samgen 0.1.2__tar.gz

samgen-0.1.2/LICENSE

@@ -0,0 +1,28 @@
+BSD 3-Clause License
+
+Copyright (c) 2026, Mayank Vats
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this
+   list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its
+   contributors may be used to endorse or promote products derived from
+   this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

samgen-0.1.2/MANIFEST.in

@@ -0,0 +1,6 @@
+graft configs
+include README.md
+include LICENSE
+global-exclude *.manifest.json
+global-exclude sam.gro sam-*.gro topol.top
+global-exclude *.pyc

samgen-0.1.2/PKG-INFO

@@ -0,0 +1,238 @@
+Metadata-Version: 2.4
+Name: samgen
+Version: 0.1.2
+Summary: Build self-assembled monolayer (SAM) surfaces for GROMACS
+Author-email: Mayank Vats <18255879+max3925vats@users.noreply.github.com>
+License-Expression: BSD-3-Clause
+Project-URL: Repository, https://github.com/max3925vats/samgen
+Keywords: SAM,self-assembled-monolayer,GROMACS,molecular-dynamics,Au(111)
+Classifier: Programming Language :: Python :: 3
+Classifier: Intended Audience :: Science/Research
+Classifier: Topic :: Scientific/Engineering :: Chemistry
+Requires-Python: >=3.11
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy>=1.24
+Requires-Dist: scipy>=1.10
+Requires-Dist: pyyaml>=6.0
+Provides-Extra: dev
+Requires-Dist: pytest>=7.0; extra == "dev"
+Dynamic: license-file
+
+# samgen
+
+[![tests](https://github.com/max3925vats/samgen/actions/workflows/tests.yml/badge.svg)](https://github.com/max3925vats/samgen/actions/workflows/tests.yml)
+[![PyPI](https://img.shields.io/pypi/v/samgen)](https://pypi.org/project/samgen/)
+[![Python 3.11+](https://img.shields.io/badge/python-3.11%2B-blue)](https://www.python.org/)
+[![License: BSD-3-Clause](https://img.shields.io/badge/license-BSD--3--Clause-green)](LICENSE)
+
+Build self-assembled monolayer (SAM) surfaces as GROMACS `.gro` / `.top` files.
+
+`samgen`'s job is to place strands correctly on a periodic Au(111) grid per a
+chosen design, for one-sided and two-sided (shared-sulfur midplane) monolayers.
+Orientation/tilt and topology assembly are provided as conveniences that **you
+must verify** before running MD.
+
+## What it does
+
+- **Hexagonal Au(111) lattice** — `(√3×√3)R30°` tiling with the staggered-row
+  offset, periodic-correct box.
+- **SAM orientation** — apply the tilt (`alpha` ≈ 28°, `beta` ≈ 53°; Love et
+  al. 2005) with an always-on orientation sanity check and opt-in,
+  chemistry-anchored canonicalization.
+- **Five placement designs** — density (default), uniform, two-component grid,
+  fraction/random (seeded), and multi-ligand (3+).
+- **Anchor / cap detection** — prompt-first with consent-to-guess.
+- **Topology assembly** — residue reordering, merged `[defaults]`/`[atomtypes]`,
+  per-component bonded params, and a `[molecules]` block with correct counts,
+  optionally gated by `gmx grompp`.
+- **Periodicity check** — verifies the built surface tiles seamlessly under PBC.
+- **Two-sided SAMs** — fuse two arms onto a single shared sulfur via a proper,
+  chirality-preserving 180° rotation; emits geometry for you to parameterize.
+
+## Install
+
+Requires **Python 3.11+**. Dependencies (`numpy`, `scipy`, `pyyaml`) install
+automatically.
+
+```bash
+# from PyPI
+pip install samgen
+
+# or the latest from GitHub
+pip install git+https://github.com/max3925vats/samgen.git
+
+# or editable, for development (adds pytest)
+git clone https://github.com/max3925vats/samgen.git
