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Fix writing to read-only array bug in nerdss_converter.py #208

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Fix writing to read-only array bug in nerdss_converter.py #208

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9 changes: 8 additions & 1 deletion simulariumio/nerdss/nerdss_converter.py
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Original file line number Diff line number Diff line change
@@ -1,6 +1,8 @@
from MDAnalysis import Universe
import os

import numpy as np

from ..trajectory_converter import TrajectoryConverter
from ..data_objects import (
AgentData,
Expand Down Expand Up @@ -131,6 +133,10 @@ def _read_pdb_files(self, input_data: NerdssData) -> AgentData:
"bonds", input_data.display_data
)
next_uid = agent_data.unique_ids.max() + 1

# need our own write-able n_subpoints array
n_subpoints = np.zeros_like(agent_data.n_subpoints)

for timestep in range(n_timesteps):
n_fibers = len(fiber_positions[timestep])
n_atoms = int(agent_data.n_agents[timestep])
Expand All @@ -139,7 +145,7 @@ def _read_pdb_files(self, input_data: NerdssData) -> AgentData:
agent_data.subpoints[timestep][agent_index + n_atoms] = fiber_positions[
timestep
][agent_index]
agent_data.n_subpoints[timestep][agent_index + n_atoms] = (
n_subpoints[timestep][agent_index + n_atoms] = (
VALUES_PER_3D_POINT * 2
)
agent_data.viz_types[timestep][agent_index + n_atoms] = VIZ_TYPE.FIBER
Expand All @@ -149,6 +155,7 @@ def _read_pdb_files(self, input_data: NerdssData) -> AgentData:
agent_data.types[timestep].append(bonds_display_data.name)
agent_data.unique_ids[timestep][agent_index + n_atoms] = next_uid
next_uid += 1
agent_data.n_subpoints = n_subpoints # overwrite with our own array
return agent_data

def _read(self, input_data: NerdssData) -> TrajectoryData:
Expand Down