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.pytest_cache/.gitignore

@@ -1,2 +0,0 @@
-# Created by pytest automatically.
-*

.pytest_cache/CACHEDIR.TAG

@@ -1,4 +0,0 @@
-Signature: 8a477f597d28d172789f06886806bc55
-# This file is a cache directory tag created by pytest.
-# For information about cache directory tags, see:
-#	https://bford.info/cachedir/spec.html

.pytest_cache/README.md

@@ -1,8 +0,0 @@
-# pytest cache directory #
-
-This directory contains data from the pytest's cache plugin,
-which provides the `--lf` and `--ff` options, as well as the `cache` fixture.
-
-**Do not** commit this to version control.
-
-See [the docs](https://docs.pytest.org/en/stable/how-to/cache.html) for more information.

.pytest_cache/v/cache/lastfailed

@@ -1 +0,0 @@
-{}

.pytest_cache/v/cache/nodeids

@@ -1,30 +0,0 @@
-[
-  "tests/test_backend_diagnostic_logic.py::TestBackendDiagnosticLogic::test_compute_rank_percentile",
-  "tests/test_backend_diagnostic_logic.py::TestBackendDiagnosticLogic::test_manual_agents_check_exists",
-  "tests/test_backend_diagnostic_logic.py::TestBackendDiagnosticLogic::test_recommend_toolchain_runtime_penalty",
-  "tests/test_backend_diagnostic_logic.py::TestBackendDiagnosticLogic::test_required_schema_constants_nonempty",
-  "tests/test_backend_diagnostic_logic.py::TestBackendDiagnosticLogic::test_select_suspicious",
-  "tests/test_backend_diagnostic_logic.py::TestBackendDiagnosticLogic::test_validate_required_columns",
-  "tests/test_pocket_modes.py::TestPocketModes::test_reference_complex_mode_uses_crystal_ligand",
-  "tests/test_pocket_modes.py::TestPocketModes::test_reference_mode_falls_back_to_receptor_centroid",
-  "tests/test_pocket_modes.py::TestPocketModes::test_relaxed_mode_increases_radius",
-  "tests/test_pocket_modes.py::TestPocketModes::test_user_fixed_override_precedence",
-  "tests/test_rdock_backend.py::TestRDockBackend::test_real_rdock_execution_and_provenance",
-  "tests/test_rdock_fixed_pocket.py::TestRDockFixedPocket::test_pocket_spec_stable_across_runs",
-  "tests/test_rdock_fixed_pocket.py::TestRDockFixedPocket::test_user_fixed_pocket_writes_sphere_mapper",
-  "tests/test_rdock_output_parsing_real.py::TestRDockOutputParsingReal::test_parser_reads_real_rdock_score_field",
-  "tests/test_rdock_real_execution.py::TestRDockRealExecution::test_rbcavity_and_rbdock_generate_real_outputs",
-  "tests/test_redocking_validation_guards.py::TestRedockingValidationGuards::test_attempt_bounds_guard",
-  "tests/test_redocking_validation_guards.py::TestRedockingValidationGuards::test_backend_guard",
-  "tests/test_reference_rank_resolution.py::TestReferenceRankResolution::test_falls_back_to_run_rank_when_oracle_missing",
-  "tests/test_reference_rank_resolution.py::TestReferenceRankResolution::test_missing_reference",
-  "tests/test_reference_rank_resolution.py::TestReferenceRankResolution::test_uses_oracle_when_available",
-  "tests/test_smina_backend_timeout.py::test_smina_timeout_returns_failed_row",
-  "tests/test_smina_score_parsing.py::TestSminaScoreParsing::test_parses_affinity_score_only_line",
-  "tests/test_smina_score_parsing.py::TestSminaScoreParsing::test_parses_minimized_affinity",
-  "tests/test_smina_score_parsing.py::TestSminaScoreParsing::test_parses_mode_table",
-  "tests/test_smina_score_parsing.py::TestSminaScoreParsing::test_parses_vina_result",
-  "tests/test_smina_score_parsing.py::TestSminaScoreParsing::test_returns_nan_when_no_score",
-  "tests/test_strict_backend_cleanup.py::TestStrictBackendCleanup::test_haddock_wrapper_removed",
-  "tests/test_strict_backend_cleanup.py::TestStrictBackendCleanup::test_thread_policy_formula_85pct"
-]

