{
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  "item": {
    "slug": "mol-render",
    "name": "Molecular 3D Renderer",
    "source": "tencent",
    "type": "skill",
    "category": "AI 智能",
    "sourceUrl": "https://clawhub.ai/Zhao-Zehua/mol-render",
    "canonicalUrl": "https://clawhub.ai/Zhao-Zehua/mol-render",
    "targetPlatform": "OpenClaw"
  },
  "install": {
    "downloadMode": "redirect",
    "downloadUrl": "/downloads/mol-render",
    "sourceDownloadUrl": "https://wry-manatee-359.convex.site/api/v1/download?slug=mol-render",
    "sourcePlatform": "tencent",
    "targetPlatform": "OpenClaw",
    "installMethod": "Manual import",
    "extraction": "Extract archive",
    "prerequisites": [
      "OpenClaw"
    ],
    "packageFormat": "ZIP package",
    "includedAssets": [
      "SKILL.md",
      "scripts/pdb_to_3d.py",
      "scripts/smiles_to_3d.py"
    ],
    "primaryDoc": "SKILL.md",
    "quickSetup": [
      "Download the package from Yavira.",
      "Extract the archive and review SKILL.md first.",
      "Import or place the package into your OpenClaw setup."
    ],
    "agentAssist": {
      "summary": "Hand the extracted package to your coding agent with a concrete install brief instead of figuring it out manually.",
      "steps": [
        "Download the package from Yavira.",
        "Extract it into a folder your agent can access.",
        "Paste one of the prompts below and point your agent at the extracted folder."
      ],
      "prompts": [
        {
          "label": "New install",
          "body": "I downloaded a skill package from Yavira. Read SKILL.md from the extracted folder and install it by following the included instructions. Tell me what you changed and call out any manual steps you could not complete."
        },
        {
          "label": "Upgrade existing",
          "body": "I downloaded an updated skill package from Yavira. Read SKILL.md from the extracted folder, compare it with my current installation, and upgrade it while preserving any custom configuration unless the package docs explicitly say otherwise. Summarize what changed and any follow-up checks I should run."
        }
      ]
    },
    "sourceHealth": {
      "source": "tencent",
      "status": "healthy",
      "reason": "direct_download_ok",
      "recommendedAction": "download",
      "checkedAt": "2026-04-30T16:55:25.780Z",
      "expiresAt": "2026-05-07T16:55:25.780Z",
      "httpStatus": 200,
      "finalUrl": "https://wry-manatee-359.convex.site/api/v1/download?slug=network",
      "contentType": "application/zip",
      "probeMethod": "head",
      "details": {
        "probeUrl": "https://wry-manatee-359.convex.site/api/v1/download?slug=network",
        "contentDisposition": "attachment; filename=\"network-1.0.0.zip\"",
        "redirectLocation": null,
        "bodySnippet": null
      },
      "scope": "source",
      "summary": "Source download looks usable.",
      "detail": "Yavira can redirect you to the upstream package for this source.",
      "primaryActionLabel": "Download for OpenClaw",
      "primaryActionHref": "/downloads/mol-render"
    },
    "validation": {
      "installChecklist": [
        "Use the Yavira download entry.",
        "Review SKILL.md after the package is downloaded.",
        "Confirm the extracted package contains the expected setup assets."
      ],
      "postInstallChecks": [
        "Confirm the extracted package includes the expected docs or setup files.",
        "Validate the skill or prompts are available in your target agent workspace.",
        "Capture any manual follow-up steps the agent could not complete."
      ]
    },
    "downloadPageUrl": "https://openagent3.xyz/downloads/mol-render",
    "agentPageUrl": "https://openagent3.xyz/skills/mol-render/agent",
    "manifestUrl": "https://openagent3.xyz/skills/mol-render/agent.json",
    "briefUrl": "https://openagent3.xyz/skills/mol-render/agent.md"
  },
  "agentAssist": {
    "summary": "Hand the extracted package to your coding agent with a concrete install brief instead of figuring it out manually.",
    "steps": [
      "Download the package from Yavira.",
      "Extract it into a folder your agent can access.",
      "Paste one of the prompts below and point your agent at the extracted folder."
    ],
    "prompts": [
      {
        "label": "New install",
        "body": "I downloaded a skill package from Yavira. Read SKILL.md from the extracted folder and install it by following the included instructions. Tell me what you changed and call out any manual steps you could not complete."
      },
      {
        "label": "Upgrade existing",
        "body": "I downloaded an updated skill package from Yavira. Read SKILL.md from the extracted folder, compare it with my current installation, and upgrade it while preserving any custom configuration unless the package docs explicitly say otherwise. Summarize what changed and any follow-up checks I should run."
      }
    ]
  },
  "documentation": {
    "source": "clawhub",
    "primaryDoc": "SKILL.md",
    "sections": [
      {
        "title": "mol-render",
        "body": "Generate high-quality 3D ball-and-stick model PNG images from SMILES strings or PDB structures, rendered with POV-Ray ray tracing."
