Mole 2.5 Command Line Input Help - Revision history

Dave at 19:01, 26 February 2014

2014-02-26T19:01:30Z

← Older revision		Revision as of 19:01, 26 February 2014
Line 81:		Line 81:
	: ''Filename of the source. Supported formats: OpenDX.''		: ''Filename of the source. Supported formats: OpenDX.''
	* '''Method''' [string], Default value = NearestValue		* '''Method''' [string], Default value = NearestValue
	: ''Method used for charge computation [NearestValue, RadiusSum, RadiusSumDividedByDistance, KNearestSum, KNearestSumDividedByDistance, Lining, WholeStructure].''		: ''Method used for charge computation [NearestValue, RadiusSum, RadiusSumDividedByDistance, RadiusMultiplicativeScale, RadiusAdditiveScale, KNearestSum, KNearestSumDividedByDistance, Lining, WholeStructure].''
	* '''Radius''' [real], Default value = 5		* '''Radius''' [real], Default value = 5
	: ''Radius used for the Radius* methods.''		: ''Radius used for the Radius* methods.''
Line 163:		Line 163:
	: ''Level of detail of mesh surface. The higher the Mesh Density, the lower the level of detail in the visualization.''		: ''Level of detail of mesh surface. The higher the Mesh Density, the lower the level of detail in the visualization.''
	==== <PyMol> attributes ====		==== <PyMol> attributes ====
			* '''ChargePalette''' [string], Default value = RedWhiteBlue
			: ''Determines the palette used for charge coloring [RedWhiteBlue, BlueWhiteRed].''
	* '''PDBId''' [string], Default value = ''none''		* '''PDBId''' [string], Default value = ''none''
	: ''If this value is present, the option for downloading the structure is incorporated in the PyMOL visualization script.''		: ''If this value is present, the option for downloading the structure is incorporated in the PyMOL visualization script.''

Dave at 12:09, 24 February 2014

2014-02-24T12:09:11Z

← Older revision		Revision as of 12:09, 24 February 2014
Line 81:		Line 81:
	: ''Filename of the source. Supported formats: OpenDX.''		: ''Filename of the source. Supported formats: OpenDX.''
	* '''Method''' [string], Default value = NearestValue		* '''Method''' [string], Default value = NearestValue
	: ''Method used for charge computation [NearestValue, RadiusSum, RadiusSumDividedByDistance, KNearestSum, KNearestSumDividedByDistance].''		: ''Method used for charge computation [NearestValue, RadiusSum, RadiusSumDividedByDistance, KNearestSum, KNearestSumDividedByDistance, Lining, WholeStructure].''
	* '''Radius''' [real], Default value = 5		* '''Radius''' [real], Default value = 5
	: ''Radius used for the Radius* methods.''		: ''Radius used for the Radius* methods.''

