ChargeCalculator:Index - Revision history

Crina: /* Analyze tab */

2015-05-29T18:01:54Z

Analyze tab

← Older revision		Revision as of 18:01, 29 May 2015
Line 151:		Line 151:
	\|''Description:'' Controls which statistics will be displayed in the graph.		\|''Description:'' Controls which statistics will be displayed in the graph.
	\|-		\|-
	\|''Possible values:'' MinimumCharge = Min, MaximumCharge = Max, Average Charge = Avg, Average Absolute Charge = \|Avg\|, Median Charge, Median Absolute Charge, Standard Charge Deviation = σ, Standard Abs. Charge Deviation = \|σ\|.		\|''Possible values:'' MinimumCharge = Min, MaximumCharge = Max, Average Charge = Avg, Average Absolute Charge = <nowiki>\|</nowiki> Avg <nowiki>\|</nowiki>, Median Charge, Median Absolute Charge, Standard Charge Deviation = σ, Standard Abs. Charge Deviation = <nowiki>\|</nowiki>σ<nowiki>\|</nowiki>.

	\|}		\|}

Crina: /* EEM parameter set */

2014-12-24T19:24:59Z

EEM parameter set

← Older revision		Revision as of 19:24, 24 December 2014
Line 54:		Line 54:
	\|'''Priority'''		\|'''Priority'''
	\|-		\|-
	\|''Description:'' Very basic grading system. Serves mainly to identify a suitable default setup. Currently curated manually.		\|''Description:'' Very basic grading system. Serves mainly to identify a suitable default setup. Currently curated manually.
			\|-
			\|''Possible values:'' For EEM parameter sets focused on ''biomolecules'', priorities are assigned based on their performance in the external validation stage of their development. For sets focused on organic molecules, priorities are assigned based on year of publication, level of theory of the QM reference data, and the results of a small in-house QM benchmark on paracetamol. Lower values are preferred.
	\|}		\|}

Crina: /* 3D Model tab */

2014-12-19T17:15:26Z

3D Model tab

← Older revision		Revision as of 17:15, 19 December 2014
Line 203:		Line 203:
	\|'''Atom Grouping'''		\|'''Atom Grouping'''
	\|-		\|-
	\|''Description:'' ~~level~~ of resolution at which the ~~atomic charges~~ will be ~~listed~~.		\|''Description:'' Level of resolution at which the 3D model will be built and colored.
	\|-		\|-
	\|''Possible values:'' Atoms, Residues (~~sum~~ of ~~atomic~~ charges ~~for each residue~~).		\|''Possible values:'' Atoms (build 3D model based on atomic positions, color based on atomic charges), Residues (build 3D model based on positions of residue centroids, color based on residue charges).
	\|}		\|}
	*'''Atom Grouping'''
	~~''Description:'' Level of resolution at which the 3D model will be built and colored.~~

	~~''Possible values:'' Atoms (build 3D model based on atomic positions, color based on atomic charges), Residues (build 3D model based on positions of residue centroids, color based on residue charges).~~

	{\| class="wikitable"		{\| class="wikitable"
	\|-		\|-
	\|'''~~Atom Grouping~~'''		\|'''Display Charges'''
	\|-		\|-
	\|''Description:'' ~~level~~ of ~~resolution at which the atomic~~ charges will be ~~listed~~.		\|''Description:'' which set of charges will be used for coloring the 3D model.
	\|-		\|-
	\|''Possible values:'' ~~Atoms, Residues (sum~~ of ~~atomic~~ charges for ~~each residue)~~.		\|''Possible values:'' any set of charges available for that molecule.
	\|}		\|}
	*'''Display Charges'''
	~~''Description:'' which set of charges will be used for coloring the 3D model~~

