Pathway Gap Filling Post-CHECKSPMUTATE - Revision history

Adk44 at 13:54, 4 June 2020

2020-06-04T13:54:47Z

← Older revision		Revision as of 13:54, 4 June 2020
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	were included.		were included.

	Before proceeding, we also required duplicates.sh, duplicates.py, duplicates2.py and reoptimise.sh, all of which can be found in '''/svn/SCRIPTS/~~CHECKSPMUTATE~~/all_launched_simult/minima'''.		Before proceeding, we also required duplicates.sh, duplicates.py, duplicates2.py and reoptimise.sh, all of which can be found in '''/svn/SCRIPTS/PATHSAMPLE/checkspmutate/all_launched_simult/minima'''.

	==== Execution ====		==== Execution ====
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	==== Note on checkts ====		==== Note on checkts ====

	Because of slightly different requirements, make sure that the auxiliary files from '''/svn/SCRIPTS/~~CHECKSPMUTATE~~/all_launched_simult/TSs''' are used instead. Also, the file to be read in by duplicates.sh should be called pathsample_checkts.out rather than pathsample_checkmin.out.		Because of slightly different requirements, make sure that the auxiliary files from '''/svn/SCRIPTS/PATHSAMPLE/checkspmutate/all_launched_simult/TSs''' are used instead. Also, the file to be read in by duplicates.sh should be called pathsample_checkts.out rather than pathsample_checkmin.out.

	=== readmin/readts ===		=== readmin/readts ===
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	</pre>		</pre>

	And the bash script, organise_mindatinfo_min.sh, to be found in '''/svn/SCRIPTS/~~CHECKSPMUTATE~~/readmin'''.		And the bash script, organise_mindatinfo_min.sh, to be found in '''/svn/SCRIPTS/PATHSAMPLE/checkspmutate/readmin'''.

	==== Execution ====		==== Execution ====
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	Rather than checkminfile and pathsample_checkmin.out, we need the files checktsfile and pathsample_checkts.out		Rather than checkminfile and pathsample_checkmin.out, we need the files checktsfile and pathsample_checkts.out

	Rather than organise_mindatainfo_min.sh, use the script organise_mindatainfo_ts.sh (to be found in '''/svn/SCRIPTS/~~CHECKSPMUTATE~~/readts''').		Rather than organise_mindatainfo_min.sh, use the script organise_mindatainfo_ts.sh (to be found in '''/svn/SCRIPTS/PATHSAMPLE/checkspmutate/readts''').

	In pathdata, stick with the READMIN (as there isn't actually a READTS keyword available). This is not a big problem - all that we need to do after running the READMIN calculation is to rename points.min to points.ts and min.data to ts.data.		In pathdata, stick with the READMIN (as there isn't actually a READTS keyword available). This is not a big problem - all that we need to do after running the READMIN calculation is to rename points.min to points.ts and min.data to ts.data.
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	</pre>		</pre>

	In addition, the following scripts, which can be accessed in '''/svn/SCRIPTS/~~CHECKSPMUTATE~~/all_opt_TSs''', are required:		In addition, the following scripts, which can be accessed in '''/svn/SCRIPTS/PATHSAMPLE/checkspmutate/all_opt_TSs''', are required:

	* addpath.sh, descents.sh		* addpath.sh, descents.sh
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	Copy ts.data from startfrompath into the sub-directory generate_connectfile		Copy ts.data from startfrompath into the sub-directory generate_connectfile

	The following files are required, which can be found in '''/svn/SCRIPTS/~~CHECKSPMUTATE~~/generate_connectfile'''.		The following files are required, which can be found in '''/svn/SCRIPTS/PATHSAMPLE/checkspmutate/generate_connectfile'''.

	* det_connections.sh, generate_connectfile_prep.py, generate_connectfile.py		* det_connections.sh, generate_connectfile_prep.py, generate_connectfile.py
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	</pre>		</pre>

	* The bash scripts, find_connections.sh (which can be found in '''/svn/SCRIPTS/~~disconnect~~''') and connect_sub_databases.sh (which can be found in '''/svn/SCRIPTS/PATHSAMPLE/connecting_sub_databases''').		* The bash scripts, find_connections.sh (which can be found in '''/svn/SCRIPTS/DISCONNECT''') and connect_sub_databases.sh (which can be found in '''/svn/SCRIPTS/PATHSAMPLE/connecting_sub_databases''').

