fixing config examples and adding correct data

coleygroup · Apr 23, 2021 · 36431d9 · 36431d9
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commit 36431d9
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Showing 17 changed files with 44 additions and 44 deletions.
diff --git a/config_expts/Enamine10k_online.ini b/config_expts/Enamine10k_online.ini
@@ -4,8 +4,8 @@ name = molpal_10k
 --write-final
 
 [pool]
-library = /nfs/ccoleylab001/dgraff/libraries/Enamine10k.csv
-fps = /nfs/ccoleylab001/dgraff/libraries/Enamine10k.h5
+library = libraries/Enamine10k.csv.gz
+fps = ...
 --validated
 
 [encoder]
@@ -15,7 +15,7 @@ radius = 2
 
 [objective]
 objective = lookup
-lookup-path = /nfs/ccoleylab001/dgraff/data//Enamine10k_scores.csv
+lookup-path = data//Enamine10k_scores.csv.gz
 lookup-smiles-col = 0
 lookup-data-col = 1
 --minimize

diff --git a/config_expts/Enamine10k_retrain.ini b/config_expts/Enamine10k_retrain.ini
@@ -5,8 +5,8 @@ name = molpal_10k
 --retrain-from-scratch
 
 [pool]
-library = /nfs/ccoleylab001/dgraff/libraries/Enamine10k.csv
-fps = /nfs/ccoleylab001/dgraff/libraries/Enamine10k.h5
+library = libraries/Enamine10k.csv.gz
+fps = ...
 --validated
 
 [encoder]
@@ -16,7 +16,7 @@ radius = 2
 
 [objective]
 objective = lookup
-lookup-path = /nfs/ccoleylab001/dgraff/data//Enamine10k_scores.csv
+lookup-path = data//Enamine10k_scores.csv.gz
 lookup-smiles-col = 0
 lookup-data-col = 1
 --minimize

diff --git a/config_expts/Enamine50k_online.ini b/config_expts/Enamine50k_online.ini
@@ -4,8 +4,8 @@ name = molpal_50k
 --write-final
 
 [pool]
-library = /nfs/ccoleylab001/dgraff/libraries/Enamine50k.csv
-fps = /nfs/ccoleylab001/dgraff/libraries/Enamine50k.h5
+library = libraries/Enamine50k.csv.gz
+fps = ...
 --validated
 
 [encoder]
@@ -15,7 +15,7 @@ radius = 2
 
 [objective]
 objective = lookup
-lookup-path = /nfs/ccoleylab001/dgraff/data//Enamine50k_scores.csv
+lookup-path = data/Enamine50k_scores.csv.gz
 lookup-smiles-col = 0
 lookup-data-col = 1
 --minimize

diff --git a/config_expts/Enamine50k_retrain.ini b/config_expts/Enamine50k_retrain.ini
@@ -5,8 +5,8 @@ name = molpal_50k
 --retrain-from-scratch
 
 [pool]
-library = /nfs/ccoleylab001/dgraff/libraries/Enamine50k.csv
-fps = /nfs/ccoleylab001/dgraff/libraries/Enamine50k.h5
+library = libraries/Enamine50k.csv.gz
+fps = ...
 --validated
 
 [encoder]
@@ -16,7 +16,7 @@ radius = 2
 
 [objective]
 objective = lookup
-lookup-path = /nfs/ccoleylab001/dgraff/data//Enamine50k_scores.csv
+lookup-path = data/Enamine50k_scores.csv.gz
 lookup-smiles-col = 0
 lookup-data-col = 1
 --minimize

diff --git a/config_expts/EnamineHTS_converge.ini b/config_expts/EnamineHTS_converge.ini
@@ -5,8 +5,8 @@ name = molpal_EnamineHTS
 --retrain-from-scratch
 
 [pool]
-library = /nfs/ccoleylab001/dgraff/libraries/EnamineHTS.csv
-fps = /nfs/ccoleylab001/dgraff/libraries/EnamineHTS_pair.h5
+library = libraries/EnamineHTS.csv.gz
+fps = ...
 --validated
 
 [encoder]
@@ -16,7 +16,7 @@ radius = 2
 
 [objective]
 objective = lookup
-lookup-path = /nfs/ccoleylab001/dgraff/data/EnamineHTS_scores.csv
+lookup-path = data/EnamineHTS_scores.csv
 lookup-smiles-col = 0
 lookup-data-col = 1
 --minimize

diff --git a/config_expts/EnamineHTS_online.ini b/config_expts/EnamineHTS_online.ini
@@ -4,8 +4,8 @@ name = molpal_EnamineHTS_retrain
 --write-final
 
 [pool]
-library = /nfs/ccoleylab001/dgraff/libraries/EnamineHTS.csv
-fps = /nfs/ccoleylab001/dgraff/libraries/EnamineHTS_pair.h5
+library = libraries/EnamineHTS.csv.gz
+fps = ...
 --validated
 
 [encoder]
@@ -15,7 +15,7 @@ radius = 2
 
 [objective]
 objective = lookup
-lookup-path = /nfs/ccoleylab001/dgraff/data/EnamineHTS_scores.csv
+lookup-path = data/EnamineHTS_scores.csv.gz
 lookup-smiles-col = 0
 lookup-data-col = 1
 --minimize

diff --git a/config_expts/EnamineHTS_retrain.ini b/config_expts/EnamineHTS_retrain.ini
@@ -5,8 +5,8 @@ name = molpal_EnamineHTS_retrain
 --retrain-from-scratch
 
