Re: [Jmol-developers] how to modify circle color of element node
Unless you are doing very major changes, there is no need to modify classes. Just be sure you are operating on the trunk code and you keep it up to date. On Fri, Aug 15, 2014 at 7:36 PM, 胡瑞 huruid...@gmail.com wrote: OH I will not change anything on your original source code, but firstly, i need test and understand jmol runing way, if i will start modify offically i will extend your Class, modify original code is really bad way :( Sir i am a new programmer, i don't know how to read your svn file, Could you give me some advice Thank you very much 2014-08-16 8:15 GMT+08:00 Robert Hanson hans...@stolaf.edu: ps -- make sure you are checking out svn.code.sf.net/p/jmol/code/trunk/Jmol On Fri, Aug 15, 2014 at 7:14 PM, Robert Hanson hans...@stolaf.edu wrote: It sounds like you are a new contributor to Jmol. Terrific! We could use someone who wants to make the Gaussian input dialog better. No one has worked on that for a long time. Before you go too far on your own, though, why not request features? It would be unwise to start changing the code in Viewer, especially, because I regularly work on that, and what I do may break what you do. And you may not think of the implications something has, the way I can if I help you. I just checked in a much more interesting Gaussian input dialog. I hope you like it. Note that: -- tabs are gone; advanced simply right side of a JSplitPane -- refresh button is new; cancel button is now close -- when you use the model kit to modify the structure, the input file is updated -- when you click on an atom, that atom is selected and highlighted on the input file -- when you click on a line in the input file, the atom is highlighted -- when you change input parameters, the input file is updated -- when you load a new model, the input file is updated Bob On Fri, Aug 15, 2014 at 6:21 PM, 胡瑞 huruid...@gmail.com wrote: Oh, sir I find there is a assignAtom function which allocate in the ModelSet Class(Figure 1) i fund two method will call this function, as i say in the photo there are all in the script package, but i just click gui and i don't input any script command. Am i going a right way ? 2014-08-16 5:48 GMT+08:00 胡瑞 huruid...@gmail.com: Thank you sir, i had saw those documents which use by script, That script just show me how to operate it. However, i need to modify jmol java source code and add a new function, i have a simple demo (Figure1). That function will provide many possible options to user to choice. But how to recored user choice? Recoding index of element is very important.I still can't find the core function in the jmol opensource,Could you tell me the point of package and core class? Jmol sourse code is a huge project, i spend one month on this opensource code, many of them i can understand , some of them look so complicated. 2014-08-16 5:06 GMT+08:00 Robert Hanson hans...@stolaf.edu: Dear 胡瑞 see below [translation] It is great to know that you have a Chinese team [to understand my point in Chinese]. Maybe I had not expressed myself well. I am student at University of New Haven, and my supervisor has asked me to add a new functionality on top of Jmol. Did you remember that Jmol has a menu item for Export Gaussian Input file? The advance option can record the data on display. When I add element at the main menu, I must first switch [to the submenu?] to change options in advance. When I add a new structure, my results are sorted in order by default (see Figure 1, where the 2nd C should be at the 5th position) . How do I get the data in original order? The second question is how to record which element is clicked by a user. This info is useful to restore to the previous state. I am not familiar with scripting languages. However, browsing the source code shows me that many functionalities are achieved by filtering strings, which is quite general strategy. I wish your team could provide a detailed documentation. There is very limit such info on the Internet. I need to know in detail the functionality of each class. [/translation] Order: There is no order sorting. The order is file order. But I see what you mean. There is a bug there, and I will look into it. I like the idea very much of being able to edit the model and see changes in the Gaussian advanced tab. Is that what you are interested in? I have never thought of doing that. Documentation for scripting is at http://chemapps.stolaf.edu/jmol/docs There is probably no need to do any actual Java programming -- you can do a lot with Jmol scripting. For example, you can run your own functions whenever atoms are clicked. Look up information on callbacks http://chemapps.stolaf.edu/jmol/docs/?search=callback No promises I can continue in Chinese -- do try English! :) Bob Hanson --
Re: [Jmol-developers] how to modify circle color of element node
