From 986613c96c9660a52653cbde0cf9f27cc90ac726 Mon Sep 17 00:00:00 2001 From: "Frolov, Andrey" Date: Wed, 19 Jan 2022 15:06:25 +0100 Subject: [PATCH] Renamed to dimorphite_dl_pka --- AUTHORS.md | 4 +- CHANGES.md | 2 +- README.md | 2 +- .../.gitignore | 0 .../README.md | 2 +- .../__init__.py | 0 .../dimorphite_dl.py | 0 .../dimorphite_dl.py.initial | 0 ...dimorphite_dl_site_substructures_smarts.py | 0 .../sample_molecules.smi | 0 .../site_substructures.smarts | 0 peptide_tools_master/README.md | 4 +- peptide_tools_master/SOURCEME.sh | 2 +- rdkit_pI/README.md | 2 +- rdkit_pI/TEST/TMP_CLAB_OUTPUT.txt | 45 ------------------- rdkit_pI/TEST/TMP_SMI_FOR_PKA.smi | 2 - rdkit_pI/TEST/run_pI.sh | 4 +- requirements.txt | 4 +- 18 files changed, 13 insertions(+), 60 deletions(-) rename {dimorphite_dl-1.2.4_for_rdkit_pI => dimorphite_dl_pka}/.gitignore (100%) rename {dimorphite_dl-1.2.4_for_rdkit_pI => dimorphite_dl_pka}/README.md (98%) rename {dimorphite_dl-1.2.4_for_rdkit_pI => dimorphite_dl_pka}/__init__.py (100%) rename {dimorphite_dl-1.2.4_for_rdkit_pI => dimorphite_dl_pka}/dimorphite_dl.py (100%) rename {dimorphite_dl-1.2.4_for_rdkit_pI => dimorphite_dl_pka}/dimorphite_dl.py.initial (100%) rename {dimorphite_dl-1.2.4_for_rdkit_pI => dimorphite_dl_pka}/dimorphite_dl_site_substructures_smarts.py (100%) rename {dimorphite_dl-1.2.4_for_rdkit_pI => dimorphite_dl_pka}/sample_molecules.smi (100%) rename {dimorphite_dl-1.2.4_for_rdkit_pI => dimorphite_dl_pka}/site_substructures.smarts (100%) delete mode 100644 rdkit_pI/TEST/TMP_CLAB_OUTPUT.txt delete mode 100644 rdkit_pI/TEST/TMP_SMI_FOR_PKA.smi diff --git a/AUTHORS.md b/AUTHORS.md index f887c2c..d81d524 100644 --- 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 index bb5eeff..affa2ac 100644 --- 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 index 7419d03..94cbc0f 100644 --- 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 b/dimorphite_dl_pka/.gitignore similarity index 100% rename from dimorphite_dl-1.2.4_for_rdkit_pI/.gitignore rename to dimorphite_dl_pka/.gitignore diff --git a/dimorphite_dl-1.2.4_for_rdkit_pI/README.md b/dimorphite_dl_pka/README.md similarity index 98% rename from dimorphite_dl-1.2.4_for_rdkit_pI/README.md rename to dimorphite_dl_pka/README.md index 29f78ef..71b54e5 100644 --- a/dimorphite_dl-1.2.4_for_rdkit_pI/README.md +++ b/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 b/dimorphite_dl_pka/__init__.py similarity index 100% rename from dimorphite_dl-1.2.4_for_rdkit_pI/__init__.py rename to dimorphite_dl_pka/__init__.py diff --git a/dimorphite_dl-1.2.4_for_rdkit_pI/dimorphite_dl.py b/dimorphite_dl_pka/dimorphite_dl.py similarity index 100% rename from dimorphite_dl-1.2.4_for_rdkit_pI/dimorphite_dl.py rename to dimorphite_dl_pka/dimorphite_dl.py diff --git a/dimorphite_dl-1.2.4_for_rdkit_pI/dimorphite_dl.py.initial b/dimorphite_dl_pka/dimorphite_dl.py.initial similarity index 100% rename from dimorphite_dl-1.2.4_for_rdkit_pI/dimorphite_dl.py.initial rename to dimorphite_dl_pka/dimorphite_dl.py.initial diff --git a/dimorphite_dl-1.2.4_for_rdkit_pI/dimorphite_dl_site_substructures_smarts.py b/dimorphite_dl_pka/dimorphite_dl_site_substructures_smarts.py similarity index 100% rename from dimorphite_dl-1.2.4_for_rdkit_pI/dimorphite_dl_site_substructures_smarts.py rename to dimorphite_dl_pka/dimorphite_dl_site_substructures_smarts.py