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from __future__ import absolute_import, division
import numpy as np
from pmda.parallel import ParallelAnalysisBase
class bsites_finder(ParallelAnalysisBase):
"""Bingding sites finder for MD simulaton trajectory
u : Universe
a Universe that contains g1 and g2.
g1 : AtomGroup
Target atoms.
g2 : AtomGroup
Potential binding sites.
cutoff : int (optional)
Maximum of the distance between ions and binding sites
def __init__(self, u, g1, g2, cutoff=5.0):
super(bsites_finder, self).__init__(u, (g1, g2))
def _prepare(self):
self.ids = None
def _single_frame(self, ts, atomgroups):
g1, g2 = atomgroups
ag = g1+g2
# Generate selection strings for ions and binding sites
id1 = ' '.join(str(id) for id in g1.resids)
id2 = ' '.join(str(id) for id in g2.resids)
# Generate AtomGroup of binding sites
sites = ag.select_atoms('resid {0} and around {1} (resid {2})'.format(
id1, self.cutoff, id2))
# Generate the list of the resids of binding sites
ids = np.unique(np.array(sites.residues.ix))
return ids
def _conclude(self,):
self.ids = np.array([])
for result in self._results:
self.ids = np.append(self.ids, result)
def _reduce(res, result_single_frame):
if isinstance(res, list) and len(res) == 0:
# Initialization of the result
# Convert res from an empty list to a numpy array
# which has the same shape as the single frame result
res = result_single_frame
# Append new single frame result to res
res = np.append(res, result_single_frame)
return res
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