yangkky

import argparse
import json
import os
from datetime import datetime
import pathlib

import torch
import torch.multiprocessing as mp
from torch.optim import Adam
from torch.optim.lr_scheduler import LambdaLR

yangkky

yangkky

import torch
import torch.nn as nn
from torch.nn import init


class MaskedBatchNorm1d(nn.Module):
    """ A masked version of nn.BatchNorm1d. Only tested for 3D inputs.

        Args:
            num_features: :math:`C` from an expected input of size

yangkky

np.random.seed(9)
X1 = np.random.rand(3,4)*2
X1 = X1.astype(int)
X2 = np.random.rand(3,4)*2
X2 = X2.astype(int)
S = np.random.rand(9,2,2)
subs1 = [S[i][x1, x2] for i, (x1, x2) in enumerate(itertools.product(X1, X2))]

def test5(X1, X2, S):
    i, n, n = S.shape

yangkky

X_list = [[1, 0, 1, 0], [1, 1, 0, 0], [0, 1, 1, 1]]
X1 = torch.tensor(X_list)
X_list = [[1, 0, 1, 1], [1, 1, 1, 0], [1, 0, 1, 1], [1, 1, 1, 0]]
X2 = torch.tensor(X_list)
b1 = 3
b2 = 4
n = 2
d = 32
e1 = torch.randn(size=(b1, n, d))
e2 = torch.randn(size=(b2, n, d))

yangkky

import numpy as np
from scipy import stats

n = 100

r = 10
x = np.linspace(-1.8, 1.8, n)
y = np.linspace(-1.8, 1.8, n)
X, Y = np.meshgrid(x, y)

yangkky

from Bio.Seq import Seq
import Bio.PDB
import Bio.SeqUtils

pdb_filename = '../inputs/1qo7.pdb'
structure = Bio.PDB.PDBParser().get_structure(pdb_code, pdb_filename)
model = structure[0]
pdb_seq = [residue.resname for residue in model['B']]
pdb_seq = ''.join([Bio.SeqUtils.seq1(s) for s in pdb_seq])
ca_coord = np.array([residue['CA'].coord for residue in model['A'] if 'CA' in residue])

yangkky

<?xml version="1.0" encoding="utf-8"?>
<style xmlns="http://purl.org/net/xbiblio/csl" class="in-text" version="1.0" demote-non-dropping-particle="sort-only" default-locale="en-GB">
  <info>
    <title>Bioinformatics - Kevin Yang</title>
    <id>http://csl.mendeley.com/styles/475547981/bioinformatics</id>
    <link href="http://www.zotero.org/styles/bioinformatics" rel="self"/>
    <link href="http://www.oxfordjournals.org/bioinformatics/for_authors/general.html" rel="documentation"/>
    <author>
      <name>Julian Onions</name>
      <email>julian.onions@gmail.com</email>