From d6f94a76b70ee303a267aba47e4c2a4299437411 Mon Sep 17 00:00:00 2001
From: Brandon Duane Walker <walkerbd@UPDATEME.HOSTNAME.COM>
Date: Fri, 3 May 2024 11:23:37 -0400
Subject: [PATCH] bash top

---
 .../amber/bash-top-tool/.bumpversion.cfg      | 29 ++++++++++
 .../amber/bash-top-tool/.dockerignore         |  4 ++
 .../amber/bash-top-tool/.gitignore            |  1 +
 .../amber/bash-top-tool/CHANGELOG.md          |  5 ++
 .../amber/bash-top-tool/Dockerfile            |  5 ++
 .../amber/bash-top-tool/README.md             | 14 +++++
 .../amber/bash-top-tool/VERSION               |  1 +
 .../amber/bash-top-tool/bash_top_0.1.0.cwl    | 50 +++++++++++++++++
 .../amber/bash-top-tool/build-docker.sh       |  4 ++
 .../gmx_add_topology_includes.sh              | 20 +++++++
 .../amber/bash-top-tool/ict.yml               | 51 ++++++++++++++++++
 .../amber/bash-top-tool/pyproject.toml        | 28 ++++++++++
 .../tests/ALL.Ala115Pro_step8_gio_gio.top     | 54 +++++++++++++++++++
 .../amber/bash-top-tool/tests/__init__.py     |  1 +
 .../bash-top-tool/tests/test_bash_top.py      | 30 +++++++++++
 15 files changed, 297 insertions(+)
 create mode 100644 utils/molecular-dynamics/amber/bash-top-tool/.bumpversion.cfg
 create mode 100644 utils/molecular-dynamics/amber/bash-top-tool/.dockerignore
 create mode 100644 utils/molecular-dynamics/amber/bash-top-tool/.gitignore
 create mode 100644 utils/molecular-dynamics/amber/bash-top-tool/CHANGELOG.md
 create mode 100644 utils/molecular-dynamics/amber/bash-top-tool/Dockerfile
 create mode 100644 utils/molecular-dynamics/amber/bash-top-tool/README.md
 create mode 100644 utils/molecular-dynamics/amber/bash-top-tool/VERSION
 create mode 100644 utils/molecular-dynamics/amber/bash-top-tool/bash_top_0.1.0.cwl
 create mode 100644 utils/molecular-dynamics/amber/bash-top-tool/build-docker.sh
 create mode 100644 utils/molecular-dynamics/amber/bash-top-tool/gmx_add_topology_includes.sh
 create mode 100644 utils/molecular-dynamics/amber/bash-top-tool/ict.yml
 create mode 100644 utils/molecular-dynamics/amber/bash-top-tool/pyproject.toml
 create mode 100644 utils/molecular-dynamics/amber/bash-top-tool/tests/ALL.Ala115Pro_step8_gio_gio.top
 create mode 100644 utils/molecular-dynamics/amber/bash-top-tool/tests/__init__.py
 create mode 100644 utils/molecular-dynamics/amber/bash-top-tool/tests/test_bash_top.py

diff --git a/utils/molecular-dynamics/amber/bash-top-tool/.bumpversion.cfg b/utils/molecular-dynamics/amber/bash-top-tool/.bumpversion.cfg
new file mode 100644
index 00000000..74a53e2b
--- /dev/null
+++ b/utils/molecular-dynamics/amber/bash-top-tool/.bumpversion.cfg
@@ -0,0 +1,29 @@
+[bumpversion]
+current_version = 0.1.0
+commit = False
+tag = False
+parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(\-(?P<release>[a-z]+)(?P<dev>\d+))?
