NEEMP:files - Revision history

Francesco at 16:58, 29 June 2016

2016-06-29T16:58:29Z

← Older revision		Revision as of 16:58, 29 June 2016
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	=SDF file=		=SDF file=
	[[File:sdf_file.png \| thumb \| 400px \| right\| '''''Figure 9:''''' V2000 MOL record extracted from '''SDF''' file ''examples/set01.sdf''. Note the atomic coordinates and bond connections blocks and the ''$$$$'' line marking the end of the record.]]		[[File:sdf_file.png \| thumb \| 400px \| right\| '''''Figure 8:''''' V2000 MOL record extracted from '''SDF''' file ''examples/set01.sdf''. Note the atomic coordinates and bond connections blocks and the ''$$$$'' line marking the end of the record.]]

	'''SDF''' file contains MOL records for each molecule separated by line consisting only of four dollar signs, i.e. $$$$. Each MOL record can be either in '''V2000''' or '''V3000''' version. The latter one is required for molecules with more than 999 atoms or bonds. For further reference on MOL format, see specification: [http://c4.cabrillo.edu/404/ctfile.pdf CTFile formats].		'''SDF''' file contains MOL records for each molecule separated by line consisting only of four dollar signs, i.e. $$$$. Each MOL record can be either in '''V2000''' or '''V3000''' version. The latter one is required for molecules with more than 999 atoms or bonds. For further reference on MOL format, see specification: [http://c4.cabrillo.edu/404/ctfile.pdf CTFile formats].

Francesco: /* SDF file */

2016-06-23T17:01:08Z

SDF file

← Older revision		Revision as of 17:01, 23 June 2016
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	=SDF file=		=SDF file=
	[[File:sdf_file.png \| thumb \| 400px \| right\| '''''Figure 5:''''' V2000 MOL record extracted from '''SDF''' file ''examples/set01.sdf''. Note the atomic coordinates and bond connections blocks and the ''$$$$'' line marking the end of the record.]]		[[File:sdf_file.png \| thumb \| 400px \| right\| '''''Figure 9:''''' V2000 MOL record extracted from '''SDF''' file ''examples/set01.sdf''. Note the atomic coordinates and bond connections blocks and the ''$$$$'' line marking the end of the record.]]

	'''SDF''' file contains MOL records for each molecule separated by line consisting only of four dollar signs, i.e. $$$$. Each MOL record can be either in '''V2000''' or '''V3000''' version. The latter one is required for molecules with more than 999 atoms or bonds. For further reference on MOL format, see specification: [http://c4.cabrillo.edu/404/ctfile.pdf CTFile formats].		'''SDF''' file contains MOL records for each molecule separated by line consisting only of four dollar signs, i.e. $$$$. Each MOL record can be either in '''V2000''' or '''V3000''' version. The latter one is required for molecules with more than 999 atoms or bonds. For further reference on MOL format, see specification: [http://c4.cabrillo.edu/404/ctfile.pdf CTFile formats].

Francesco: /* SDF file */

2016-05-30T12:36:50Z

SDF file

← Older revision		Revision as of 12:36, 30 May 2016
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	=SDF file=		=SDF file=
	[[File:sdf_file.png \| thumb \| 400px \| right\| '''''Figure 4:''''' V2000 MOL record extracted from '''SDF''' file ''examples/set01.sdf''. Note the atomic coordinates and bond connections blocks and the ''$$$$'' line marking the end of the record.]]		[[File:sdf_file.png \| thumb \| 400px \| right\| '''''Figure 5:''''' V2000 MOL record extracted from '''SDF''' file ''examples/set01.sdf''. Note the atomic coordinates and bond connections blocks and the ''$$$$'' line marking the end of the record.]]

	'''SDF''' file contains MOL records for each molecule separated by line consisting only of four dollar signs, i.e. $$$$. Each MOL record can be either in '''V2000''' or '''V3000''' version. The latter one is required for molecules with more than 999 atoms or bonds. For further reference on MOL format, see specification: [http://c4.cabrillo.edu/404/ctfile.pdf CTFile formats].		'''SDF''' file contains MOL records for each molecule separated by line consisting only of four dollar signs, i.e. $$$$. Each MOL record can be either in '''V2000''' or '''V3000''' version. The latter one is required for molecules with more than 999 atoms or bonds. For further reference on MOL format, see specification: [http://c4.cabrillo.edu/404/ctfile.pdf CTFile formats].

Francesco: /* CHG file */

2016-05-29T13:15:41Z

CHG file

← Older revision		Revision as of 13:15, 29 May 2016
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	</pre>		</pre>

	Note that only the third column (the actual charge) is read, the first two are silently ignored. This implies that the order of the atoms in the structure and charge records must be the same ~~in order~~ to get a perfect pairing.		Note that only the third column (the actual charge) is read, the first two are silently ignored. This implies that the order of the atoms in the structure and charge records must be the same to get a perfect pairing.

	Every other record is separated from the previous one by a blank line.		Every other record is separated from the previous one by a blank line.

