From 3fa9418d0480ec3377d5d8577e8e9fc63001d91f Mon Sep 17 00:00:00 2001
From: root <Yorgo EL MOUBAYED>
Date: Fri, 9 Jul 2021 10:03:20 +0200
Subject: [PATCH] Add new files and update folder structure
---
.../autoproc_summary/autoproc_summary.json | 106 +++++++++++
.../{ => pipedream}/1-pipedream_summary.json | 0
.../{ => pipedream}/2-pipedream_summary.json | 0
.../{ => pipedream}/3-pipedream_summary.json | 0
.../{ => pipedream}/4-pipedream_summary.json | 0
.../pipedream/5-pipedream_summary.json | 172 ++++++++++++++++++
.../{ => summary.out}/1-summary.out | 0
.../{ => summary.out}/2-summary.out | 0
.../{ => summary.out}/3-summary.out | 0
.../{ => summary.out}/4-summary.out | 0
.../pipedream}/pipedream_summary.json | 0
.../pipedream_summary_original.json | 0
.../pipedream}/pipedream_summary_v0.json | 0
.../pipedream}/pipedream_summary_v1.json | 0
.../sample_data.json | 0
15 files changed, 278 insertions(+)
create mode 100644 data/jsonexamples_andrew/autoproc_summary/autoproc_summary.json
rename data/jsonexamples_andrew/{ => pipedream}/1-pipedream_summary.json (100%)
rename data/jsonexamples_andrew/{ => pipedream}/2-pipedream_summary.json (100%)
rename data/jsonexamples_andrew/{ => pipedream}/3-pipedream_summary.json (100%)
rename data/jsonexamples_andrew/{ => pipedream}/4-pipedream_summary.json (100%)
create mode 100644 data/jsonexamples_andrew/pipedream/5-pipedream_summary.json
rename data/jsonexamples_andrew/{ => summary.out}/1-summary.out (100%)
rename data/jsonexamples_andrew/{ => summary.out}/2-summary.out (100%)
rename data/jsonexamples_andrew/{ => summary.out}/3-summary.out (100%)
rename data/jsonexamples_andrew/{ => summary.out}/4-summary.out (100%)
rename data/{ => jsonexamples_raphael/pipedream}/pipedream_summary.json (100%)
rename data/{ => jsonexamples_raphael/pipedream}/pipedream_summary_original.json (100%)
rename data/{ => jsonexamples_raphael/pipedream}/pipedream_summary_v0.json (100%)
rename data/{ => jsonexamples_raphael/pipedream}/pipedream_summary_v1.json (100%)
rename data/{ => jsonexamples_raphael}/sample_data.json (100%)
diff --git a/data/jsonexamples_andrew/autoproc_summary/autoproc_summary.json b/data/jsonexamples_andrew/autoproc_summary/autoproc_summary.json
new file mode 100644
index 0000000..165fcda
--- /dev/null
+++ b/data/jsonexamples_andrew/autoproc_summary/autoproc_summary.json
@@ -0,0 +1,106 @@
+{
+ "AutoProcContainer" : {
+ "AutoProc" : {
+ "spaceGroup" : "P 1 21 1",
+ "refinedCell_gamma" : "90.000",
+ "wavelength" : ".97926",
+ "refinedCell_alpha" : "90.000",
+ "refinedCell_b" : "116.975",
+ "refinedCell_a" : "57.988",
+ "refinedCell_beta" : "92.547",
+ "refinedCell_c" : "64.389"
+ },
+ "AutoProcScalingContainer" : {
+ "AutoProcScaling" : {
+ "resolutionEllipsoidAxis21" : ".00000",
+ "resolutionEllipsoidAxis32" : ".00000",
+ "resolutionEllipsoidAxis13" : ".22319",
+ "resolutionEllipsoidValue3" : "1.87200",
+ "resolutionEllipsoidValue2" : "1.81000",
+ "resolutionEllipsoidAxis31" : "-.22319",
+ "resolutionEllipsoidAxis22" : "1.00000",
+ "resolutionEllipsoidAxis33" : ".97475",
+ "resolutionEllipsoidAxis11" : ".97475",
+ "recordTimeStamp" : "2021-07-05 08:46:02",
+ "resolutionEllipsoidAxis12" : ".00000",