	~~''Possible values:'' any set of charges available for that molecule~~

	{\| class="wikitable"		{\| class="wikitable"
	\|-		\|-
	\|'''~~Atom Grouping~~'''		\|'''Show Differences'''
	\|-		\|-
	\|''Description:'' ~~level of resolution~~ at ~~which~~ the ~~atomic charges will be listed~~.		\|''Description:'' allow to color the 3D model based on differences in charges from individual charge sets. Each atom or residue is colored according to the difference which results as the value in the set chosen at ''Display Charges'', minus the value in the set chosen at ''Show Differences''.
	\|-		\|-
	\|''Possible values:'' ~~Atoms, Residues (sum~~ of ~~atomic~~ charges for ~~each residue)~~.		\|''Possible values:'' any set of charges available for that molecule, and not chosen at ''Display Charges''.
	\|}		\|}
	*'''Show Differences'''
	''Description:'' allow to color the 3D model based on differences in charges from individual charge sets. Each atom or residue is colored according to the difference which results as the value in the set chosen at ''Display Charges'', minus the value in the set chosen at ''Show Differences''.

	~~''Possible values:'' any set of charges available for that molecule, and not chosen at ''Display Charges''.~~		{\| class="wikitable"
			\|-
	*'''Display Mode'''		\|'''Display Mode'''
	''Description:'' Type of graphical representation used for building the 3D model.		\|-
			\|''Description:'' Type of graphical representation used for building the 3D model.
	''Possible values:'' Depend on Atom Grouping.		\|-
			\|''Possible values:'' Depend on Atom Grouping.

	For ''Atom Grouping = Atoms'':		For ''Atom Grouping = Atoms'':
	**Balls and Sticks - render atoms as spheres and bonds as tubes.		*Balls and Sticks - render atoms as spheres and bonds as tubes.
	**Surface - surface built as a set of points given by the potential of each atom at that point in space; potential computed as a function of the VDW radius and ''Probe Radius'' parameter.		*Surface - surface built as a set of points given by the potential of each atom at that point in space; potential computed as a function of the VDW radius and ''Probe Radius'' parameter.
	**Cartoons - render amino acids and nucleotides as cartoons; secondary structure is approximated if not explicit in input file.		*Cartoons - render amino acids and nucleotides as cartoons; secondary structure is approximated if not explicit in input file.
	**C-α trace - smooth trace of the molecule backbone based on the position of C-α atoms.		*C-α trace - smooth trace of the molecule backbone based on the position of C-α atoms.
	**VDW spheres - render atoms as spheres with VDW radius.		*VDW spheres - render atoms as spheres with VDW radius.
	For ''Atom Grouping = Residues'':		For ''Atom Grouping = Residues'':
	**Balls and Sticks - render residue centroids as spheres connected in the amino acid sequence by tubes		*Balls and Sticks - render residue centroids as spheres connected in the amino acid sequence by tubes
	**Surface - surface built as a set of points given by the potential of each residue at that point in space; potential computed as a function of the ''Probe Radius'' parameter.		*Surface - surface built as a set of points given by the potential of each residue at that point in space; potential computed as a function of the ''Probe Radius'' parameter.
			\|}

	{\| class="wikitable"		{\| class="wikitable"

Crina: /* 3D Model tab */

2014-12-19T17:11:58Z

3D Model tab

← Older revision		Revision as of 17:11, 19 December 2014
Line 197:		Line 197:

	==3D Model tab==		==3D Model tab==
			'''ACC''' allows a few basic charge visualization options to aid in interpreting the results of the atomic charge calculation.

			{\| class="wikitable"
			\|-
			\|'''Atom Grouping'''
			\|-
			\|''Description:'' level of resolution at which the atomic charges will be listed.
			\|-
			\|''Possible values:'' Atoms, Residues (sum of atomic charges for each residue).
			\|}
	*'''Atom Grouping'''		*'''Atom Grouping'''
	''Description:'' Level of resolution at which the 3D model will be built and colored.		''Description:'' Level of resolution at which the 3D model will be built and colored.
Line 202:		Line 212:
	''Possible values:'' Atoms (build 3D model based on atomic positions, color based on atomic charges), Residues (build 3D model based on positions of residue centroids, color based on residue charges).		''Possible values:'' Atoms (build 3D model based on atomic positions, color based on atomic charges), Residues (build 3D model based on positions of residue centroids, color based on residue charges).