.venv_haddock/bin/Activate.ps1

@@ -1,247 +0,0 @@
-<#
-.Synopsis
-Activate a Python virtual environment for the current PowerShell session.
-
-.Description
-Pushes the python executable for a virtual environment to the front of the
-$Env:PATH environment variable and sets the prompt to signify that you are
-in a Python virtual environment. Makes use of the command line switches as
-well as the `pyvenv.cfg` file values present in the virtual environment.
-
-.Parameter VenvDir
-Path to the directory that contains the virtual environment to activate. The
-default value for this is the parent of the directory that the Activate.ps1
-script is located within.
-
-.Parameter Prompt
-The prompt prefix to display when this virtual environment is activated. By
-default, this prompt is the name of the virtual environment folder (VenvDir)
-surrounded by parentheses and followed by a single space (ie. '(.venv) ').
-
-.Example
-Activate.ps1
-Activates the Python virtual environment that contains the Activate.ps1 script.
-
-.Example
-Activate.ps1 -Verbose
-Activates the Python virtual environment that contains the Activate.ps1 script,
-and shows extra information about the activation as it executes.
-
-.Example
-Activate.ps1 -VenvDir C:\Users\MyUser\Common\.venv
-Activates the Python virtual environment located in the specified location.
-
-.Example
-Activate.ps1 -Prompt "MyPython"
-Activates the Python virtual environment that contains the Activate.ps1 script,
-and prefixes the current prompt with the specified string (surrounded in
-parentheses) while the virtual environment is active.
-
-.Notes
-On Windows, it may be required to enable this Activate.ps1 script by setting the
-execution policy for the user. You can do this by issuing the following PowerShell
-command:
-
-PS C:\> Set-ExecutionPolicy -ExecutionPolicy RemoteSigned -Scope CurrentUser
-
-For more information on Execution Policies: 
-https://go.microsoft.com/fwlink/?LinkID=135170
-
-#>
-Param(
-    [Parameter(Mandatory = $false)]
-    [String]
-    $VenvDir,
-    [Parameter(Mandatory = $false)]
-    [String]
-    $Prompt
-)
-
-<# Function declarations --------------------------------------------------- #>
-
-<#
-.Synopsis
-Remove all shell session elements added by the Activate script, including the
-addition of the virtual environment's Python executable from the beginning of
-the PATH variable.
-
-.Parameter NonDestructive
-If present, do not remove this function from the global namespace for the
-session.
-
-#>
-function global:deactivate ([switch]$NonDestructive) {
-    # Revert to original values
-
-    # The prior prompt:
-    if (Test-Path -Path Function:_OLD_VIRTUAL_PROMPT) {
-        Copy-Item -Path Function:_OLD_VIRTUAL_PROMPT -Destination Function:prompt
-        Remove-Item -Path Function:_OLD_VIRTUAL_PROMPT
-    }
-
-    # The prior PYTHONHOME:
-    if (Test-Path -Path Env:_OLD_VIRTUAL_PYTHONHOME) {
-        Copy-Item -Path Env:_OLD_VIRTUAL_PYTHONHOME -Destination Env:PYTHONHOME
-        Remove-Item -Path Env:_OLD_VIRTUAL_PYTHONHOME
-    }
-
-    # The prior PATH:
-    if (Test-Path -Path Env:_OLD_VIRTUAL_PATH) {
-        Copy-Item -Path Env:_OLD_VIRTUAL_PATH -Destination Env:PATH
-        Remove-Item -Path Env:_OLD_VIRTUAL_PATH
-    }
-
-    # Just remove the VIRTUAL_ENV altogether:
-    if (Test-Path -Path Env:VIRTUAL_ENV) {
-        Remove-Item -Path env:VIRTUAL_ENV
-    }
-
-    # Just remove VIRTUAL_ENV_PROMPT altogether.
-    if (Test-Path -Path Env:VIRTUAL_ENV_PROMPT) {
-        Remove-Item -Path env:VIRTUAL_ENV_PROMPT
-    }
-
-    # Just remove the _PYTHON_VENV_PROMPT_PREFIX altogether:
-    if (Get-Variable -Name "_PYTHON_VENV_PROMPT_PREFIX" -ErrorAction SilentlyContinue) {
-        Remove-Variable -Name _PYTHON_VENV_PROMPT_PREFIX -Scope Global -Force
-    }
-
-    # Leave deactivate function in the global namespace if requested:
-    if (-not $NonDestructive) {
-        Remove-Item -Path function:deactivate
-    }
-}
-
-<#
-.Description
-Get-PyVenvConfig parses the values from the pyvenv.cfg file located in the
-given folder, and returns them in a map.
-
-For each line in the pyvenv.cfg file, if that line can be parsed into exactly
-two strings separated by `=` (with any amount of whitespace surrounding the =)
-then it is considered a `key = value` line. The left hand string is the key,
-the right hand is the value.
-
-If the value starts with a `'` or a `"` then the first and last character is
-stripped from the value before being captured.
-
-.Parameter ConfigDir