+cd samgen
+pip install -e ".[dev]"
+```
+
+**GROMACS is optional** — it's only used for the `gmx grompp` topology check
+(`--validate`) and any boxing/centering you do yourself. Install it however you
+like (e.g. `brew install gromacs`, conda, or your cluster module).
+
+## Quick start
+
+The default design places a methyl-terminated (`ch3`) ligand on a
+hydroxyl-terminated (`coh`) matrix at a target areal density:
+
+```bash
+samgen build configs/ch3_density.yaml -o sam.gro --top topol.top
+# -> 132 CH3 ligands on a COH matrix (528 strands), with topol.top
+```
+
+## Three stages (run together or separately)
+
+All stages share one config, so you can run them piecewise or in one shot:
+
+```bash
+# 1) tile the surface geometry (no force field needed)
+samgen geometry configs/ch3_grid.yaml -o sam.gro
+
+# 2) assemble the topology for that surface (--validate runs the gmx grompp gate)
+samgen topology configs/ch3_grid.yaml --gro sam.gro -o topol.top --validate
+
+# ...or do both at once:
+samgen build    configs/ch3_grid.yaml -o sam.gro --top topol.top
+
+# two-sided (shared-S) strand + geometry-only surface:
+samgen twosided configs/ch3_grid.yaml --component ch3 -o strand.gro --surface twosided-sam.gro
+```
+
+For `twosided`, the anchor is prompt-first: it uses the config's `anchor:` if
+set, otherwise prompts in an interactive terminal and only auto-detects with your
+consent. In batch (no TTY) it requires `anchor:` in the config unless
+`allow_anchor_autodetect: true`.
+
+From Python:
+
+```python
+from samgen import generate_geometry, assemble_topology, build
+```
+
+## Placement designs
+
+A design decides which component sits at each Au(111) lattice site. Set it in the
+`design:` block of the config.
+
+- **`density`** (default) — ligands at a target areal density (ligands/nm²),
+  placed on a uniform sub-lattice of the gold sites. samgen keeps the grid
+  perfectly periodic; the realized density is quantized to the Au spacing and is
+  reported. If your box and density don't tile uniquely, samgen offers two
+  periodic choices (a smaller box with fewer ligands, or a larger box with more)
+  and you pick — or set `density_choice: below|above` for batch runs.
+
+  ```yaml
+  design: {type: density, base: coh, ligand: ch3, density: 1.0}
+  ```
+
+  Example: density 1.0/nm² in a ~10×10 nm box → a 22×24 Au grid, stride 2 →
+  **11×12 = 132 ligands** (box 10.978×10.368 nm in rounded-lattice mode).
+
+  For full manual control, `ligand_grid: [nx, ny]` places exactly nx×ny ligands
+  (the box is grown so the grid stays periodic; per-axis spacing may differ, so
+  anisotropic grids are allowed). It overrides `density` when both are set.
+
+- **`fraction`** — random ligands at a target fraction (0–1), seeded for
+  reproducibility.
+
+  ```yaml
+  design: {type: fraction, base: coh, ligand: ch3, fraction: 0.25, seed: 42}
+  ```
+
+- **`uniform`** — one component on every site.
+
+  ```yaml
+  design: {type: uniform, component: ch3}
+  ```
+
+- **`grid`** — two components from a 0/1 pattern file.
+
+  ```yaml
+  design: {type: grid, pattern: inputs/pattern.dat, mapping: {0: coh, 1: ch3}}
+  ```
+
+- **`multilig`** — 3+ components from an integer pattern file.
+
+The config `box: {x, y}` sets the surface area; the lattice fills it and snaps
+x,y to whole Au cells for periodicity. The pattern file (for `grid`/`multilig`)
+does not set the box — it is sampled per site and padded with the base component