You need to learn how to check out code properly using SVN within Eclipse. Are you already using Eclipse? On Fri, Aug 15, 2014 at 7:49 PM, 胡瑞 huruid...@gmail.com wrote: I mean i don't know how to start to read. i connect your trunk address through svn, but there are many files. 2014-08-16 8:36 GMT+08:00 胡瑞 huruid...@gmail.com: OH I will not change anything on your original source code, but firstly, i need test and understand jmol runing way, if i will start modify offically i will extend your Class, modify original code is really bad way :( Sir i am a new programmer, i don't know how to read your svn file, Could you give me some advice Thank you very much 2014-08-16 8:15 GMT+08:00 Robert Hanson hans...@stolaf.edu: ps -- make sure you are checking out svn.code.sf.net/p/jmol/code/trunk/Jmol On Fri, Aug 15, 2014 at 7:14 PM, Robert Hanson hans...@stolaf.edu wrote: It sounds like you are a new contributor to Jmol. Terrific! We could use someone who wants to make the Gaussian input dialog better. No one has worked on that for a long time. Before you go too far on your own, though, why not request features? It would be unwise to start changing the code in Viewer, especially, because I regularly work on that, and what I do may break what you do. And you may not think of the implications something has, the way I can if I help you. I just checked in a much more interesting Gaussian input dialog. I hope you like it. Note that: -- tabs are gone; advanced simply right side of a JSplitPane -- refresh button is new; cancel button is now close -- when you use the model kit to modify the structure, the input file is updated -- when you click on an atom, that atom is selected and highlighted on the input file -- when you click on a line in the input file, the atom is highlighted -- when you change input parameters, the input file is updated -- when you load a new model, the input file is updated Bob On Fri, Aug 15, 2014 at 6:21 PM, 胡瑞 huruid...@gmail.com wrote: Oh, sir I find there is a assignAtom function which allocate in the ModelSet Class(Figure 1) i fund two method will call this function, as i say in the photo there are all in the script package, but i just click gui and i don't input any script command. Am i going a right way ? 2014-08-16 5:48 GMT+08:00 胡瑞 huruid...@gmail.com: Thank you sir, i had saw those documents which use by script, That script just show me how to operate it. However, i need to modify jmol java source code and add a new function, i have a simple demo (Figure1). That function will provide many possible options to user to choice. But how to recored user choice? Recoding index of element is very important.I still can't find the core function in the jmol opensource,Could you tell me the point of package and core class? Jmol sourse code is a huge project, i spend one month on this opensource code, many of them i can understand , some of them look so complicated. 2014-08-16 5:06 GMT+08:00 Robert Hanson hans...@stolaf.edu: Dear 胡瑞 see below [translation] It is great to know that you have a Chinese team [to understand my point in Chinese]. Maybe I had not expressed myself well. I am student at University of New Haven, and my supervisor has asked me to add a new functionality on top of Jmol. Did you remember that Jmol has a menu item for Export Gaussian Input file? The advance option can record the data on display. When I add element at the main menu, I must first switch [to the submenu?] to change options in advance. When I add a new structure, my results are sorted in order by default (see Figure 1, where the 2nd C should be at the 5th position) . How do I get the data in original order? The second question is how to record which element is clicked by a user. This info is useful to restore to the previous state. I am not familiar with scripting languages. However, browsing the source code shows me that many functionalities are achieved by filtering strings, which is quite general strategy. I wish your team could provide a detailed documentation. There is very limit such info on the Internet. I need to know in detail the functionality of each class. [/translation] Order: There is no order sorting. The order is file order. But I see what you mean. There is a bug there, and I will look into it. I like the idea very much of being able to edit the model and see changes in the Gaussian advanced tab. Is that what you are interested in? I have never thought of doing that. Documentation for scripting is at http://chemapps.stolaf.edu/jmol/docs There is probably no need to do any actual Java programming -- you can do a lot with Jmol scripting. For example, you can run your own functions whenever atoms are clicked. Look up information on callbacks http://chemapps.stolaf.edu/jmol/docs/?search=callback No promises I can continue in Chinese -- do try English! :) Bob
Re: [Jmol-developers] how to modify circle color of element node