			{\| class="wikitable"
			\|-
			\|'''Atom Grouping'''
			\|-
			\|''Description:'' level of resolution at which the atomic charges will be listed.
			\|-
			\|''Possible values:'' Atoms, Residues (sum of atomic charges for each residue).
			\|}
	*'''Display Charges'''		*'''Display Charges'''
	''Description:'' which set of charges will be used for coloring the 3D model		''Description:'' which set of charges will be used for coloring the 3D model
Line 207:		Line 225:
	''Possible values:'' any set of charges available for that molecule		''Possible values:'' any set of charges available for that molecule

			{\| class="wikitable"
			\|-
			\|'''Atom Grouping'''
			\|-
			\|''Description:'' level of resolution at which the atomic charges will be listed.
			\|-
			\|''Possible values:'' Atoms, Residues (sum of atomic charges for each residue).
			\|}
	*'''Show Differences'''		*'''Show Differences'''
	''Description:'' allow to color the 3D model based on differences in charges from individual charge sets. Each atom or residue is colored according to the difference which results as the value in the set chosen at ''Display Charges'', minus the value in the set chosen at ''Show Differences''.		''Description:'' allow to color the 3D model based on differences in charges from individual charge sets. Each atom or residue is colored according to the difference which results as the value in the set chosen at ''Display Charges'', minus the value in the set chosen at ''Show Differences''.
Line 227:		Line 253:
	**Surface - surface built as a set of points given by the potential of each residue at that point in space; potential computed as a function of the ''Probe Radius'' parameter.		**Surface - surface built as a set of points given by the potential of each residue at that point in space; potential computed as a function of the ''Probe Radius'' parameter.

	*'''Additional display options for each ''Display Mode''		{\| class="wikitable"
	''Description:'' Certain ''Display Modes'' allow further tuning of what parts of the model are displayed, and how.		\|-
			\|'''Additional display options for each ''Display Mode'''
	''Possible values:'' Depend on ''Display Mode''.		\|-
			\|''Description:'' Certain ''Display Modes'' allow further tuning of what parts of the model are displayed, and how.
			\|-
			\|''Possible values:'' Depend on ''Display Mode''.
	For ''Display Mode = Balls and sticks'':		For ''Display Mode = Balls and sticks'':
	**Charge Scaling - Scales the size of the balls (atoms or residue centroids) according to the absolute value of the corresponding (atomic or residue) charge. Possible values: Yes (default), No.		*Charge Scaling - Scales the size of the balls (atoms or residue centroids) according to the absolute value of the corresponding (atomic or residue) charge. Possible values: Yes (default), No.
	For ''Display Mode = Surface'':		For ''Display Mode = Surface'':
	**Probe Radius - determines the shape of the surface. Lower values lead to a more VDW-like surface.		*Probe Radius - determines the shape of the surface. Lower values lead to a more VDW-like surface.
	For ''Display Mode = Cartoons'' or ''C-α trace'':		For ''Display Mode = Cartoons'' or ''C-α trace'':
	**Show HET atoms - render atoms annotated as HETATM (typically ligand or cofactor atoms) as ''Balls and Sticks''. Possible values: Yes (default), No.		*Show HET atoms - render atoms annotated as HETATM (typically ligand or cofactor atoms) as ''Balls and Sticks''. Possible values: Yes (default), No.
	**Show Waters - render atoms annotated as water (residue names HOH, H2O, WAT) as ''Balls and Sticks''. Possible values: Yes, No (default).		*Show Waters - render atoms annotated as water (residue names HOH, H2O, WAT) as ''Balls and Sticks''. Possible values: Yes, No (default).
			\|}
	*'''Display Quality'''
	~~''Description:'' Number of tetrahedrons used to display 3D objects. Finer detail is achieved by using a higher number of tetrahedrons.~~

