A tool to find between two selections.
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__init__(self,
protein_sel,
ligand_sel,
tol=0.01,
*args,
**kwargs)
Initialize frame slicing information. |
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isOrthogonal(self,
box,
tol) |
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getResCa(self,
atom_index) |
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getClosestHydrophobicDist(self,
res,
frag) |
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getProteinChargedAtoms(self,
st) |
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getLigandChargedAtoms(self,
st) |
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Centroid
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find_centroid(self,
atomlist)
Computes the centroid of a group of atoms |
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convert_index_to_asl(self,
index_list) |
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findLigFrag(self,
atm_index) |
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labelProtAtm(self,
atm_idx) |
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labelProtRes(self,
atm_idx) |
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labelLigAtm(self,
atm_idx,
frag='') |
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labelLigFrag(self,
atm_idx=-1,
frag='') |
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doFrameInit(self,
frame)
initialize parameters on the first frame |
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updatePositions(self,
st,
frame) |
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updateProteinNearResidues(self,
frame) |
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processFrame(self,
frame)
Collect data for the provided frame. |
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processWatersFrame(self,
frame) |
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get_distance(self,
box,
atom1,
atom2)
Return the distance of the two atoms in the periodic box |
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processMetalFrame(self,
frame)
This function is searches for ions or metals that either interact
with protein and a ligand or just a ligand. |
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processHydrophobic(self,
frame) |
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processPiFrame(self,
frame) |
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processSbFrame(self,
frame) |
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processHbFrame(self,
frame) |
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getDictionaries(self)
This function returns a dictionary of dictionaries of various system
atoms, so the labels can be mapped back to the structure atoms. |
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getFrameResults(self)
For each frame, return a list of (acceptor, donor) integer tuples,
each value being a 1-based atom index into the overall simulation
structure. |
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getResults(self)
Return results for all values and frames as a numpy array with the
first index across analyses. |
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getAllBonds(self)
Return a set of all hydrogen bonds found by the analysis. |
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getLigandUniquePDBName(self,
st)
If all s_m_pdb_atom_name in the ligand are unique, then return true
else return false |
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Inherited from analysistool.AnalysisTool :
getDataLabels ,
getLabel ,
plot ,
plot2D ,
postProcess ,
setSlice ,
shouldProcessFrame
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