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Merge PR biopython#1360 from JoaoRodrigues
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JoaoRodrigues authored and Sarah committed Dec 3, 2020
1 parent 536ead7 commit 59ac318
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Showing 6 changed files with 388 additions and 76 deletions.
77 changes: 77 additions & 0 deletions Bio/PDB/Atom.py
View file
Expand Up @@ -70,6 +70,79 @@ def __init__(self, name, coord, bfactor, occupancy, altloc, fullname, serial_num
self.element = self._assign_element(element)
self.mass = self._assign_atom_mass()

# For atom sorting (protein backbone atoms first)
self._sorting_keys = {'N': 0, 'CA': 1, 'C': 2, 'O': 3}

# Sorting Methods
# standard across different objects and allows direct comparison
def __eq__(self, other):
if isinstance(other, Atom):
return (self.id, self.altloc) == (other.id, other.altloc)
else:
return NotImplemented

def __ne__(self, other):
if isinstance(other, Atom):
return (self.id, self.altloc) != (other.id, other.altloc)
else:
return NotImplemented

def __gt__(self, other):
if isinstance(other, Atom):
order_s = self._sorting_keys.get(self.name, 4)
order_o = self._sorting_keys.get(other.name, 4)
if order_s != order_o:
return order_s > order_o
elif self.name != other.name:
return self.name > other.name
else:
return self.altloc > other.altloc
else:
return NotImplemented

def __ge__(self, other):
if isinstance(other, Atom):
order_s = self._sorting_keys.get(self.name, 4)
order_o = self._sorting_keys.get(other.name, 4)
if order_s != order_o:
return order_s >= order_o
elif self.name != other.name:
return self.name >= other.name
else:
return self.altloc >= other.altloc
else:
return NotImplemented

def __lt__(self, other):
if isinstance(other, Atom):
order_s = self._sorting_keys.get(self.name, 4)
order_o = self._sorting_keys.get(other.name, 4)
if order_s != order_o:
return order_s < order_o
elif self.name != other.name:
return self.name < other.name
else:
return self.altloc < other.altloc
else:
return NotImplemented

def __le__(self, other):
if isinstance(other, Atom):
order_s = self._sorting_keys.get(self.name, 4)
order_o = self._sorting_keys.get(other.name, 4)
if order_s != order_o:
return order_s <= order_o
elif self.name != other.name:
return self.name <= other.name
else:
return self.altloc <= other.altloc
else:
return NotImplemented

# Hash method to allow uniqueness (set)
def __hash__(self):
return hash(self.get_full_id())

def _assign_element(self, element):
"""Tries to guess element from atom name if not recognised."""
if not element or element.capitalize() not in IUPACData.atom_weights:
Expand Down Expand Up @@ -311,6 +384,10 @@ def __init__(self, id):
DisorderedEntityWrapper.__init__(self, id)

# Special methods
# Override parent class __iter__ method
def __iter__(self):
for i in self.disordered_get_list():
yield i

def __repr__(self):
return "<Disordered Atom %s>" % self.get_id()
Expand Down
45 changes: 45 additions & 0 deletions Bio/PDB/Chain.py
View file
Expand Up @@ -13,6 +13,51 @@ def __init__(self, id):
self.level = "C"
Entity.__init__(self, id)

# Sorting methods: empty chain IDs come last.
def __gt__(self, other):
if isinstance(other, Chain):
if self.id == ' ' and other.id != ' ':
return 0
elif self.id != ' ' and other.id == ' ':
return 1
else:
return self.id > other.id
else:
return NotImplemented

def __ge__(self, other):
if isinstance(other, Chain):
if self.id == ' ' and other.id != ' ':
return 0
elif self.id != ' ' and other.id == ' ':
return 1
else:
return self.id >= other.id
else:
return NotImplemented

def __lt__(self, other):
if isinstance(other, Chain):
if self.id == ' ' and other.id != ' ':
return 0
elif self.id != ' ' and other.id == ' ':
return 1
else:
return self.id < other.id
else:
return NotImplemented

def __le__(self, other):
if isinstance(other, Chain):
if self.id == ' ' and other.id != ' ':
return 0
elif self.id != ' ' and other.id == ' ':
return 1
else:
return self.id <= other.id
else:
return NotImplemented

# Private methods

def _sort(self, r1, r2):
Expand Down
56 changes: 56 additions & 0 deletions Bio/PDB/Entity.py
View file
Expand Up @@ -51,6 +51,48 @@ def __iter__(self):
for child in self.child_list:
yield child