-Path to the directory that contains the `pyvenv.cfg` file.
-#>
-function Get-PyVenvConfig(
-    [String]
-    $ConfigDir
-) {
-    Write-Verbose "Given ConfigDir=$ConfigDir, obtain values in pyvenv.cfg"
-
-    # Ensure the file exists, and issue a warning if it doesn't (but still allow the function to continue).
-    $pyvenvConfigPath = Join-Path -Resolve -Path $ConfigDir -ChildPath 'pyvenv.cfg' -ErrorAction Continue
-
-    # An empty map will be returned if no config file is found.
-    $pyvenvConfig = @{ }
-
-    if ($pyvenvConfigPath) {
-
-        Write-Verbose "File exists, parse `key = value` lines"
-        $pyvenvConfigContent = Get-Content -Path $pyvenvConfigPath
-
-        $pyvenvConfigContent | ForEach-Object {
-            $keyval = $PSItem -split "\s*=\s*", 2
-            if ($keyval[0] -and $keyval[1]) {
-                $val = $keyval[1]
-
-                # Remove extraneous quotations around a string value.
-                if ("'""".Contains($val.Substring(0, 1))) {
-                    $val = $val.Substring(1, $val.Length - 2)
-                }
-
-                $pyvenvConfig[$keyval[0]] = $val
-                Write-Verbose "Adding Key: '$($keyval[0])'='$val'"
-            }
-        }
-    }
-    return $pyvenvConfig
-}
-
-
-<# Begin Activate script --------------------------------------------------- #>
-
-# Determine the containing directory of this script
-$VenvExecPath = Split-Path -Parent $MyInvocation.MyCommand.Definition
-$VenvExecDir = Get-Item -Path $VenvExecPath
-
-Write-Verbose "Activation script is located in path: '$VenvExecPath'"
-Write-Verbose "VenvExecDir Fullname: '$($VenvExecDir.FullName)"
-Write-Verbose "VenvExecDir Name: '$($VenvExecDir.Name)"
-
-# Set values required in priority: CmdLine, ConfigFile, Default
-# First, get the location of the virtual environment, it might not be
-# VenvExecDir if specified on the command line.
-if ($VenvDir) {
-    Write-Verbose "VenvDir given as parameter, using '$VenvDir' to determine values"
-}
-else {
-    Write-Verbose "VenvDir not given as a parameter, using parent directory name as VenvDir."
-    $VenvDir = $VenvExecDir.Parent.FullName.TrimEnd("\\/")
-    Write-Verbose "VenvDir=$VenvDir"
-}
-
-# Next, read the `pyvenv.cfg` file to determine any required value such
-# as `prompt`.
-$pyvenvCfg = Get-PyVenvConfig -ConfigDir $VenvDir
-
-# Next, set the prompt from the command line, or the config file, or
-# just use the name of the virtual environment folder.
-if ($Prompt) {
-    Write-Verbose "Prompt specified as argument, using '$Prompt'"
-}
-else {
-    Write-Verbose "Prompt not specified as argument to script, checking pyvenv.cfg value"
-    if ($pyvenvCfg -and $pyvenvCfg['prompt']) {
-        Write-Verbose "  Setting based on value in pyvenv.cfg='$($pyvenvCfg['prompt'])'"
-        $Prompt = $pyvenvCfg['prompt'];
-    }
-    else {
-        Write-Verbose "  Setting prompt based on parent's directory's name. (Is the directory name passed to venv module when creating the virtual environment)"
-        Write-Verbose "  Got leaf-name of $VenvDir='$(Split-Path -Path $venvDir -Leaf)'"
-        $Prompt = Split-Path -Path $venvDir -Leaf
-    }
-}
-
-Write-Verbose "Prompt = '$Prompt'"
-Write-Verbose "VenvDir='$VenvDir'"
-
-# Deactivate any currently active virtual environment, but leave the
-# deactivate function in place.
-deactivate -nondestructive
-
-# Now set the environment variable VIRTUAL_ENV, used by many tools to determine
-# that there is an activated venv.
-$env:VIRTUAL_ENV = $VenvDir
-
-if (-not $Env:VIRTUAL_ENV_DISABLE_PROMPT) {
-
-    Write-Verbose "Setting prompt to '$Prompt'"
-
-    # Set the prompt to include the env name
-    # Make sure _OLD_VIRTUAL_PROMPT is global
-    function global:_OLD_VIRTUAL_PROMPT { "" }
-    Copy-Item -Path function:prompt -Destination function:_OLD_VIRTUAL_PROMPT
-    New-Variable -Name _PYTHON_VENV_PROMPT_PREFIX -Description "Python virtual environment prompt prefix" -Scope Global -Option ReadOnly -Visibility Public -Value $Prompt
-
-    function global:prompt {
-        Write-Host -NoNewline -ForegroundColor Green "($_PYTHON_VENV_PROMPT_PREFIX) "
-        _OLD_VIRTUAL_PROMPT
-    }
-    $env:VIRTUAL_ENV_PROMPT = $Prompt
-}
-
-# Clear PYTHONHOME
-if (Test-Path -Path Env:PYTHONHOME) {
-    Copy-Item -Path Env:PYTHONHOME -Destination Env:_OLD_VIRTUAL_PYTHONHOME
-    Remove-Item -Path Env:PYTHONHOME
-}
-
-# Add the venv to the PATH
-Copy-Item -Path Env:PATH -Destination Env:_OLD_VIRTUAL_PATH
-$Env:PATH = "$VenvExecDir$([System.IO.Path]::PathSeparator)$Env:PATH"

