求助! 如何把化学结构的文件mol格式,转化为SVG矢量图格式?

[ispotato]

各位好!

我是化学信息学的初学者, 最近正在研究如何将mol转化为svg图的问题,我是初学者,对svg不太熟悉,希望和请教以下,

1. 如何将mol中的原子坐标与键转化为svg的点和边?
2. 如何着色处理? 还有一些特殊的化学键如何处理?
3. 可有现成的mol2svg转化工具,我想学习一下, 各位高手可否给予一些知识和帮助?

万分感谢您!

[eexpress]

自己看描述。
● as ~dmolfile~dchem
p jmol - Molecular Viewer
p jmol-applet - Jmol Java applet
p libchemistry-openbabel-perl - Chemical toolbox library (perl bindings)
p libopenbabel-dev - Chemical toolbox library (development file
p libopenbabel-doc - Chemical toolbox library (documentation)
p libopenbabel4 - Chemical toolbox library
p openbabel - Chemical toolbox utilities (cli)
p pymol - Molecular Graphics System
p python-openbabel - Chemical toolbox library (python bindings)

[eexpress]

http://forum.ubuntu.org.cn/viewtopic.php?f=35&t=298243

[ispotato]

谢谢楼上的详细资料, 我正在逐个尝试,

看来论坛里藏龙卧虎阿 都是对化学信息学很有研究的高手

[xiooli]

用Indigo吧

代码： 全选

from indigo import *
from indigo_renderer import *
import os

class Mol2pic():
    def __init__(self, mol_string = '', width = 600, height = 600):
        self.idg = Indigo()
        self.renderer = IndigoRenderer(self.idg)
        self.idg.setOption("render-comment-position", "top")
        self.idg.setOption("render-image-size", width, height)
#        self.idg.setOption("render-background-color", 1.0, 1.0, 1.0)
        self.idg.setOption('render-label-mode', 'forcehide')
        self.idg.setOption('render-margins', 5, 5)
        self.idg.setOption('render-coloring', True)
        self.idg.setOption('render-stereo-old-style', True)

        if mol_string:
            self.set_mol(mol_string)

    def set_mol(self, string, fmt = 'mol'):
        #print string
        string = string.replace('\\n', '\n')
        if os.path.exists(string):
            self.mol = self.idg.loadMoleculeFromFile(string)
        else:
            self.mol = self.idg.loadMolecule(string)
        self.mol.foldHydrogens()

    def to_pic(self, out_fmt = 'svg', auto_layout = False, filename = None):
        self.idg.setOption("render-output-format", out_fmt)
        if auto_layout:
            self.mol.layout()
        if filename:
            try:
                self.renderer.renderToFile(self.mol, filename)
                return filename
            except Exception, e:
                print e
                pass
        return self.renderer.renderToBuffer(self.mol).tostring()

[ispotato]

自己看描述。
● as ~dmolfile~dchem
p jmol - Molecular Viewer
p jmol-applet - Jmol Java applet
p libchemistry-openbabel-perl - Chemical toolbox library (perl bindings)
p libopenbabel-dev - Chemical toolbox library (development file
p libopenbabel-doc - Chemical toolbox library (documentation)
p libopenbabel4 - Chemical toolbox library
p openbabel - Chemical toolbox utilities (cli)
p pymol - Molecular Graphics System
p python-openbabel - Chemical toolbox library (python bindings)

请教一个很棘手的问题,我现在通过调用openbabel,生成化合物SVG图, 经常出现化学键手性的错误问题,这是不是openbabel的bug?
另外,jmol如何生成svg图片?我找了半天 没有找到.. 麻烦您说详细些?

[ispotato]

用Indigo吧

代码： 全选

from indigo import *
from indigo_renderer import *
import os

class Mol2pic():
    def __init__(self, mol_string = '', width = 600, height = 600):
        self.idg = Indigo()
        self.renderer = IndigoRenderer(self.idg)
        self.idg.setOption("render-comment-position", "top")
        self.idg.setOption("render-image-size", width, height)
#        self.idg.setOption("render-background-color", 1.0, 1.0, 1.0)
        self.idg.setOption('render-label-mode', 'forcehide')
        self.idg.setOption('render-margins', 5, 5)
        self.idg.setOption('render-coloring', True)
        self.idg.setOption('render-stereo-old-style', True)

        if mol_string:
            self.set_mol(mol_string)

    def set_mol(self, string, fmt = 'mol'):
        #print string
        string = string.replace('\\n', '\n')
        if os.path.exists(string):
            self.mol = self.idg.loadMoleculeFromFile(string)
        else:
            self.mol = self.idg.loadMolecule(string)
        self.mol.foldHydrogens()

    def to_pic(self, out_fmt = 'svg', auto_layout = False, filename = None):
        self.idg.setOption("render-output-format", out_fmt)
        if auto_layout:
            self.mol.layout()
        if filename:
            try:
                self.renderer.renderToFile(self.mol, filename)
                return filename
            except Exception, e:
                print e
                pass
        return self.renderer.renderToBuffer(self.mol).tostring()

Indigo是什么工具?我搜了很久,找不到 可否给个链接?谢谢!

[xiooli]

http://ggasoftware.com/download

[ispotato]

用Indigo吧

代码： 全选

from indigo import *
from indigo_renderer import *
import os

class Mol2pic():
    def __init__(self, mol_string = '', width = 600, height = 600):
        self.idg = Indigo()
        self.renderer = IndigoRenderer(self.idg)
        self.idg.setOption("render-comment-position", "top")
        self.idg.setOption("render-image-size", width, height)
#        self.idg.setOption("render-background-color", 1.0, 1.0, 1.0)
        self.idg.setOption('render-label-mode', 'forcehide')
        self.idg.setOption('render-margins', 5, 5)
        self.idg.setOption('render-coloring', True)
        self.idg.setOption('render-stereo-old-style', True)

        if mol_string:
            self.set_mol(mol_string)

    def set_mol(self, string, fmt = 'mol'):
        #print string
        string = string.replace('\\n', '\n')
        if os.path.exists(string):
            self.mol = self.idg.loadMoleculeFromFile(string)
        else:
            self.mol = self.idg.loadMolecule(string)
        self.mol.foldHydrogens()

    def to_pic(self, out_fmt = 'svg', auto_layout = False, filename = None):
        self.idg.setOption("render-output-format", out_fmt)
        if auto_layout:
            self.mol.layout()
        if filename:
            try:
                self.renderer.renderToFile(self.mol, filename)
                return filename
            except Exception, e:
                print e
                pass
        return self.renderer.renderToBuffer(self.mol).tostring()

Indigo是什么工具?我搜了很久,找不到 可否给个链接?谢谢!

我用java调用，类似self.idg.setOption("render-comment-position", 这一类的参数设置，一律不能通过编译，也找不到相关的使用说明，
可有java调用的例子？setOption的这些参数从哪里可以看到如何设置呢？初学者，还请您详细指点了，谢谢！

[ispotato]

问题已经解决，java用Indigo
非常感谢各位牛人的大力协助！学到了不少东西！
谢谢！