Renamed to dimorphite_dl_pka

AstraZeneca · Jan 19, 2022 · 986613c · 986613c
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diff --git a/AUTHORS.md b/AUTHORS.md
@@ -16,7 +16,7 @@ smi2scrambledfasta_v1.0/
     Andrey I. Frolov
     Johan Ulander - contributed idea to do SMARTS pattern matching Smiles into scrambled FASTA
 
-dimorphite_dl-1.2.4_for_rdkit_pI/
-    Andrey I. Frolov - changes for dimorphite_dl-1.2.4_for_rdkit_pI
+dimorphite_dl_pka/
+    Andrey I. Frolov - changes for dimorphite_dl_pka
     Contributors to the original dimorphite_dl-1.2.4 repo: Jacob Durrant, Jesse Kaminsky, Patrick Ropp, Jacob Spiegel, Sara Yablonski
 
diff --git a/CHANGES.md b/CHANGES.md
@@ -38,7 +38,7 @@ smi2scrambledfasta_v1.0/
 
 
 
-dimorphite_dl-1.2.4_for_rdkit_pI/
+dimorphite_dl_pka/
 
 1.2.4_for_rdkit_pI
 -----

diff --git a/README.md b/README.md
@@ -18,7 +18,7 @@ OVERVIEW
     4) extn_coeff_fasta_v2.1  (depends on 2)
     program to calculate extinction coefficients.
 
-    5) dimorphite_dl-1.2.4_for_rdkit_pI  
+    5) dimorphite_dl_pka  
     slightly modified version of the Dimorphite_DL-1.2.4 code, avaialble on GitHub, to enable pKa predition of unknown nonatural amino-acids side-chains.  
     https://github.com/UnixJunkie/dimorphite_dl
 

diff --git a/dimorphite_dl-1.2.4_for_rdkit_pI/.gitignore → dimorphite_dl_pka/.gitignore b/dimorphite_dl-1.2.4_for_rdkit_pI/.gitignore → dimorphite_dl_pka/.gitignore
diff --git a/dimorphite_dl-1.2.4_for_rdkit_pI/README.md → dimorphite_dl_pka/README.md b/dimorphite_dl-1.2.4_for_rdkit_pI/README.md → dimorphite_dl_pka/README.md
@@ -1,4 +1,4 @@
-dimorphite_dl-1.2.4_for_rdkit_pI
+dimorphite_dl_pka
 ===================
 
 What is it?

diff --git a/dimorphite_dl-1.2.4_for_rdkit_pI/__init__.py → dimorphite_dl_pka/__init__.py b/dimorphite_dl-1.2.4_for_rdkit_pI/__init__.py → dimorphite_dl_pka/__init__.py
diff --git a/...te_dl-1.2.4_for_rdkit_pI/dimorphite_dl.py → dimorphite_dl_pka/dimorphite_dl.py b/...te_dl-1.2.4_for_rdkit_pI/dimorphite_dl.py → dimorphite_dl_pka/dimorphite_dl.py
diff --git a/...2.4_for_rdkit_pI/dimorphite_dl.py.initial → dimorphite_dl_pka/dimorphite_dl.py.initial b/...2.4_for_rdkit_pI/dimorphite_dl.py.initial → dimorphite_dl_pka/dimorphite_dl.py.initial
diff --git a/...imorphite_dl_site_substructures_smarts.py → ...imorphite_dl_site_substructures_smarts.py b/...imorphite_dl_site_substructures_smarts.py → ...imorphite_dl_site_substructures_smarts.py
diff --git a/...l-1.2.4_for_rdkit_pI/sample_molecules.smi → dimorphite_dl_pka/sample_molecules.smi b/...l-1.2.4_for_rdkit_pI/sample_molecules.smi → dimorphite_dl_pka/sample_molecules.smi
diff --git a/....4_for_rdkit_pI/site_substructures.smarts → dimorphite_dl_pka/site_substructures.smarts b/....4_for_rdkit_pI/site_substructures.smarts → dimorphite_dl_pka/site_substructures.smarts
diff --git a/peptide_tools_master/README.md b/peptide_tools_master/README.md
@@ -18,7 +18,7 @@ HOW TO RUN
     export PYTHONPATH=${PYTHONPATH}:${PEPTIDE_TOOLS_PATH}/../smi2scrambledfasta_v1.0
     export PYTHONPATH=${PYTHONPATH}:${PEPTIDE_TOOLS_PATH}/../extn_coeff_fasta_v2.2
     export PYTHONPATH=${PYTHONPATH}:${PEPTIDE_TOOLS_PATH}/../pI_fasta_v1.4
-    export PYTHONPATH=${PYTHONPATH}:${PEPTIDE_TOOLS_PATH}/../dimorphite_dl-1.2.4_for_rdkit_pI
+    export PYTHONPATH=${PYTHONPATH}:${PEPTIDE_TOOLS_PATH}/../dimorphite_dl_pka
     export PYTHONPATH=${PYTHONPATH}:${PEPTIDE_TOOLS_PATH}/../rdkit_pI_v3.2
 