.venv_haddock/bin/__init__

@@ -1,6 +0,0 @@
-#!/Users/makardorohuntsev/docking_project/.venv_haddock/bin/python
-import sys
-from pdbtools.__init__ import main
-if __name__ == '__main__':
-    sys.argv[0] = sys.argv[0].removesuffix('.exe')
-    sys.exit(main())

.venv_haddock/bin/activate

@@ -1,70 +0,0 @@
-# This file must be used with "source bin/activate" *from bash*
-# You cannot run it directly
-
-deactivate () {
-    # reset old environment variables
-    if [ -n "${_OLD_VIRTUAL_PATH:-}" ] ; then
-        PATH="${_OLD_VIRTUAL_PATH:-}"
-        export PATH
-        unset _OLD_VIRTUAL_PATH
-    fi
-    if [ -n "${_OLD_VIRTUAL_PYTHONHOME:-}" ] ; then
-        PYTHONHOME="${_OLD_VIRTUAL_PYTHONHOME:-}"
-        export PYTHONHOME
-        unset _OLD_VIRTUAL_PYTHONHOME
-    fi
-
-    # Call hash to forget past commands. Without forgetting
-    # past commands the $PATH changes we made may not be respected
-    hash -r 2> /dev/null
-
-    if [ -n "${_OLD_VIRTUAL_PS1:-}" ] ; then
-        PS1="${_OLD_VIRTUAL_PS1:-}"
-        export PS1
-        unset _OLD_VIRTUAL_PS1
-    fi
-
-    unset VIRTUAL_ENV
-    unset VIRTUAL_ENV_PROMPT
-    if [ ! "${1:-}" = "nondestructive" ] ; then
-    # Self destruct!
-        unset -f deactivate
-    fi
-}
-
-# unset irrelevant variables
-deactivate nondestructive
-
-# on Windows, a path can contain colons and backslashes and has to be converted:
-if [ "${OSTYPE:-}" = "cygwin" ] || [ "${OSTYPE:-}" = "msys" ] ; then
-    # transform D:\path\to\venv to /d/path/to/venv on MSYS
-    # and to /cygdrive/d/path/to/venv on Cygwin
-    export VIRTUAL_ENV=$(cygpath "/Users/makardorohuntsev/docking_project/.venv_haddock")
-else
-    # use the path as-is
-    export VIRTUAL_ENV="/Users/makardorohuntsev/docking_project/.venv_haddock"
-fi
-
-_OLD_VIRTUAL_PATH="$PATH"
-PATH="$VIRTUAL_ENV/bin:$PATH"
-export PATH
-
-# unset PYTHONHOME if set
-# this will fail if PYTHONHOME is set to the empty string (which is bad anyway)
-# could use `if (set -u; : $PYTHONHOME) ;` in bash
-if [ -n "${PYTHONHOME:-}" ] ; then
-    _OLD_VIRTUAL_PYTHONHOME="${PYTHONHOME:-}"
-    unset PYTHONHOME
-fi
-
-if [ -z "${VIRTUAL_ENV_DISABLE_PROMPT:-}" ] ; then
-    _OLD_VIRTUAL_PS1="${PS1:-}"
-    PS1="(.venv_haddock) ${PS1:-}"
-    export PS1
-    VIRTUAL_ENV_PROMPT="(.venv_haddock) "
-    export VIRTUAL_ENV_PROMPT
-fi
-
-# Call hash to forget past commands. Without forgetting
-# past commands the $PATH changes we made may not be respected
-hash -r 2> /dev/null