+serialize = 
+	{major}.{minor}.{patch}-{release}{dev}
+	{major}.{minor}.{patch}
+
+[bumpversion:part:release]
+optional_value = _
+first_value = dev
+values = 
+	dev
+	_
+
+[bumpversion:part:dev]
+
+[bumpversion:file:pyproject.toml]
+search = version = "{current_version}"
+replace = version = "{new_version}"
+
+[bumpversion:file:VERSION]
+
+[bumpversion:file:README.md]
+
+[bumpversion:file:plugin.json]
+
+[bumpversion:file:src/polus/mm/utils/bash_top/__init__.py]
diff --git a/utils/molecular-dynamics/amber/bash-top-tool/.dockerignore b/utils/molecular-dynamics/amber/bash-top-tool/.dockerignore
new file mode 100644
index 00000000..7c603f81
--- /dev/null
+++ b/utils/molecular-dynamics/amber/bash-top-tool/.dockerignore
@@ -0,0 +1,4 @@
+.venv
+out
+tests
+__pycache__
diff --git a/utils/molecular-dynamics/amber/bash-top-tool/.gitignore b/utils/molecular-dynamics/amber/bash-top-tool/.gitignore
new file mode 100644
index 00000000..c04bc49f
--- /dev/null
+++ b/utils/molecular-dynamics/amber/bash-top-tool/.gitignore
@@ -0,0 +1 @@
+poetry.lock
diff --git a/utils/molecular-dynamics/amber/bash-top-tool/CHANGELOG.md b/utils/molecular-dynamics/amber/bash-top-tool/CHANGELOG.md
new file mode 100644
index 00000000..b67793f7
--- /dev/null
+++ b/utils/molecular-dynamics/amber/bash-top-tool/CHANGELOG.md
@@ -0,0 +1,5 @@
+# CHANGELOG
+
+## 0.1.0
+
+Initial release.
diff --git a/utils/molecular-dynamics/amber/bash-top-tool/Dockerfile b/utils/molecular-dynamics/amber/bash-top-tool/Dockerfile
new file mode 100644
index 00000000..a09b5ff6
--- /dev/null
+++ b/utils/molecular-dynamics/amber/bash-top-tool/Dockerfile
@@ -0,0 +1,5 @@
+# docker build -f Dockerfile -t polusai/bash-top-tool .
+FROM bash
+
+ADD gmx_add_topology_includes.sh .
+ADD Dockerfile .
diff --git a/utils/molecular-dynamics/amber/bash-top-tool/README.md b/utils/molecular-dynamics/amber/bash-top-tool/README.md
new file mode 100644
index 00000000..6b0ca987
--- /dev/null
+++ b/utils/molecular-dynamics/amber/bash-top-tool/README.md
@@ -0,0 +1,14 @@
+# bash_top (0.1.0)
+
+Concatentate import statements in AMBER topology file
+
+## Options
+
+This plugin takes 3 input arguments and 1 output argument:
+
+| Name          | Description             | I/O    | Type   | Default |
+|---------------|-------------------------|--------|--------|---------|
+| script | Bash script name | Input | string | string |
+| input_top_path | Gromacs topology file | Input | File | File |
+| output_top_path | Output topology file name | Input | string | string |
+| output_top_path | Output topology file | Output | File | File |
diff --git a/utils/molecular-dynamics/amber/bash-top-tool/VERSION b/utils/molecular-dynamics/amber/bash-top-tool/VERSION
new file mode 100644
index 00000000..6e8bf73a
--- /dev/null
+++ b/utils/molecular-dynamics/amber/bash-top-tool/VERSION
@@ -0,0 +1 @@
+0.1.0
diff --git a/utils/molecular-dynamics/amber/bash-top-tool/bash_top_0.1.0.cwl b/utils/molecular-dynamics/amber/bash-top-tool/bash_top_0.1.0.cwl
new file mode 100644
index 00000000..8eeb6dba
--- /dev/null
+++ b/utils/molecular-dynamics/amber/bash-top-tool/bash_top_0.1.0.cwl
@@ -0,0 +1,50 @@
+#!/usr/bin/env cwl-runner
+cwlVersion: v1.0
+
+class: CommandLineTool
+
+label: Concatentate import statements in AMBER topology file
+
+doc: |
+  Concatentate import statements in AMBER topology file
+
+baseCommand: bash
+
+hints:
+  DockerRequirement:
+    dockerPull: polusai/bash-top-tool@sha256:881d3634bd000a931b3339e8328ee9701190e6ac7b1227082bd095e317d2e551
+
+inputs:
+  script:
+    type: string
+    inputBinding:
+      position: 1
+
+  input_top_path:
+    type: File
+    format: edam:format_3880
+    inputBinding:
+      position: 2
+
+  output_top_path:
+    type: string?
