update installation scripts

Author: fspoendlin

.gitignore

@@ -1,3 +1,3 @@
 **/__pychache__/**
 **/*.pyc
-**.egg-info/
+**/*.egg-info/**

CALVADOS3_Fv/cleanup_amber.py …DOS3_Fv/CV3_Fv_pipeline/cleanup_amber.pyCALVADOS3_Fv/cleanup_amber.py renamed to CALVADOS3_Fv/CV3_Fv_pipeline/cleanup_amber.py CALVADOS3_Fv/cleanup_amber.py renamed to CALVADOS3_Fv/CV3_Fv_pipeline/cleanup_amber.py

@@ -11,8 +11,8 @@
 
 from pdbtools import pdb_selchain,pdb_selres,pdb_tofasta,pdb_keepcoord,pdb_reres,pdb_merge,pdb_chain,pdb_reatom,pdb_delhetatm,pdb_tidy,pdb_delelem
 
-# RELAX_path = os.path.abspath('/projects/prism/people/bqm193/software/CALVADOS/openmm_relax.py')
-RELAX_path = os.path.abspath('/vols/opig/projects/cagiada-CDRsimulations/analysis_files/CDRsimulations/CALVADOS/openmm_relax.py')
+SCRIPT_DIR = os.path.dirname(os.path.abspath(__file__))
+RELAX_path = os.path.abspath(f'{SCRIPT_DIR}/openmm_relax.py')
 
 def create_parser():
     def parse_tuple(value):

CALVADOS3_Fv/CV3_Fv_pipeline/imgt2relax2calvados3.py

@@ -1,5 +1,4 @@
-import argparse 
-import Bio.PDB as PDB
+import argparse
 import os
 
 from Bio.PDB import PDBParser, PDBIO, Select

CALVADOS3_Fv/openmm_relax.py …ADOS3_Fv/CV3_Fv_pipeline/openmm_relax.pyCALVADOS3_Fv/openmm_relax.py renamed to CALVADOS3_Fv/CV3_Fv_pipeline/openmm_relax.py CALVADOS3_Fv/openmm_relax.py renamed to CALVADOS3_Fv/CV3_Fv_pipeline/openmm_relax.py

@@ -3,13 +3,15 @@
 import subprocess
 import argparse
 
+SCRIPT_DIR = os.path.dirname(os.path.abspath(__file__))
+
 def create_parser():
     parser = argparse.ArgumentParser(description='Prepare script for Calvados2COM AB simulation')
     parser.add_argument('--temp', type=float, help='Temperature in K',default=293)
     parser.add_argument('--ionic', type=float, help='Ionic strength in molar',default=0.15)
     parser.add_argument('--pH', type=float, help='pH',default=7.0)
     parser.add_argument('--k-harmonic', type=float, help='Restraint force constant',default=700)
-    parser.add_argument('--fresidues-file', type=str, help='Residue definitions file',default='/projects/prism/people/bqm193/software/CALVADOS/residues_C3.csv')
+    parser.add_argument('--fresidues-file', type=str, help='Residue definitions file',default=f'{SCRIPT_DIR}/residues_C3.csv')
     parser.add_argument('--wfreq', type=int, help='DCD writing frequency',default=5000)
     parser.add_argument('--steps', type=int, help='Number of simulation steps (total: wfreq*steps)',default=1010)
     parser.add_argument('--platform', type=str, help='Platform (CPU or CUDA)',default='CPU')

CALVADOS3_Fv/convert_top.py

@@ -1,11 +1,10 @@
-import pandas as pd
 import subprocess
 import argparse
 import os
 
 argparser = argparse.ArgumentParser()
 argparser.add_argument('--simulation_dir', type=str)
-argparser.add_argument('--pdb_id', type=int)
+argparser.add_argument('--pdb_id', type=str)
 argparser.add_argument('--h_chain', type=str)
 argparser.add_argument('--l_chain', type=str)
 

CALVADOS3_Fv/prepare_ABrun.py

@@ -58,7 +58,7 @@ echo "[INFO] Creating constraints for contacts"
 python CALVADOS3_Fv/CV3_Fv_pipeline/pdb2ij_energy_relaxed.py --pdb-file ${OUTDIR}/${NAME}_Fv_${CHAINH}${CHAINL}.pdb --energy-HB-file ${OUTDIR}/${NAME}_Fv_${CHAINH}${CHAINL}_ij_energy.csv --out-dir ${OUTDIR} --map-file ${OUTDIR}/${NAME}_dict_Fv_${CHAINH}${CHAINL}.txt --chains ${CHAINH}${CHAINL}
 
 echo "[INFO] Preparing simulation"
-python CALVADOS3_Fv/prepare_ABrun.py --input-pdb ${OUTDIR}/${NAME}_Fv_${CHAINH}${CHAINL}.pdb --fdomains-file ${OUTDIR}/constraints_folded/${NAME}_Fv_${CHAINH}${CHAINL}_constraints.yaml --custom-restraints-file ${OUTDIR}/${NAME}_Fv_${CHAINH}${CHAINL}_ij_energy_contact.csv --out-dir $OUTDIR --fresidues-file /vols/opig/projects/cagiada-CDRsimulations/analysis_files/CDRsimulations/CALVADOS/residues_C3.csv #--steps 3010
+python CALVADOS3_Fv/prepare_ABrun.py --input-pdb ${OUTDIR}/${NAME}_Fv_${CHAINH}${CHAINL}.pdb --fdomains-file ${OUTDIR}/constraints_folded/${NAME}_Fv_${CHAINH}${CHAINL}_constraints.yaml --custom-restraints-file ${OUTDIR}/${NAME}_Fv_${CHAINH}${CHAINL}_ij_energy_contact.csv --out-dir $OUTDIR
 
 echo "[INFO] Running simulation"
 cd $OUTDIR

scripts/convert2all_atom.py

@@ -1,20 +1,20 @@
 #!/usr/bin/env bash
 
 ### script to install environments for simulation
-
+eval "$(conda shell.bash hook)"
 
 ## prep environment
 echo "[INFO] Setting up prep_env"
 # For prep environment install openmm 8.2.0 (in yaml) from pip followed by openmm 7.7.0
 # This is a hack for a current issue and will be fixed in future releases
 conda env create -f prep_env.yaml
 conda activate prep_env
-conda install openmm=7.7.0
+conda install -c conda-forge openmm=7.7.0
 conda deactivate
 
 
-## calvados environment
-echo "[INFO] Setting up calvados environment"
+# ## calvados environment
+# echo "[INFO] Setting up calvados environment"
 conda create -n calvados python=3.10 -y
 conda activate calvados
 cd CALVADOS3_Fv
@@ -28,10 +28,10 @@ echo "[INFO] Setting up cg2all environment"
 # This is an example with cudatoolkit=11.3.
 # Set a proper cudatoolkit version that is compatible with your CUDA driver and DGL library.
 # dgl>=1.1 occasionally raises some errors, so please use dgl<=1.0.
-conda create --name cg2all pip cudatoolkit=12.8 dgl=1.0 -c dglteam/label/cu128 python=3.10 -y
+conda create --name cg2all pip cudatoolkit=11.3 dgl=1.0 -c dglteam/label/cu113 -y
 conda activate cg2all
-pip install git+http://github.com/huhlim/cg2all
-pip install pandas
+pip install git+https://github.com/huhlim/cg2all.git@cuda-12
+conda install -c conda-forge biopython MDAnalysis -y
 conda deactivate
 
 echo "Done"