+ "resolutionEllipsoidAxis23" : ".00000",
+ "resolutionEllipsoidValue1" : "1.68100"
+ },
+ "AutoProcScalingStatistics" : [
+ {
+ "nTotalObservations" : "393991",
+ "rMeasWithinIPlusIMinus" : ".097",
+ "anomalousMultiplicity" : "2.7",
+ "anomalousCompleteness" : "91.7",
+ "nTotalUniqueObservations" : "75926",
+ "anomalousCompletenessSpherical" : "76.7",
+ "scalingStatisticsType" : "overall",
+ "ccHalf" : "0.999",
+ "completeness" : "93.2",
+ "meanIOverSigI" : "12.6",
+ "completenessSpherical" : "78.1",
+ "rPimWithinIPlusIMinus" : ".057",
+ "ccAnomalous" : "0.033",
+ "DanoOverSigDano" : ".848",
+ "anomalousCompletenessEllipsoidal" : "91.7",
+ "resolutionLimitLow" : "64.325",
+ "rMeasAllIPlusIMinus" : ".097",
+ "rMerge" : ".087",
+ "multiplicity" : "5.2",
+ "rPimAllIPlusIMinus" : ".042",
+ "completenessEllipsoidal" : "93.2",
+ "resolutionLimitHigh" : "1.681"
+ },
+ {
+ "completeness" : "98.3",
+ "ccHalf" : "0.999",
+ "anomalousCompletenessSpherical" : "96.4",
+ "scalingStatisticsType" : "innerShell",
+ "anomalousCompleteness" : "96.4",
+ "anomalousMultiplicity" : "2.7",
+ "nTotalUniqueObservations" : "4050",
+ "rMeasWithinIPlusIMinus" : ".033",
+ "nTotalObservations" : "20598",
+ "rPimAllIPlusIMinus" : ".015",
+ "completenessEllipsoidal" : "98.3",
+ "resolutionLimitHigh" : "4.853",
+ "multiplicity" : "5.1",
+ "resolutionLimitLow" : "64.325",
+ "DanoOverSigDano" : "1.021",
+ "ccAnomalous" : "0.206",
+ "anomalousCompletenessEllipsoidal" : "96.4",
+ "rMerge" : ".032",
+ "rMeasAllIPlusIMinus" : ".035",
+ "completenessSpherical" : "98.3",
+ "meanIOverSigI" : "38.7",
+ "rPimWithinIPlusIMinus" : ".019"
+ },
+ {
+ "resolutionLimitHigh" : "1.681",
+ "rPimAllIPlusIMinus" : ".540",
+ "completenessEllipsoidal" : "53.6",
+ "multiplicity" : "5.6",
+ "rMeasAllIPlusIMinus" : "1.296",
+ "rMerge" : "1.175",
+ "anomalousCompletenessEllipsoidal" : "52.7",
+ "DanoOverSigDano" : ".793",
+ "ccAnomalous" : "-0.000",
+ "resolutionLimitLow" : "1.830",
+ "rPimWithinIPlusIMinus" : ".758",
+ "meanIOverSigI" : "1.6",
+ "completenessSpherical" : "16.7",
+ "completeness" : "53.6",
+ "ccHalf" : "0.480",
+ "anomalousCompletenessSpherical" : "16.3",
+ "scalingStatisticsType" : "outerShell",
+ "nTotalUniqueObservations" : "3642",
+ "anomalousMultiplicity" : "2.8",
+ "anomalousCompleteness" : "52.7",
+ "nTotalObservations" : "20258",
+ "rMeasWithinIPlusIMinus" : "1.320"
+ }
+ ]
+ }
+ }
+}
+
diff --git a/data/jsonexamples_andrew/1-pipedream_summary.json b/data/jsonexamples_andrew/pipedream/1-pipedream_summary.json
similarity index 100%
rename from data/jsonexamples_andrew/1-pipedream_summary.json
rename to data/jsonexamples_andrew/pipedream/1-pipedream_summary.json
diff --git a/data/jsonexamples_andrew/2-pipedream_summary.json b/data/jsonexamples_andrew/pipedream/2-pipedream_summary.json
similarity index 100%
rename from data/jsonexamples_andrew/2-pipedream_summary.json
rename to data/jsonexamples_andrew/pipedream/2-pipedream_summary.json
diff --git a/data/jsonexamples_andrew/3-pipedream_summary.json b/data/jsonexamples_andrew/pipedream/3-pipedream_summary.json
similarity index 100%
rename from data/jsonexamples_andrew/3-pipedream_summary.json