	~~''Possible values:'' Very Low, Low, Medium (default), High, Very High~~

	*'''~~Min. Value, Mid. Value, Max. Value~~'''		{\| class="wikitable"
	''Description:'' ~~Enable in order~~ to ~~adjust lowest/highest limit and middle point of the charge scale~~. ~~The default~~ is ~~given~~ by ~~the~~ values ~~in each particular set of charges~~ (~~or of differences in charges~~).		\|-
			\|'''Display Quality'''
			\|-
			\|''Description:'' Number of tetrahedrons used to display 3D objects. Finer detail is achieved by using a higher number of tetrahedrons.
			\|-
			\|''Possible values:'' Very Low, Low, Medium (default), High, Very High
			\|}

	*'''Value ~~Gap~~'''		{\| class="wikitable"
	''Description:'' ~~Further adjustment~~ to the ~~coloring scheme can be achieved~~ by ~~using fewer discrete~~ values of ~~the color scheme. Charges which are similar~~ (~~absolute difference smaller than ''Value Gap''~~) ~~are displayed in the same color. This allows to visually emphasize the difference in charge distribution in different areas of the molecule. Emphasis increases with ''Value Gap''~~.		\|-
			\|'''Min. Value, Mid. Value, Max. Value'''
			\|-
			\|''Description:'' Enable in order to adjust lowest/highest limit and middle point of the charge scale. The default is given by the values in each particular set of charges (or of differences in charges).
			\|}

	''Possible values:'' 0.05-1.		{\| class="wikitable"
			\|-
			\|'''Value Gap'''
			\|-
			\|''Description:'' Further adjustment to the coloring scheme can be achieved by using fewer discrete values of the color scheme. Charges which are similar (absolute difference smaller than ''Value Gap'') are displayed in the same color. This allows to visually emphasize the difference in charge distribution in different areas of the molecule. Emphasis increases with ''Value Gap''.
			\|-
			\|''Possible values:'' 0.05-1.
			\|}

Crina: /* Compare tab */

2014-12-19T17:08:02Z

Compare tab

← Older revision		Revision as of 17:08, 19 December 2014
Line 163:		Line 163:

	==Compare tab==		==Compare tab==
	*'''~~Atom Grouping~~'''		'''ACC''' allows to compare sets of charges at more levels of resolution, in graphical and tabular form. These sets of charges may have resulted from different jobs, or were read from the input file.
	~~''Description:'' Level~~ of resolution ~~at which~~ the ~~charges will be compared~~.

	''Possible values:'' Atoms, Residues.		{\| class="wikitable"
			\|-
			\|'''Atom Grouping'''
			\|-
			\|''Description:'' Level of resolution at which the charges will be compared.
			\|-
			\|''Possible values:'' Atoms, Residues.
			\|}

	*'''X Axis, Y Axis'''		{\| class="wikitable"
	''Description:'' Which two sets of charges will be compared.		\|-
			\|'''X Axis, Y Axis'''
			\|-
			\|''Description:'' Which two sets of charges will be compared.
			\|-
			\|''Possible values:'' any sets of charges available for that molecule. ''X Axis'' must be different from ''Y Axis''.
			\|}

	~~''Possible values:'' any sets of charges available for that molecule. ''X Axis'' must be different from ''Y Axis''.~~		{\| class="wikitable"
			\|-
	*'''Raw Data'''		\|'''Raw Data'''
	''Description:'' Display descriptors for each pairwise comparison between the set of charges on the ''X Axis'' and all other sets of charges available for that molecule (resulted from '''ACC''' jobs, or read from the input file).		\|-
			\|''Description:'' Display descriptors for each pairwise comparison between the set of charges on the ''X Axis'' and all other sets of charges available for that molecule (resulted from '''ACC''' jobs, or read from the input file).
	''Possible values:'' The values of the following descriptors are displayed for each pairwise comparison: R² = Pearson (squared Pearson's correlation coefficient), ρ = Spearman (Spearman's rank correlation coefficient), δ² = RMSD (root mean square deviation), Diff. (sum of absolute differences).		\|-
			\|''Possible values:'' The values of the following descriptors are displayed for each pairwise comparison:
			*''R², Pearson'' - squared Pearson's correlation coefficient
			*''ρ, Spearman'' - Spearman's rank correlation coefficient
			*''δ², RMSD'' - root mean square deviation
			*''Diff.'' - sum of absolute differences.
			\|}