Dave at 21:52, 14 November 2013

2013-11-14T21:52:15Z

← Older revision		Revision as of 21:52, 14 November 2013
Line 111:		Line 111:
	* '''MinDepth''' [int], Default value = 8		* '''MinDepth''' [int], Default value = 8
	: ''Minimum cavity depth in the number of tetrahedrons.''		: ''Minimum cavity depth in the number of tetrahedrons.''
			* '''MinDepthLength''' [real], Default value = 5
			: ''Minimum depth of a cavity in angstroms.''
	* '''ProbeRadius''' [real], Default value = 3		* '''ProbeRadius''' [real], Default value = 3
	: ''Regulates level of detail of the molecular surface. Higher Probe Radius produces less detail.''		: ''Regulates level of detail of the molecular surface. Higher Probe Radius produces less detail.''
	==== <Tunnel> attributes ====		==== <Tunnel> attributes ====
			* '''AutoOriginCoverRadius''' [real], Default value = 10
			: ''The minimal distance between two auto origins in a given cavity.''
	* '''BottleneckRadius''' [real], Default value = 1.25		* '''BottleneckRadius''' [real], Default value = 1.25
	: ''Minimal radius of a valid tunnel if BottleneckLength is 0.''		: ''Minimal radius of a valid tunnel if BottleneckLength is 0.''
	* '''BottleneckTolerance''' [real], Default value = 0		* '''BottleneckTolerance''' [real], Default value = 0
	: ''Maximum length of a valid tunnel for which the radius is less than Bottleneck Radius.''		: ''Maximum length of a valid tunnel for which the radius is less than Bottleneck Radius.''
			* '''FilterBoundaryLayers''' [bool], Default value = False
			: ''Determines whether to remove layers with boundary residues from the tunnel.''
			* '''MaxAutoOriginsPerCavity''' [int], Default value = 5
			: ''The maximum number of automatically computed origins per cavity.''
	* '''MaxTunnelSimilarity''' [real], Default value = 0.9		* '''MaxTunnelSimilarity''' [real], Default value = 0.9
	: ''Maximum degree of similarity between two tunnels before one tunnel is discarded.''		: ''Maximum degree of similarity between two tunnels before one tunnel is discarded.''
Line 130:		Line 138:
	* '''UseCustomExitsOnly''' [bool], Default value = False		* '''UseCustomExitsOnly''' [bool], Default value = False
	: ''Only user defined exits are used for tunnel computation.''		: ''Only user defined exits are used for tunnel computation.''
	* '''WeightFunction''' [string], Default value = ~~LengthAndRadius~~		* '''WeightFunction''' [string], Default value = VoronoiScale
	: ''Determines the weight function used to compute channels [LengthAndRadius, Length, Constant].''		: ''Determines the weight function used to compute channels [VoronoiScale, LengthAndRadius, Length, Constant].''
	==== <Filter> element ====		==== <Filter> element ====
	''A MotiveQuery lambda expression that returns True to keep the given channel or False to discard it.''		''A MotiveQuery lambda expression that returns True to keep the given channel or False to discard it.''

Dave at 17:16, 6 November 2013

2013-11-06T17:16:55Z

← Older revision		Revision as of 17:16, 6 November 2013
Line 120:		Line 120:
	* '''MaxTunnelSimilarity''' [real], Default value = 0.9		* '''MaxTunnelSimilarity''' [real], Default value = 0.9
	: ''Maximum degree of similarity between two tunnels before one tunnel is discarded.''		: ''Maximum degree of similarity between two tunnels before one tunnel is discarded.''
	* '''~~MinLength~~''' [real], Default value = 0		* '''MinPoreLength''' [real], Default value = 0
			: ''Determines the minimal length (in ang) of a pore.''
			* '''MinTunnelLength''' [real], Default value = 0
	: ''Determines the minimal length (in ang) of a tunnel.''		: ''Determines the minimal length (in ang) of a tunnel.''
	* '''OriginRadius''' [real], Default value = 5		* '''OriginRadius''' [real], Default value = 5
Line 167:		Line 169:
	: ''Controls whether user exit pores will be computed.''		: ''Controls whether user exit pores will be computed.''
	* '''Tunnels''' [bool], Default value = True		* '''Tunnels''' [bool], Default value = True
	: ''Controls tunnels will be computed.''		: ''Controls whether tunnels will be computed.''
	-----------------------		-----------------------
	=== <Origin> attributes ===		=== <Origin> attributes ===
	* '''Auto''' [bool], Default value = False		* '''Auto''' [bool], Default value = False
	: ''Determines whether to (also) use automatically computed tunnel start points.''		: ''Determines whether to (also) use automatically computed tunnel start points.''

Dave at 17:20, 5 November 2013

2013-11-05T17:20:48Z

Show changes

Dave: Created page with "== General XML input shape ==

    filename             
2013-11-05T17:13:11Z
Created page with "== General XML input shape == <pre> <Tunnels>   <Input Attributes="...">filename</Input>   <ChargeSources>     <ScalarGrid Attributes="..." />     <AtomValues Attributes="..."..."
New page
== General XML input shape ==

<pre>

<Tunnels>

  <Input Attributes="...">filename</Input>

  <ChargeSources>

    <ScalarGrid Attributes="..." />

    <AtomValues Attributes="..." />

    <RandomGrid Attributes="..." />

    <!--More optional Field elements-->

  </ChargeSources>

  <WorkingDirectory>path</WorkingDirectory>

  <Params>

    <Cavity Attributes="..." />

    <Tunnel Attributes="..." />

    <Filter>MotiveQuery expression (see http://webchem.ncbr.muni.cz/Wiki for help)</Filter>