+beyond its extent.
+
+### Lattice constants
+
+The default Au(111) spacing is the exact `colsep = √3·a` (`a = 0.288 nm`). Set
+`lattice: {rounded: true}` to use rounded constants (`colsep = 0.499`) when you
+need to reproduce a specific box exactly (e.g. 10.978 × 10.368 nm); ligand counts
+are identical either way.
+
+### Periodicity check
+
+Every build is checked for periodicity under PBC (on by default, warn-only): the
+box is a whole Au-lattice multiple, the ligand grid has no seam (uniform
+nearest-neighbour spacing including the wrap), and no two strands fall closer
+than `min_spacing` across the periodic boundary. Configure or disable it:
+
+```yaml
+periodicity_check: {enabled: true, on_failure: warn, min_spacing: 0.40, tol: 0.002}
+```
+
+Set `on_failure: error` to make a non-periodic surface a hard failure instead of
+a warning.
+
+## Input files
+
+The examples ship with ready-to-run strands under `configs/inputs/`: a
+methyl-terminated (`ch3`) and a hydroxyl-terminated (`coh`) alkanethiol, each as
+a single-strand `.gro` (pre-oriented along z) plus a self-contained `.itp`, and a
+design `pattern.dat` for the grid. So `configs/ch3_density.yaml`,
+`configs/ch3_onesided.yaml`, and `configs/ch3_grid.yaml` run out of the box.
+
+To use **your own** molecules, drop a single-strand `.gro` (canonically oriented
+along z, or pre-tilted with `apply_tilt: false`) and a matching `.itp`/`.top`
+into `configs/inputs/` and point the config's component paths at them.
+
+## You finish run-readiness
+
+`samgen` builds the geometry and assembles a topology, but deliberately leaves two
+simulation-setup steps to you (it prints a reminder when you assemble a
+topology):
+
+1. **Position restraints** — restrain the anchor sulfur (and typically the 7th
+   chain carbon) so the SAM stays anchored. Add a `[ position_restraints ]`
+   block / `#ifdef POSRES` to each component `.itp` and define `POSRES` in your
+   `.mdp`.
+2. **Center / box the structure** — e.g.
+   `gmx editconf -f sam.gro -o centered.gro -c -d <pad>` before
+   solvation/equilibration.
+
+## Orientation applicability
+
+samgen derives a strand's tilt/twist frame from the anchor sulfur and the first N
+backbone carbons of a linear alkyl spacer (default N=9, set per component with
+`backbone_carbons`). This matches the canonical alkanethiol-on-Au(111) SAM motif.
+Strands that depart from it — non-thiol anchors; branched, short, rigid, or
+aromatic spacers; or headgroups attached within the first N carbons — may not be
+oriented correctly. In those cases, supply a pre-oriented strand
+(`apply_tilt: false`) or verify and correct the generated frame yourself. samgen
+does not guarantee orientation for arbitrary strand chemistries.
+
+## Surface types
+
+samgen places strands on a periodic Au(111) grid — that placement is the
+guarantee. One-sided and two-sided (shared-sulfur midplane) surfaces are
+supported. Orientation and topology assembly are provided as conveniences;
+**verify both before running MD** (see "You finish run-readiness" and
+"Orientation applicability" above).
+
+## Two-sided SAMs
+
+The tool builds the **geometry** of a two-sided (shared-S) strand and surface.
+Because forming the shared sulfur removes the methyl caps and changes local
+charges, you **parameterize the generated strand yourself** (acpype/RESP), then
+hand the `.itp`/`.top` back to assemble the integrated topology.
+
+## License
+
+BSD-3-Clause — see [LICENSE](LICENSE).