oh, i fix it ~Thank you to response me. I fund it in the* CircleRenderer* Package and there is *plot8CircleCenteredUnclipped* funtion control it. but another question is how to record the element node sequence? And i also want record the element postion which select by user, but in the result of Gaussian input advance tap all result have been sorted. Do you know which functions sort them? i just want to export original data. Thank you 2014-08-15 13:15 GMT+08:00 Robert Hanson hans...@stolaf.edu: Do you mean the red thin line that is active in modelKit mode? Or something else? Can you say a bit more about what you are trying to do? On Thu, Aug 14, 2014 at 10:57 PM, 胡瑞 huruid...@gmail.com wrote: as i talk about the title, please tell me how can i find the node circle function when i move my mouse to a node. There is no any document to reference, i really need your help Thanks -- ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers -- Robert M. Hanson Larson-Anderson Professor of Chemistry Chair, Department of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 -- ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers -- ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
Re: [Jmol-developers] how to modify circle color of element node
If I understand, you are working at the Java level, not the scripting level. Those rendering methods are not anything you should be working with. They are very low-level operations at the pixel level of the final display. I cannot imagine how that would help you. If you explain more about what you mean by I just want to export original data I might be able help you. What exactly do you want to do. Can you give an example, starting with a Gaussian file? If you send your message in Chinese, not English, we may be able to help you better. Bob Hanson On Fri, Aug 15, 2014 at 1:27 AM, 胡瑞 huruid...@gmail.com wrote: oh, i fix it ~Thank you to response me. I fund it in the* CircleRenderer* Package and there is *plot8CircleCenteredUnclipped* funtion control it. but another question is how to record the element node sequence? And i also want record the element postion which select by user, but in the result of Gaussian input advance tap all result have been sorted. Do you know which functions sort them? i just want to export original data. Thank you 2014-08-15 13:15 GMT+08:00 Robert Hanson hans...@stolaf.edu: Do you mean the red thin line that is active in modelKit mode? Or something else? Can you say a bit more about what you are trying to do? On Thu, Aug 14, 2014 at 10:57 PM, 胡瑞 huruid...@gmail.com wrote: as i talk about the title, please tell me how can i find the node circle function when i move my mouse to a node. There is no any document to reference, i really need your help Thanks -- ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers -- Robert M. Hanson Larson-Anderson Professor of Chemistry Chair, Department of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 -- ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers -- ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers -- Robert M. Hanson Larson-Anderson Professor of Chemistry Chair, Department of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 -- ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
Re: [Jmol-developers] how to modify circle color of element node
哇，你们有中国团队，太好了，可能我表达意思有点不对，我是就读于university of new haven的学生，我的教授需要我在jmol的原有基础上增加一个功能，那个jmol里面有个菜单里面不是有个Export Gaussian Input file 的选项卡嘛？那个advance里面会记录你display的数据，当我在主界面增加元素的时候，只有再次切换才能改变advance里面的结果，当我发现我增加一个结构的时候，内部的函数会给我的结果进行排序（图1）如何获得原始数据？ 第二个问题如何获取当用户单击某个元素节点的时候，我可以记录下他单击的是哪儿一个具体的节点序号，以便用户保存后下次提取可以还原》 脚本语言确实没有怎么接触过，不过纵观代码很多都是过滤字符串来达到实现功能的目的，这一点做得做得很通用。 希望贵组织能够给一份详细的开发文档，网上的资料太少了，我需要详细的每个类做什么事的具体功能即可。 谢谢 2014-08-15 20:33 GMT+08:00 Robert Hanson hans...@stolaf.edu: If I understand, you are working at the Java level, not the scripting level. Those rendering methods are not anything you should be working with. They are very low-level operations at the pixel level of the final display. I cannot imagine how that would help you. If you explain more about what you mean by I just want to export original data I might be able help you. What exactly do you want to do. Can you give an example, starting with a Gaussian file? If you send your message in Chinese, not English, we may be able to help you better. Bob Hanson On Fri, Aug 15, 2014 at 1:27 AM, 胡瑞 huruid...@gmail.com wrote: oh, i fix it ~Thank you to response me. I fund it in the* CircleRenderer* Package and there is *plot8CircleCenteredUnclipped* funtion control it. but another question is how to record the element node sequence? And i also want record the element postion which select by user, but in the result of Gaussian input advance tap all result have been sorted. Do you know which functions sort them? i just want to export original data. Thank you 2014-08-15 13:15 GMT+08:00 Robert Hanson hans...