+    format: edam:format_2330 # 'Textual format'
+#    inputBinding:
+#      position: 3
+    default: system.top
+
+outputs:
+  output_top_path:
+    type: File
+    format: edam:format_3880
+    streamable: true
+    outputBinding:
+      glob: $(inputs.output_top_path)
+
+stdout: $(inputs.output_top_path)
+
+$namespaces:
+  edam: https://edamontology.org/
+
+$schemas:
+- https://raw.githubusercontent.com/edamontology/edamontology/master/EDAM_dev.owl
diff --git a/utils/molecular-dynamics/amber/bash-top-tool/build-docker.sh b/utils/molecular-dynamics/amber/bash-top-tool/build-docker.sh
new file mode 100644
index 00000000..fea1a3c9
--- /dev/null
+++ b/utils/molecular-dynamics/amber/bash-top-tool/build-docker.sh
@@ -0,0 +1,4 @@
+#!/bin/bash
+
+version=$(<VERSION)
+docker build . -t polusai/bash-top-tool:${version}
diff --git a/utils/molecular-dynamics/amber/bash-top-tool/gmx_add_topology_includes.sh b/utils/molecular-dynamics/amber/bash-top-tool/gmx_add_topology_includes.sh
new file mode 100644
index 00000000..61b2f3c0
--- /dev/null
+++ b/utils/molecular-dynamics/amber/bash-top-tool/gmx_add_topology_includes.sh
@@ -0,0 +1,20 @@
+#!/bin/bash -e
+# NOTE: These include statements MUST be in this order. In particular, we
+# cannot simply use cat $1 because we need to interleave the amber99sb-ildn.ff
+# includes around ligand_GMX.itp, and because we need to remove the [ defaults ]
+# directive (which is included in forcefield.itp)
+echo '#include "amber99sb-ildn.ff/forcefield.itp"'
+
+echo '#include "ligand_GMX.itp"'
+
+echo '#include "amber99sb-ildn.ff/spce.itp"'
+echo '#include "amber99sb-ildn.ff/ions.itp"'
+
+echo "[ system ]"
+echo " ligand "
+echo ""
+echo "[ molecules ]"
+echo "; Compound        nmols"
+echo " ligand           1     "
+
+#cat $1
diff --git a/utils/molecular-dynamics/amber/bash-top-tool/ict.yml b/utils/molecular-dynamics/amber/bash-top-tool/ict.yml
new file mode 100644
index 00000000..bee015e4
--- /dev/null
+++ b/utils/molecular-dynamics/amber/bash-top-tool/ict.yml
@@ -0,0 +1,51 @@
+specVersion: "0.1.0"
+name: bash_top
+version: 0.1.0
+container: bash-top-tool
+entrypoint:
+title: bash_top
+description: Concatentate import statements in AMBER topology file
+author: Data Scientist
+contact: data.scientist@labshare.org
+repository:
+documentation:
+citation:
+
+inputs:
+  - name: script
+    required: true
+    description:
+    type: string
+  - name: input_top_path
+    required: true
+    description:
+    type: File
+    format:
+      uri: edam:format_3880
+  - name: output_top_path
+    required: true
+    description:
+    type: string
+    defaultValue: system.top
+    format:
+      uri: edam:format_2330
+outputs:
+  - name: output_top_path
+    required: true
+    description:
+    type: File
+    format:
+      uri: edam:format_3880
+ui:
+  - key: inputs.script
+    title: "script: "
+    description: ""
+    type: string
+  - key: inputs.input_top_path
+    title: "input_top_path: "
+    description: ""
+    type: File
+  - key: inputs.output_top_path
+    title: "output_top_path: "
+    description: ""
+    type: string
diff --git a/utils/molecular-dynamics/amber/bash-top-tool/pyproject.toml b/utils/molecular-dynamics/amber/bash-top-tool/pyproject.toml
new file mode 100644
index 00000000..d78ed09b
--- /dev/null
+++ b/utils/molecular-dynamics/amber/bash-top-tool/pyproject.toml
@@ -0,0 +1,28 @@
+[tool.poetry]
+name = "polus-mm-utils-bash-top"
+version = "0.1.0"
+description = "Run a Bash script"
+authors = ["Data Scientist <data.scientist@labshare.org>"]
+readme = "README.md"
+
+[tool.poetry.dependencies]
+python = ">=3.9,<3.12"
+sophios = "0.1.0"
+
+[tool.poetry.group.dev.dependencies]
+bump2version = "^1.0.1"
+pytest = "^7.4"
+pytest-sugar = "^0.9.6"
+pre-commit = "^3.2.1"
+black = "^23.3.0"
+mypy = "^1.1.1"
+ruff = "^0.0.270"
+
+[build-system]
+requires = ["poetry-core"]
+build-backend = "poetry.core.masonry.api"
+
+[tool.pytest.ini_options]
+pythonpath = [
+  "."
