YingyingJin/ProteinLigandInteractionAnalysis

YingyingJin`ProteinLigandInteractionAnalysis`

LabelPose

LabelPose[

metrics_Association,barrelParams_Association, finStrong_:0.70,(*required Fin for strong “inside”*) finBorder_:0.10,(*min Fin for “borderline”*) rInnerMargin_:0.4,(*how far inside Rpore COM must be for strong inside*) rOuterMargin_:0.8,(*how far outside Rpore COM can be for borderline*) zInnerMargin_:0.3,(*tighten Z window for strong inside*) zOuterMargin_:0.7,(*loosen Z window for borderline*) fracInsideContactsStrong_:0.5,(*fraction of contacts that must come from inside atoms*) minContactDistSafety_:0.5 (*extra distance buffer vs cutoff for strong inside*)]

Examples

(1)

Basic Examples

(1)

In[1]:=

cylFile="/Users/yingyingjin/Dropbox/NewMoleculeProject/DynamicBind/cylindrinA.pdb";barrelParams=ComputeProteinParameters[cylFile];poseFile="/Users/yingyingjin/Dropbox/NewMoleculeProject/DynamicBind/NAC6mer_ZINC11/rank_50.pdb";

Number of CA atoms used: 66

In[2]:=

metrics=PoseMetrics[poseFile,barrelParams,4.0];label=LabelPose[metrics,barrelParams]

Out[2]=

Inside

SeeAlso

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