n-yoshikawa

import cv2
import numpy as np
from datetime import datetime


# Get initial image
cap = cv2.VideoCapture(0)
ret, frame = cap.read()

# Select ROI for reference (background)

n-yoshikawa

1. Generate problem.pddl by running xdl_to_pddl.py.

python xdl_to_pddl.py procedure.xdl

Three problems will be generated. Save one of them as problem.pddl

(define (problem tmp)
  (:domain xdl)
 (:objects beaker red_cabbage_soup baking_soda_solution vinegar)

n-yoshikawa

import numpy as np
from selfies import encoder, decoder, selfies_alphabet

gene_length = 300
# assign 5 bits for each alphabet (0 - 31)
bits_per_symbol = 5  
gene_max = 2**bits_per_symbol - 1

def chromosome_to_selfies(chromosome):
    alphabets = selfies_alphabet() 

n-yoshikawa

n-yoshikawa

Benchmarking XYZ2mol

This is a small benchmark for xyz2mol by Jan Jensen.

I used a criteria that the conversion is successful when canonical SMILES from SDF file and XYZ files are the same. I compared xyz2mol and Open Babel 3.0.

Requirements

• xyz2mol.py from xyz2mol
• RDKit
• networkx

n-yoshikawa

import torch
import torch.nn as nn
from torch.nn import Softplus
from torch.utils.data import Dataset, DataLoader
import dgl
import dgl.function as fn
from dgl.batched_graph import sum_nodes
from dgl.data.chem.utils import mol_to_complete_graph
import numpy as np
from collections import defaultdict

n-yoshikawa

(smiles
  (chain
    (chain
      (chain
        (chain
          (chain
            (chain
              (chain (branched_atom (atom (aliphatic_organic C))))
              (branched_atom (atom (aliphatic_organic C))))
            (branched_atom

n-yoshikawa

0CO_3CS6_A
 OpenBabel06211905503D

 76 79  0  0  1  0  0  0  0  0999 V2000
    3.9824    3.9435   -1.1687 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3558    3.9999    0.0052 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9598    4.3426   -0.2972 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3168    3.2716   -0.4635 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0541    3.2334   -0.2169 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.4429    1.8599   -0.1287 C   0  0  2  0  0  0  0  0  0  0  0  0

n-yoshikawa

%chk=/home/yoshikawa/naphthalene_excited.chk
#p HF/3-21G Opt CIS

Naphthalene excited structure calculation

0  1
C           2.44670        -0.67152         0.02374
C           2.42779         0.72015         0.01820
C           1.20948         1.40137         0.00470
C          -0.00617         0.69817        -0.00343

n-yoshikawa