samgen-0.1.2/README.md

@@ -0,0 +1,217 @@
+# samgen
+
+[![tests](https://github.com/max3925vats/samgen/actions/workflows/tests.yml/badge.svg)](https://github.com/max3925vats/samgen/actions/workflows/tests.yml)
+[![PyPI](https://img.shields.io/pypi/v/samgen)](https://pypi.org/project/samgen/)
+[![Python 3.11+](https://img.shields.io/badge/python-3.11%2B-blue)](https://www.python.org/)
+[![License: BSD-3-Clause](https://img.shields.io/badge/license-BSD--3--Clause-green)](LICENSE)
+
+Build self-assembled monolayer (SAM) surfaces as GROMACS `.gro` / `.top` files.
+
+`samgen`'s job is to place strands correctly on a periodic Au(111) grid per a
+chosen design, for one-sided and two-sided (shared-sulfur midplane) monolayers.
+Orientation/tilt and topology assembly are provided as conveniences that **you
+must verify** before running MD.
+
+## What it does
+
+- **Hexagonal Au(111) lattice** — `(√3×√3)R30°` tiling with the staggered-row
+  offset, periodic-correct box.
+- **SAM orientation** — apply the tilt (`alpha` ≈ 28°, `beta` ≈ 53°; Love et
+  al. 2005) with an always-on orientation sanity check and opt-in,
+  chemistry-anchored canonicalization.
+- **Five placement designs** — density (default), uniform, two-component grid,
+  fraction/random (seeded), and multi-ligand (3+).
+- **Anchor / cap detection** — prompt-first with consent-to-guess.
+- **Topology assembly** — residue reordering, merged `[defaults]`/`[atomtypes]`,
+  per-component bonded params, and a `[molecules]` block with correct counts,
+  optionally gated by `gmx grompp`.
+- **Periodicity check** — verifies the built surface tiles seamlessly under PBC.
+- **Two-sided SAMs** — fuse two arms onto a single shared sulfur via a proper,
+  chirality-preserving 180° rotation; emits geometry for you to parameterize.
+
+## Install
+
+Requires **Python 3.11+**. Dependencies (`numpy`, `scipy`, `pyyaml`) install
+automatically.
+
+```bash
+# from PyPI
+pip install samgen
+
+# or the latest from GitHub
+pip install git+https://github.com/max3925vats/samgen.git
+
+# or editable, for development (adds pytest)
+git clone https://github.com/max3925vats/samgen.git
+cd samgen
+pip install -e ".[dev]"
+```
+
+**GROMACS is optional** — it's only used for the `gmx grompp` topology check
+(`--validate`) and any boxing/centering you do yourself. Install it however you
+like (e.g. `brew install gromacs`, conda, or your cluster module).
+
+## Quick start
+
+The default design places a methyl-terminated (`ch3`) ligand on a
+hydroxyl-terminated (`coh`) matrix at a target areal density:
+
+```bash
+samgen build configs/ch3_density.yaml -o sam.gro --top topol.top
+# -> 132 CH3 ligands on a COH matrix (528 strands), with topol.top
+```
+
+## Three stages (run together or separately)
+
+All stages share one config, so you can run them piecewise or in one shot:
+
+```bash
+# 1) tile the surface geometry (no force field needed)
+samgen geometry configs/ch3_grid.yaml -o sam.gro
+
+# 2) assemble the topology for that surface (--validate runs the gmx grompp gate)
+samgen topology configs/ch3_grid.yaml --gro sam.gro -o topol.top --validate
+
+# ...or do both at once:
+samgen build    configs/ch3_grid.yaml -o sam.gro --top topol.top
+
+# two-sided (shared-S) strand + geometry-only surface:
+samgen twosided configs/ch3_grid.yaml --component ch3 -o strand.gro --surface twosided-sam.gro
+```
+
+For `twosided`, the anchor is prompt-first: it uses the config's `anchor:` if
+set, otherwise prompts in an interactive terminal and only auto-detects with your
+consent. In batch (no TTY) it requires `anchor:` in the config unless
+`allow_anchor_autodetect: true`.
+
+From Python:
+
+```python
+from samgen import generate_geometry, assemble_topology, build
+```
+
+## Placement designs
+
+A design decides which component sits at each Au(111) lattice site. Set it in the
+`design:` block of the config.
+
+- **`density`** (default) — ligands at a target areal density (ligands/nm²),
+  placed on a uniform sub-lattice of the gold sites. samgen keeps the grid
+  perfectly periodic; the realized density is quantized to the Au spacing and is
+  reported. If your box and density don't tile uniquely, samgen offers two
+  periodic choices (a smaller box with fewer ligands, or a larger box with more)
+  and you pick — or set `density_choice: below|above` for batch runs.
+
+  ```yaml
+  design: {type: density, base: coh, ligand: ch3, density: 1.0}
+  ```
+
+  Example: density 1.0/nm² in a ~10×10 nm box → a 22×24 Au grid, stride 2 →
