User:Wayne Decatur/Code for Molecular Structure and Visualization Work - Revision history

Wayne Decatur: /* Related Python resources by others */

2019-09-19T19:12:42Z

Related Python resources by others

← Older revision		Revision as of 19:12, 19 September 2019
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	==Related Python resources by others==		==Related Python resources by others==

	[~~atomium](~~https://github.com/samirelanduk/atomium) is a Python library for opening and saving .pdb, .cif and .xyz files, and presenting and manipulating the information contained within. Documentation is at https://atomium.samireland.com/ .		*[https://github.com/samirelanduk/atomium atomium] is a Python library for opening and saving .pdb, .cif and .xyz files, and presenting and manipulating the information contained within. Documentation is at https://atomium.samireland.com/ .

	[~~Biopandas](~~https://github.com/rasbt/biopandas) for working with molecular structures in pandas DataFrames. Documentation at http://rasbt.github.io/biopandas/.		*[https://github.com/rasbt/biopandas Biopandas] for working with molecular structures in pandas DataFrames. Documentation at http://rasbt.github.io/biopandas/.

Wayne Decatur: add more of my stuff

2019-09-19T19:09:44Z

add more of my stuff

← Older revision		Revision as of 19:09, 19 September 2019
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	*** A script written in Python 2.x to merge multiple PDB files as individual models in a single PDB file. The individual models are placed in a single folder..		*** A script written in Python 2.x to merge multiple PDB files as individual models in a single PDB file. The individual models are placed in a single folder..
	*** It has advanced options that let you control the order of the individual models or control the starting numbering for the first model.		*** It has advanced options that let you control the order of the individual models or control the starting numbering for the first model.
			** And more available [https://github.com/fomightez/structurework/tree/master/python_scripts here], with several of them demonstrated actively in Jupyter notebooks by launching 'binder' sessions from .[https://github.com/fomightez/cl_demo-binder here].
			* In addition to my [https://github.com/fomightez/structurework/tree/master/python_scripts Python Scripts for Molecular Structure Analysis], my [https://github.com/fomightez/pymol-binder pymol-binder] adds some of my own code in for handling structures via PyMOL.

	==Webserver for Python code==		==Webserver for Python code==

Wayne Decatur: adds biopandas and atomium links

2018-08-24T01:03:06Z

adds biopandas and atomium links

← Older revision		Revision as of 01:03, 24 August 2018
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	* [https://github.com/fomightez/cnssolve1pt21_docker Dockerfile] to build images that will compile CNSsolve 1.21. A modified version of CNS to run the scripts for XL-MS Protein assembly, that software is referred to as XL-MOD in the publication [https://www.ncbi.nlm.nih.gov/pubmed/27111507 here].		* [https://github.com/fomightez/cnssolve1pt21_docker Dockerfile] to build images that will compile CNSsolve 1.21. A modified version of CNS to run the scripts for XL-MS Protein assembly, that software is referred to as XL-MOD in the publication [https://www.ncbi.nlm.nih.gov/pubmed/27111507 here].
	* [https://github.com/fomightez/xlmod_docker Dockerfile] for a modified version of CNS to run the scripts for XL-MS Protein assembly, that software is referred to as XL-MOD in the publication [https://www.ncbi.nlm.nih.gov/pubmed/27111507 here].		* [https://github.com/fomightez/xlmod_docker Dockerfile] for a modified version of CNS to run the scripts for XL-MS Protein assembly, that software is referred to as XL-MOD in the publication [https://www.ncbi.nlm.nih.gov/pubmed/27111507 here].

			==Related Python resources by others==

			[atomium](https://github.com/samirelanduk/atomium) is a Python library for opening and saving .pdb, .cif and .xyz files, and presenting and manipulating the information contained within. Documentation is at https://atomium.samireland.com/ .

			[Biopandas](https://github.com/rasbt/biopandas) for working with molecular structures in pandas DataFrames. Documentation at http://rasbt.github.io/biopandas/.

Wayne Decatur: add Dockerfiles I have made for molecular structure work

2018-06-18T16:56:30Z

add Dockerfiles I have made for molecular structure work

← Older revision		Revision as of 16:56, 18 June 2018
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	==Webserver==		==Webserver for Python code==
	* Much of the more involved code featured ~~here~~ is running in a webserver form [http://fomightez.pythonanywhere.com/spartan_fixer/ here]. You can enter your data and have it analyzed without needing to download anything.		* Much of the more involved code featured for Spartan_Fixer is running in a webserver form [http://fomightez.pythonanywhere.com/spartan_fixer/ here]. You can enter your data and have it analyzed without needing to download anything.