	==3D Model tab==		==3D Model tab==

Crina: /* Analyze tab */

2014-12-19T17:04:43Z

Analyze tab

← Older revision		Revision as of 17:04, 19 December 2014
Line 133:		Line 133:
	\|'''Group Property'''		\|'''Group Property'''
	\|-		\|-
	\|''Description:'' Type of property based on which the statistics will be calculated. ''ResidueName'' gives statistics for all atoms/residues with a certain residue name appropriately annotated in the input file. ''ChemicalElement'' gives statistics for all atoms of a certain chemical element. ResidueChargeType gives statistics for all atoms/residues with a residue name recognized by '''ACC''' to be of a certain type (polar/nonpolar, positively/negatively charged). ''AtomicComposition'' gives statistics for all residues with a certain atomic composition (number of atoms of different chemical elements).		\|''Description:'' Type of property based on which the statistics will be calculated.
			*''ResidueName'' gives statistics for all atoms/residues with a certain residue name appropriately annotated in the input file.
			*''ChemicalElement'' gives statistics for all atoms of a certain chemical element.
			*''ResidueChargeType'' gives statistics for all atoms/residues with a residue name recognized by '''ACC''' to be of a certain type (polar/nonpolar, positively/negatively charged).
			*''AtomicComposition'' gives statistics for all residues with a certain atomic composition (number of atoms of different chemical elements).
	\|-		\|-
	\|''Possible values:'' Depend on ''Atom Grouping''. For ''Atom Grouping = Atoms'': ResidueName, ChemicalElement, ResidueChargeType, For ''Atom Grouping = Residues'': ResidueName, AtomicComposition, ResidueChargeType.		\|''Possible values:'' Depend on ''Atom Grouping''. For ''Atom Grouping = Atoms'': ResidueName, ChemicalElement, ResidueChargeType, For ''Atom Grouping = Residues'': ResidueName, AtomicComposition, ResidueChargeType.

Crina: /* Analyze tab */

2014-12-19T17:03:29Z

Analyze tab

← Older revision		Revision as of 17:03, 19 December 2014
Line 120:		Line 120:
	'''ACC''' provides several statistical descriptors for the results at more levels of resolution, in graphical and tabular form.		'''ACC''' provides several statistical descriptors for the results at more levels of resolution, in graphical and tabular form.

	*'''Atom Grouping'''		{\| class="wikitable"
	''Description:'' Level of resolution at which the statistics will be calculated.		\|-
			\|'''Atom Grouping'''
			\|-
			\|''Description:'' Level of resolution at which the statistics will be calculated.
			\|-
			\|''Possible values:'' Atoms, Residues.
			\|}

	''Possible values:'' Atoms, Residues.		{\| class="wikitable"
			\|-
			\|'''Group Property'''
			\|-
			\|''Description:'' Type of property based on which the statistics will be calculated. ''ResidueName'' gives statistics for all atoms/residues with a certain residue name appropriately annotated in the input file. ''ChemicalElement'' gives statistics for all atoms of a certain chemical element. ResidueChargeType gives statistics for all atoms/residues with a residue name recognized by '''ACC''' to be of a certain type (polar/nonpolar, positively/negatively charged). ''AtomicComposition'' gives statistics for all residues with a certain atomic composition (number of atoms of different chemical elements).
			\|-
			\|''Possible values:'' Depend on ''Atom Grouping''. For ''Atom Grouping = Atoms'': ResidueName, ChemicalElement, ResidueChargeType, For ''Atom Grouping = Residues'': ResidueName, AtomicComposition, ResidueChargeType.

