n-yoshikawa

# Generate 3D structure

from rdkit import Chem
from rdkit.Chem import AllChem

# https://github.com/n-yoshikawa/ob-fragment-generation/blob/master/rdkit/platinum-rdkit-etkdg.sdf
w = Chem.SDWriter('platinum-rdkit-etkdg.sdf')

# https://github.com/n-yoshikawa/ob-fragment-generation/blob/master/data/platinum.smi
with open("platinum.smi", "r") as f:

n-yoshikawa

0Q1_4GPJ_A
 OpenBabel02211917303D
Protoss
 42 45  0  0  0  0  0  0  0  0999 V2000
   32.9220   14.8880   -1.0770 C   0  0  0  0  0  0  0  0  0  0  0  0
   32.5830   16.1240   -0.2780 C   0  0  0  0  0  0  0  0  0  0  0  0
   33.5890   16.9660    0.0910 O   0  0  0  0  0  0  0  0  0  0  0  0
   32.9790   18.0380    0.7860 N   0  0  0  0  0  0  0  0  0  0  0  0
   31.6660   17.8070    0.8060 C   0  0  0  0  0  0  0  0  0  0  0  0
   30.7590   18.8380    1.5090 C   0  0  0  0  0  0  0  0  0  0  0  0

n-yoshikawa

FROM ubuntu:16.04
# COD version
RUN apt-get update && apt-get install -y \
  build-essential \
  cmake \
  git \
  libcairo2-dev \
  libeigen2-dev \
  zlib1g-dev
RUN git clone https://github.com/n-yoshikawa/openbabel.git && \

n-yoshikawa

In Google Summer of Code 2018, I worked on Fast, Efficient Fragment-Based Coordinate Generation. My contribution was as follows:

• Implement fragment-based coordinate generation (Pull Request)
• Debug distance geometry method (Pull Request

Fragment-based coordinate generation

I implemented a faster coordinate generation method in this task. In this method, molecules are separated into fragments by rotable bonds. If a fragment is in our database, the coordinates of atoms in the fragment are set according to the information from the database.

n-yoshikawa

#include <iostream>
#include <string>
#include <sstream>

#include <openbabel/mol.h>
#include <openbabel/obconversion.h>
#include <openbabel/builder.h>

using namespace std;
using namespace OpenBabel;

n-yoshikawa

#include <openbabel/mol.h>
#include <openbabel/obconversion.h>

#include <iostream>
#include <fstream>
#include <iterator>
#include <string>
#include <map>
#include <vector>

n-yoshikawa

#include <iostream>
#include <sstream>

#include <openbabel/mol.h>
#include <openbabel/obconversion.h>
#include <openbabel/builder.h>
#include <openbabel/math/align.h>

using namespace std;
using namespace OpenBabel;