Editing Mole 2.5 Command Line Input Help

== 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''' [string], Default value = ''none''
: ''One or more characters that specify which chains should participate in the computation. If empty or non present, all chains are loaded.''
* '''ReadAllModels''' [bool], Default value = False
: ''Determines whether to read all models from the PDB file. All models are read automatically for PDB assemblies (.pdb0 extension).''
-----------------------
=== &lt;ChargeSources&gt; elements ===
==== &lt;AtomValues&gt; attributes ====
* '''Name''' [string], Default value = ''none''
: ''Name of the field.''
* '''Source''' [string], Default value = ''none''
: ''Filename of the source. Supported formats: OpenDX.''
* '''Method''' [string], Default value = NearestValue
: ''Method used for charge computation [NearestValue, RadiusSum, RadiusSumDividedByDistance, RadiusMultiplicativeScale, RadiusAdditiveScale, KNearestSum, KNearestSumDividedByDistance, Lining, WholeStructure].''
* '''Radius''' [real], Default value = 5
: ''Radius used for the Radius* methods.''
* '''K''' [int], Default value = 5
: ''Number of neighbors used used for the KNearest* methods.''
* '''IgnoreHydrogens''' [bool], Default value = False
: ''Determines if to consider hydrogens for value assignment.''
==== &lt;RandomGrid&gt; attributes ====
* '''Name''' [string], Default value = ''none''
: ''Name of the field.''
* '''MinValue''' [real], Default value = -1
: ''Minimum value to generate.''
* '''MaxValue''' [real], Default value = 1
: ''Maximum value to generate.''
==== &lt;ScalarGrid&gt; attributes ====
* '''Name''' [string], Default value = ''none''
: ''Name of the field.''
* '''Source''' [string], Default value = ''none''
: ''Filename of the source. Supported formats: OpenDX.''
-----------------------
=== &lt;Params&gt; elements ===
==== &lt;Cavity&gt; attributes ====
* '''IgnoreHETAtoms''' [bool], Default value = False
: ''Allows to exclude the HET atoms from the calculation.''
* '''IgnoreHydrogens''' [bool], Default value = False
: ''Allows to exclude the hydrogen atoms from the calculation.''
* '''InteriorThreshold''' [real], Default value = 1.25
: ''Minimum radius of void inside the protein structure, so that the void would be considered a cavity.''
* '''MinDepth''' [int], Default value = 8
: ''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
: ''Regulates level of detail of the molecular surface. Higher Probe Radius produces less detail.''
==== &lt;Tunnel&gt; attributes ====
* '''AutoOriginCoverRadius''' [real], Default value = 10
: ''The minimal distance between two auto origins in a given cavity.''
* '''BottleneckRadius''' [real], Default value = 1.25
: ''Minimal radius of a valid tunnel if BottleneckLength is 0.''
* '''BottleneckTolerance''' [real], Default value = 0
: ''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
: ''Maximum degree of similarity between two tunnels before one tunnel is discarded.''
* '''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.''
* '''OriginRadius''' [real], Default value = 5
: ''If the user defined a tunnel start point, expand the search for tunnel start points to a sphere of radius.''
* '''SurfaceCoverRadius''' [real], Default value = 10
: ''Regulates the density of exit points tested at each outer boundary. Higher Surface Cover radius produces a lower density of exit points.''
* '''UseCustomExitsOnly''' [bool], Default value = False
: ''Only user defined exits are used for tunnel computation.''
* '''WeightFunction''' [string], Default value = VoronoiScale
: ''Determines the weight function used to compute channels [VoronoiScale, LengthAndRadius, Length, Constant].''
==== &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''' [bool], Default value = True
: ''Controls if XML representation of surface with charges is created.''
* '''CSV''' [bool], Default value = False
: ''Controls if CSV export or channel profiles created.''
* '''Mesh''' [bool], Default value = False
: ''Controls storing information about the mesh of detected tunnels, for subsequent visualization in PyMol or Jmol.''
* '''PDBProfile''' [bool], Default value = False
: ''Controls if channel profiles are exported in PDB format.''
* '''PDBStructure''' [bool], Default value = False
: ''Controls if channel residues (surrounding atoms) are exported in PDB format.''
* '''PyMol''' [bool], Default value = False
: ''Controls whether a PyMol script will be generated, for subsequent visualization in PyMol.''
==== &lt;Mesh&gt; attributes ====
* '''Compress''' [bool], Default value = False
: ''Controls storing of mesh information in a GZip file archive.''
* '''Density''' [real], Default value = 1.33
: ''Level of detail of mesh surface. The higher the Mesh Density, the lower the level of detail in the visualization.''
==== &lt;PyMol&gt; attributes ====
* '''ChargePalette''' [string], Default value = RedWhiteBlue
: ''Determines the palette used for charge coloring [RedWhiteBlue, BlueWhiteRed].''
* '''PDBId''' [string], Default value = ''none''
: ''If this value is present, the option for downloading the structure is incorporated in the PyMOL visualization script.''
* '''SurfaceType''' [string], Default value = Surface
: ''Controls, if channels are displayed in PyMOL as isosurface or as a set of spheres [Surface, Spheres].''
==== &lt;Types&gt; attributes ====
* '''Cavities''' [bool], Default value = True
: ''Controls whether cavities will be exported.''
* '''PoresAuto''' [bool], Default value = False
: ''Controls whether 'auto' pores will be computed.''
* '''PoresMerged''' [bool], Default value = False
: ''Controls whether merged pores will be computed.''
* '''PoresUser''' [bool], Default value = False
: ''Controls whether user exit pores will be computed.''
* '''Tunnels''' [bool], Default value = True
: ''Controls whether tunnels will be computed.''
-----------------------
=== &lt;Origin&gt; attributes ===
* '''Auto''' [bool], Default value = False
: ''Determines whether to (also) use automatically computed tunnel start points.''