	==Code==		==Obtaining the Python Code==
	See [http://fomightez.github.io/ here] for getting my code in a form you can use on your machine or that you can modify.		See [http://fomightez.github.io/ here] for getting my code in a form you can use on your machine or that you can modify.


			==Dockerfiles==
			* [https://github.com/fomightez/cnssolve1pt21_docker Dockerfile] to build images that will compile CNSsolve 1.21. A modified version of CNS to run the scripts for XL-MS Protein assembly, that software is referred to as XL-MOD in the publication [https://www.ncbi.nlm.nih.gov/pubmed/27111507 here].
			* [https://github.com/fomightez/xlmod_docker Dockerfile] for a modified version of CNS to run the scripts for XL-MS Protein assembly, that software is referred to as XL-MOD in the publication [https://www.ncbi.nlm.nih.gov/pubmed/27111507 here].

Wayne Decatur at 02:21, 2 November 2015

2015-11-02T02:21:05Z

← Older revision		Revision as of 02:21, 2 November 2015
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	*** It takes a multiple model PDB file and splits up the models to produce as output each of the models as a separate PDB file.		*** It takes a multiple model PDB file and splits up the models to produce as output each of the models as a separate PDB file.
	*** This basic version requires you to paste the complete PDB file text into the script before you run it. I put this out here in case it helps anyone understand what is going on; it was inspired by code at [http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Split_NMR-style_multiple_model_pdb_files_into_individual_models here]		*** This basic version requires you to paste the complete PDB file text into the script before you run it. I put this out here in case it helps anyone understand what is going on; it was inspired by code at [http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Split_NMR-style_multiple_model_pdb_files_into_individual_models here]
			** [https://github.com/fomightez/structurework/blob/master/python_scripts/super_basic_multiple_model_PDB_file_splitter.py merge_multi_PDBs_into_single_file.py]
			*** A script written in Python 2.x to merge multiple PDB files as individual models in a single PDB file. The individual models are placed in a single folder..
			*** It has advanced options that let you control the order of the individual models or control the starting numbering for the first model.

Wayne Decatur at 20:56, 21 July 2015

2015-07-21T20:56:29Z

@@ Line 4: / Line 4: @@
 ** a Python (2.x) program  that fixes Spartan'08 output files in so-called PDB format, converting them to be true PDB format. The fixed files can then easily be used in Jmol.
 ** A webserver version of this is is running [http://fomightez.pythonanywhere.com/spartan_fixer/ here]. You can enter your data and have it analyzed without needing to download anything.
 * [https://github.com/fomightez/structurework/tree/master/python_scripts Wayne Decatur's Python Scripts for Molecular Structure Analysis]
 ==Webserver==

Wayne Decatur at 19:40, 15 June 2015

2015-06-15T19:40:07Z

← Older revision		Revision as of 19:40, 15 June 2015
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	* [https://github.com/fomightez/structurework/tree/master/spartan_fixer SPARTAN_FIXER]		* [https://github.com/fomightez/structurework/tree/master/spartan_fixer SPARTAN_FIXER]
	** a ~~python~~ program that fixes Spartan'08 output files in so-called PDB format, converting them to be true PDB format. The fixed files can then easily be used in Jmol.		** a Python (2.x) program that fixes Spartan'08 output files in so-called PDB format, converting them to be true PDB format. The fixed files can then easily be used in Jmol.
	** A webserver version of this is is running [http://fomightez.pythonanywhere.com/spartan_fixer/ here]. You can enter your data and have it analyzed without needing to download anything.		** A webserver version of this is is running [http://fomightez.pythonanywhere.com/spartan_fixer/ here]. You can enter your data and have it analyzed without needing to download anything.
	** Written in Python 2.x.
	* [https://github.com/fomightez/structurework/blob/master/python_scripts/multiple_model_PDB_file_splitter.py multiple_model_PDB_file_splitter.py]		* [https://github.com/fomightez/structurework/blob/master/python_scripts/multiple_model_PDB_file_splitter.py multiple_model_PDB_file_splitter.py]
	** It takes a multiple model PDB file and splits up the models to produce as output each of the models as a separate PDB file.		** It takes a multiple model PDB file and splits up the models to produce as output each of the models as a separate PDB file.