	==== Execution ====		==== Execution ====

Adk44: /* A Few Notes */

2020-06-04T09:33:08Z

A Few Notes

← Older revision		Revision as of 09:33, 4 June 2020
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	As mentioned at the top of this article, this method to plug in the gaps of a new pathway is highly idiosyncratic, and was particularly useful for the system I was working on. I don't necessarily anticipate it being useful for everybody, and that's why I haven't really generalised the various scripts I've used. Should this prove more popular than I suspect, I would be happy to generalise this code.		As mentioned at the top of this article, this method to plug in the gaps of a new pathway is highly idiosyncratic, and was particularly useful for the system I was working on. I don't necessarily anticipate it being useful for everybody, and that's why I haven't really generalised the various scripts I've used. Should this prove more popular than I suspect, I would be happy to generalise this code.

	One thing to note is that, if you have a really big database describing a large system, it ~~make~~ not be practical to create so many directories, and copy over the large points.min and points.ts files. In which case, some of my scripts will have to be adapted. Again, if anybody struggles doing this, I would be happy to step in and help.		One thing to note is that, if you have a really big database describing a large system, it may not be practical to create so many directories, and copy over the large points.min and points.ts files. In which case, some of my scripts will have to be adapted. Again, if anybody struggles doing this, I would be happy to step in and help.

	--adk44 18.15, 3 June 2020 (BST)		--adk44 18.15, 3 June 2020 (BST)

Adk44: /* Execution */

2020-06-04T09:30:34Z

Execution

← Older revision		Revision as of 09:30, 4 June 2020
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	==== Execution ====		==== Execution ====

	First of all, the minima need to be grouped into sub-databases. I found that the easiest way to do this is by running disconnectionDPS in a loop until all the minima in the database are assigned. This is done by executing find_connections.sh. Before doing so, ensure that the argument to CONNECTMIN is set to 1 and the PRINTCONNECTED keyword is included. Also, make sure to change the disconnectionDPS binary in the bash script to whatever you've called your binary.		First of all, the minima need to be grouped into sub-databases. I found that the easiest way to do this is by running [[disconnectionDPS]] in a loop until all the minima in the database are assigned. This is done by executing find_connections.sh. Before doing so, ensure that the argument to CONNECTMIN is set to 1 and the PRINTCONNECTED keyword is included. Also, make sure to change the [[disconnectionDPS]] binary in the bash script to whatever you've called your binary.

	I tend to find it a bit of a waste of time to consider really small sub-databases. I only tend to consider sub-databases with 10 minima or more in them. It's up to you what cutoff, if any, you wish to have. For these sub-databases, the '''connected_''' files which list the minima comprising them are copied to '''relevant_connected_''' files. Following the completion of find_connections.sh, the '''connected_''' can simply be deleted, but keep the '''relevant_connected_''' ones. Just make sure that the two minima at the beginning and end of the pathway that you are interested in are retained (i.e. if one of these minima is contained in a '''connected_''' file beneath the cutoff, ensure that this file is also renamed to a '''relevant_connected_''' file).		I tend to find it a bit of a waste of time to consider really small sub-databases. I only tend to consider sub-databases with 10 minima or more in them. It's up to you what cutoff, if any, you wish to have. For these sub-databases, the '''connected_''' files which list the minima comprising them are copied to '''relevant_connected_''' files. Following the completion of find_connections.sh, the '''connected_''' can simply be deleted, but keep the '''relevant_connected_''' ones. Just make sure that the two minima at the beginning and end of the pathway that you are interested in are retained (i.e. if one of these minima is contained in a '''connected_''' file beneath the cutoff, ensure that this file is also renamed to a '''relevant_connected_''' file).

Adk44: /* Files Required */

2020-06-04T09:29:57Z

Files Required

← Older revision		Revision as of 09:29, 4 June 2020
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	</pre>		</pre>

	* The bash scripts, find_connections.sh (which can be found in /svn/SCRIPTS/disconnect) and connect_sub_databases.sh (which can be found in /svn/SCRIPTS/PATHSAMPLE/connecting_sub_databases).		* The bash scripts, find_connections.sh (which can be found in '''/svn/SCRIPTS/disconnect''') and connect_sub_databases.sh (which can be found in '''/svn/SCRIPTS/PATHSAMPLE/connecting_sub_databases''').

	==== Execution ====		==== Execution ====

Adk44: /* Files Required */

2020-06-04T09:25:33Z

Files Required

← Older revision		Revision as of 09:25, 4 June 2020
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	Copy ts.data from startfrompath into the sub-directory generate_connectfile		Copy ts.data from startfrompath into the sub-directory generate_connectfile

	The following files are required, which can be found in /svn/SCRIPTS/CHECKSPMUTATE/generate_connectfile		The following files are required, which can be found in '''/svn/SCRIPTS/CHECKSPMUTATE/generate_connectfile'''.