rename to data/jsonexamples_andrew/pipedream/3-pipedream_summary.json
diff --git a/data/jsonexamples_andrew/4-pipedream_summary.json b/data/jsonexamples_andrew/pipedream/4-pipedream_summary.json
similarity index 100%
rename from data/jsonexamples_andrew/4-pipedream_summary.json
rename to data/jsonexamples_andrew/pipedream/4-pipedream_summary.json
diff --git a/data/jsonexamples_andrew/pipedream/5-pipedream_summary.json b/data/jsonexamples_andrew/pipedream/5-pipedream_summary.json
new file mode 100644
index 0000000..83da7a5
--- /dev/null
+++ b/data/jsonexamples_andrew/pipedream/5-pipedream_summary.json
@@ -0,0 +1,172 @@
+{
+ "dataprocessing" : {
+ "inputdata" : {
+ "symmetry" : 19,
+ "reslo" : 19.8514,
+ "cell" : {
+ "b" : 57.911,
+ "alpha" : 90,
+ "beta" : 90,
+ "a" : 54.537,
+ "gamma" : 90,
+ "c" : 66.625
+ },
+ "reshigh" : 1.6982
+ },
+ "referencedata" : {
+ "symmetry" : 19,
+ "cell" : {
+ "a" : 54.268,
+ "gamma" : 90,
+ "c" : 66.267,
+ "b" : 58.462,
+ "alpha" : 90,
+ "beta" : 90
+ }
+ },
+ "datatype" : "mtz",
+ "processingtype" : "unknown"
+ },
+ "refinement" : {
+ "models" : [
+ {
+ "number" : 1,
+ "LMRscore" : 27.3,
+ "modelname" : "input"
+ }
+ ],
+ "refinementprotocol" : "Default",
+ "Cycles" : [
+ {
+ "MeanB" : null,
+ "Rfree" : 0.253753,
+ "RMSangles" : 1.01017,
+ "WatersPresent" : null,
+ "RMSbonds" : 0.00676186,
+ "step" : "initial",
+ "R" : 0.250732,
+ "type" : "BUSTER",
+ "WilsonB" : null,
+ "cycle_number" : 0
+ },
+ {
+ "type" : "BUSTER",
+ "WilsonB" : 17.79,
+ "step" : "refinement",
+ "R" : 0.186006,
+ "cycle_number" : 1,
+ "Rfree" : 0.22027,
+ "MeanB" : 17.74,
+ "WatersPresent" : null,
+ "RMSangles" : 1.07758,
+ "RMSbonds" : 0.00812835
+ },
+ {
+ "cycle_number" : 2,
+ "R" : 0.184953,
+ "step" : "final",
+ "WilsonB" : 17.79,
+ "type" : "BUSTER",
+ "RMSbonds" : 0.00823198,
+ "WatersPresent" : 306,
+ "RMSangles" : 1.0751,
+ "Rfree" : 0.21906,
+ "MeanB" : 17.71
+ }
+ ],
+ "selectedmodel" : "input.pdb"
+ },
+ "GPhL_pipedream" : {
+ "version" : "__VERSION__ <__DATE__>",
+ "runfrom" : "/.net/fs3/scratch_fs1/asharff/pipedream-tutorials/tutorial3",
+ "output" : "/.net/fs3/scratch_fs1/asharff/pipedream-tutorials/tutorial3/fff8",
+ "jsonversion" : "0.0.4",
+ "runby" : "asharff : escher : 14:07:37 on Thu Jul 8 2021",
+ "jobid" : "a8a37dea-2380-435e-90e8-f9d2ee6ab493",
+ "terminationstatus" : "COMPLETED",
+ "command" : "pipedream -hklin 3rxt.mtz -xyzin input.pdb -hklref 3rxe.mtz -keepwater -nowateradd -rhofit grade-L01.cif -postquick -v1 -d fff8"
+ },
+ "ligandfitting" : {
+ "ligands" : [
+ {
+ "postrefinement" : [
+ {
+ "cycle_number" : 0,
+ "type" : "BUSTER",
+ "WilsonB" : 17.79,
+ "R" : 0.186098,
+ "step" : "initial",
+ "RMSbonds" : 0.0081761,
+ "RMSangles" : 1.07068,
+ "WatersPresent" : null,
+ "MeanB" : 17.71,
+ "Rfree" : 0.2237
+ },
+ {
+ "WilsonB" : 17.79,
+ "type" : "BUSTER",
+ "R" : 0.184739,
+ "step" : "final",
+ "cycle_number" : 1,
+ "Rfree" : 0.223065,
+ "MeanB" : 17.76,
+ "RMSangles" : 1.07073,
+ "WatersPresent" : 304,
+ "RMSbonds" : 0.00808843
+ }
+ ],
+ "ligandname" : "grade-L01",
+ "solutions" : [
+ {
+ "chain" : "A",
+ "rhofitscore" : -172.7,
+ "poorfit" : "0/10",
+ "correlationcoefficient" : 0.729,
+ "contactscore" : 0,