  </Params>

  <Export>

    <Formats Attributes="..." />

    <Types Attributes="..." />

    <Mesh Attributes="..." />

    <PyMol Attributes="..." />

  </Export>

  <CustomVdw>

    <Radius Element="C" Value="1.75" />

    <!--More optional Radius elements-->

  </CustomVdw>

  <NonActiveResidues>

    <Residue SequenceNumber="123" Chain="A" />

    <Query>MotiveQuery expression (see http://webchem.ncbr.muni.cz/Wiki for help)</Query>

    <!--More optional Residues or Query elements-->

  </NonActiveResidues>

  <CustomExits>

    <Exit>Point specification</Exit>

    <!--More optional Exit elements-->

  </CustomExits>

  <Origins Auto="0 or 1">

    <Origin>Point specification</Origin>

    <!--More optional Origin elements-->

  </Origins>

  <Paths>

    <!--Optional-->

    <Path>

      <Start>Point specification</Start>

      <End>Point specification</End>

    </Path>

    <!--More optional Path elements.-->

  </Paths>

</Tunnels>

</pre>

== Point specification ==

Points can be specified in 4 ways:

; One or more residue elements

: <code><Residue SequenceNumber="123" Chain="A" InsertionCode=" " /></code>

; One or more 3D points that 'snaps' to the closest residue

: <code><ResidueFromPoint X="1.0" Y="2.0" Z="3.0" /></code>

; One or more 3D points

: <code><Point X="1.0" Y="2.0" Z="3.0" /></code>

; MotiveQuery expression (see http://webchem.ncbr.muni.cz/Wiki for help)

: <code><Query>expression</Query></code>

: Creates a point from each motif returned by the query.

<br/>

The final start point is defined as the centroid of atomic centers or defined points.

== Parameter Descriptions ==

=== Types ===

: [string] - a sequence of characters

: [real] - a floating point number (1.23)

: [int] - an integer (123)

: [bool] - 0/1 or True/False

-----------------------

=== &lt;Input&gt; attributes ===

; SpecificChains

: ''One or more characters that specify which chains should participate in the computation. If empty or non present, all chains are loaded.''

: Type = [string]

: Default value = ''none''

; ReadAllModels

: ''Determines whether to read all models from the PDB file. All models are read automatically for PDB assemblies (.pdb0 extension).''

: Type = [bool]

: Default value = False

-----------------------

=== &lt;ChargeSources&gt; elements ===

==== &lt;AtomValues&gt; attributes ====

; Name

: ''Name of the field.''

: Type = [string]

: Default value = ''none''

; Source

: ''Filename of the source. Supported formats: OpenDX.''

: Type = [string]

: Default value = ''none''

; Method

: ''Method used for charge computation [NearestValue, RadiusSum, RadiusSumDividedByDistance, KNearestSum, KNearestSumDividedByDistance].''

: Type = [string]

: Default value = NearestValue

; Radius

: ''Radius used for the Radius* methods.''

: Type = [real]

: Default value = 5

; K

: ''Number of neighbors used used for the KNearest* methods.''

: Type = [int]

: Default value = 5

; IgnoreHydrogens

: ''Determines if to consider hydrogens for value assignment.''

: Type = [bool]

: Default value = False

==== &lt;RandomGrid&gt; attributes ====

; Name

: ''Name of the field.''

: Type = [string]

: Default value = ''none''

; MinValue

: ''Minimum value to generate.''

: Type = [real]

: Default value = -1

; MaxValue

: ''Maximum value to generate.''

: Type = [real]

: Default value = 1

==== &lt;ScalarGrid&gt; attributes ====

; Name

: ''Name of the field.''

: Type = [string]

: Default value = ''none''

; Source

: ''Filename of the source. Supported formats: OpenDX.''

: Type = [string]

: Default value = ''none''

-----------------------

=== &lt;Params&gt; elements ===

==== &lt;Cavity&gt; attributes ====

; IgnoreHETAtoms

: ''Allows to exclude the HET atoms from the calculation.''

: Type = [bool]

: Default value = False

; IgnoreHydrogens

: ''Allows to exclude the hydrogen atoms from the calculation.''