	* det_connections.sh, generate_connectfile_prep.py, generate_connectfile.py		* det_connections.sh, generate_connectfile_prep.py, generate_connectfile.py

Adk44: /* Execution */

2020-06-04T09:24:57Z

Execution

← Older revision		Revision as of 09:24, 4 June 2020
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	</pre>		</pre>

	Then, move back into the all_opt_TSs directory, and execute addpath.sh. Now, all of the TSs and their associated minima shall be added to the database in the startfrompath directory. Thus now, we don't just have a database of transition states, but of transition states and their associated minima (note that the database of minima obtained in the readmin directory have not yet been added. This will come later.		Then, move back into the all_opt_TSs directory, and execute addpath.sh. Now, all of the TSs and their associated minima shall be added to the database in the startfrompath directory. Thus now, we don't just have a database of transition states, but of transition states and their associated minima (note that the database of minima obtained in the readmin directory have not yet been added. This will come later).

	=== generate_connectfile ===		=== generate_connectfile ===

Adk44: /* Execution */

2020-06-04T09:24:05Z

Execution

← Older revision		Revision as of 09:24, 4 June 2020
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	==== Execution ====		==== Execution ====

	First, descents.sh is executed. This extracts all of the transition states in the database, moves them to a subdirectory with an index corresponding to where it appears in ts.data, and then performs the descent calculations to determine the two minima directly connected to this TS. Additionally, this script creates another subdirectory called startfrompath, in which the path.info file generated from the first TS and its two associated minima is used to create a new database (i.e. two minima should appear in min.data and one in ts.data).		First, descents.sh is executed. This extracts all of the transition states in the database, moves them to a subdirectory with an index corresponding to where it appears in ts.data, and then performs the descent calculations to determine the two minima directly connected to this TS. Additionally, this script creates another subdirectory called startfrompath, in which the path.info file generated from the first TS and its two associated minima is used to create a new database (i.e. two minima should appear in min.data and one TS in ts.data).

	Once all of the calculations are complete, move into the startfrompath directory and change pathdata to:		Once all of the calculations are complete, move into the startfrompath directory and change pathdata to:

Adk44: /* Files Required */

2020-06-04T09:23:14Z

Files Required

← Older revision		Revision as of 09:23, 4 June 2020
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	</pre>		</pre>

	In addition, the following scripts, which can be accessed in /svn/SCRIPTS/CHECKSPMUTATE/all_opt_TSs, are required:		In addition, the following scripts, which can be accessed in '''/svn/SCRIPTS/CHECKSPMUTATE/all_opt_TSs''', are required:

	* addpath.sh, descents.sh		* addpath.sh, descents.sh

Adk44: /* Note on readts */

2020-06-04T09:21:41Z

Note on readts

← Older revision		Revision as of 09:21, 4 June 2020
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	Rather than checkminfile and pathsample_checkmin.out, we need the files checktsfile and pathsample_checkts.out		Rather than checkminfile and pathsample_checkmin.out, we need the files checktsfile and pathsample_checkts.out

	Rather than organise_mindatainfo_min.sh, use the script organise_mindatainfo_ts.sh (to be found in /svn/SCRIPTS/CHECKSPMUTATE/readts).		Rather than organise_mindatainfo_min.sh, use the script organise_mindatainfo_ts.sh (to be found in '''/svn/SCRIPTS/CHECKSPMUTATE/readts''').

	In pathdata, stick with the READMIN (as there isn't actually a READTS keyword available). This is not a big problem - all that we need to do after running the READMIN calculation is to rename points.min to points.ts and min.data to ts.data.		In pathdata, stick with the READMIN (as there isn't actually a READTS keyword available). This is not a big problem - all that we need to do after running the READMIN calculation is to rename points.min to points.ts and min.data to ts.data.

Adk44: /* Files Required */

2020-06-04T09:21:03Z

Files Required

← Older revision		Revision as of 09:21, 4 June 2020
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	</pre>		</pre>

	And the bash script, organise_mindatinfo_min.sh, to be found in /svn/SCRIPTS/CHECKSPMUTATE/readmin		And the bash script, organise_mindatinfo_min.sh, to be found in '''/svn/SCRIPTS/CHECKSPMUTATE/readmin'''.

	==== Execution ====		==== Execution ====