.venv_haddock/bin/activate.csh

@@ -1,27 +0,0 @@
-# This file must be used with "source bin/activate.csh" *from csh*.
-# You cannot run it directly.
-
-# Created by Davide Di Blasi <davidedb@gmail.com>.
-# Ported to Python 3.3 venv by Andrew Svetlov <andrew.svetlov@gmail.com>
-
-alias deactivate 'test $?_OLD_VIRTUAL_PATH != 0 && setenv PATH "$_OLD_VIRTUAL_PATH" && unset _OLD_VIRTUAL_PATH; rehash; test $?_OLD_VIRTUAL_PROMPT != 0 && set prompt="$_OLD_VIRTUAL_PROMPT" && unset _OLD_VIRTUAL_PROMPT; unsetenv VIRTUAL_ENV; unsetenv VIRTUAL_ENV_PROMPT; test "\!:*" != "nondestructive" && unalias deactivate'
-
-# Unset irrelevant variables.
-deactivate nondestructive
-
-setenv VIRTUAL_ENV "/Users/makardorohuntsev/docking_project/.venv_haddock"
-
-set _OLD_VIRTUAL_PATH="$PATH"
-setenv PATH "$VIRTUAL_ENV/bin:$PATH"
-
-
-set _OLD_VIRTUAL_PROMPT="$prompt"
-
-if (! "$?VIRTUAL_ENV_DISABLE_PROMPT") then
-    set prompt = "(.venv_haddock) $prompt"
-    setenv VIRTUAL_ENV_PROMPT "(.venv_haddock) "
-endif
-
-alias pydoc python -m pydoc
-
-rehash

.venv_haddock/bin/activate.fish

@@ -1,69 +0,0 @@
-# This file must be used with "source <venv>/bin/activate.fish" *from fish*
-# (https://fishshell.com/). You cannot run it directly.
-
-function deactivate  -d "Exit virtual environment and return to normal shell environment"
-    # reset old environment variables
-    if test -n "$_OLD_VIRTUAL_PATH"
-        set -gx PATH $_OLD_VIRTUAL_PATH
-        set -e _OLD_VIRTUAL_PATH
-    end
-    if test -n "$_OLD_VIRTUAL_PYTHONHOME"
-        set -gx PYTHONHOME $_OLD_VIRTUAL_PYTHONHOME
-        set -e _OLD_VIRTUAL_PYTHONHOME
-    end
-
-    if test -n "$_OLD_FISH_PROMPT_OVERRIDE"
-        set -e _OLD_FISH_PROMPT_OVERRIDE
-        # prevents error when using nested fish instances (Issue #93858)
-        if functions -q _old_fish_prompt
-            functions -e fish_prompt
-            functions -c _old_fish_prompt fish_prompt
-            functions -e _old_fish_prompt
-        end
-    end
-
-    set -e VIRTUAL_ENV
-    set -e VIRTUAL_ENV_PROMPT
-    if test "$argv[1]" != "nondestructive"
-        # Self-destruct!
-        functions -e deactivate
-    end
-end
-
-# Unset irrelevant variables.
-deactivate nondestructive
-
-set -gx VIRTUAL_ENV "/Users/makardorohuntsev/docking_project/.venv_haddock"
-
-set -gx _OLD_VIRTUAL_PATH $PATH
-set -gx PATH "$VIRTUAL_ENV/bin" $PATH
-
-# Unset PYTHONHOME if set.
-if set -q PYTHONHOME
-    set -gx _OLD_VIRTUAL_PYTHONHOME $PYTHONHOME
-    set -e PYTHONHOME
-end
-
-if test -z "$VIRTUAL_ENV_DISABLE_PROMPT"
-    # fish uses a function instead of an env var to generate the prompt.
-
-    # Save the current fish_prompt function as the function _old_fish_prompt.
-    functions -c fish_prompt _old_fish_prompt
-
-    # With the original prompt function renamed, we can override with our own.
-    function fish_prompt
-        # Save the return status of the last command.
-        set -l old_status $status
-
-        # Output the venv prompt; color taken from the blue of the Python logo.
-        printf "%s%s%s" (set_color 4B8BBE) "(.venv_haddock) " (set_color normal)
-
-        # Restore the return status of the previous command.
-        echo "exit $old_status" | .
-        # Output the original/"old" prompt.
-        _old_fish_prompt
-    end
-
-    set -gx _OLD_FISH_PROMPT_OVERRIDE "$VIRTUAL_ENV"
-    set -gx VIRTUAL_ENV_PROMPT "(.venv_haddock) "
-end

.venv_haddock/bin/f2py

@@ -1,6 +0,0 @@
-#!/Users/makardorohuntsev/docking_project/.venv_haddock/bin/python
-import sys
-from numpy.f2py.f2py2e import main
-if __name__ == '__main__':
-    sys.argv[0] = sys.argv[0].removesuffix('.exe')
-    sys.exit(main())