     ### Example peptide structure
@@ -42,7 +42,7 @@ DEPENDENCIES
         acdperceptabatch     # "perceptabat" executable should be callable
 
     if --use_dimorphite enabled:
-        dimorphite_dl-1.2.4_for_rdkit_pI
+        dimorphite_dl_pka
 
 
 PLATFORM

diff --git a/peptide_tools_master/SOURCEME.sh b/peptide_tools_master/SOURCEME.sh
@@ -10,7 +10,7 @@ PEPTIDE_TOOLS_PATH=`echo $PWD`
 export PYTHONPATH=${PYTHONPATH}:${PEPTIDE_TOOLS_PATH}/../smi2scrambledfasta_v1.0
 export PYTHONPATH=${PYTHONPATH}:${PEPTIDE_TOOLS_PATH}/../extn_coeff_fasta_v2.2
 export PYTHONPATH=${PYTHONPATH}:${PEPTIDE_TOOLS_PATH}/../pI_fasta_v1.4
-export PYTHONPATH=${PYTHONPATH}:${PEPTIDE_TOOLS_PATH}/../dimorphite_dl-1.2.4_for_rdkit_pI
+export PYTHONPATH=${PYTHONPATH}:${PEPTIDE_TOOLS_PATH}/../dimorphite_dl_pka
 export PYTHONPATH=${PYTHONPATH}:${PEPTIDE_TOOLS_PATH}/../rdkit_pI_v3.2
 
 ### Example peptide structure

diff --git a/rdkit_pI/README.md b/rdkit_pI/README.md
@@ -34,7 +34,7 @@ DEPENDENCIES
         acdperceptabatch     # "perceptabat" executable should be callable
 
     if --use_dimorphite enabled:
-        dimorphite_dl-1.2.4_for_rdkit_pI
+        dimorphite_dl_pka
 
 
 PLATFORM

diff --git a/rdkit_pI/TEST/TMP_CLAB_OUTPUT.txt b/rdkit_pI/TEST/TMP_CLAB_OUTPUT.txt
diff --git a/rdkit_pI/TEST/TMP_SMI_FOR_PKA.smi b/rdkit_pI/TEST/TMP_SMI_FOR_PKA.smi
diff --git a/rdkit_pI/TEST/run_pI.sh b/rdkit_pI/TEST/run_pI.sh
@@ -1,11 +1,11 @@
 # example usage. currently set to run from teh "rdkit_pI" folder.
 # Make sure to have RDkit avaialble. 
-# Make sure to set teh proper path to dimorphite_dl-1.2.4_for_rdkit_pI (see below) - if intent to use it.
+# Make sure to set teh proper path to dimorphite_dl_pka (see below) - if intent to use it.
 # Or make sure to have ACD Perceptabat avaialble - if intent to use it. 
 
 module load rdkit
 #module load acdperceptabatch
-export PYTHONPATH=$PYTHONPATH:${pwd}/../dimorphite_dl-1.2.4_for_rdkit_pI
+export PYTHONPATH=$PYTHONPATH:${pwd}/../dimorphite_dl_pka
 
 i=$1
 o=$2

diff --git a/requirements.txt b/requirements.txt
@@ -7,7 +7,7 @@ peptide_tools_master_v1.0/
     and all tools below
 
 
-dimorphite_dl-1.2.4_for_rdkit_pI/
+dimorphite_dl_pka/
 
     Python3
     check this for the original repo:
@@ -38,7 +38,7 @@ rdkit_pI_v3.2/
         acdperceptabatch     # "perceptabat" executable should be callable
 
     if --use_dimorphite enabled:
-        dimorphite_dl-1.2.4_for_rdkit_pI
+        dimorphite_dl_pka
 
 smi2scrambledfasta_v1.0/