@stolaf.edu: Do you mean the red thin line that is active in modelKit mode? Or something else? Can you say a bit more about what you are trying to do? On Thu, Aug 14, 2014 at 10:57 PM, 胡瑞 huruid...@gmail.com wrote: as i talk about the title, please tell me how can i find the node circle function when i move my mouse to a node. There is no any document to reference, i really need your help Thanks -- ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers -- Robert M. Hanson Larson-Anderson Professor of Chemistry Chair, Department of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 -- ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers -- ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers -- Robert M. Hanson Larson-Anderson Professor of Chemistry Chair, Department of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 -- ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers -- ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
Re: [Jmol-developers] how to modify circle color of element node
Dear 胡瑞 see below [translation] It is great to know that you have a Chinese team [to understand my point in Chinese]. Maybe I had not expressed myself well. I am student at University of New Haven, and my supervisor has asked me to add a new functionality on top of Jmol. Did you remember that Jmol has a menu item for Export Gaussian Input file? The advance option can record the data on display. When I add element at the main menu, I must first switch [to the submenu?] to change options in advance. When I add a new structure, my results are sorted in order by default (see Figure 1, where the 2nd C should be at the 5th position) . How do I get the data in original order? The second question is how to record which element is clicked by a user. This info is useful to restore to the previous state. I am not familiar with scripting languages. However, browsing the source code shows me that many functionalities are achieved by filtering strings, which is quite general strategy. I wish your team could provide a detailed documentation. There is very limit such info on the Internet. I need to know in detail the functionality of each class. [/translation] Order: There is no order sorting. The order is file order. But I see what you mean. There is a bug there, and I will look into it. I like the idea very much of being able to edit the model and see changes in the Gaussian advanced tab. Is that what you are interested in? I have never thought of doing that. Documentation for scripting is at http://chemapps.stolaf.edu/jmol/docs There is probably no need to do any actual Java programming -- you can do a lot with Jmol scripting. For example, you can run your own functions whenever atoms are clicked. Look up information on callbacks http://chemapps.stolaf.edu/jmol/docs/?search=callback No promises I can continue in Chinese -- do try English! :) Bob Hanson -- ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
Re: [Jmol-developers] how to modify circle color of element node
Thank you sir, i had saw those documents which use by script, That script just show me how to operate it. However, i need to modify jmol java source code and add a new function, i have a simple demo (Figure1). That function will provide many possible options to user to choice. But how to recored user choice? Recoding index of element is very important.I still can't find the core function in the jmol opensource,Could you tell me the point of package and core class? Jmol sourse code is a huge project, i spend one month on this opensource code, many of them i can understand , some of them look so complicated. 2014-08-16 5:06 GMT+08:00 Robert Hanson hans...@stolaf.edu: Dear 胡瑞 see below [translation] It is great to know that you have a Chinese team [to understand my point in Chinese]. Maybe I had not expressed myself well. I am student at University of New Haven, and my supervisor has asked me to add a new functionality on top of Jmol. Did you remember that Jmol has a menu item for Export Gaussian Input file? The advance option can record the data on display. When I add element at the main menu, I must first switch [to the submenu?] to change options in advance. When I add a new structure, my results are sorted in order by default (see Figure 1, where the 2nd C should be at the 5th position) . How do I get the data in original order? The second question is how to record which element is clicked by a user. This info is useful to restore to the previous state. I am not familiar with scripting languages. However, browsing the source code shows me that many functionalities are achieved by filtering strings, which is quite general strategy. I wish your team could provide a detailed documentation. There is very limit such info on the Internet. I need to know in detail the functionality of each class. [/translation] Order: There is no order sorting. The order is file order. But I see what you