.venv_haddock/bin/haddock-restraints

@@ -1,6 +0,0 @@
-#!/Users/makardorohuntsev/docking_project/.venv_haddock/bin/python
-import sys
-from haddock.clis.wrapper_haddock_restraints import main
-if __name__ == '__main__':
-    sys.argv[0] = sys.argv[0].removesuffix('.exe')
-    sys.exit(main())

.venv_haddock/bin/haddock3

@@ -1,6 +0,0 @@
-#!/Users/makardorohuntsev/docking_project/.venv_haddock/bin/python
-import sys
-from haddock.clis.cli import maincli
-if __name__ == '__main__':
-    sys.argv[0] = sys.argv[0].removesuffix('.exe')
-    sys.exit(maincli())

.venv_haddock/bin/haddock3-analyse

@@ -1,6 +0,0 @@
-#!/Users/makardorohuntsev/docking_project/.venv_haddock/bin/python
-import sys
-from haddock.clis.cli_analyse import maincli
-if __name__ == '__main__':
-    sys.argv[0] = sys.argv[0].removesuffix('.exe')
-    sys.exit(maincli())

.venv_haddock/bin/haddock3-cfg

@@ -1,6 +0,0 @@
-#!/Users/makardorohuntsev/docking_project/.venv_haddock/bin/python
-import sys
-from haddock.clis.cli_cfg import maincli
-if __name__ == '__main__':
-    sys.argv[0] = sys.argv[0].removesuffix('.exe')
-    sys.exit(maincli())

.venv_haddock/bin/haddock3-clean

@@ -1,6 +0,0 @@
-#!/Users/makardorohuntsev/docking_project/.venv_haddock/bin/python
-import sys
-from haddock.clis.cli_clean import maincli
-if __name__ == '__main__':
-    sys.argv[0] = sys.argv[0].removesuffix('.exe')
-    sys.exit(maincli())

.venv_haddock/bin/haddock3-copy

@@ -1,6 +0,0 @@
-#!/Users/makardorohuntsev/docking_project/.venv_haddock/bin/python
-import sys
-from haddock.clis.cli_cp import maincli
-if __name__ == '__main__':
-    sys.argv[0] = sys.argv[0].removesuffix('.exe')
-    sys.exit(maincli())

.venv_haddock/bin/haddock3-dmn

@@ -1,6 +0,0 @@
-#!/Users/makardorohuntsev/docking_project/.venv_haddock/bin/python
-import sys
-from haddock.clis.cli_dmn import maincli
-if __name__ == '__main__':
-    sys.argv[0] = sys.argv[0].removesuffix('.exe')
-    sys.exit(maincli())

.venv_haddock/bin/haddock3-mpitask

@@ -1,6 +0,0 @@
-#!/Users/makardorohuntsev/docking_project/.venv_haddock/bin/python
-import sys
-from haddock.clis.cli_mpi import maincli
-if __name__ == '__main__':
-    sys.argv[0] = sys.argv[0].removesuffix('.exe')
-    sys.exit(maincli())

.venv_haddock/bin/haddock3-pp

@@ -1,6 +0,0 @@
-#!/Users/makardorohuntsev/docking_project/.venv_haddock/bin/python
-import sys
-from haddock.clis.cli_pp import maincli
-if __name__ == '__main__':
-    sys.argv[0] = sys.argv[0].removesuffix('.exe')
-    sys.exit(maincli())

.venv_haddock/bin/haddock3-re

@@ -1,6 +0,0 @@
-#!/Users/makardorohuntsev/docking_project/.venv_haddock/bin/python
-import sys
-from haddock.clis.cli_re import maincli
-if __name__ == '__main__':
-    sys.argv[0] = sys.argv[0].removesuffix('.exe')
-    sys.exit(maincli())

.venv_haddock/bin/haddock3-restraints

@@ -1,6 +0,0 @@
-#!/Users/makardorohuntsev/docking_project/.venv_haddock/bin/python
-import sys
-from haddock.clis.cli_restraints import maincli
-if __name__ == '__main__':
-    sys.argv[0] = sys.argv[0].removesuffix('.exe')
-    sys.exit(maincli())

.venv_haddock/bin/haddock3-score

@@ -1,6 +0,0 @@
-#!/Users/makardorohuntsev/docking_project/.venv_haddock/bin/python
-import sys
-from haddock.clis.cli_score import maincli
-if __name__ == '__main__':
-    sys.argv[0] = sys.argv[0].removesuffix('.exe')
-    sys.exit(maincli())

.venv_haddock/bin/haddock3-traceback

@@ -1,6 +0,0 @@
-#!/Users/makardorohuntsev/docking_project/.venv_haddock/bin/python
-import sys
-from haddock.clis.cli_traceback import maincli
-if __name__ == '__main__':
-    sys.argv[0] = sys.argv[0].removesuffix('.exe')
-    sys.exit(maincli())

