Skip to content

Instantly share code, notes, and snippets.

View fabian-paul's full-sized avatar

fabian-paul

42 followers · 49 following
View GitHub Profile
@fabian-paul
fabian-paul / pubsub.py
Last active May 19, 2025 21:35
publish-subscribe with Starlette
import typing
import asyncio
import uvicorn
import random
import weakref
from pydantic import BaseModel
#from starlette.applications import Starlette
#from starlette.routing import Route
from fastapi import FastAPI, Query
from sse_starlette.sse import EventSourceResponse
@fabian-paul
fabian-paul / switch_network_renderer.py
Last active August 29, 2021 21:17
switch_network_renderer
class Renderer:
def __init__(self, root):
self.root = root
def svg(self):
leftmost = self.root.leftmost(0)
s = min(300 / self.root.w, 300 / self.root.h)
svg = f"""
<!DOCTYPE html>
<html>
@fabian-paul
fabian-paul / Taschenkalender.ipynb
Created December 23, 2020 20:54
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
@fabian-paul
fabian-paul / pcca.py
Last active May 19, 2025 21:34
PCCA
import typing
import numpy as np
import scipy.optimize
def _pcca_plus_score(partial_coarse_graining_matrix_flat: np.ndarray, eigenvectors: np.ndarray, n: int) -> float:
"""Implementation of the PCCA+ score.
Parameters
----------
@fabian-paul
fabian-paul / npy_append.py
Created September 27, 2020 20:48
create npy in append mode
dtype = np.dtype([("row", np.int32, ), ("col", np.int32, ), ("cov", np.float32, )])
a = np.zeros((3,), dtype=dtype)
for i in range(3):
a[i]["row"] = np.random.randint(2*15)
a[i]["col"] = np.random.randint(2*15)
a[i]["cov"] = np.random.randn()
with NpyStream("test.npy") as s:
s.append(a[0])
s.append(a[1])
s.append(a[2])
@fabian-paul
fabian-paul / short_widest_path.c
Created July 30, 2020 07:53
An implementation of Dijkstra's algorithm for the shortest path, the widest path, and an "interpolation" between shortest and widest path.
#include <math.h>
#include <stddef.h>
#include <signal.h>
#include <assert.h>
static volatile sig_atomic_t interrupted;
static void (*old_handler)(int);
static void signal_handler(int signo) {
interrupted = 1;
@fabian-paul
fabian-paul / induced_fit_parameter_inference.ipynb
Created March 27, 2020 18:04
parameter inference for kinetic model using HMC
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
@fabian-paul
fabian-paul / reorder-atoms.py
Created January 30, 2020 17:30
Reorder small molecule atoms in PDB file to match the order in template PDB file. Uses RDKit.
import numpy as np
import rdkit.Chem
def reorder_atoms(mol_pdb_fname, template_pdb_fname, output_pdb_fname):
from rdkit.Chem import rdmolfiles
mol_to_transform = rdkit.Chem.rdmolfiles.MolFromPDBFile(mol_pdb_fname, removeHs=False)
transform_order = list(rdmolfiles.CanonicalRankAtoms(mol_to_transform))
mol_template = rdkit.Chem.rdmolfiles.MolFromPDBFile(template_pdb_fname, removeHs=False)
@fabian-paul
fabian-paul / mutate.py
Last active April 5, 2020 08:18
Generate trajectories for computational alanine scan (mass generation of mutant structures)
import numpy as np
import mdtraj
import os
import os.path
import argparse
def prepare_maps(mut_pdb='mutant.pdb', wt_pdb=None):
if wt_pdb is None:
wt_pdb = os.path.expanduser('~/system/crystal.pdb')
@fabian-paul
fabian-paul / colvars_def_reader.py
Last active October 16, 2019 16:13
Reads some NAMD colvar defintions in Python
import pyparsing as pp
from pyparsing import pyparsing_common as ppc
__all__ = ['load_colvars', 'handle_colvars']
pp.ParserElement.setDefaultWhitespaceChars(' \t')
vector = pp.Group(pp.Literal('(').suppress() +
pp.delimitedList(ppc.number, delim=',') +
pp.Literal(')').suppress())