# Generic id-based comparison methods
# Works for Structures and Models (id is numeric)
def __eq__(self, other):
if isinstance(other, Entity):
return self.id == other.id
else:
return NotImplemented

def __ne__(self, other):
if isinstance(other, Entity):
return self.id != other.id
else:
return NotImplemented

def __gt__(self, other):
if isinstance(other, Entity):
return self.id > other.id
else:
return NotImplemented

def __ge__(self, other):
if isinstance(other, Entity):
return self.id >= other.id
else:
return NotImplemented

def __lt__(self, other):
if isinstance(other, Entity):
return self.id < other.id
else:
return NotImplemented

def __le__(self, other):
if isinstance(other, Entity):
return self.id <= other.id
else:
return NotImplemented

# Hash method to allow uniqueness (set)
def __hash__(self):
return hash(self.id)

# Private methods

def _reset_full_id(self):
Expand Down Expand Up @@ -281,6 +323,20 @@ def __sub__(self, other):
"""Subtraction with another object."""
return self.selected_child - other

# Sorting
# Directly compare the selected child
def __gt__(self, other):
return self.selected_child > other

def __ge__(self, other):
return self.selected_child >= other

def __lt__(self, other):
return self.selected_child < other

def __le__(self, other):
return self.selected_child <= other

# Public methods

def get_id(self):
Expand Down
66 changes: 65 additions & 1 deletion Bio/PDB/Residue.py
View file
Expand Up @@ -35,6 +35,60 @@ def __repr__(self):
full_id = (resname, hetflag, resseq, icode)
return "<Residue %s het=%s resseq=%s icode=%s>" % full_id

# Residue-specific sorting methods
# Sort first by HETATM flag, then by resseq, finally by insertion code
def __gt__(self, other):
if isinstance(other, Residue):
hetflag_s, resseq_s, icode_s = self.id
hetflag_o, resseq_o, icode_o = other.id
if hetflag_o != hetflag_s:
return hetflag_s > hetflag_o
elif resseq_o != resseq_s:
return resseq_s > resseq_o
else:
return icode_s > icode_o
else:
return NotImplemented

def __ge__(self, other):
if isinstance(other, Residue):
hetflag_s, resseq_s, icode_s = self.id
hetflag_o, resseq_o, icode_o = other.id
if hetflag_o != hetflag_s:
return hetflag_s >= hetflag_o
elif resseq_o != resseq_s:
return resseq_s >= resseq_o
else:
return icode_s >= icode_o
else:
return NotImplemented

def __lt__(self, other):
if isinstance(other, Residue):
hetflag_s, resseq_s, icode_s = self.id
hetflag_o, resseq_o, icode_o = other.id
if hetflag_o != hetflag_s:
return hetflag_s < hetflag_o
elif resseq_o != resseq_s:
return resseq_s < resseq_o
else:
return icode_s < icode_o
else:
return NotImplemented

def __le__(self, other):
if isinstance(other, Residue):
hetflag_s, resseq_s, icode_s = self.id
hetflag_o, resseq_o, icode_o = other.id
if hetflag_o != hetflag_s:
return hetflag_s < hetflag_o
elif resseq_o != resseq_s:
return resseq_s < resseq_o
else:
return icode_s < icode_o
else:
return NotImplemented

# Private methods

def _sort(self, a1, a2):
Expand Down Expand Up @@ -81,7 +135,17 @@ def add(self, atom):
Entity.add(self, atom)

def sort(self):
self.child_list.sort(self._sort)
"""Sort child atoms.
Atoms N, CA, C, O always come first, thereafter alphabetically
by name, with any alternative location specifier for disordered
atoms (altloc) as a tie-breaker.
"""
warnings.warn("The custom sort() method will be removed in the "
"future in favour of rich comparison methods. Use the "
"built-in sorted() function instead.",
BiopythonDeprecationWarning)
self.child_list.sort()