.venv_haddock/bin/haddock3-unpack

@@ -1,6 +0,0 @@
-#!/Users/makardorohuntsev/docking_project/.venv_haddock/bin/python
-import sys
-from haddock.clis.cli_unpack import maincli
-if __name__ == '__main__':
-    sys.argv[0] = sys.argv[0].removesuffix('.exe')
-    sys.exit(maincli())

.venv_haddock/bin/numpy-config

@@ -1,6 +0,0 @@
-#!/Users/makardorohuntsev/docking_project/.venv_haddock/bin/python
-import sys
-from numpy._configtool import main
-if __name__ == '__main__':
-    sys.argv[0] = sys.argv[0].removesuffix('.exe')
-    sys.exit(main())

.venv_haddock/bin/pdb_b

@@ -1,6 +0,0 @@
-#!/Users/makardorohuntsev/docking_project/.venv_haddock/bin/python
-import sys
-from pdbtools.pdb_b import main
-if __name__ == '__main__':
-    sys.argv[0] = sys.argv[0].removesuffix('.exe')
-    sys.exit(main())

.venv_haddock/bin/pdb_chain

@@ -1,6 +0,0 @@
-#!/Users/makardorohuntsev/docking_project/.venv_haddock/bin/python
-import sys
-from pdbtools.pdb_chain import main
-if __name__ == '__main__':
-    sys.argv[0] = sys.argv[0].removesuffix('.exe')
-    sys.exit(main())

.venv_haddock/bin/pdb_chainbows

@@ -1,6 +0,0 @@
-#!/Users/makardorohuntsev/docking_project/.venv_haddock/bin/python
-import sys
-from pdbtools.pdb_chainbows import main
-if __name__ == '__main__':
-    sys.argv[0] = sys.argv[0].removesuffix('.exe')
-    sys.exit(main())

.venv_haddock/bin/pdb_chainxseg

@@ -1,6 +0,0 @@
-#!/Users/makardorohuntsev/docking_project/.venv_haddock/bin/python
-import sys
-from pdbtools.pdb_chainxseg import main
-if __name__ == '__main__':
-    sys.argv[0] = sys.argv[0].removesuffix('.exe')
-    sys.exit(main())

.venv_haddock/bin/pdb_chkensemble

@@ -1,6 +0,0 @@
-#!/Users/makardorohuntsev/docking_project/.venv_haddock/bin/python
-import sys
-from pdbtools.pdb_chkensemble import main
-if __name__ == '__main__':
-    sys.argv[0] = sys.argv[0].removesuffix('.exe')
-    sys.exit(main())

.venv_haddock/bin/pdb_delchain

@@ -1,6 +0,0 @@
-#!/Users/makardorohuntsev/docking_project/.venv_haddock/bin/python
-import sys
-from pdbtools.pdb_delchain import main
-if __name__ == '__main__':
-    sys.argv[0] = sys.argv[0].removesuffix('.exe')
-    sys.exit(main())

.venv_haddock/bin/pdb_delelem

@@ -1,6 +0,0 @@
-#!/Users/makardorohuntsev/docking_project/.venv_haddock/bin/python
-import sys
-from pdbtools.pdb_delelem import main
-if __name__ == '__main__':
-    sys.argv[0] = sys.argv[0].removesuffix('.exe')
-    sys.exit(main())

.venv_haddock/bin/pdb_delhetatm

@@ -1,6 +0,0 @@
-#!/Users/makardorohuntsev/docking_project/.venv_haddock/bin/python
-import sys
-from pdbtools.pdb_delhetatm import main
-if __name__ == '__main__':
-    sys.argv[0] = sys.argv[0].removesuffix('.exe')
-    sys.exit(main())

.venv_haddock/bin/pdb_delinsertion

@@ -1,6 +0,0 @@
-#!/Users/makardorohuntsev/docking_project/.venv_haddock/bin/python
-import sys
-from pdbtools.pdb_delinsertion import main
-if __name__ == '__main__':
-    sys.argv[0] = sys.argv[0].removesuffix('.exe')
-    sys.exit(main())

.venv_haddock/bin/pdb_delres

@@ -1,6 +0,0 @@
-#!/Users/makardorohuntsev/docking_project/.venv_haddock/bin/python
-import sys
-from pdbtools.pdb_delres import main
-if __name__ == '__main__':
-    sys.argv[0] = sys.argv[0].removesuffix('.exe')
-    sys.exit(main())

