Skip to content

Add point keyword to MolSys object for selection atoms neara point in space #198

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
mtessmer merged 2 commits into from
Oct 13, 2025
Merged

Add point keyword to MolSys object for selection atoms neara point in space #198

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
c44e1ce
Add point keyword to molses selection syntax
mtessmer Oct 13, 2025
6157178
Fix AF Fetch
mtessmer Oct 13, 2025
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
97 changes: 75 additions & 22 deletions src/chilife/MolSys.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -233,24 +233,24 @@ class MolSys(MolecularSystemBase):
Name of molecular system
"""
def __init__(
self,
record_types: np.ndarray,
atomids: np.ndarray,
names: np.ndarray,
altlocs: np.ndarray,
resnames: np.ndarray,
resnums: np.ndarray,
icodes: np.ndarray,
chains: np.ndarray,
trajectory: np.ndarray,
occupancies: np.ndarray,
bs: np.ndarray,
segs: np.ndarray,
atypes: np.ndarray,
charges: np.ndarray,
bonds: ArrayLike = None,
name: str = 'Noname_MolSys'

self,
record_types: np.ndarray,
atomids: np.ndarray,
names: np.ndarray,
altlocs: np.ndarray,
resnames: np.ndarray,
resnums: np.ndarray,
icodes: np.ndarray,
chains: np.ndarray,
trajectory: np.ndarray,
occupancies: np.ndarray,
bs: np.ndarray,
segs: np.ndarray,
atypes: np.ndarray,
charges: np.ndarray,
chiral: ArrayLike =None,
bonds: ArrayLike = None,
name: str = "Noname_MolSys",
):

self.molsys = self
Expand All @@ -268,6 +268,7 @@ def __init__(
self.segs = segs.copy()
self.atypes = atypes.copy()
self.charges = charges.copy()
self.chiral = chiral.copy() if chiral is not None else None
self._fname = name

self.ix = np.arange(len(self.atomids))
Expand Down Expand Up @@ -310,6 +311,7 @@ def __init__(
'chain': self.chains,
'occupancies': self.occupancies,
'b': self.bs,
'chiral': self.chiral,
'segid': self.chains,
'type': self.atypes,
'charges': self.charges,
Expand Down Expand Up @@ -341,7 +343,8 @@ def __init__(
'!=': operator.ne,
'byres': partial(byres, molsys=self.molsys),
'within': update_wrapper(partial(within, molsys=self.molsys), within),
'around': update_wrapper(partial(within, molsys=self.molsys), within)}
'around': update_wrapper(partial(within, molsys=self.molsys), within),
'point': update_wrapper(partial(point, molsys=self.molsys), point),}


# Aliases
Expand Down Expand Up @@ -783,6 +786,12 @@ def process_statement(statement, logickws, subjectkws):
continue

stat_split = stat.split()
if stat_split[0] not in logickws and stat_split[0] not in subjectkws:
raise ValueError(
f"Invalid selection keyword: {stat_split[0]}. All selections statements and substatements must start "
f"with a valid selection keyword"
)

subject = None
values = []
while len(stat_split) > 0:
Expand Down Expand Up @@ -810,6 +819,9 @@ def process_statement(statement, logickws, subjectkws):
mask = operation(mask, tmp) if operation else tmp
operation = None

elif not values and hasattr(operation, 'novals'):
mask = operation(mask, np.ones_like(mask, dtype=bool))

return mask


Expand Down Expand Up @@ -879,7 +891,7 @@ def check_operation(operation, stat_split, logickws):
operation : callable
A simplified version of the provided operation now accounting for the user provided parameters.
"""
advanced_operators = (logickws['within'], logickws['around'], logickws['byres'])
advanced_operators = (logickws['within'], logickws['around'], logickws['byres'], logickws['point'])
if operation in advanced_operators:
outer_operation = logickws['and']
args = [stat_split.pop(i) for i in range(1, 1 + operation.nargs)]
Expand Down Expand Up @@ -915,7 +927,7 @@ def build_operator(stat_split, logickws):
operation = logickws['and']
unary_operators = (logickws['not'], logickws['byres'])
binary_operators = (logickws['and'], logickws['or'])
advanced_operators = (logickws['within'], logickws['around'])
advanced_operators = (logickws['within'], logickws['around'], logickws['point'])

while _io := logickws.get(stat_split[0], False):