      },
      {
        "title": "Dependencies",
        "body": "Required:\n\nrdkit — SMILES parsing & 3D conformer generation\nnumpy — coordinate transforms\npovray — ray tracing renderer\n\nOptional (PDB mode only):\n\nbiopython — PDB file parsing\n\nInstall:\n\npip install rdkit numpy\napt-get install -y povray\n\n# For PDB support:\npip install biopython"
      },
      {
        "title": "SMILES Mode",
        "body": "python3 scripts/smiles_to_3d.py \"SMILES\" -o output.png\n\nArguments:\n\nSMILES — (positional) SMILES string (required)\n-o, --output — output PNG path (default: molecule.png)\n--bg — background color: black / white / blue (default: blue)\n--no-hydrogen — hide hydrogen atoms\n--kekulize — convert aromatic bonds to alternating single/double bonds\n\nExamples:\n\n# Ethanol\npython3 scripts/smiles_to_3d.py \"CCO\" -o ethanol.png\n\n# Benzene (white background, Kekulé style)\npython3 scripts/smiles_to_3d.py \"c1ccccc1\" -o benzene.png --bg white --kekulize\n\n# Caffeine\npython3 scripts/smiles_to_3d.py \"CN1C=NC2=C1C(=O)N(C(=O)N2C)C\" -o caffeine.png\n\n# Aspirin (no hydrogens)\npython3 scripts/smiles_to_3d.py \"CC(=O)OC1=CC=CC=C1C(=O)O\" -o aspirin.png --no-hydrogen"
      },
      {
        "title": "PDB Mode",
        "body": "python3 scripts/pdb_to_3d.py --pdb <PDB_ID_or_file> -o output.png\n\nArguments:\n\n--pdb — PDB file path or 4-character PDB ID (auto-downloads from RCSB) (required)\n-o, --output — output PNG path (default: pdb_molecule.png)\n--chain — select specific chain (e.g., A)\n--residues — residue range (e.g., 1-50 or 10,20,30-40)\n--ligand-only — render only ligands (HETATM, excluding water)\n--no-hydrogen — hide hydrogen atoms\n--no-water / --keep-water — filter/keep water molecules (default: filter)\n--bg — background color: black / white / blue (default: blue)\n--view — viewing angle: auto / side / top / front or θ,φ in degrees (default: auto)\n--resolution — resolution multiplier, e.g., 0.5 for half, 2.0 for double (default: 1.0)\n--sphere-scale — override sphere scale factor (default: auto)\n--bond-radius — override bond radius (default: auto)\n\nExamples:\n\n# Download and render G-quadruplex from RCSB\npython3 scripts/pdb_to_3d.py --pdb 1KF1 --no-hydrogen -o g4.png\n\n# Side view\npython3 scripts/pdb_to_3d.py --pdb 1KF1 --no-hydrogen --view side -o g4_side.png\n\n# Ligands only\npython3 scripts/pdb_to_3d.py --pdb 1KF1 --ligand-only -o ligands.png\n\n# Specific chain and residues\npython3 scripts/pdb_to_3d.py --pdb 1KF1 --chain A --residues 1-12 -o partial.png\n\n# Local PDB file\npython3 scripts/pdb_to_3d.py --pdb structure.pdb -o out.png\n\n# Large protein at lower resolution\npython3 scripts/pdb_to_3d.py --pdb 2HYY --no-hydrogen --resolution 0.5 -o protein.png"
      },
      {
        "title": "Output",
        "body": "1200×1200 PNG with POV-Ray ray tracing\nCPK color scheme (C=dark gray, O=red, N=blue, H=white, P=orange, S=yellow, K=purple, ...)\nAromatic bonds rendered as solid + dashed lines (SMILES mode)\nDouble bonds rendered as two parallel solid lines\n--kekulize option converts aromatic bonds to alternating single/double\nMetal ions displayed with ionic radius (large spheres), no coordination bonds drawn\nAuto-selects best viewing angle (PCA-based)\nAuto-scales sphere/bond sizes for large molecules\nWater molecules filtered by default (PDB mode)"
      },
      {
        "title": "Known Limitations",
        "body": "Very large molecules (>2000 atoms) may be slow to render (use --resolution 0.5)\nPDB mode renders all bonds as single bonds (no double/aromatic distinction)\nMetal coordination bonds are not rendered\nPOV-Ray must be installed (which povray)\nbiopython required only for PDB mode (optional dependency)"
      },
      {
        "title": "License",
        "body": "MIT"
      }
    ],
    "body": "mol-render\n\nGenerate high-quality 3D ball-and-stick model PNG images from SMILES strings or PDB structures, rendered with POV-Ray ray tracing.\n\nDependencies\n\nRequired:\n\nrdkit — SMILES parsing & 3D conformer generation\nnumpy — coordinate transforms\npovray — ray tracing renderer\n\nOptional (PDB mode only):\n\nbiopython — PDB file parsing\n\nInstall:\n\npip install rdkit numpy\napt-get install -y povray\n\n# For PDB support:\npip install biopython\n\nUsage\nSMILES Mode\npython3 scripts/smiles_to_3d.py \"SMILES\" -o output.png\n\n\nArguments:\n\nSMILES — (positional) SMILES string (required)\n-o, --output — output PNG path (default: molecule.png)\n--bg — background color: black / white / blue (default: blue)\n--no-hydrogen — hide hydrogen atoms\n--kekulize — convert aromatic bonds to alternating single/double bonds\n\nExamples:\n\n# