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Removing selection functionality from xray_structure that relies on s…
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…catterer.label content
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@olegsobolev
olegsobolev committed Sep 21, 2023
1 parent f19b80e commit ac5fa52
Showing 1 changed file with 0 additions and 219 deletions.
219 changes: 0 additions & 219 deletions cctbx/xray/structure.py
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Original file line number Diff line number Diff line change
Expand Up @@ -979,198 +979,6 @@ def hd_selection(self):
else: result.append(False)
return result


# MARKED_FOR_DELETION_OLEG
# Reason: this functionality relies on content of scatterer.label, which should be
# identical to atom.id_str(). Now when it becomes of variable lenghts, slicing it to extract
# atom names or residue names will not work.

def heavy_selection(self,
ignore_atoms_with_alternative_conformations=False,
include_only_atoms_with_alternative_conformations=False,
only_protein=False,
):
"""Get a selector array for heavy (= non H or D) scatterers of the structure.
:param ignore_atoms_with_alternative_conformations: select normal atoms/conformations only
:type ignore_atoms_with_alternative_conformations: boolean
:param include_only_atoms_with_alternative_conformations: select only scatterers with alternative conformations
:type include_only_atoms_with_alternative_conformations: boolean
:param only_protein: select only protein scatterers
:type only_protein: boolean
:returns: an array to select the desired scatterers of the structure
:rtype: boolean[]
"""
if ( ignore_atoms_with_alternative_conformations and
include_only_atoms_with_alternative_conformations
):
raise Sorry("Mutually exclusive alternative location options")
scattering_types = self._scatterers.extract_scattering_types()
scatterers = self.scatterers()
result = flex.bool()
for i, sct in enumerate(scattering_types):
if ignore_atoms_with_alternative_conformations:
if scatterers[i].label[9:10]!=" ":
result.append(False)
continue
if include_only_atoms_with_alternative_conformations:
if scatterers[i].label[9:10]==" ":
result.append(False)
continue
if only_protein:
for resname in [
"ALA",
"CYS",
"ASP",
"GLU",
"PHE",
"GLY",
"HIS",
"ILE",
"LYS",
"LEU",
"MET",
"ASN",
"PRO",
"GLN",
"ARG",
"SER",
"THR",
"VAL",
"TRP",
"TYR",
]:
if scatterers[i].label[10:13]==resname:
break
else:
result.append(False)
continue

if(sct.strip() in ['H','D']): result.append(False)
else: result.append(True)
return result

def atom_names_selection(self,
atom_names=["C","O","CA","N"],
ignore_atoms_with_alternative_conformations=False,
include_only_atoms_with_alternative_conformations=False,
):
"""Get a selector array for scatterers of the structure by "atom" names.
:param atom_names: list of labels of scatterers to select
:type atom_names: list(string)
:param ignore_atoms_with_alternative_conformations: select normal atoms/conformations only
:type ignore_atoms_with_alternative_conformations: boolean
:param include_only_atoms_with_alternative_conformations: select only scatterers with alternative conformations
:type include_only_atoms_with_alternative_conformations: boolean
:returns: an array to select the desired scatterers of the structure
:rtype: boolean[]
"""
#XXX may need a better function
assert 0
if ( ignore_atoms_with_alternative_conformations and
include_only_atoms_with_alternative_conformations
):
raise Sorry("Mutually exclusive alternative location options")
scattering_types = self._scatterers.extract_scattering_types()
result = flex.bool()
for sc in self.scatterers():
if(sc.label.find("HOH")>-1):
result.append(False)
continue
if ignore_atoms_with_alternative_conformations:
if sc.label[9:10]!=" ":
result.append(False)
continue
if include_only_atoms_with_alternative_conformations:
if sc.label[9:10]==" ":
result.append(False)
continue
for name in atom_names:
if(sc.label[5:9].find("%s " % name)>-1 and
sc.scattering_type==name[0]
):
result.append(True)
break
else: result.append(False)
return result

def backbone_selection(self,
atom_names=["C","O","CA","N"],
ignore_atoms_with_alternative_conformations=False,
include_only_atoms_with_alternative_conformations=False,
):
"""Get a selector array for scatterers of the backbone of the structure.
(This is just an alias for atom_names_selection.)
:param atom_names: list of labels of scatterers to select
:type atom_names: list(string)
:param ignore_atoms_with_alternative_conformations: select normal atoms/conformations only
:type ignore_atoms_with_alternative_conformations: boolean
:param include_only_atoms_with_alternative_conformations: select only scatterers with alternative conformations
:type include_only_atoms_with_alternative_conformations: boolean
:returns: an array to select the desired scatterers of the structure
:rtype: boolean[]
"""
return self.atom_names_selection(
atom_names=atom_names,
ignore_atoms_with_alternative_conformations=ignore_atoms_with_alternative_conformations,
include_only_atoms_with_alternative_conformations=include_only_atoms_with_alternative_conformations,
)

def main_chain_selection(self,
atom_names=["C","O","CA","N","CB"],
ignore_atoms_with_alternative_conformations=False,
include_only_atoms_with_alternative_conformations=False,
):
"""Get a selector array for scatterers of the main chain of the structure.
(This is just an alias for atom_names_selection with a different default selection.)
:param atom_names: list of labels of scatterers to select
:type atom_names: list(string)
:param ignore_atoms_with_alternative_conformations: select normal atoms/conformations only
:type ignore_atoms_with_alternative_conformations: boolean
:param include_only_atoms_with_alternative_conformations: select only scatterers with alternative conformations
:type include_only_atoms_with_alternative_conformations: boolean
:returns: an array to select the desired scatterers of the structure
:rtype: boolean[]
"""
return self.atom_names_selection(
atom_names=atom_names,
ignore_atoms_with_alternative_conformations=ignore_atoms_with_alternative_conformations,
include_only_atoms_with_alternative_conformations=include_only_atoms_with_alternative_conformations,
)

def peptide_dihedral_selection(self,
atom_names=["C","CA","N"],
ignore_atoms_with_alternative_conformations=False,
include_only_atoms_with_alternative_conformations=False,
):
"""Get a selector array for peptide dihedral scatterers of the structure.
(This is just an alias for atom_names_selection with a different default selection.)
:param atom_names: list of labels of scatterers to select
:type atom_names: list(string)
:param ignore_atoms_with_alternative_conformations: select normal atoms/conformations only
:type ignore_atoms_with_alternative_conformations: boolean
:param include_only_atoms_with_alternative_conformations: select only scatterers with alternative conformations
:type include_only_atoms_with_alternative_conformations: boolean
:returns: an array to select the desired scatterers of the structure
:rtype: boolean[]
"""
return self.atom_names_selection(
atom_names=atom_names,
ignore_atoms_with_alternative_conformations=ignore_atoms_with_alternative_conformations,
include_only_atoms_with_alternative_conformations=include_only_atoms_with_alternative_conformations,
)

# END_MARKED_FOR_DELETION_OLEG

def element_selection(self, *elements):
"""Get a selector array for scatterers of specified element type(s) of the structure.
Expand All @@ -1183,33 +991,6 @@ def element_selection(self, *elements):
return flex.bool([ sc.element_symbol().strip() in elements
for sc in self.scatterers() ])

def label_selection(self, *labels):
"""Get a selector array for scatterers of specified labels from the structure.
:param labels: tuple of scatterer labels to select
:type labels: list(string) or set(string) or tuple(string)
:returns: an array to select the desired scatterers of the structure
:rtype: boolean[]
"""
return flex.bool([ sc.label in labels for sc in self.scatterers() ])

def label_regex_selection(self, label_regex):
"""Get a selector array for scatterers of specified labels (via regular
expression) from the structure.
:param label_regex: a regular expression matching scatterer labels to select
:type label_regex: string or re
:returns: an array to select the desired scatterers of the structure
:rtype: boolean[]
"""
if is_string(label_regex):
import re
label_regex = re.compile(label_regex)
return flex.bool([ label_regex.search(sc.label) is not None
for sc in self.scatterers() ])

def by_index_selection(self, selected_scatterers):
"""Get a selector array for scatterers with specified index from the
structure. For example you can select scatterers 1,4 and 5 by passing
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