+]
diff --git a/utils/molecular-dynamics/amber/bash-top-tool/tests/ALL.Ala115Pro_step8_gio_gio.top b/utils/molecular-dynamics/amber/bash-top-tool/tests/ALL.Ala115Pro_step8_gio_gio.top
new file mode 100644
index 00000000..5d86f4df
--- /dev/null
+++ b/utils/molecular-dynamics/amber/bash-top-tool/tests/ALL.Ala115Pro_step8_gio_gio.top
@@ -0,0 +1,54 @@
+;
+;	File 'ALL.Ala115Pro_step4_p2g_p2g.top' was generated
+;	By user: unknown (3373)
+;	On host: s04r1b41
+;	At date: Tue Apr 10 08:32:54 2018
+
+;
+;	This is a standalone topology file
+;
+;	Created by:
+;	                 :-) GROMACS - gmx pdb2gmx, VERSION 5.1.2 (-:
+;
+;	Executable:   /gpfs/home/bsc23/bsc23210/gromacs/bin/gmx
+;	Data prefix:  /gpfs/home/bsc23/bsc23210/gromacs
+;	Command line:
+;	  gmx pdb2gmx -f /gpfs/scratch/bsc23/bsc23210/tmp.pjwGKiFyti/dd33c756-035a-41ec-9e5c-ad722dd9f4e7/s04r1b41-ib0/sandBox/job_203/mutated.pdb -o /gpfs/scratch/bsc23/bsc23210/tmp.pjwGKiFyti/dd33c756-035a-41ec-9e5c-ad722dd9f4e7/s04r1b41-ib0/sandBox/job_203/p2g.gro -p ALL.Ala115Pro_step4_p2g_p2g.top -water tip3p -ff amber99sb -i ALL.Ala115Pro_step4_p2g_p2g.itp -ignh
+;	Force field was read from the standard GROMACS share directory.
+;
+
+; Include forcefield parameters
+#include "amber99sb.ff/forcefield.itp"
+
+; Include chain topologies
+#include "ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_A.itp"
+#include "ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_B.itp"
+#include "ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_C.itp"
+#include "ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_D.itp"
+
+; Include water topology
+#include "amber99sb.ff/tip3p.itp"
+
+#ifdef POSRES_WATER
+; Position restraint for each water oxygen
+[ position_restraints ]
+;  i funct       fcx        fcy        fcz
+   1    1       1000       1000       1000
+#endif
+
+; Include topology for ions
+#include "amber99sb.ff/ions.itp"
+
+[ system ]
+; Name
+Protein in water
+
+[ molecules ]
+; Compound        #mols
+Protein_chain_A     1
+Protein_chain_B     1
+Protein_chain_C     1
+Protein_chain_D     1
+SOL         121173
+NA               128
+CL               120
diff --git a/utils/molecular-dynamics/amber/bash-top-tool/tests/__init__.py b/utils/molecular-dynamics/amber/bash-top-tool/tests/__init__.py
new file mode 100644
index 00000000..0cf21055
--- /dev/null
+++ b/utils/molecular-dynamics/amber/bash-top-tool/tests/__init__.py
@@ -0,0 +1 @@
+"""Tests for bash_top."""
diff --git a/utils/molecular-dynamics/amber/bash-top-tool/tests/test_bash_top.py b/utils/molecular-dynamics/amber/bash-top-tool/tests/test_bash_top.py
new file mode 100644
index 00000000..a8f89dfe
--- /dev/null
+++ b/utils/molecular-dynamics/amber/bash-top-tool/tests/test_bash_top.py
@@ -0,0 +1,30 @@
+"""Tests for bash_top."""
+from pathlib import Path
+
+from sophios.api.pythonapi import Step
+from sophios.api.pythonapi import Workflow
+
+
+def test_bash_top() -> None:
+    """Test bash topology CWL."""
+    input_top_path = Path(__file__).resolve().parent / Path(
+        "ALL.Ala115Pro_step8_gio_gio.top",
+    )
+    cwl_file_str = "bash_top_0.1.0.cwl"
+    cwl_file = Path(__file__).resolve().parent.parent / Path(cwl_file_str)
+    bash_top = Step(clt_path=cwl_file)
+    bash_top.script = "/gmx_add_topology_includes.sh"
+    bash_top.input_top_path = input_top_path
+
+    steps = [bash_top]
+    filename = "bash_top"
+    viz = Workflow(steps, filename)
+
+    viz.run()
+
+    outdir = Path("outdir")
+    files = list(outdir.rglob("system.top"))
+
+    assert (
+        files
+    ), f"The file 'system.top' does not exist in any subdirectory of '{outdir}'."