+ "output" : "Hit_00_00_000.pdb",
+ "closecontacts" : "",
+ "solution_number" : 1,
+ "ligandstrain" : 1.9
+ }
+ ],
+ "validationstatistics" : {
+ "ligandstatistics" : [
+ {
+ "mogulbond" : "0/9",
+ "ligandid" : "L01 A4000",
+ "ligandomax" : 0.99,
+ "mogulzbond" : 0.637,
+ "ligandomin" : 0.99,
+ "mogulring" : "0/1",
+ "mogulangl" : "0/11",
+ "ligandbavg" : 20.88,
+ "moguldihe" : "1/1",
+ "ligandbmin" : 19.71,
+ "mogulzangl" : 0.524,
+ "ligandbmax" : 24.22,
+ "ligandresno" : "A4000",
+ "ligandcc" : 0.842
+ }
+ ],
+ "molprobity" : {
+ "rmsbonds" : 0.0136,
+ "rmsangles" : 1.59,
+ "ramaoutlierpercent" : 0,
+ "ramaoutliers" : 0,
+ "cbetadeviations" : 0,
+ "ramafavoredpercent" : 98.19,
+ "poorrotamerspercent" : 0.54,
+ "ramafavored" : 217,
+ "molprobitypercentile" : "(percentile: 98.6 N=40830, 1.70A+/-0.25A) ",
+ "poorrotamers" : 1,
+ "clashscore" : 0.6,
+ "clashpercentile" : "(percentile: 97.4 N=41457, 1.70A+/-0.25A) ",
+ "molprobityscore" : 0.7
+ }
+ }
+ }
+ ],
+ "type" : "Rhofit"
+ }
+}
+
diff --git a/data/jsonexamples_andrew/1-summary.out b/data/jsonexamples_andrew/summary.out/1-summary.out
similarity index 100%
rename from data/jsonexamples_andrew/1-summary.out
rename to data/jsonexamples_andrew/summary.out/1-summary.out
diff --git a/data/jsonexamples_andrew/2-summary.out b/data/jsonexamples_andrew/summary.out/2-summary.out
similarity index 100%
rename from data/jsonexamples_andrew/2-summary.out
rename to data/jsonexamples_andrew/summary.out/2-summary.out
diff --git a/data/jsonexamples_andrew/3-summary.out b/data/jsonexamples_andrew/summary.out/3-summary.out
similarity index 100%
rename from data/jsonexamples_andrew/3-summary.out
rename to data/jsonexamples_andrew/summary.out/3-summary.out
diff --git a/data/jsonexamples_andrew/4-summary.out b/data/jsonexamples_andrew/summary.out/4-summary.out
similarity index 100%
rename from data/jsonexamples_andrew/4-summary.out
rename to data/jsonexamples_andrew/summary.out/4-summary.out
diff --git a/data/pipedream_summary.json b/data/jsonexamples_raphael/pipedream/pipedream_summary.json
similarity index 100%
rename from data/pipedream_summary.json
rename to data/jsonexamples_raphael/pipedream/pipedream_summary.json
diff --git a/data/pipedream_summary_original.json b/data/jsonexamples_raphael/pipedream/pipedream_summary_original.json
similarity index 100%
rename from data/pipedream_summary_original.json
rename to data/jsonexamples_raphael/pipedream/pipedream_summary_original.json
diff --git a/data/pipedream_summary_v0.json b/data/jsonexamples_raphael/pipedream/pipedream_summary_v0.json
similarity index 100%
rename from data/pipedream_summary_v0.json
rename to data/jsonexamples_raphael/pipedream/pipedream_summary_v0.json
diff --git a/data/pipedream_summary_v1.json b/data/jsonexamples_raphael/pipedream/pipedream_summary_v1.json
similarity index 100%
rename from data/pipedream_summary_v1.json
rename to data/jsonexamples_raphael/pipedream/pipedream_summary_v1.json
diff --git a/data/sample_data.json b/data/jsonexamples_raphael/sample_data.json
similarity index 100%
rename from data/sample_data.json
rename to data/jsonexamples_raphael/sample_data.json
--
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