Wayne Decatur at 19:39, 15 June 2015

2015-06-15T19:39:24Z

← Older revision		Revision as of 19:39, 15 June 2015
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	** a python program that fixes Spartan'08 output files in so-called PDB format, converting them to be true PDB format. The fixed files can then easily be used in Jmol.		** a python program that fixes Spartan'08 output files in so-called PDB format, converting them to be true PDB format. The fixed files can then easily be used in Jmol.
	** A webserver version of this is is running [http://fomightez.pythonanywhere.com/spartan_fixer/ here]. You can enter your data and have it analyzed without needing to download anything.		** A webserver version of this is is running [http://fomightez.pythonanywhere.com/spartan_fixer/ here]. You can enter your data and have it analyzed without needing to download anything.
			** Written in Python 2.x.
	* [https://github.com/fomightez/structurework/blob/master/python_scripts/multiple_model_PDB_file_splitter.py multiple_model_PDB_file_splitter.py]		* [https://github.com/fomightez/structurework/blob/master/python_scripts/multiple_model_PDB_file_splitter.py multiple_model_PDB_file_splitter.py]
	** It takes a multiple model PDB file and splits up the models to produce as output each of the models as a separate PDB file.		** It takes a multiple model PDB file and splits up the models to produce as output each of the models as a separate PDB file.

Wayne Decatur at 19:38, 15 June 2015

2015-06-15T19:38:38Z

← Older revision		Revision as of 19:38, 15 June 2015
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	** A very basic multiple model PDB file splitting script written in Python 2.x.		** A very basic multiple model PDB file splitting script written in Python 2.x.
	** It takes a multiple model PDB file and splits up the models to produce as output each of the models as a separate PDB file.		** It takes a multiple model PDB file and splits up the models to produce as output each of the models as a separate PDB file.
	** This basic version requires you to paste the complete PDB file text into the script before you run it. I put this out here in case it helps anyone understand what is going on; it was inspired by code [~~here~~ http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Split_NMR-style_multiple_model_pdb_files_into_individual_models ]		** This basic version requires you to paste the complete PDB file text into the script before you run it. I put this out here in case it helps anyone understand what is going on; it was inspired by code at [http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Split_NMR-style_multiple_model_pdb_files_into_individual_models here]
	* [https://github.com/fomightez/structurework/tree/master/python_scripts Wayne Decatur's Python Scripts for Molecular Structure Analysis]		* [https://github.com/fomightez/structurework/tree/master/python_scripts Wayne Decatur's Python Scripts for Molecular Structure Analysis]

Wayne Decatur at 19:38, 15 June 2015

2015-06-15T19:38:01Z

← Older revision		Revision as of 19:38, 15 June 2015
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	** It takes a multiple model PDB file and splits up the models to produce as output each of the models as a separate PDB file.		** It takes a multiple model PDB file and splits up the models to produce as output each of the models as a separate PDB file.
	**You specify the structure file when you call the program.		**You specify the structure file when you call the program.
			** Written in Python 2.x.
	* [https://github.com/fomightez/structurework/blob/master/python_scripts/super_basic_multiple_model_PDB_file_splitter.py super_basic_multiple_model_PDB_file_splitter.py]		* [https://github.com/fomightez/structurework/blob/master/python_scripts/super_basic_multiple_model_PDB_file_splitter.py super_basic_multiple_model_PDB_file_splitter.py]
	** A very basic multiple model PDB file splitting script written in Python.		** A very basic multiple model PDB file splitting script written in Python 2.x.
	** It takes a multiple model PDB file and splits up the models to produce as output each of the models as a separate PDB file.		** It takes a multiple model PDB file and splits up the models to produce as output each of the models as a separate PDB file.
	** This basic version requires you to paste the complete PDB file text into the script before you run it. I put this out here in case it helps anyone understand what is going on; it was inspired by code [here http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Split_NMR-style_multiple_model_pdb_files_into_individual_models ]		** This basic version requires you to paste the complete PDB file text into the script before you run it. I put this out here in case it helps anyone understand what is going on; it was inspired by code [here http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Split_NMR-style_multiple_model_pdb_files_into_individual_models ]