mean. There is a bug there, and I will look into it. I like the idea very much of being able to edit the model and see changes in the Gaussian advanced tab. Is that what you are interested in? I have never thought of doing that. Documentation for scripting is at http://chemapps.stolaf.edu/jmol/docs There is probably no need to do any actual Java programming -- you can do a lot with Jmol scripting. For example, you can run your own functions whenever atoms are clicked. Look up information on callbacks http://chemapps.stolaf.edu/jmol/docs/?search=callback No promises I can continue in Chinese -- do try English! :) Bob Hanson -- ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers -- ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
Re: [Jmol-developers] how to modify circle color of element node
It sounds like you are a new contributor to Jmol. Terrific! We could use someone who wants to make the Gaussian input dialog better. No one has worked on that for a long time. Before you go too far on your own, though, why not request features? It would be unwise to start changing the code in Viewer, especially, because I regularly work on that, and what I do may break what you do. And you may not think of the implications something has, the way I can if I help you. I just checked in a much more interesting Gaussian input dialog. I hope you like it. Note that: -- tabs are gone; advanced simply right side of a JSplitPane -- refresh button is new; cancel button is now close -- when you use the model kit to modify the structure, the input file is updated -- when you click on an atom, that atom is selected and highlighted on the input file -- when you click on a line in the input file, the atom is highlighted -- when you change input parameters, the input file is updated -- when you load a new model, the input file is updated Bob On Fri, Aug 15, 2014 at 6:21 PM, 胡瑞 huruid...@gmail.com wrote: Oh, sir I find there is a assignAtom function which allocate in the ModelSet Class(Figure 1) i fund two method will call this function, as i say in the photo there are all in the script package, but i just click gui and i don't input any script command. Am i going a right way ? 2014-08-16 5:48 GMT+08:00 胡瑞 huruid...@gmail.com: Thank you sir, i had saw those documents which use by script, That script just show me how to operate it. However, i need to modify jmol java source code and add a new function, i have a simple demo (Figure1). That function will provide many possible options to user to choice. But how to recored user choice? Recoding index of element is very important.I still can't find the core function in the jmol opensource,Could you tell me the point of package and core class? Jmol sourse code is a huge project, i spend one month on this opensource code, many of them i can understand , some of them look so complicated. 2014-08-16 5:06 GMT+08:00 Robert Hanson hans...@stolaf.edu: Dear 胡瑞 see below [translation] It is great to know that you have a Chinese team [to understand my point in Chinese]. Maybe I had not expressed myself well. I am student at University of New Haven, and my supervisor has asked me to add a new functionality on top of Jmol. Did you remember that Jmol has a menu item for Export Gaussian Input file? The advance option can record the data on display. When I add element at the main menu, I must first switch [to the submenu?] to change options in advance. When I add a new structure, my results are sorted in order by default (see Figure 1, where the 2nd C should be at the 5th position) . How do I get the data in original order? The second question is how to record which element is clicked by a user. This info is useful to restore to the previous state. I am not familiar with scripting languages. However, browsing the source code shows me that many functionalities are achieved by filtering strings, which is quite general strategy. I wish your team could provide a detailed documentation. There is very limit such info on the Internet. I need to know in detail the functionality of each class. [/translation] Order: There is no order sorting. The order is file order. But I see what you mean. There is a bug there, and I will look into it. I like the idea very much of being able to edit the model and see changes in the Gaussian advanced tab. Is that what you are interested in? I have never thought of doing that. Documentation for scripting is at http://chemapps.stolaf.edu/jmol/docs There is probably no need to do any actual Java programming -- you can do a lot with Jmol scripting. For example, you can run your own functions whenever atoms are clicked. Look up information on callbacks http://chemapps.stolaf.edu/jmol/docs/?search=callback No promises I can continue in Chinese -- do try English! :) Bob Hanson -- ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers -- ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers -- Robert M. Hanson Larson-Anderson Professor of Chemistry Chair, Department of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 --