def flag_disordered(self):
"""Set the disordered flag."""
Expand Down
65 changes: 33 additions & 32 deletions Tests/PDB/a_structure.pdb
View file
Expand Up @@ -573,15 +573,15 @@ ATOM 558 N GLY A 73 17.694 -3.324 28.982 1.00 25.36 N
ATOM 559 CA GLY A 73 18.291 -4.645 28.942 1.00 26.44 C
ATOM 560 C GLY A 73 17.283 -5.775 28.973 1.00 27.24 C
ATOM 561 O GLY A 73 16.086 -5.595 29.157 1.00 26.15 O
ATOM 562 N ASN A 74 17.798 -7.004 28.869 1.00 27.53 N
ATOM 563 CA ASN A 74 17.013 -8.206 28.788 1.00 27.66 C
ATOM 562 CA ASN A 74 17.013 -8.206 28.788 1.00 27.66 C
ATOM 563 N ASN A 74 17.798 -7.004 28.869 1.00 27.53 N
ATOM 564 C ASN A 74 16.001 -8.395 29.892 1.00 25.55 C
ATOM 565 O ASN A 74 14.915 -8.955 29.662 1.00 26.18 O
ATOM 566 CB ASN A 74 17.981 -9.421 28.763 1.00 32.27 C
ATOM 567 CG AASN A 74 17.279 -10.749 28.825 0.50 33.40 C
ATOM 568 CG BASN A 74 18.917 -9.356 27.574 0.50 34.22 C
ATOM 569 OD1AASN A 74 17.230 -11.395 29.878 0.50 35.56 O
ATOM 570 OD1BASN A 74 18.479 -9.218 26.432 0.50 36.46 O
ATOM 569 OD1BASN A 74 18.479 -9.218 26.432 0.50 36.46 O
ATOM 570 OD1AASN A 74 17.230 -11.395 29.878 0.50 35.56 O
ATOM 571 ND2AASN A 74 16.736 -11.203 27.699 0.50 34.86 N
ATOM 572 ND2BASN A 74 20.215 -9.465 27.831 0.50 36.27 N
ATOM 573 N ASP A 75 16.355 -8.036 31.129 1.00 25.87 N
Expand Down Expand Up @@ -696,6 +696,7 @@ ATOM 681 O CYS A 86 9.846 -3.464 22.105 1.00 25.66 O
ATOM 682 CB CYS A 86 8.644 -5.399 24.430 1.00 21.37 C
ATOM 683 SG CYS A 86 7.527 -5.528 25.832 1.00 19.98 S
TER 684 CYS A 86
HETATM 685 O HOH B 0 6.997 5.537 34.149 1.00 15.09 O
HETATM 685 C1 NAG B 1 2.845 5.730 8.410 1.00 13.00 C
HETATM 686 C2 NAG B 1 2.980 4.600 7.346 1.00 14.42 C
HETATM 687 C3 NAG B 1 2.175 3.411 7.793 1.00 14.65 C
Expand Down Expand Up @@ -724,34 +725,34 @@ HETATM 709 O4 NAG B 2 3.695 6.769 8.064 1.00 13.33 O
HETATM 710 O5 NAG B 2 3.294 10.396 8.215 1.00 16.15 O
HETATM 711 O6 NAG B 2 2.067 9.786 5.669 1.00 21.57 O
HETATM 712 O7 NAG B 2 4.383 10.784 12.792 1.00 13.02 O
HETATM 713 C1 NAG B 3 4.558 15.870 8.029 1.00 22.68 C
HETATM 714 C2 NAG B 3 3.781 14.939 7.134 1.00 23.40 C
HETATM 715 C3 NAG B 3 3.385 13.670 7.891 1.00 21.15 C
HETATM 716 C4 NAG B 3 4.638 13.082 8.560 1.00 19.08 C
HETATM 717 C5 NAG B 3 5.387 14.135 9.404 1.00 20.09 C
HETATM 718 C6 NAG B 3 6.662 13.594 9.979 1.00 20.74 C
HETATM 719 C7 NAG B 3 2.333 15.941 5.366 1.00 30.04 C
HETATM 720 C8 NAG B 3 0.935 16.346 5.056 1.00 30.86 C
HETATM 721 N2 NAG B 3 2.536 15.585 6.659 1.00 26.09 N
HETATM 722 O3 NAG B 3 2.831 12.779 6.934 1.00 22.73 O
HETATM 723 O4 NAG B 3 4.253 12.032 9.493 1.00 16.48 O
HETATM 724 O5 NAG B 3 5.732 15.223 8.531 1.00 21.12 O