Expand All @@ -936,6 +948,9 @@ def toperation(a, b, operation, _io):

operation = partial(toperation, operation=operation, _io=_io)

if hasattr(_io.func, 'novals'):
operation.novals = _io.func.novals

elif _io in binary_operators:
if operation != logickws['and']:
raise RuntimeError('Cannot have two binary logical operators in succession')
Expand Down Expand Up @@ -1323,7 +1338,7 @@ def unot(mask):

def within(distance, mask, molsys):
"""
Advanced logic operator to identify atoms within a user defined distance.
Advanced logic operator to identify atoms within a user defined distance of another selection.

Parameters
----------
Expand Down Expand Up @@ -1355,6 +1370,44 @@ def within(distance, mask, molsys):
within.nargs = 1


def point(x, y, z, distance, mask, molsys):
"""
Advanced logic operator to identify atoms within a user defined distance of a point in cartesian space.

Parameters
----------
x : float
The x coordinate of the point in cartesian space.
y : float
The y coordinate of the point in cartesian space.
z : float
The z coordinate of the point in cartesian space.
distance : float
The distance window defining which atoms will be included in the selection.
mask : np.ndarray
A boolean array defining a subset of atoms of a :class:`~MolSys` from which the distance cutoff will be
measured by.
molsys : :class:`~MolSys`
A chiLife :class:`~MolSys` from which to select atoms from .

Returns
-------
out_mask : np.ndarray
A boolean array defining a subset of atoms of a :class:`~MolSys` that are within the user defined distance
of the user defined selection.
"""

tree1 = cKDTree(molsys.coords[mask])
args = tree1.query_ball_point(np.array([x, y, z], dtype=float), distance)
out_mask = np.zeros_like(mask, dtype=bool)
out_mask[args] = True

return out_mask


point.nargs = 4
point.novals = True

def concat_molsys(systems):
"""
Function to concatenate two or more :class:`~MolSys` objects into a single :class:`~MolSys` object. Atoms will be
Expand Down
10 changes: 5 additions & 5 deletions src/chilife/io.py
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
from typing import Tuple, Dict, Union, BinaryIO, TextIO, Protocol
from typing import Tuple, Dict, Union, BinaryIO, TextIO
import warnings
import os
import urllib
Expand All @@ -9,7 +9,7 @@
from pathlib import Path
import pickle
import shutil
from io import StringIO, BytesIO
from io import StringIO
import zipfile

import numpy as np
Expand Down Expand Up @@ -507,8 +507,8 @@ def fetch(accession_number: str, save: bool = False) -> MDAnalysis.Universe:
pdb_name = accession_number + '.pdb'

if accession_number.startswith('AF-'):
print(f"https://alphafold.ebi.ac.uk/files/{accession_number}-F1-model_v3.pdb")
urllib.request.urlretrieve(f"https://alphafold.ebi.ac.uk/files/{accession_number}-F1-model_v3.pdb", pdb_name)
print(f"https://alphafold.ebi.ac.uk/files/{accession_number}-F1-model_v6.pdb")
urllib.request.urlretrieve(f"https://alphafold.ebi.ac.uk/files/{accession_number}-F1-model_v6.pdb", pdb_name)
else:
urllib.request.urlretrieve(f"http://files.rcsb.org/download/{pdb_name}", pdb_name)

Expand Down Expand Up @@ -631,7 +631,7 @@ def write_frame(pdb_file: TextIO, atoms, frame=None, coords=None):
pdb_file.write("TER\n")

if frame is not None:
pdb_file.write(f"ENDMDL\n")
pdb_file.write("ENDMDL\n")


def write_ic(pdb_file: TextIO,
Expand Down
Loading