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Mole 2.5 Command Line Input Help

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Revision as of 17:13, 5 November 2013 by Dave (talk | contribs) (Created page with "== General XML input shape == <pre> <Tunnels> <Input Attributes="...">filename</Input> <ChargeSources> <ScalarGrid Attributes="..." /> <AtomValues Attributes="..."...")
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General XML input shape

<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>

Point specification

Points can be specified in 4 ways:

One or more residue elements
<Residue SequenceNumber="123" Chain="A" InsertionCode=" " />
One or more 3D points that 'snaps' to the closest residue
<ResidueFromPoint X="1.0" Y="2.0" Z="3.0" />
One or more 3D points
<Point X="1.0" Y="2.0" Z="3.0" />
MotiveQuery expression (see http://webchem.ncbr.muni.cz/Wiki for help)
<Query>expression</Query>
Creates a point from each motif returned by the query.


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

<Input> 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

<ChargeSources> elements

<AtomValues> 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

<RandomGrid> 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

<ScalarGrid> attributes

Name
Name of the field.
Type = [string]
Default value = none
Source
Filename of the source. Supported formats: OpenDX.
Type = [string]
Default value = none

<Params> elements

<Cavity> 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

<Tunnel> 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

<Filter> element

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

<Export> elements

<Formats> 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

<Mesh> 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

<PyMol> 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

<Types> 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

<Origin> attributes:

Auto
Determines whether to (also) use automatically computed tunnel start points.
Type = [bool]
Default value = False
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