NEEMP:Getting started - Revision history

Krab1k at 13:56, 5 July 2016

2016-07-05T13:56:08Z

← Older revision		Revision as of 13:56, 5 July 2016
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	'''NEEMP''''s binary ~~file is~~ available online ([http://www.fi.muni.cz/~xracek/neemp/ http://ncbr.muni.cz/NEEMP]) together with the ''examples.~~tar.bz2~~'' file containing all the inputs needed to run the [[NEEMP:Examples \| examples]] and get acquainted with the tool. These files include:		'''NEEMP''''s binary and source codes are available online ([http://www.fi.muni.cz/~xracek/neemp/ http://ncbr.muni.cz/NEEMP]) together with the ''examples.zip'' file containing all the inputs needed to run the [[NEEMP:Examples \| examples]] and get acquainted with the tool. These files include:

	* '''set01.sdf''' -- 500 molecules extracted from DTP NCI with a low atomic element complexity (H, C, N, O, S) and encoded in MOL V2000		* '''set01.sdf''' -- 500 molecules extracted from DTP NCI with a low atomic element complexity (H, C, N, O, S) and encoded in MOL V2000

Krab1k at 20:58, 28 June 2016

2016-06-28T20:58:36Z

← Older revision		Revision as of 20:58, 28 June 2016
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	* '''set01.sdf''' -- 500 molecules extracted from DTP NCI with a low atomic element complexity (H, C, N, O, S) and encoded in MOL V2000		* '''set01.sdf''' -- 500 molecules extracted from DTP NCI with a low atomic element complexity (H, C, N, O, S) and encoded in MOL V2000

	* '''set02.sdf''' -- 4443 molecules extracted from LigandExpo (ideal coordinates) with high atomic element complexity (H, C, N, O, S, F, Cl, P, Br) and encoded in MOL ~~V2000~~		* '''set02.sdf''' -- 4443 molecules extracted from LigandExpo (ideal coordinates) with high atomic element complexity (H, C, N, O, S, F, Cl, P, Br) and encoded in MOL V3000

	* '''set01.chg''' -- Reference QM charges for all molecules in set01. Theory level, basis set and population analysis: HF/6-31GH/Mulliken		* '''set01.chg''' -- Reference QM charges for all molecules in set01. Theory level, basis set and population analysis: HF/6-31GH/Mulliken

Francesco at 13:30, 28 June 2016

2016-06-28T13:30:47Z

← Older revision		Revision as of 13:30, 28 June 2016
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	* '''Element.par''' -- parameters calculated using set01 for atomic types determined by element only		* '''Element.par''' -- parameters calculated using set01 for atomic types determined by element only

	* '''ElemBond.par''' -- parameters calculated using set01 for atomic types determined by element + ~~maximum~~ bond order		* '''ElemBond.par''' -- parameters calculated using set01 for atomic types determined by element + maximal bond order

	'''NEEMP''' can then be run simply by calling the command <code>./neemp</code>. For instance, to get information about basic usage, use:		'''NEEMP''' can then be run simply by calling the command <code>./neemp</code>. For instance, to get information about basic usage, use:

Francesco at 13:30, 28 June 2016

2016-06-28T13:30:00Z

← Older revision		Revision as of 13:30, 28 June 2016
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	* '''set02.chg''' -- Reference QM charges for all molecules in set02. Theory level, basis set and population analysis: B3LYP/6-311G/NPA		* '''set02.chg''' -- Reference QM charges for all molecules in set02. Theory level, basis set and population analysis: B3LYP/6-311G/NPA

	* '''Element.par''' -- parameters calculated using ~~set03~~ for ~~atom~~ types determined by element only		* '''Element.par''' -- parameters calculated using set01 for atomic types determined by element only

	* '''ElemBond.par''' -- parameters calculated using ~~set03~~ for ~~atom~~ types determined by element + maximum bond order		* '''ElemBond.par''' -- parameters calculated using set01 for atomic types determined by element + maximum bond order

	'''NEEMP''' can then be run simply by calling the command <code>./neemp</code>. For instance, to get information about basic usage, use:		'''NEEMP''' can then be run simply by calling the command <code>./neemp</code>. For instance, to get information about basic usage, use:

Francesco at 13:03, 28 June 2016

2016-06-28T13:03:06Z

← Older revision		Revision as of 13:03, 28 June 2016
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	'''NEEMP''''s binary file is available online ([http://www.fi.muni.cz/~xracek/neemp/ http://ncbr.muni.cz/NEEMP]) together with the ''examples.tar.bz2'' file containing all the inputs needed to run the [[NEEMP:Examples \| examples]] and get acquainted with the tool. These files include:		'''NEEMP''''s binary file is available online ([http://www.fi.muni.cz/~xracek/neemp/ http://ncbr.muni.cz/NEEMP]) together with the ''examples.tar.bz2'' file containing all the inputs needed to run the [[NEEMP:Examples \| examples]] and get acquainted with the tool. These files include:

	* '''set01.sdf''' -- 500 molecules extracted from DTP NCI ~~database~~ with a low atomic element complexity (H, C, N, O, S) and encoded in MOL V2000		* '''set01.sdf''' -- 500 molecules extracted from DTP NCI with a low atomic element complexity (H, C, N, O, S) and encoded in MOL V2000

	* '''set02.sdf''' --		* '''set02.sdf''' -- 4443 molecules extracted from LigandExpo (ideal coordinates) with high atomic element complexity (H, C, N, O, S, F, Cl, P, Br) and encoded in MOL V2000

