalForm] = _load_xtalforms(source_fs_model.xtalforms, self.assemblies_file)
Expand Down Expand Up @@ -506,7 +509,7 @@ def _perform_alignments(self, meta):
# }

# Add the canonical sites
canonical_sites = read_yaml(fs_model.canonical_sites)
canonical_sites = read_yaml(updated_fs_model.canonical_sites)
new_meta[Constants.META_CANONICAL_SITES] = canonical_sites
# canonical_sites_meta = new_meta[Constants.META_CANONICAL_SITES] = {}
# for canonical_site_id, canonical_site in zip(canonical_sites.site_ids, canonical_sites.sites):
Expand All @@ -525,7 +528,7 @@ def _perform_alignments(self, meta):
# }

# Add the xtalform sites - note the chain is that of the original crystal structure, NOT the assembly
xtalform_sites = read_yaml(fs_model.xtalform_sites)
xtalform_sites = read_yaml(updated_fs_model.xtalform_sites)
new_meta[Constants.META_XTALFORM_SITES] = xtalform_sites
# xtalform_sites_meta = new_meta[Constants.META_XTALFORM_SITES] = {}
# for xtalform_site_id, xtalform_site in xtalform_sites.xtalform_sites.items():
Expand All @@ -541,7 +544,7 @@ def _perform_alignments(self, meta):
# }

# Add the output aligned files
assigned_xtalforms = read_yaml(fs_model.dataset_assignments)
assigned_xtalforms = read_yaml(updated_fs_model.dataset_assignments)

# for dtag, crystal in crystals.items():
# # Skip if no output for this dataset
Expand Down Expand Up @@ -586,47 +589,48 @@ def _perform_alignments(self, meta):
crystal_output[Constants.META_ASSIGNED_XTALFORM] = assigned_xtalform

# Skip if no output for this dataset
if dtag not in fs_model.alignments:
if dtag not in updated_fs_model.alignments:
self.logger.warn('skipping {} as aligned structures not found'.format(dtag))
continue

crystal_output[Constants.META_ALIGNED_FILES] = {}
aligned_output = crystal_output[Constants.META_ALIGNED_FILES]
dataset_output = fs_model.alignments[dtag]
dataset_output = updated_fs_model.alignments[dtag]
for chain_name, chain_output in dataset_output.items():
aligned_chain_output = aligned_output[chain_name] = {}
for ligand_residue, ligand_output in chain_output.items():
aligned_ligand_output = aligned_chain_output[ligand_residue] = {}
for site_id, aligned_structure_path in ligand_output.aligned_structures.items():
aligned_artefacts_path = ligand_output.aligned_artefacts[site_id]
aligned_event_map_path = ligand_output.aligned_event_maps[site_id]
aligned_xmap_path = ligand_output.aligned_xmaps[site_id]
aligned_diff_map_path = ligand_output.aligned_diff_maps[site_id]
aligned_ligand_output[site_id] = {
Constants.META_AIGNED_STRUCTURE: aligned_structure_path,
# Constants.META_AIGNED_ARTEFACTS: aligned_artefacts_path,
Constants.META_AIGNED_EVENT_MAP: aligned_event_map_path,
Constants.META_AIGNED_X_MAP: aligned_xmap_path,
Constants.META_AIGNED_DIFF_MAP: aligned_diff_map_path,
}
for version, version_output in ligand_output.items():
for site_id, aligned_structure_path in version_output.aligned_structures.items():
aligned_artefacts_path = version_output.aligned_artefacts[site_id]
aligned_event_map_path = version_output.aligned_event_maps[site_id]
aligned_xmap_path = version_output.aligned_xmaps[site_id]
aligned_diff_map_path = version_output.aligned_diff_maps[site_id]
aligned_ligand_output[site_id] = {
Constants.META_AIGNED_STRUCTURE: aligned_structure_path,
# Constants.META_AIGNED_ARTEFACTS: aligned_artefacts_path,
Constants.META_AIGNED_EVENT_MAP: aligned_event_map_path,
Constants.META_AIGNED_X_MAP: aligned_xmap_path,
Constants.META_AIGNED_DIFF_MAP: aligned_diff_map_path,
}

## Add the reference alignments
new_meta[Constants.META_REFERENCE_ALIGNMENTS] = {}
for dtag, crystal in crystals.items():
# Skip if no output for this dataset
if dtag not in fs_model.reference_alignments:
if dtag not in updated_fs_model.reference_alignments:
continue

crystal_output = new_meta[Constants.META_REFERENCE_ALIGNMENTS][dtag] = {}

# for dtag, canonical_site_aligned_files in fs_model.reference_alignments.items():
for canonical_site_id, aligned_files in fs_model.reference_alignments[dtag].items():
for canonical_site_id, aligned_files in updated_fs_model.reference_alignments[dtag].items():
crystal_output[canonical_site_id] = aligned_files

new_meta[Constants.META_TRANSFORMS] = {}

## Get the observation to conformer site transforms
ligand_neighbourhood_transforms = read_yaml(fs_model.ligand_neighbourhood_transforms)
ligand_neighbourhood_transforms = read_yaml(updated_fs_model.ligand_neighbourhood_transforms)
new_meta[Constants.META_TRANSFORMS][
Constants.META_TRANSFORMS_OBSERVATION_TO_CONFORMER_SITES
] = ligand_neighbourhood_transforms
Expand All @@ -651,7 +655,7 @@ def _perform_alignments(self, meta):
# new_meta[Constants.META_TRANSFORMS][Constants.META_TRANSFORMS_OBSERVATION_TO_CONFORMER_SITES].append(transform_record)