Francesco: /* CHG file */

2016-05-29T13:13:36Z

CHG file

← Older revision		Revision as of 13:13, 29 May 2016
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	Each record (charges for one molecule) in the '''CHG''' file consists of 3 parts. First line is the name of the molecule (it must be the same as in the '''SDF''' file to pair the charges to the structural information), second line contains number of atoms N and then N lines for each atom with its charges:		Each record (charges for one molecule) in the '''CHG''' file consists of 3 parts. First line is the name of the molecule (it must be the same as in the '''SDF''' file to pair the charges to the structural information), second line contains number of atoms N and then N lines for each atom with its charges:

	<~~nowiki~~>		<pre>
	My dummy molecule name		My dummy molecule name
	5		5
			1 C -0.921539
			2 H -0.507788
			3 H -0.565167
			4 H -0.200822
			5 H 0.110252

	</~~nowiki~~>		</pre>

			Note that only the third column (the actual charge) is read, the first two are silently ignored. This implies that the order of the atoms in the structure and charge records must be the same in order to get a perfect pairing.

			Every other record is separated from the previous one by a blank line.

	=PAR file=		=PAR file=

Francesco: /* CHG file */

2016-05-29T13:02:40Z

CHG file

← Older revision		Revision as of 13:02, 29 May 2016
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	=CHG file=		=CHG file=

			Each record (charges for one molecule) in the '''CHG''' file consists of 3 parts. First line is the name of the molecule (it must be the same as in the '''SDF''' file to pair the charges to the structural information), second line contains number of atoms N and then N lines for each atom with its charges:

			<nowiki>
			My dummy molecule name
			5

			</nowiki>

	=PAR file=		=PAR file=

Francesco: /* PAR file */

2016-05-29T12:23:32Z

PAR file

← Older revision		Revision as of 12:23, 29 May 2016
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	'''PAR''' file is used for storing EEM parameters. It's a simple XML file of the following form. All fields are pretty self-explanatory. The ''AtomType'' parameter corresponds to the <code>--atom-types-by</code> option.		'''PAR''' file is used for storing EEM parameters. It's a simple XML file of the following form. All fields are pretty self-explanatory. The ''AtomType'' parameter corresponds to the <code>--atom-types-by</code> option.

	<~~code~~>		<pre>
	<?xml version="1.0"?>		<?xml version="1.0"?>
	<ParameterSet>		<ParameterSet>
Line 42:		Line 42:
	</Parameters>		</Parameters>
	</ParameterSet>		</ParameterSet>
	</~~code~~>		</pre>

Francesco: /* PAR file */

2016-05-29T12:20:15Z

PAR file

← Older revision		Revision as of 12:20, 29 May 2016
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	'''PAR''' file is used for storing EEM parameters. It's a simple XML file of the following form. All fields are pretty self-explanatory. The ''AtomType'' parameter corresponds to the <code>--atom-types-by</code> option.		'''PAR''' file is used for storing EEM parameters. It's a simple XML file of the following form. All fields are pretty self-explanatory. The ''AtomType'' parameter corresponds to the <code>--atom-types-by</code> option.

			<code>
			<?xml version="1.0"?>
			<ParameterSet>
			<Parameters AtomType="ElemBond" Kappa="0.1976">
			<Element Name=" O">
			<Bond Type="1" A="2.6730" B="0.4091"/>
			<Bond Type="2" A="2.7759" B="0.6434"/>
			</Element>
			<Element Name=" C">
			<Bond Type="2" A="2.4880" B="0.2348"/>
			<Bond Type="1" A="2.4787" B="0.2722"/>
			</Element>
			<Element Name=" H">
			<Bond Type="1" A="2.3827" B="0.5701"/>
			</Element>
			<Element Name=" N">
			<Bond Type="2" A="2.5440" B="0.2370"/>
			<Bond Type="1" A="2.5370" B="0.2526"/>
			</Element>
			<Element Name=" S">
			<Bond Type="2" A="2.4945" B="0.1454"/>
			<Bond Type="1" A="2.4050" B="0.3687"/>
			</Element>
			</Parameters>
			</ParameterSet>
			</code>

Francesco: /* PAR file */

2016-05-29T12:12:27Z

PAR file

← Older revision		Revision as of 12:12, 29 May 2016
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	=PAR file=		=PAR file=

			'''PAR''' file is used for storing EEM parameters. It's a simple XML file of the following form. All fields are pretty self-explanatory. The ''AtomType'' parameter corresponds to the <code>--atom-types-by</code> option.

Francesco: /* SDF file */

2016-05-29T11:18:52Z

SDF file

← Older revision		Revision as of 11:18, 29 May 2016
Line 4:		Line 4:

	=SDF file=		=SDF file=
	[[File:sdf_file.png \| thumb \| 400px \| right\| '''''Figure 4:''''' V2000 MOL record extracted from '''SDF''' file ''examples/set01.sdf''. Note the ~~blocks with~~ atomic coordinates and bond connections and the ''$$$$'' line marking the end of the record.]]		[[File:sdf_file.png \| thumb \| 400px \| right\| '''''Figure 4:''''' V2000 MOL record extracted from '''SDF''' file ''examples/set01.sdf''. Note the atomic coordinates and bond connections blocks and the ''$$$$'' line marking the end of the record.]]

	'''SDF''' file contains MOL records for each molecule separated by line consisting only of four dollar signs, i.e. $$$$. Each MOL record can be either in '''V2000''' or '''V3000''' version. The latter one is required for molecules with more than 999 atoms or bonds. For further reference on MOL format, see specification: [http://c4.cabrillo.edu/404/ctfile.pdf CTFile formats].		'''SDF''' file contains MOL records for each molecule separated by line consisting only of four dollar signs, i.e. $$$$. Each MOL record can be either in '''V2000''' or '''V3000''' version. The latter one is required for molecules with more than 999 atoms or bonds. For further reference on MOL format, see specification: [http://c4.cabrillo.edu/404/ctfile.pdf CTFile formats].