+  **11×12 = 132 ligands** (box 10.978×10.368 nm in rounded-lattice mode).
+
+  For full manual control, `ligand_grid: [nx, ny]` places exactly nx×ny ligands
+  (the box is grown so the grid stays periodic; per-axis spacing may differ, so
+  anisotropic grids are allowed). It overrides `density` when both are set.
+
+- **`fraction`** — random ligands at a target fraction (0–1), seeded for
+  reproducibility.
+
+  ```yaml
+  design: {type: fraction, base: coh, ligand: ch3, fraction: 0.25, seed: 42}
+  ```
+
+- **`uniform`** — one component on every site.
+
+  ```yaml
+  design: {type: uniform, component: ch3}
+  ```
+
+- **`grid`** — two components from a 0/1 pattern file.
+
+  ```yaml
+  design: {type: grid, pattern: inputs/pattern.dat, mapping: {0: coh, 1: ch3}}
+  ```
+
+- **`multilig`** — 3+ components from an integer pattern file.
+
+The config `box: {x, y}` sets the surface area; the lattice fills it and snaps
+x,y to whole Au cells for periodicity. The pattern file (for `grid`/`multilig`)
+does not set the box — it is sampled per site and padded with the base component
+beyond its extent.
+
+### Lattice constants
+
+The default Au(111) spacing is the exact `colsep = √3·a` (`a = 0.288 nm`). Set
+`lattice: {rounded: true}` to use rounded constants (`colsep = 0.499`) when you
+need to reproduce a specific box exactly (e.g. 10.978 × 10.368 nm); ligand counts
+are identical either way.
+
+### Periodicity check
+
+Every build is checked for periodicity under PBC (on by default, warn-only): the
+box is a whole Au-lattice multiple, the ligand grid has no seam (uniform
+nearest-neighbour spacing including the wrap), and no two strands fall closer
+than `min_spacing` across the periodic boundary. Configure or disable it:
+
+```yaml
+periodicity_check: {enabled: true, on_failure: warn, min_spacing: 0.40, tol: 0.002}
+```
+
+Set `on_failure: error` to make a non-periodic surface a hard failure instead of
+a warning.
+
+## Input files
+
+The examples ship with ready-to-run strands under `configs/inputs/`: a
+methyl-terminated (`ch3`) and a hydroxyl-terminated (`coh`) alkanethiol, each as
+a single-strand `.gro` (pre-oriented along z) plus a self-contained `.itp`, and a
+design `pattern.dat` for the grid. So `configs/ch3_density.yaml`,
+`configs/ch3_onesided.yaml`, and `configs/ch3_grid.yaml` run out of the box.
+
+To use **your own** molecules, drop a single-strand `.gro` (canonically oriented
+along z, or pre-tilted with `apply_tilt: false`) and a matching `.itp`/`.top`
+into `configs/inputs/` and point the config's component paths at them.
+
+## You finish run-readiness
+
+`samgen` builds the geometry and assembles a topology, but deliberately leaves two
+simulation-setup steps to you (it prints a reminder when you assemble a
+topology):
+
+1. **Position restraints** — restrain the anchor sulfur (and typically the 7th
+   chain carbon) so the SAM stays anchored. Add a `[ position_restraints ]`
+   block / `#ifdef POSRES` to each component `.itp` and define `POSRES` in your
+   `.mdp`.
+2. **Center / box the structure** — e.g.
+   `gmx editconf -f sam.gro -o centered.gro -c -d <pad>` before
+   solvation/equilibration.
+
+## Orientation applicability
+
+samgen derives a strand's tilt/twist frame from the anchor sulfur and the first N
+backbone carbons of a linear alkyl spacer (default N=9, set per component with
+`backbone_carbons`). This matches the canonical alkanethiol-on-Au(111) SAM motif.
+Strands that depart from it — non-thiol anchors; branched, short, rigid, or
+aromatic spacers; or headgroups attached within the first N carbons — may not be
+oriented correctly. In those cases, supply a pre-oriented strand
+(`apply_tilt: false`) or verify and correct the generated frame yourself. samgen
+does not guarantee orientation for arbitrary strand chemistries.
+
+## Surface types
+
+samgen places strands on a periodic Au(111) grid — that placement is the
+guarantee. One-sided and two-sided (shared-sulfur midplane) surfaces are
+supported. Orientation and topology assembly are provided as conveniences;
+**verify both before running MD** (see "You finish run-readiness" and
+"Orientation applicability" above).
+
+## Two-sided SAMs
+
+The tool builds the **geometry** of a two-sided (shared-S) strand and surface.
+Because forming the shared sulfur removes the methyl caps and changes local
+charges, you **parameterize the generated strand yourself** (acpype/RESP), then
+hand the `.itp`/`.top` back to assemble the integrated topology.
+
+## License
+
+BSD-3-Clause — see [LICENSE](LICENSE).