HETATM 725 O6 NAG B 3 7.565 13.140 9.015 1.00 23.92 O
HETATM 726 O7 NAG B 3 3.172 15.935 4.593 1.00 31.92 O
HETATM 727 C1 NAG B 4 6.424 20.761 7.837 1.00 35.33 C
HETATM 728 C2 NAG B 4 7.333 19.637 8.339 1.00 35.66 C
HETATM 729 C3 NAG B 4 6.907 18.331 7.686 1.00 35.20 C
HETATM 730 C4 NAG B 4 5.422 18.072 8.014 1.00 33.37 C
HETATM 731 C5 NAG B 4 4.527 19.299 7.696 1.00 33.27 C
HETATM 732 C6 NAG B 4 3.173 19.102 8.406 1.00 32.57 C
HETATM 733 C7 NAG B 4 9.448 20.235 9.622 0.00 40.22 C
HETATM 734 C8 NAG B 4 10.921 20.272 9.570 0.00 40.07 C
HETATM 735 N2 NAG B 4 8.744 19.920 8.013 1.00 37.41 N
HETATM 736 O3 NAG B 4 7.711 17.283 8.235 1.00 36.78 O
HETATM 737 O4 NAG B 4 4.923 16.987 7.202 1.00 29.35 O
HETATM 738 O5 NAG B 4 5.078 20.464 8.245 1.00 34.32 O
HETATM 739 O6 NAG B 4 3.314 19.212 9.787 1.00 31.85 O
HETATM 740 O7 NAG B 4 8.849 20.404 10.603 0.00 43.75 O
HETATM 713 C1 NAG B 4 4.558 15.870 8.029 1.00 22.68 C
HETATM 714 C2 NAG B 4 3.781 14.939 7.134 1.00 23.40 C
HETATM 715 C3 NAG B 4 3.385 13.670 7.891 1.00 21.15 C
HETATM 716 C4 NAG B 4 4.638 13.082 8.560 1.00 19.08 C
HETATM 717 C5 NAG B 4 5.387 14.135 9.404 1.00 20.09 C
HETATM 718 C6 NAG B 4 6.662 13.594 9.979 1.00 20.74 C
HETATM 719 C7 NAG B 4 2.333 15.941 5.366 1.00 30.04 C
HETATM 720 C8 NAG B 4 0.935 16.346 5.056 1.00 30.86 C
HETATM 721 N2 NAG B 4 2.536 15.585 6.659 1.00 26.09 N
HETATM 722 O3 NAG B 4 2.831 12.779 6.934 1.00 22.73 O
HETATM 723 O4 NAG B 4 4.253 12.032 9.493 1.00 16.48 O
HETATM 724 O5 NAG B 4 5.732 15.223 8.531 1.00 21.12 O
HETATM 725 O6 NAG B 4 7.565 13.140 9.015 1.00 23.92 O
HETATM 726 O7 NAG B 4 3.172 15.935 4.593 1.00 31.92 O
HETATM 727 C1 NAG B 3 6.424 20.761 7.837 1.00 35.33 C
HETATM 728 C2 NAG B 3 7.333 19.637 8.339 1.00 35.66 C
HETATM 729 C3 NAG B 3 6.907 18.331 7.686 1.00 35.20 C
HETATM 730 C4 NAG B 3 5.422 18.072 8.014 1.00 33.37 C
HETATM 731 C5 NAG B 3 4.527 19.299 7.696 1.00 33.27 C
HETATM 732 C6 NAG B 3 3.173 19.102 8.406 1.00 32.57 C
HETATM 733 C7 NAG B 3 9.448 20.235 9.622 0.00 40.22 C
HETATM 734 C8 NAG B 3 10.921 20.272 9.570 0.00 40.07 C
HETATM 735 N2 NAG B 3 8.744 19.920 8.013 1.00 37.41 N
HETATM 736 O3 NAG B 3 7.711 17.283 8.235 1.00 36.78 O
HETATM 737 O4 NAG B 3 4.923 16.987 7.202 1.00 29.35 O
HETATM 738 O5 NAG B 3 5.078 20.464 8.245 1.00 34.32 O
HETATM 739 O6 NAG B 3 3.314 19.212 9.787 1.00 31.85 O
HETATM 740 O7 NAG B 3 8.849 20.404 10.603 0.00 43.75 O
HETATM 741 O HOH 1 6.997 5.537 34.149 1.00 15.09 O
HETATM 742 O HOH 2 10.295 3.302 26.095 1.00 16.76 O
HETATM 743 O HOH 3 10.019 12.949 25.133 1.00 20.11 O
Expand Down

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