From 079d7ef32e168f2c253cd0c167219fe2d79a5f5c Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?S=C3=B6ren=20von=20B=C3=BClow?= <soren.bulow@bio.ku.dk>
Date: Tue, 15 Apr 2025 14:54:08 +0200
Subject: [PATCH] Remove top level prepare

---
 prepare.py         | 62 ----------------------------------------------
 prepare_minimal.py | 36 ---------------------------
 2 files changed, 98 deletions(-)
 delete mode 100644 prepare.py
 delete mode 100644 prepare_minimal.py

diff --git a/prepare.py b/prepare.py
deleted file mode 100644
index a828528..0000000
--- a/prepare.py
+++ /dev/null
@@ -1,62 +0,0 @@
-import os
-from calvados.cfg import Config, Job, Components
-import subprocess
-
-cwd = os.getcwd()
-
-config = Config(
-  # GENERAL
-  sysname = 'test', # name of simulation system
-  box = [25., 25., 150.], # nm
-  temp = 293, # K
-  ionic = 0.15, # molar
-  pH = 7.0,
-  topol = 'slab',
-
-  # RUNTIME SETTINGS
-  wfreq = 1000, # dcd writing frequency, 1 = 10fs
-  steps = 100000, # number of simulation steps
-  runtime = 0, # overwrites 'steps' keyword if > 0
-  platform = 'CPU', # 'CUDA'
-  restart = None,
-  verbose = True,
-  threads = 1,
-)
-
-job = Job(
-  batch_sys = 'SLURM', # PBS
-  envname = 'calvados', # conda environment
-  template = 'robust.jinja',
-  fbash = '/home/sobuelow/.bashrc', # path to .bashrc
-)
-
-# PATH
-path = f'{cwd}/{config.config["sysname"]}'
-subprocess.run(f'mkdir -p {path}',shell=True)
-
-config.write(path,name='config.yaml')
-
-components = Components(
-  # Defaults
-  molecule_type = 'protein',
-  nmol = 1, # number of molecules
-  restraint = False, # apply restraints
-  restraint_type = 'harmonic',
-  charge_termini = 'both', # charge N or C or both
-  use_com = True, # center-of-mass (only if read from PDB)
-  colabfold = 1, # PAE format (EBI AF=0, Colabfold=1&2)
-  k_harmonic = 700., # Restraint force constant
-  # INPUT
-  ffasta = f'{cwd}/test.fasta', # input fasta file
-  fresidues = f'{cwd}/residues_C3.csv', # residue definitions
-  pdb_folder = f'{cwd}/pdbs', # directory for pdb and PAE files
-  fdomains = f'{cwd}/domains.yaml', # domain definitions (harmonic restraints)
-)
-
-components.add(name='hSUMO_hnRNPA1S', nmol=1, restraint=True)
-components.add(name='Gal3', nmol=5, charge_termini='C')
-
-components.write(path,name='components.yaml')
-
-job.write(path,config,components,name='job.sh')
-# job.submit(path,njobs=3)
diff --git a/prepare_minimal.py b/prepare_minimal.py
deleted file mode 100644
index 8b44c4a..0000000
--- a/prepare_minimal.py
+++ /dev/null
@@ -1,36 +0,0 @@
-import os
-from calvados.cfg import Config, Job, Components
-import subprocess
-
-cwd = os.getcwd()
-
-config = Config(
-  # GENERAL
-  sysname = 'test_A1', # name of simulation system
-  box = [25., 25., 25.], # nm
-  temp = 293, # K
-  ionic = 0.15, # molar
-  pH = 7.0,
-
-
-  # RUNTIME SETTINGS
-  wfreq = 1000, # dcd writing frequency, 1 = 10fs
-  steps = 100000, # number of simulation steps
-)
-
-# PATH
-path = f'{cwd}/{config.config["sysname"]}'
-subprocess.run(f'mkdir -p {path}',shell=True)
-
-config.write(path,name='config.yaml')
-
-components = Components(
-    # INPUT
-  ffasta = f'{cwd}/test.fasta', # input fasta file
-  fresidues = f'{cwd}/residues.csv', # residue definitions
-)
-components.add(name='A1', nmol=1, restraint=False, charge_termini='both')
-components.write(path,name='components.yaml')
-
-# navigate to path followed by
-# python run.py