samgen-0.1.2/configs/ch3_density.yaml

@@ -0,0 +1,43 @@
+# configs/ch3_density.yaml
+# Default design: areal-density placement of a CH3 ligand on a COH base.
+# Paths resolve relative to this file. Bundled inputs are pre-oriented along z.
+# samgen keeps the ligand grid perfectly periodic on Au(111); if your box +
+# density don't tile uniquely it offers a 'below'/'above' choice (interactive),
+# or set design.density_choice for batch runs.
+lattice:
+  a: 0.288
+  tilt_alpha: 28
+  tilt_beta: 53
+  # rounded: true       # opt in for exact legacy box dims (10.978 x 10.368)
+box:
+  x: 10.0
+  y: 10.0
+  z: 10.0
+leaflets: 1
+components:
+  coh:
+    gro: inputs/coh.gro
+    itp: inputs/coh.itp
+    resname: COH
+    anchor: S13
+  ch3:
+    gro: inputs/ch3.gro
+    itp: inputs/ch3.itp
+    resname: CH3
+    anchor: S12
+design:
+  type: density           # the default; may be omitted
+  base: coh
+  ligand: ch3
+  density: 1.0            # ligands/nm^2
+  # density_choice: above # batch pick when the box doesn't tile uniquely
+  # ligand_grid: [11, 12] # explicit override (exact nx x ny; wins over density)
+output:
+  gro: sam.gro
+  order: [COH, CH3]
+periodicity_check:        # on by default, warn-only; shown here for reference
+  enabled: true
+  on_failure: warn        # warn | error
+  min_spacing: 0.40       # nm
+  tol: 0.002              # nm
+allow_anchor_autodetect: false

samgen-0.1.2/configs/ch3_grid.yaml

@@ -0,0 +1,33 @@
+# Two-component mixed CH3/OH SAM from a 0/1 design grid:
+#   methyl-terminated (CH3) ligand on a hydroxyl-terminated (COH) base.
+# Paths are resolved relative to this config file's directory.
+# The bundled inputs/ strands are pre-oriented (chain along z); samgen applies
+# the SAM tilt. Swap in your own strand .gro/.itp the same way.
+lattice:
+  a: 0.288
+  tilt_alpha: 28
+  tilt_beta: 53
+box:
+  x: 5.0
+  y: 5.0
+  z: 10.0
+leaflets: 1
+components:
+  coh:
+    gro: inputs/coh.gro
+    itp: inputs/coh.itp
+    resname: COH
+    anchor: S13         # gold-facing (methyl-capped) sulfur
+  ch3:
+    gro: inputs/ch3.gro
+    itp: inputs/ch3.itp
+    resname: CH3
+    anchor: S12
+design:
+  type: grid
+  pattern: inputs/pattern.dat
+  mapping: {0: coh, 1: ch3}
+output:
+  gro: sam.gro
+  order: [COH, CH3]     # [molecules] order; base first
+allow_anchor_autodetect: false

samgen-0.1.2/configs/ch3_onesided.yaml

@@ -0,0 +1,26 @@
+# Single-component CH3 SAM (one-sided), methyl-terminated alkanethiol.
+# Paths are resolved relative to this config file's directory.
+# The bundled inputs/ strands are pre-oriented (chain along z); samgen applies
+# the SAM tilt. Swap in your own strand .gro/.itp the same way.
+lattice:
+  a: 0.288          # Au(111) lattice constant, nm
+  tilt_alpha: 28    # tilt from surface normal, deg (Love et al. 2005)
+  tilt_beta: 53     # twist about chain axis, deg
+box:
+  x: 8.0
+  y: 8.0
+  z: 5.0
+leaflets: 1
+components:
+  ch3:
+    gro: inputs/ch3.gro
+    itp: inputs/ch3.itp
+    resname: CH3
+    anchor: S12       # gold-facing (methyl-capped) sulfur
+design:
+  type: uniform
+  component: ch3
+output:
+  gro: sam.gro
+  order: [CH3]
+allow_anchor_autodetect: false

samgen-0.1.2/configs/example-patterns/dense-grid.dat

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samgen-0.1.2/configs/example-patterns/four-lig.dat

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samgen-0.1.2/configs/example-patterns/one-lig.dat

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samgen-0.1.2/configs/example-patterns/three-lig.dat

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