diff --git a/dimorphite_dl-1.2.4_for_rdkit_pI/sample_molecules.smi b/dimorphite_dl_pka/sample_molecules.smi similarity index 100% rename from dimorphite_dl-1.2.4_for_rdkit_pI/sample_molecules.smi rename to dimorphite_dl_pka/sample_molecules.smi diff --git a/dimorphite_dl-1.2.4_for_rdkit_pI/site_substructures.smarts b/dimorphite_dl_pka/site_substructures.smarts similarity index 100% rename from dimorphite_dl-1.2.4_for_rdkit_pI/site_substructures.smarts rename to dimorphite_dl_pka/site_substructures.smarts diff --git a/peptide_tools_master/README.md b/peptide_tools_master/README.md index 7f92650..993362c 100644 --- 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 index 9904816..442e318 100644 --- 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 index 5ddf6da..5bddc79 100644 --- 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 deleted file mode 100644 index 8473840..0000000 --- a/rdkit_pI/TEST/TMP_CLAB_OUTPUT.txt +++ /dev/null @@ -1,45 +0,0 @@ -PKA: Calculate apparent values using classic algorithm -1 ID: 1 -1 ACD_pKa_IonicForm_Apparent: HL -1 ACD_pKa_Apparent_1: 14.778 -1 ACD_pKa_Error_Apparent_1: 0.46 -1 ACD_pKa_DissAtom_Apparent_1: 4 -1 ACD_pKa_DissType_Apparent_1: MA -1 ACD_pKa_Equation_Apparent_1: HL/H+L -1 ACD_pKa_AccuracyExplanation_Apparent_1: Adjacent Reaction Center ; Strong Hammet Equation -1 ACD_pKa_All_Apparent_1: pKa(HL/H+L; 4) = 14.78+/-0.46 -1 ACD_pKa_Apparent_2: 10.061 -1 ACD_pKa_Error_Apparent_2: 0.10 -1 ACD_pKa_DissAtom_Apparent_2: 9 -1 ACD_pKa_DissType_Apparent_2: MB -1 ACD_pKa_Equation_Apparent_2: H2L/H+HL -1 ACD_pKa_All_Apparent_2: pKa(H2L/H+HL; 9) = 10.06+/-0.10 -1 ACD_pKa_Apparent_3: -0.867 -1 ACD_pKa_Error_Apparent_3: 0.70 -1 ACD_pKa_DissAtom_Apparent_3: 4 -1 ACD_pKa_DissType_Apparent_3: B -1 ACD_pKa_Equation_Apparent_3: H3L/H+H2L -1 ACD_pKa_AccuracyExplanation_Apparent_3: Adjacent Reaction Center -1 ACD_pKa_All_Apparent_3: pKa(H3L/H+H2L; 4) = -0.87+/-0.70 -2 ID: 2 -2 ACD_pKa_IonicForm_Apparent: H2L -2 ACD_pKa_Apparent_1: 14.109 -2 ACD_pKa_Error_Apparent_1: 0.46 -2 ACD_pKa_DissAtom_Apparent_1: 4 -2 ACD_pKa_DissType_Apparent_1: A -2 ACD_pKa_Equation_Apparent_1: HL/H+L -2 ACD_pKa_AccuracyExplanation_Apparent_1: Adjacent Reaction Center ; Strong Hammet Equation -2 ACD_pKa_All_Apparent_1: pKa(HL/H+L; 4) = 14.11+/-0.46 -2 ACD_pKa_Apparent_2: 4.327 -2 ACD_pKa_Error_Apparent_2: 0.21 -2 ACD_pKa_DissAtom_Apparent_2: 10 -2 ACD_pKa_DissType_Apparent_2: MA -2 ACD_pKa_Equation_Apparent_2: H2L/H+HL -2 ACD_pKa_All_Apparent_2: pKa(H2L/H+HL; 10) = 4.33+/-0.21 -2 ACD_pKa_Apparent_3: -1.041 -2 ACD_pKa_Error_Apparent_3: 0.70 -2 ACD_pKa_DissAtom_Apparent_3: 4 -2 ACD_pKa_DissType_Apparent_3: MB -2 ACD_pKa_Equation_Apparent_3: H3L/H+H2L -2 ACD_pKa_AccuracyExplanation_Apparent_3: Adjacent Reaction Center -2 ACD_pKa_All_Apparent_3: pKa(H3L/H+H2L; 4) = -1.04+/-0.70 diff --git a/rdkit_pI/TEST/TMP_SMI_FOR_PKA.smi b/rdkit_pI/TEST/TMP_SMI_FOR_PKA.smi deleted file mode 100644 index bc086fd..0000000 --- a/rdkit_pI/TEST/TMP_SMI_FOR_PKA.smi +++ /dev/null @@ -1,2 +0,0 @@ -CC(=O)N[C@@H](CCCN)C(C)=O tmpname1 -CC(=O)N[C@@](C)(CC(=O)O)C(C)=O tmpname2 diff --git a/rdkit_pI/TEST/run_pI.sh b/rdkit_pI/TEST/run_pI.sh index 6056c4e..0eb30de 100755 --- 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 index 53f7a39..3d82919 100644 --- 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/