Re: [Jmol-developers] how to modify circle color of element node
ps -- make sure you are checking out svn.code.sf.net/p/jmol/code/trunk/Jmol On Fri, Aug 15, 2014 at 7:14 PM, Robert Hanson hans...@stolaf.edu wrote: It sounds like you are a new contributor to Jmol. Terrific! We could use someone who wants to make the Gaussian input dialog better. No one has worked on that for a long time. Before you go too far on your own, though, why not request features? It would be unwise to start changing the code in Viewer, especially, because I regularly work on that, and what I do may break what you do. And you may not think of the implications something has, the way I can if I help you. I just checked in a much more interesting Gaussian input dialog. I hope you like it. Note that: -- tabs are gone; advanced simply right side of a JSplitPane -- refresh button is new; cancel button is now close -- when you use the model kit to modify the structure, the input file is updated -- when you click on an atom, that atom is selected and highlighted on the input file -- when you click on a line in the input file, the atom is highlighted -- when you change input parameters, the input file is updated -- when you load a new model, the input file is updated Bob On Fri, Aug 15, 2014 at 6:21 PM, 胡瑞 huruid...@gmail.com wrote: Oh, sir I find there is a assignAtom function which allocate in the ModelSet Class(Figure 1) i fund two method will call this function, as i say in the photo there are all in the script package, but i just click gui and i don't input any script command. Am i going a right way ? 2014-08-16 5:48 GMT+08:00 胡瑞 huruid...@gmail.com: Thank you sir, i had saw those documents which use by script, That script just show me how to operate it. However, i need to modify jmol java source code and add a new function, i have a simple demo (Figure1). That function will provide many possible options to user to choice. But how to recored user choice? Recoding index of element is very important.I still can't find the core function in the jmol opensource,Could you tell me the point of package and core class? Jmol sourse code is a huge project, i spend one month on this opensource code, many of them i can understand , some of them look so complicated. 2014-08-16 5:06 GMT+08:00 Robert Hanson hans...@stolaf.edu: Dear 胡瑞 see below [translation] It is great to know that you have a Chinese team [to understand my point in Chinese]. Maybe I had not expressed myself well. I am student at University of New Haven, and my supervisor has asked me to add a new functionality on top of Jmol. Did you remember that Jmol has a menu item for Export Gaussian Input file? The advance option can record the data on display. When I add element at the main menu, I must first switch [to the submenu?] to change options in advance. When I add a new structure, my results are sorted in order by default (see Figure 1, where the 2nd C should be at the 5th position) . How do I get the data in original order? The second question is how to record which element is clicked by a user. This info is useful to restore to the previous state. I am not familiar with scripting languages. However, browsing the source code shows me that many functionalities are achieved by filtering strings, which is quite general strategy. I wish your team could provide a detailed documentation. There is very limit such info on the Internet. I need to know in detail the functionality of each class. [/translation] Order: There is no order sorting. The order is file order. But I see what you mean. There is a bug there, and I will look into it. I like the idea very much of being able to edit the model and see changes in the Gaussian advanced tab. Is that what you are interested in? I have never thought of doing that. Documentation for scripting is at http://chemapps.stolaf.edu/jmol/docs There is probably no need to do any actual Java programming -- you can do a lot with Jmol scripting. For example, you can run your own functions whenever atoms are clicked. Look up information on callbacks http://chemapps.stolaf.edu/jmol/docs/?search=callback No promises I can continue in Chinese -- do try English! :) Bob Hanson -- ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers -- ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers -- Robert M. Hanson Larson-Anderson Professor of Chemistry Chair, Department of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is
Re: [Jmol-developers] how to modify circle color of element node
