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ViewerFramework.VFCommand.Command --+ | mvCommand.MVCommand --+ | ViewerFramework.VFCommand.ICOM --+ | | | mvCommand.MVICOM --+ | | | mvCommand.MVAtomICOM --+ | ComputeMSMS
The computeMSMS command will compute a triangulated solvent excluded surface for the current selection. Package : Pmv Module : msmsCommands Class : ComputeMSMS Command name : computeMSMS Synopsis : None <--- mv.computeMSMS(nodes, surfName=None, pRadius=1.5, density=1.0, perMol=True, display=1) Required Arguments : nodes --- current selection Optional Arguments: surfName --- name of the surfname which will be used as the key in mol.geomContainer.msms dictionary. If the surfName is already a key of the msms dictionary the surface is recreated. By default mol.name-MSMS pRadius --- probe radius (1.5) density --- triangle density to represent the surface. (1.0) perMol --- when this flag is True a surface is computed for each molecule having at least one node in the current selection else the surface is computed for the current selection. (True) display --- flag when set to 1 the displayMSMS will be executed to display the new msms surface.
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| __init__(self, func=None) | ||
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checkDependencies(self) virtual method. |
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onAddCmdToViewer(self) method called when an instance of this command is added to the viewer. |
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| onAddObjectToViewer(self, obj) | ||
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atomPropToVertices(self,
geom,
atoms,
propName,
propIndex=None) Function called to map atomic properties to the vertices of the geometry |
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| pickedVerticesToBonds(self, geom, parts, vertex) | ||
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pickedVerticesToAtoms(self,
geom,
vertInd) Function called to convert picked vertices into atoms |
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__call__(self,
nodes,
surfName='MSMS-MOL',
pRadius=1.5,
density=3.0,
perMol=True,
display=True,
hdset='None',
hdensity=6.0,
**kw) None <- mv.computeMSMS(nodes, surfName='MSMSMOL', pRadius=1.5,density=1.0,perMol=True, display=1) Required Arguments : nodes --- atomic fragment (string or objects) Optional Arguments : surfName --- name of the surfname which will be used as the key in mol.geomContainer.msms dictionary. |
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| fixValues(self, val) | ||
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guiCallback(self) Default callback function called by the gui |
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doit(self,
nodes,
surfName='MSMS-MOL',
pRadius=1.5,
density=1.0,
perMol=True,
display=True,
hdset=None,
hdensity=6.0) Required Arguments: nodes --- current selection surfName --- name of the surfname which will be used as the key in mol.geomContainer.msms dictionary. |
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buildFormDescr(self,
formName='default') descr <- buildFormDescr(self, formName): this virtual method is implemented in the classes derived from Command. |
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| setTexCoords(self, mol, values) | ||
| updateTexCoords(self, mol) | ||
| updateForm(self, surfName) | ||
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entryValidate(self,
text) Method to validate the name of the msms surface. |
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| updateCBB(self) | ||
| perMol_cb(self, event=None) | ||
| saveSel_cb(self, event=None) | ||
Inherited from Inherited from Inherited from Inherited from Inherited from |
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Inherited from |
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None <- mv.computeMSMS(nodes, surfName='MSMSMOL', pRadius=1.5,density=1.0,perMol=True, display=1) Required Arguments : nodes --- atomic fragment (string or objects) Optional Arguments : surfName --- name of the surfname which will be used as the key in mol.geomContainer.msms dictionary. If the surfName is already a key of the msms dictionary the surface is recomputed. (default MSMS-MOL) pRadius --- probe radius (1.5) density --- triangle density to represent the surface. (1.0) perMol --- when this flag is True a surface is computed for each molecule having at least one node in the current selection else the surface is computed for the current selection. (True) display --- flag when set to 1 the displayMSMS will be executed with the surfName else not. hdset --- Atom set (or name) for which high density triangualtion will be generated hdensity --- vertex density for high density
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Required Arguments: nodes --- current selection surfName --- name of the surfname which will be used as the key in mol.geomContainer.msms dictionary. Optional Arguments: pRadius --- probe radius (1.5) density --- triangle density to represent the surface. (1.0) perMol --- when this flag is True a surface is computed for each molecule having at least one node in the current selection else the surface is computed for the current selection. (True) display --- flag when set to True the displayMSMS will be executed with the surfName else not. hdset --- Atom set for which high density triangualtion will be generated hdensity --- vertex density for high density
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