## Get the conformer site to canonical site transforms
conformer_site_transforms = read_yaml(fs_model.conformer_site_transforms)
conformer_site_transforms = read_yaml(updated_fs_model.conformer_site_transforms)
new_meta[Constants.META_TRANSFORMS][
Constants.META_TRANSFORMS_CONFORMER_SITES_TO_CANON
] = conformer_site_transforms
Expand Down Expand Up @@ -730,52 +734,54 @@ def _extract_components(self, crystals, aligner_meta):

for k2, v2 in v1[Constants.META_ALIGNED_FILES].items(): # chain
for k3, v3 in v2.items(): # ligand
for k4, v4 in v3.items(): # conf site
pdb = v4[Constants.META_AIGNED_STRUCTURE]
self.logger.info("extracting components", k1, k2, k3, k4, pdb)
# pth = self.version_dir / pdb
pth = Path(pdb)
if not pth.is_file():
self.logger.error("can't find file", pth)
num_errors += 1
else:
pdbxtal = PDBXtal(pth, pth.parent, logger=self.logger)
errs = pdbxtal.validate()
if errs:
self.logger.error("validation errors - can't extract components")
for k4, v4 in v3.items(): # version

for k5, v5 in v4.items():# conf site
pdb = v5[Constants.META_AIGNED_STRUCTURE]
self.logger.info("extracting components", k1, k2, k3, k4,, k5, pdb)
# pth = self.version_dir / pdb
pth = Path(pdb)
if not pth.is_file():
self.logger.error("can't find file", pth)
num_errors += 1
else:
pdbxtal.create_apo_file()
pdbxtal.create_apo_solv_desolv()

v4[Constants.META_PDB_APO] = str(pdbxtal.apo_file.relative_to(self.base_dir))
v4[Constants.META_PDB_APO_SOLV] = str(
pdbxtal.apo_solv_file.relative_to(self.base_dir)
)
v4[Constants.META_PDB_APO_DESOLV] = str(
pdbxtal.apo_desolv_file.relative_to(self.base_dir)
)
if cif_file:
try:
pdbxtal.create_ligands(k2, k3, str(self.base_dir / cif_file))
v4[Constants.META_LIGAND_MOL] = (
str(pdbxtal.ligand_base_file.relative_to(self.base_dir)) + '.mol'
)
v4[Constants.META_LIGAND_PDB] = (
str(pdbxtal.ligand_base_file.relative_to(self.base_dir)) + '.pdb'
)
v4[Constants.META_LIGAND_SMILES] = (
str(pdbxtal.ligand_base_file.relative_to(self.base_dir)) + '.smi'
)
v4[Constants.META_LIGAND_SMILES_STRING] = pdbxtal.smiles
except:
num_errors += 1
self.logger.warn(
"failed to create ligand for",
k1,
"Check that the ligand in PDB file and the CIF file are compatible",
)
traceback.print_exc()
pdbxtal = PDBXtal(pth, pth.parent, logger=self.logger)
errs = pdbxtal.validate()
if errs:
self.logger.error("validation errors - can't extract components")
num_errors += 1
else:
pdbxtal.create_apo_file()
pdbxtal.create_apo_solv_desolv()

v5[Constants.META_PDB_APO] = str(pdbxtal.apo_file.relative_to(self.base_dir))
v5[Constants.META_PDB_APO_SOLV] = str(
pdbxtal.apo_solv_file.relative_to(self.base_dir)
)
v5[Constants.META_PDB_APO_DESOLV] = str(
pdbxtal.apo_desolv_file.relative_to(self.base_dir)
)
if cif_file:
try:
pdbxtal.create_ligands(k2, k3, str(self.base_dir / cif_file))
v5[Constants.META_LIGAND_MOL] = (
str(pdbxtal.ligand_base_file.relative_to(self.base_dir)) + '.mol'
)
v5[Constants.META_LIGAND_PDB] = (
str(pdbxtal.ligand_base_file.relative_to(self.base_dir)) + '.pdb'
)
v5[Constants.META_LIGAND_SMILES] = (
str(pdbxtal.ligand_base_file.relative_to(self.base_dir)) + '.smi'
)
v5[Constants.META_LIGAND_SMILES_STRING] = pdbxtal.smiles
except:
num_errors += 1
self.logger.warn(
"failed to create ligand for",
k1,
"Check that the ligand in PDB file and the CIF file are compatible",
)
traceback.print_exc()

return num_errors

Expand Down

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