OH I will not change anything on your original source code, but firstly, i need test and understand jmol runing way, if i will start modify offically i will extend your Class, modify original code is really bad way :( Sir i am a new programmer, i don't know how to read your svn file, Could you give me some advice Thank you very much 2014-08-16 8:15 GMT+08:00 Robert Hanson hans...@stolaf.edu: ps -- make sure you are checking out svn.code.sf.net/p/jmol/code/trunk/Jmol On Fri, Aug 15, 2014 at 7:14 PM, Robert Hanson hans...@stolaf.edu wrote: It sounds like you are a new contributor to Jmol. Terrific! We could use someone who wants to make the Gaussian input dialog better. No one has worked on that for a long time. Before you go too far on your own, though, why not request features? It would be unwise to start changing the code in Viewer, especially, because I regularly work on that, and what I do may break what you do. And you may not think of the implications something has, the way I can if I help you. I just checked in a much more interesting Gaussian input dialog. I hope you like it. Note that: -- tabs are gone; advanced simply right side of a JSplitPane -- refresh button is new; cancel button is now close -- when you use the model kit to modify the structure, the input file is updated -- when you click on an atom, that atom is selected and highlighted on the input file -- when you click on a line in the input file, the atom is highlighted -- when you change input parameters, the input file is updated -- when you load a new model, the input file is updated Bob On Fri, Aug 15, 2014 at 6:21 PM, 胡瑞 huruid...@gmail.com wrote: Oh, sir I find there is a assignAtom function which allocate in the ModelSet Class(Figure 1) i fund two method will call this function, as i say in the photo there are all in the script package, but i just click gui and i don't input any script command. Am i going a right way ? 2014-08-16 5:48 GMT+08:00 胡瑞 huruid...@gmail.com: Thank you sir, i had saw those documents which use by script, That script just show me how to operate it. However, i need to modify jmol java source code and add a new function, i have a simple demo (Figure1). That function will provide many possible options to user to choice. But how to recored user choice? Recoding index of element is very important.I still can't find the core function in the jmol opensource,Could you tell me the point of package and core class? Jmol sourse code is a huge project, i spend one month on this opensource code, many of them i can understand , some of them look so complicated. 2014-08-16 5:06 GMT+08:00 Robert Hanson hans...@stolaf.edu: Dear 胡瑞 see below [translation] It is great to know that you have a Chinese team [to understand my point in Chinese]. Maybe I had not expressed myself well. I am student at University of New Haven, and my supervisor has asked me to add a new functionality on top of Jmol. Did you remember that Jmol has a menu item for Export Gaussian Input file? The advance option can record the data on display. When I add element at the main menu, I must first switch [to the submenu?] to change options in advance. When I add a new structure, my results are sorted in order by default (see Figure 1, where the 2nd C should be at the 5th position) . How do I get the data in original order? The second question is how to record which element is clicked by a user. This info is useful to restore to the previous state. I am not familiar with scripting languages. However, browsing the source code shows me that many functionalities are achieved by filtering strings, which is quite general strategy. I wish your team could provide a detailed documentation. There is very limit such info on the Internet. I need to know in detail the functionality of each class. [/translation] Order: There is no order sorting. The order is file order. But I see what you mean. There is a bug there, and I will look into it. I like the idea very much of being able to edit the model and see changes in the Gaussian advanced tab. Is that what you are interested in? I have never thought of doing that. Documentation for scripting is at http://chemapps.stolaf.edu/jmol/docs There is probably no need to do any actual Java programming -- you can do a lot with Jmol scripting. For example, you can run your own functions whenever atoms are clicked. Look up information on callbacks http://chemapps.stolaf.edu/jmol/docs/?search=callback No promises I can continue in Chinese -- do try English! :) Bob Hanson -- ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers --
Re: [Jmol-developers] how to modify circle color of element node