	*'''Group Property'''		\|}
	''Description:'' Type of property based on which the statistics will be calculated. ''ResidueName'' gives statistics for all atoms/residues with a certain residue name appropriately annotated in the input file. ''ChemicalElement'' gives statistics for all atoms of a certain chemical element. ResidueChargeType gives statistics for all atoms/residues with a residue name recognized by '''ACC''' to be of a certain type (polar/nonpolar, positively/negatively charged). ''AtomicComposition'' gives statistics for all residues with a certain atomic composition (number of atoms of different chemical elements).

	''~~Possible values:~~'' ~~Depend on~~ ''~~Atom Grouping~~''. ~~For~~ ''~~Atom Grouping = Atoms~~''~~: ResidueName~~, ~~ChemicalElement~~, ~~ResidueChargeType~~, ~~For ''Atom Grouping~~ = ~~Residues'': ResidueName~~, ~~AtomicComposition~~, ~~ResidueChargeType~~.		{\| class="wikitable"
			\|-
			\|'''Plot Value, Property Value'''
			\|-
			\|''Description:'' Controls which statistics will be displayed in the graph.
			\|-
			\|''Possible values:'' MinimumCharge = Min, MaximumCharge = Max, Average Charge = Avg, Average Absolute Charge = \|Avg\|, Median Charge, Median Absolute Charge, Standard Charge Deviation = σ, Standard Abs. Charge Deviation = \|σ\|.

	*'''Plot Value, Property Value'''		\|}
	~~''Description:'' Controls which statistics will be displayed in the graph.~~

	~~''Possible values:'' MinimumCharge = Min, MaximumCharge = Max, Average Charge = Avg, Average Absolute Charge = \|Avg~~\|~~, Median Charge, Median Absolute Charge, Standard Charge Deviation = σ, Standard Abs. Charge Deviation~~ = \|~~σ~~\|		{\| class="wikitable"
			\|-
	*'''Raw Data'''		\|'''Raw Data'''
	''Description:'' Display statistics for a certain set of charges (resulted from a single job, or read from the input file).		\|-
			\|''Description:'' Display statistics for a certain set of charges (resulted from a single job, or read from the input file).
	''Possible values:'' any set of charges available for that molecule		\|-
			\|''Possible values:'' any set of charges available for that molecule.
			\|}

	==Compare tab==		==Compare tab==

Crina: /* Analyze tab */

2014-12-19T17:01:17Z

Analyze tab

← Older revision		Revision as of 17:01, 19 December 2014
Line 118:		Line 118:

	==Analyze tab==		==Analyze tab==
			'''ACC''' provides several statistical descriptors for the results at more levels of resolution, in graphical and tabular form.

	*'''Atom Grouping'''		*'''Atom Grouping'''
	''Description:'' Level of resolution at which the statistics will be calculated.		''Description:'' Level of resolution at which the statistics will be calculated.

Crina: /* Raw Data tab */

2014-12-19T17:00:21Z

Raw Data tab

← Older revision		Revision as of 17:00, 19 December 2014
Line 106:		Line 106:

	==Raw Data tab==		==Raw Data tab==
			The ''raw data'' is available in tabular form, and refers to the actual values of atomic charges resulted from the EEM calculation, or read in from the input file. Residue charges are also available if residue annotations are available in the input file. No additional statistics are included here.

	{\| class="wikitable"		{\| class="wikitable"
	\|-		\|-

Crina: /* Raw Data tab */

2014-12-19T16:58:37Z

Raw Data tab

← Older revision		Revision as of 16:58, 19 December 2014
Line 106:		Line 106:

	==Raw Data tab==		==Raw Data tab==
	*'''Atom Grouping'''		{\| class="wikitable"
	''Description:'' ~~Controls the~~ level of resolution at which the atomic charges will be listed.		\|-
			\|'''Atom Grouping'''
	''Possible values:'' Atoms, Residues (sum of atomic charges for each residue).		\|-
			\|''Description:'' level of resolution at which the atomic charges will be listed.
			\|-
			\|''Possible values:'' Atoms, Residues (sum of atomic charges for each residue).
			\|}

	==Analyze tab==		==Analyze tab==