Update config

README.md

@@ -24,7 +24,6 @@ You also need to install NVIDIA's SE(3)-Transformer (**please use SE3Transformer
 ```
 conda activate RF2NA
 cd SE3Transformer
-pip install --no-cache-dir -r requirements.txt
 python setup.py install
 cd ..
 ```

RF2na-linux.yml

@@ -1,24 +1,28 @@
 name: RF2NA
-channels:
-  - pytorch
-  - nvidia
-  - defaults
-  - conda-forge
 dependencies:
-  - python=3.10
+  - python==3.10.14
   - pip
-  - pytorch
-  - requests
-  - pytorch-cuda=11.7
-  - dglteam/label/cu117::dgl
-  - pyg::pyg
   - bioconda::mafft
   - bioconda::hhsuite
   - bioconda::blast
   - bioconda::hmmer>=3.3
   - bioconda::infernal
   - bioconda::cd-hit
   - bioconda::csblast
+  - conda-forge::llvm-openmp
   - pip:
+    - pandas
+    - torch==2.2.1 
+    - torchvision 
+    - torchaudio 
+    - torchdata 
+    - torch_geometric
     - psutil
-    - tqdm
+    - tqdm
+    - torchdata
+    - pydantic 
+    - e3nn 
+    - wandb 
+    - pynvml 
+    - git+https://github.com/NVIDIA/dllogger#egg=dllogger
+    - https://data.dgl.ai/wheels/cu121/dgl-2.0.0%2Bcu121-cp310-cp310-manylinux1_x86_64.whl

input_prep/make_rna_msa.sh

@@ -6,7 +6,7 @@ out_dir="$2"
 out_tag="$3"
 
 overwrite=true
-if [ -f $out_dir/$out_tag.afa -a $overwrite = false]
+if [ -f $out_dir/$out_tag.afa -a $overwrite == false ]
 then
     exit 0
 fi

network/predict.py

@@ -360,9 +360,12 @@ def _run_model(self, L_s, msa_orig, ins_orig, t1d, t2d, xyz_t, xyz, alpha_t, sam
 
     # Read template database
     FFDB = args.db
-    FFindexDB = namedtuple("FFindexDB", "index, data")
-    ffdb = FFindexDB(read_index(FFDB+'_pdb.ffindex'),
-                     read_data(FFDB+'_pdb.ffdata'))
+    if FFDB is not None:
+        FFindexDB = namedtuple("FFindexDB", "index, data")
+        ffdb = FFindexDB(read_index(FFDB+'_pdb.ffindex'),
+                         read_data(FFDB+'_pdb.ffdata'))
+    else:
+        ffdb = None
 
     if (torch.cuda.is_available()):
         print ("Running on GPU")

run_RF2NA.sh

@@ -6,9 +6,9 @@ set -e
 ############################################################
 # >>> conda initialize >>>
 # !! Contents within this block are managed by 'conda init' !!
-__conda_setup="$('conda' 'shell.bash' 'hook' 2> /dev/null)"
-eval "$__conda_setup"
-unset __conda_setup
+#__conda_setup="$('conda' 'shell.bash' 'hook' 2> /dev/null)"
+#eval "$__conda_setup"
+#unset __conda_setup
 # <<< conda initialize <<<
 ############################################################
 
@@ -22,7 +22,7 @@ MEM="64" # max memory (in GB)
 WDIR=`realpath -s $1`  # working folder
 mkdir -p $WDIR/log
 
-conda activate RF2NA
+#conda activate RF2NA
 
 # process protein (MSA + homology search)
 function proteinMSA {
@@ -36,7 +36,7 @@ function proteinMSA {
     then
         echo "Running HHblits"
         echo " -> Running command: $PIPEDIR/input_prep/make_protein_msa.sh $seqfile $WDIR $tag $CPU $MEM"
-        $PIPEDIR/input_prep/make_protein_msa.sh $seqfile $WDIR $tag $CPU $MEM > $WDIR/log/make_msa.$tag.stdout 2> $WDIR/log/make_msa.$tag.stderr
+        $PIPEDIR/input_prep/make_protein_msa.sh $seqfile $WDIR $tag $CPU $MEM > $WDIR/log/make_msa.$tag.stdout #2> $WDIR/log/make_msa.$tag.stderr
     fi
 
 
@@ -48,7 +48,7 @@ function proteinMSA {
         echo "Running hhsearch"
         HH="hhsearch -b 50 -B 500 -z 50 -Z 500 -mact 0.05 -cpu $CPU -maxmem $MEM -aliw 100000 -e 100 -p 5.0 -d $HHDB"
         echo " -> Running command: $HH -i $WDIR/$tag.msa0.ss2.a3m -o $WDIR/$tag.hhr -atab $WDIR/$tag.atab -v 0"
-        $HH -i $WDIR/$tag.msa0.a3m -o $WDIR/$tag.hhr -atab $WDIR/$tag.atab -v 0 > $WDIR/log/hhsearch.$tag.stdout 2> $WDIR/log/hhsearch.$tag.stderr
+        $HH -i $WDIR/$tag.msa0.a3m -o $WDIR/$tag.hhr -atab $WDIR/$tag.atab -v 0 > $WDIR/log/hhsearch.$tag.stdout #2> $WDIR/log/hhsearch.$tag.stderr
     fi
 }
 
@@ -64,7 +64,7 @@ function RNAMSA {
     then
         echo "Running rMSA (lite)"
         echo " -> Running command: $PIPEDIR/input_prep/make_rna_msa.sh $seqfile $WDIR $tag $CPU $MEM"
-        $PIPEDIR/input_prep/make_rna_msa.sh $seqfile $WDIR $tag $CPU $MEM > $WDIR/log/make_msa.$tag.stdout 2> $WDIR/log/make_msa.$tag.stderr
+        $PIPEDIR/input_prep/make_rna_msa.sh $seqfile $WDIR $tag $CPU $MEM > $WDIR/log/make_msa.$tag.stdout #2> $WDIR/log/make_msa.$tag.stderr
     fi
 }
 
@@ -85,24 +85,25 @@ do
 
     if [ $type = 'P' ]
     then
-        proteinMSA $fasta $tag
+        proteinMSA $fasta_name $tag
         argstring+="P:$WDIR/$tag.msa0.a3m:$WDIR/$tag.hhr:$WDIR/$tag.atab "
         nP=$((nP+1))
         lastP="$tag"
     elif [ $type = 'R' ]
     then
-        RNAMSA $fasta $tag
+        echo $fasta_name $tag
+        RNAMSA $fasta_name $tag
         argstring+="R:$WDIR/$tag.afa "
         nR=$((nR+1))
         lastR="$tag"
     elif [ $type = 'D' ]
     then
-        cp $fasta $WDIR/$tag.fa
+        cp $fasta_name $WDIR/$tag.fa
         argstring+="D:$WDIR/$tag.fa "
         nD=$((nD+2))
     elif [ $type = 'S' ]
     then
-        cp $fasta $WDIR/$tag.fa
+        cp $fasta_name $WDIR/$tag.fa
         argstring+="S:$WDIR/$tag.fa "
         nD=$((nD+1))
     fi