I mean i don't know how to start to read. i connect your trunk address through svn, but there are many files. 2014-08-16 8:36 GMT+08:00 胡瑞 huruid...@gmail.com: OH I will not change anything on your original source code, but firstly, i need test and understand jmol runing way, if i will start modify offically i will extend your Class, modify original code is really bad way :( Sir i am a new programmer, i don't know how to read your svn file, Could you give me some advice Thank you very much 2014-08-16 8:15 GMT+08:00 Robert Hanson hans...@stolaf.edu: ps -- make sure you are checking out svn.code.sf.net/p/jmol/code/trunk/Jmol On Fri, Aug 15, 2014 at 7:14 PM, Robert Hanson hans...@stolaf.edu wrote: It sounds like you are a new contributor to Jmol. Terrific! We could use someone who wants to make the Gaussian input dialog better. No one has worked on that for a long time. Before you go too far on your own, though, why not request features? It would be unwise to start changing the code in Viewer, especially, because I regularly work on that, and what I do may break what you do. And you may not think of the implications something has, the way I can if I help you. I just checked in a much more interesting Gaussian input dialog. I hope you like it. Note that: -- tabs are gone; advanced simply right side of a JSplitPane -- refresh button is new; cancel button is now close -- when you use the model kit to modify the structure, the input file is updated -- when you click on an atom, that atom is selected and highlighted on the input file -- when you click on a line in the input file, the atom is highlighted -- when you change input parameters, the input file is updated -- when you load a new model, the input file is updated Bob On Fri, Aug 15, 2014 at 6:21 PM, 胡瑞 huruid...@gmail.com wrote: Oh, sir I find there is a assignAtom function which allocate in the ModelSet Class(Figure 1) i fund two method will call this function, as i say in the photo there are all in the script package, but i just click gui and i don't input any script command. Am i going a right way ? 2014-08-16 5:48 GMT+08:00 胡瑞 huruid...@gmail.com: Thank you sir, i had saw those documents which use by script, That script just show me how to operate it. However, i need to modify jmol java source code and add a new function, i have a simple demo (Figure1). That function will provide many possible options to user to choice. But how to recored user choice? Recoding index of element is very important.I still can't find the core function in the jmol opensource,Could you tell me the point of package and core class? Jmol sourse code is a huge project, i spend one month on this opensource code, many of them i can understand , some of them look so complicated. 2014-08-16 5:06 GMT+08:00 Robert Hanson hans...@stolaf.edu: Dear 胡瑞 see below [translation] It is great to know that you have a Chinese team [to understand my point in Chinese]. Maybe I had not expressed myself well. I am student at University of New Haven, and my supervisor has asked me to add a new functionality on top of Jmol. Did you remember that Jmol has a menu item for Export Gaussian Input file? The advance option can record the data on display. When I add element at the main menu, I must first switch [to the submenu?] to change options in advance. When I add a new structure, my results are sorted in order by default (see Figure 1, where the 2nd C should be at the 5th position) . How do I get the data in original order? The second question is how to record which element is clicked by a user. This info is useful to restore to the previous state. I am not familiar with scripting languages. However, browsing the source code shows me that many functionalities are achieved by filtering strings, which is quite general strategy. I wish your team could provide a detailed documentation. There is very limit such info on the Internet. I need to know in detail the functionality of each class. [/translation] Order: There is no order sorting. The order is file order. But I see what you mean. There is a bug there, and I will look into it. I like the idea very much of being able to edit the model and see changes in the Gaussian advanced tab. Is that what you are interested in? I have never thought of doing that. Documentation for scripting is at http://chemapps.stolaf.edu/jmol/docs There is probably no need to do any actual Java programming -- you can do a lot with Jmol scripting. For example, you can run your own functions whenever atoms are clicked. Look up information on callbacks http://chemapps.stolaf.edu/jmol/docs/?search=callback No promises I can continue in Chinese -- do try English! :) Bob Hanson -- ___ Jmol-developers mailing list
Re: [Jmol-developers] how to modify circle color of element node
Do you mean the red thin line that is active in modelKit mode? Or something else? Can you say a bit more about what you are trying to do? On Thu, Aug 14, 2014 at 10:57 PM, 胡瑞 huruid...@gmail.com wrote: as i talk about the title, please tell me how can i find the node circle function when i move my mouse to a node. There is no any document to reference, i really need your help Thanks -- ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers -- Robert M. Hanson Larson-Anderson Professor of Chemistry Chair, Department of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 -- ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