	* '''~~charges~~.chg''' -- Reference QM charges for all molecules in set01~~, set02 and set03~~. Theory level, basis set and population analysis: HF/6-31GH/Mulliken		* '''set01.chg''' -- Reference QM charges for all molecules in set01. Theory level, basis set and population analysis: HF/6-31GH/Mulliken

			* '''set02.chg''' -- Reference QM charges for all molecules in set02. Theory level, basis set and population analysis: B3LYP/6-311G/NPA

	* '''Element.par''' -- parameters calculated using set03 for atom types determined by element only		* '''Element.par''' -- parameters calculated using set03 for atom types determined by element only

Francesco at 13:23, 27 June 2016

2016-06-27T13:23:37Z

← Older revision		Revision as of 13:23, 27 June 2016
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	'''NEEMP''''s binary file is available online ([http://www.fi.muni.cz/~xracek/neemp/ http://ncbr.muni.cz/NEEMP]) together with the ''examples.tar.bz2'' file containing all the inputs needed to run the [[NEEMP:Examples \| examples]] and get acquainted with the tool. These files include:		'''NEEMP''''s binary file is available online ([http://www.fi.muni.cz/~xracek/neemp/ http://ncbr.muni.cz/NEEMP]) together with the ''examples.tar.bz2'' file containing all the inputs needed to run the [[NEEMP:Examples \| examples]] and get acquainted with the tool. These files include:

	* '''set01.sdf''' -- 500 molecules (H, C, N, O, S)~~, records~~ in MOL V2000		* '''set01.sdf''' -- 500 molecules extracted from DTP NCI database with a low atomic element complexity (H, C, N, O, S) and encoded in MOL V2000

	* '''set02.sdf''' -- ~~500 molecules (H, C, N, O, S), records in MOL V2000~~		* '''set02.sdf''' --

	* '''set03.sdf''' -- 500 molecules (H, C, N, O, S), records in MOL V3000

	* '''charges.chg''' -- Reference QM charges for all molecules in set01, set02 and set03. Theory level, basis set and population analysis: HF/6-31GH/Mulliken		* '''charges.chg''' -- Reference QM charges for all molecules in set01, set02 and set03. Theory level, basis set and population analysis: HF/6-31GH/Mulliken

Francesco at 11:00, 21 June 2016

2016-06-21T11:00:02Z

← Older revision		Revision as of 11:00, 21 June 2016
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	'''NEEMP''''s binary file is available online ([http://www.fi.muni.cz/~xracek/neemp/ http://ncbr.muni.cz/NEEMP]) together with the ''examples.tar.bz2'' file containing all the ~~input files~~ needed to run the [[NEEMP:Examples \| examples]] and get acquainted with the tool. These files include:		'''NEEMP''''s binary file is available online ([http://www.fi.muni.cz/~xracek/neemp/ http://ncbr.muni.cz/NEEMP]) together with the ''examples.tar.bz2'' file containing all the inputs needed to run the [[NEEMP:Examples \| examples]] and get acquainted with the tool. These files include:

	* '''set01.sdf''' -- 500 molecules (H, C, N, O, S), records in MOL V2000		* '''set01.sdf''' -- 500 molecules (H, C, N, O, S), records in MOL V2000

Francesco at 10:57, 21 June 2016

2016-06-21T10:57:14Z

@@ Line 1: / Line 1: @@
-<span style="color:#FF0000"> waiting for instructions on how to retrieve the executable file </span>
+'''NEEMP''''s binary file is available online ([http://www.fi.muni.cz/~xracek/neemp/ http://ncbr.muni.cz/NEEMP]) together with the ''examples.tar.bz2'' file containing all the input files needed to run the [[NEEMP:Examples | examples]] and get acquainted with the tool. These files include:
 '''NEEMP''' can then be run simply by calling the command <code>./neemp</code>. For instance, to get information about basic usage, use:
@@ Line 6: / Line 18: @@
 Click on the link to see the complete [[NEEMP:Options | options list]].

Francesco: Created page with " waiting for instructions on how to retrieve the executable file '''NEEMP''' can then be run simply by calling the command ./neemp 2016-06-20T11:13:33Z Created page with "<span style="color:#FF0000"> waiting for instructions on how to retrieve the executable file </span> '''NEEMP''' can then be run simply by calling the command <code>./neemp</..." New page <span style="color:#FF0000"> waiting for instructions on how to retrieve the executable file </span> '''NEEMP''' can then be run simply by calling the command <code>./neemp</code>. For instance, to get information about basic usage, use: <code>~/neemp/$ ./neemp --help</code> Click on the link to see the complete [[NEEMP:Options | options list]]. Before proceeding in the description of '''NEEMP''''s modes, here we introduce a tree representation of '''NEEMP''''s main directory to assist the user in the examples understanding. '''NB:''' the ''examples'' directory contains all the files employed in the [[NEEMP:examples]] section. ''src'' directory has not been expanded to improve the readability. <nowiki> /neemp ├── examples │ ├── charges.chg │ ├── ElemBond.par │ ├── Element.par │ ├── NOTES │ ├── set01.sdf │ ├── set02.sdf │ └── set03.sdf ├── LICENCE ├── Makefile ├── misc │ ├── template │ ├── valgrind-suppresions │ └── web-update.sh ├── README └── src </nowiki>