.venv_haddock/bin/pdb_delresname

@@ -1,6 +0,0 @@
-#!/Users/makardorohuntsev/docking_project/.venv_haddock/bin/python
-import sys
-from pdbtools.pdb_delresname import main
-if __name__ == '__main__':
-    sys.argv[0] = sys.argv[0].removesuffix('.exe')
-    sys.exit(main())

.venv_haddock/bin/pdb_element

@@ -1,6 +0,0 @@
-#!/Users/makardorohuntsev/docking_project/.venv_haddock/bin/python
-import sys
-from pdbtools.pdb_element import main
-if __name__ == '__main__':
-    sys.argv[0] = sys.argv[0].removesuffix('.exe')
-    sys.exit(main())

.venv_haddock/bin/pdb_fetch

@@ -1,6 +0,0 @@
-#!/Users/makardorohuntsev/docking_project/.venv_haddock/bin/python
-import sys
-from pdbtools.pdb_fetch import main
-if __name__ == '__main__':
-    sys.argv[0] = sys.argv[0].removesuffix('.exe')
-    sys.exit(main())

.venv_haddock/bin/pdb_fixinsert

@@ -1,6 +0,0 @@
-#!/Users/makardorohuntsev/docking_project/.venv_haddock/bin/python
-import sys
-from pdbtools.pdb_fixinsert import main
-if __name__ == '__main__':
-    sys.argv[0] = sys.argv[0].removesuffix('.exe')
-    sys.exit(main())

.venv_haddock/bin/pdb_fromcif

@@ -1,6 +0,0 @@
-#!/Users/makardorohuntsev/docking_project/.venv_haddock/bin/python
-import sys
-from pdbtools.pdb_fromcif import main
-if __name__ == '__main__':
-    sys.argv[0] = sys.argv[0].removesuffix('.exe')
-    sys.exit(main())

.venv_haddock/bin/pdb_gap

@@ -1,6 +0,0 @@
-#!/Users/makardorohuntsev/docking_project/.venv_haddock/bin/python
-import sys
-from pdbtools.pdb_gap import main
-if __name__ == '__main__':
-    sys.argv[0] = sys.argv[0].removesuffix('.exe')
-    sys.exit(main())

.venv_haddock/bin/pdb_head

@@ -1,6 +0,0 @@
-#!/Users/makardorohuntsev/docking_project/.venv_haddock/bin/python
-import sys
-from pdbtools.pdb_head import main
-if __name__ == '__main__':
-    sys.argv[0] = sys.argv[0].removesuffix('.exe')
-    sys.exit(main())

.venv_haddock/bin/pdb_intersect

@@ -1,6 +0,0 @@
-#!/Users/makardorohuntsev/docking_project/.venv_haddock/bin/python
-import sys
-from pdbtools.pdb_intersect import main
-if __name__ == '__main__':
-    sys.argv[0] = sys.argv[0].removesuffix('.exe')
-    sys.exit(main())

.venv_haddock/bin/pdb_keepcoord

@@ -1,6 +0,0 @@
-#!/Users/makardorohuntsev/docking_project/.venv_haddock/bin/python
-import sys
-from pdbtools.pdb_keepcoord import main
-if __name__ == '__main__':
-    sys.argv[0] = sys.argv[0].removesuffix('.exe')
-    sys.exit(main())

.venv_haddock/bin/pdb_merge

@@ -1,6 +0,0 @@
-#!/Users/makardorohuntsev/docking_project/.venv_haddock/bin/python
-import sys
-from pdbtools.pdb_merge import main
-if __name__ == '__main__':
-    sys.argv[0] = sys.argv[0].removesuffix('.exe')
-    sys.exit(main())

.venv_haddock/bin/pdb_mkensemble

@@ -1,6 +0,0 @@
-#!/Users/makardorohuntsev/docking_project/.venv_haddock/bin/python
-import sys
-from pdbtools.pdb_mkensemble import main
-if __name__ == '__main__':
-    sys.argv[0] = sys.argv[0].removesuffix('.exe')
-    sys.exit(main())

.venv_haddock/bin/pdb_occ

@@ -1,6 +0,0 @@
-#!/Users/makardorohuntsev/docking_project/.venv_haddock/bin/python
-import sys
-from pdbtools.pdb_occ import main
-if __name__ == '__main__':
-    sys.argv[0] = sys.argv[0].removesuffix('.exe')
-    sys.exit(main())

.venv_haddock/bin/pdb_reatom

@@ -1,6 +0,0 @@
-#!/Users/makardorohuntsev/docking_project/.venv_haddock/bin/python
-import sys
-from pdbtools.pdb_reatom import main
-if __name__ == '__main__':
-    sys.argv[0] = sys.argv[0].removesuffix('.exe')
-    sys.exit(main())