 [pool]
-library = /nfs/ccoleylab001/dgraff/libraries/EnamineHTS.csv
-fps = /nfs/ccoleylab001/dgraff/libraries/EnamineHTS_pair.h5
+library = libraries/EnamineHTS.csv.gz
+fps = ...
 --validated
 
 [encoder]
@@ -16,7 +16,7 @@ radius = 2
 
 [objective]
 objective = lookup
-lookup-path = /nfs/ccoleylab001/dgraff/data/EnamineHTS_scores.csv
+lookup-path = data/EnamineHTS_scores.csv.gz
 lookup-smiles-col = 0
 lookup-data-col = 1
 --minimize

diff --git a/config_expts/EnamineHTS_single_batch.ini b/config_expts/EnamineHTS_single_batch.ini
@@ -5,8 +5,8 @@ name = EnamineHTS_singleBatch_mpn_greedy_0
 --retrain-from-scratch
 
 [pool]
-library = /nfs/ccoleylab001/dgraff/libraries/EnamineHTS.csv
-fps = /nfs/ccoleylab001/dgraff/libraries/EnamineHTS_pair.h5
+library = libraries/EnamineHTS.csv.gz
+fps = ...
 --validated
 
 [acquisition]
@@ -25,7 +25,7 @@ conf-method = mve
 
 [objective]
 objective = lookup
-lookup-path = /nfs/ccoleylab001/dgraff/data/EnamineHTS_scores.csv
+lookup-path = data/EnamineHTS_scores.csv.gz
 lookup-smiles-col = 0
 lookup-data-col = 1
 --minimize

diff --git a/config_expts/HCEP_pce.ini b/config_expts/HCEP_pce.ini
@@ -5,8 +5,8 @@ name = molpal_HCEP
 --retrain-from-scratch
 
 [pool]
-library = /nfs/ccoleylab001/dgraff/data/HCEP_pce.csv
-fps = /nfs/ccoleylab001/dgraff/libraries/HCEP_morgan.h5
+library = ...
+fps = ...
 
 [encoder]
 fingerprint = morgan
@@ -23,9 +23,9 @@ metric = greedy
 
 [objective]
 objective = lookup
-lookup-path = /nfs/ccoleylab001/dgraff/data/HCEP_pce.csv
-lookup-smiles-col = 0
-lookup-data-col = 1
+lookup-path = ...
+lookup-smiles-col = ...
+lookup-data-col = ...
 
 [stopping]
 top-k = 0.005

diff --git a/config_expts/config_AmpC_online.ini b/config_expts/config_AmpC_online.ini
@@ -4,8 +4,8 @@ name = AmpC_100M
 --write-final
 
 [pool]
-library = /nfs/ccoleylab001/dgraff/libraries/AmpC_100M.csv.gz
-fps = /nfs/ccoleylab001/dgraff/libraries/AmpC_100M.h5
+library = ...
+fps = ...
 --validated
 
 [encoder]
@@ -15,9 +15,9 @@ radius = 2
 
 [objective]
 objective = lookup
-lookup-path = /nfs/ccoleylab001/dgraff/data/AmpC_100M_scores.csv.gz
-lookup-smiles-col = 1
-lookup-data-col = 2
+lookup-path = ...
+lookup-smiles-col = ...
+lookup-data-col = ...
 --minimize
 
 [stopping]

diff --git a/config_expts/config_AmpC_retrain.ini b/config_expts/config_AmpC_retrain.ini
@@ -5,8 +5,8 @@ name = AmpC_100M
 --retrain-from-scratch
 
 [pool]
-library = /nfs/ccoleylab001/dgraff/libraries/AmpC_100M.csv.gz
-fps = /nfs/ccoleylab001/dgraff/libraries/AmpC_100M.h5
+library = ...
+fps = ...
 --validated
 
 [encoder]
@@ -16,9 +16,9 @@ radius = 2
 
 [objective]
 objective = lookup
-lookup-path = /nfs/ccoleylab001/dgraff/data/AmpC_100M_scores.csv.gz
-lookup-smiles-col = 1
-lookup-data-col = 2
+lookup-path = ...
+lookup-smiles-col = ...
+lookup-data-col = ...
 --minimize
 
 [stopping]

diff --git a/config_expts/config_D4.ini b/config_expts/config_D4.ini
@@ -6,8 +6,8 @@ name = D4_140M
 --retrain-from-scratch
 
 [pool]
-library = /nfs/ccoleylab001/dgraff/libraries/D4_140M.csv.gz
-fps = /nfs/ccoleylab001/dgraff/libraries/D4_140M.h5
+library = ...
+fps = ...
 --validated
 
 [encoder]
@@ -17,9 +17,9 @@ radius = 2
 
 [objective]
 objective = lookup
-lookup-path = /nfs/ccoleylab001/dgraff/data/D4_scores.csv.gz
-lookup-smiles-col = 0
-lookup-data-col = 1
+lookup-path = ...
+lookup-smiles-col = ...
+lookup-data-col = ...
 --minimize
 
 [stopping]

diff --git a/data/4UNN_Enamine10k_scores.csv.gz b/data/4UNN_Enamine10k_scores.csv.gz
diff --git a/data/4UNN_Enamine50k_scores.csv.gz b/data/4UNN_Enamine50k_scores.csv.gz
diff --git a/data/Enamine10k_scores.csv.gz b/data/Enamine10k_scores.csv.gz
diff --git a/data/Enamine50k_scores.csv.gz b/data/Enamine50k_scores.csv.gz
diff --git a/data/4UNN_EnamineHTS_scores.csv.gz → data/EnamineHTS_scores.csv.gz b/data/4UNN_EnamineHTS_scores.csv.gz → data/EnamineHTS_scores.csv.gz