: Type = [bool]

: Default value = False

; InteriorThreshold

: ''Minimum radius of void inside the protein structure, so that the void would be considered a cavity.''

: Type = [real]

: Default value = 1.25

; MinDepth

: ''Minimum cavity depth in the number of tetrahedrons.''

: Type = [int]

: Default value = 8

; ProbeRadius

: ''Regulates level of detail of the molecular surface. Higher Probe Radius produces less detail.''

: Type = [real]

: Default value = 3

==== &lt;Tunnel&gt; attributes ====

; BottleneckRadius

: ''Minimal radius of a valid tunnel if BottleneckLength is 0.''

: Type = [real]

: Default value = 1.25

; BottleneckTolerance

: ''Maximum length of a valid tunnel for which the radius is less than Bottleneck Radius.''

: Type = [real]

: Default value = 0

; MaxTunnelSimilarity

: ''Maximum degree of similarity between two tunnels before one tunnel is discarded.''

: Type = [real]

: Default value = 0.9

; MinLength

: ''Determines the minimal length (in ang) of a tunnel.''

: Type = [real]

: Default value = 0

; OriginRadius

: ''If the user defined a tunnel start point, expand the search for tunnel start points to a sphere of radius.''

: Type = [real]

: Default value = 5

; SurfaceCoverRadius

: ''Regulates the density of exit points tested at each outer boundary. Higher Surface Cover radius produces a lower density of exit points.''

: Type = [real]

: Default value = 10

; UseCustomExitsOnly

: ''Only user defined exits are used for tunnel computation.''

: Type = [bool]

: Default value = False

; WeightFunction

: ''Determines the weight function used to compute channels [LengthAndRadius, Length, Constant].''

: Type = [string]

: Default value = LengthAndRadius

==== &lt;Filter&gt; element ====

''A MotiveQuery lambda expression that returns True to keep the given channel or False to discard it.''

-----------------------

=== &lt;Export&gt; elements ===

==== &lt;Formats&gt; attributes ====

; ChargeSurface

: ''Controls if XML representation of surface with charges is created.''

: Type = [bool]

: Default value = True

; CSV

: ''Controls if CSV export or channel profiles created.''

: Type = [bool]

: Default value = False

; Mesh

: ''Controls storing information about the mesh of detected tunnels, for subsequent visualization in PyMol or Jmol.''

: Type = [bool]

: Default value = False

; PDBProfile

: ''Controls if channel profiles are exported in PDB format.''

: Type = [bool]

: Default value = False

; PDBStructure

: ''Controls if channel residues (surrounding atoms) are exported in PDB format.''

: Type = [bool]

: Default value = False

; PyMol

: ''Controls whether a PyMol script will be generated, for subsequent visualization in PyMol.''

: Type = [bool]

: Default value = False

==== &lt;Mesh&gt; attributes ====

; Compress

: ''Controls storing of mesh information in a GZip file archive.''

: Type = [bool]

: Default value = False

; Density

: ''Level of detail of mesh surface. The higher the Mesh Density, the lower the level of detail in the visualization.''

: Type = [real]

: Default value = 1.33

==== &lt;PyMol&gt; attributes ====

; PDBId

: ''If this value is present, the option for downloading the structure is incorporated in the PyMOL visualization script.''

: Type = [string]

: Default value = ''none''

; SurfaceType

: ''Controls, if channels are displayed in PyMOL as isosurface or as a set of spheres [Surface, Spheres].''

: Type = [string]

: Default value = Surface

==== &lt;Types&gt; attributes ====

; Cavities

: ''Controls whether cavities will be exported.''

: Type = [bool]

: Default value = True

; PoresAuto

: ''Controls whether 'auto' pores will be computed.''

: Type = [bool]

: Default value = False

; PoresMerged

: ''Controls whether merged pores will be computed.''

: Type = [bool]

: Default value = False

; PoresUser

: ''Controls whether user exit pores will be computed.''

: Type = [bool]

: Default value = False

; Tunnels

: ''Controls tunnels will be computed.''

: Type = [bool]

: Default value = True

-----------------------

=== &lt;Origin&gt; attributes: ===

; Auto

: ''Determines whether to (also) use automatically computed tunnel start points.''

: Type = [bool]

: Default value = False