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mol2ps-a freeware tool for 2D depiction of molecular structures

Eric.Zhou — Fri, 20 Nov 2009 07:26:00 GMT

mol2ps is a freely available command-line utility program which reads molecular structure files in different formats (see below) and generates Postscript output for 2D display. The Postscript file can then be used e.g. for creating a bitmap file, using a Postscript interpreter like Ghostscript.

As an example, the following 2D representation of caffeine in PNG (Portable Network Graphics) format was created from the corresponding MDL molfile (PubChem CID 2519), using mol2ps in combination with Ghostscript:

As input files, MDL molfiles and SD files (*.mol, *.sdf; 2D and 3D), Alchemy molfiles (*.mol), and Sybyl mol2 files (*.mol2) are accepted by mol2ps, the preferred format is the MDL molfile format. At present, it is not intended to extend the number of supported input file formats, as there are powerful file format converters available, such as OpenBabel.

The main purpose of mol2ps is to create small, but high-quality 2D pictures of molecules for display on web pages. Especially for web-based molecular structure databases it is quite useful to have pre-built pictures for display in hitlists instead of invoking browser plugins, Java applets, or server-side programs for display of the individual structures. A description of how such structure databases can be created with free software is given here.

Availability

mol2ps is freely available under the terms of the GNU General Public License (GPL), for a detailed description of this license, please visit http://www.gnu.org/copyleft/gpl.html.
It is written in Pascal and it was compiled with the Free Pascal compiler for the following platforms: Linux i386, FreeBSD i386, Windows (Win32 console application). You may use it on your own risk, there is no warranty for anything.

Download

source code: mol2ps.pas (approx. 139 KB)
Linux (i386) executable: mol2ps-latest-linux-i386.gz (approx. 81 KB)
FreeBSD (i386) executable: mol2ps-latest-freebsd-i386.gz (approx. 114 KB)
Win32 console application: mol2ps-latest-win32.zip (approx. 62 KB)
example color definition file: color.conf

Eric.Zhou 2009-11-20 15:26 发表评论

在Python中使用openbabel

Eric.Zhou — Sun, 25 Oct 2009 04:37:00 GMT

如果你的环境还没准备好, 可以官方网站看如何配置环境:http://openbabel.org/wiki/Install_Python_bindings
1. 通过使用OBMol, OBAtom和OBBond来创建原子和键
import openbabel

mol = openbabel.OBMol()
print 'Should print 0 (atoms)'
print mol.NumAtoms()

a = mol.NewAtom()
a.SetAtomicNum(6)   # carbon atom
a.SetVector(0.0, 1.0, 2.0) # coordinates

b = mol.NewAtom()
mol.AddBond(1, 2, 1)   # atoms indexed from 1
print 'Should print 2 (atoms)'
print mol.NumAtoms()
print 'Should print 1 (bond)'
print mol.NumBonds()

mol.Clear();

2. 通过OBConversion来读取分子, 并输出不同格式文件或字符串值
import openbabel

obConversion = openbabel.OBConversion()
obConversion.SetInAndOutFormats("smi", "mdl")    //读取smiles值, 然后输出mdl值

mol = openbabel.OBMol()
obConversion.ReadString(mol, "C1=CC=CS1")

print 'Should print 5 (atoms)'
print mol.NumAtoms()

mol.AddHydrogens()
print 'Should print 9 (atoms) after adding hydrogens'
print mol.NumAtoms()      //输出原子个数

outMDL = obConversion.WriteString(mol)

3. 计算fp值
import pybel
smiles = ['CCCC', 'CCCN']
mols = [pybel.readstring("smi", x) for x in smiles]   # Create two molecules from the SMILES
fps = [x.calcfp() for x in mols]   # Calculate their fingerprints
print fps[0].bits, fps[1].bits
print fps[0].fp[0]

mol2 = pybel.readstring('smi', 'c2ccc1ccccc1c2')
fp2 = mol2.calcfp("FP4")
print fp2
print fp2.bits

mol3 = pybel.readstring('smi', 'C1CCCCC1')
fp3 = mol3.calcfp()

print fp3.__or__(fp2) //计算相似度值

4. 读取sdf文件
#encoding=utf-8
import pybel
for mymol in pybel.readfile("sdf", "structures_all.sdf"):
fp = mymol.calcfp("FP2")
print fp

5. 输出txt文件和sdf文件

print mymol.write("smi") //'CCCC'
mymol.write("smi", "outputfile.txt")
largeSDfile = Outputfile("sdf", "multipleSD.sdf")
largeSDfile.write(mymol)
largeSDfile.write(myothermol)
largeSDfile.close()

Eric.Zhou 2009-10-25 12:37 发表评论

Openbabel子结构匹配

Eric.Zhou — Wed, 21 Oct 2009 00:55:00 GMT

package com.founder.openbabel;

import org.openbabel.OBConversion;
import org.openbabel.OBMol;
import org.openbabel.OBSmartsPattern;

public class Test {

public static void main(String[] args) {
// Initialise
System.loadLibrary("openbabel_java");

        // Read molecule from SMILES string
        OBConversion conv = new OBConversion();
        OBMol mol = new OBMol();
        conv.SetInFormat("smi");
        conv.ReadString(mol, "C(Cl)(=O)CCC(=O)Cl");

        // What are the indices of the carbon atoms
        // of the acid chloride groups?
        OBSmartsPattern acidpattern = new OBSmartsPattern();
        acidpattern.Init("C(=O)Cl");
        long t1 = System.currentTimeMillis();
        boolean flag = acidpattern.Match(mol);
        long t2 = System.currentTimeMillis();
        System.out.println("Cost time:" + (t2-t1) + "ms");
        System.out.println(flag);
    }

}

Eric.Zhou 2009-10-21 08:55 发表评论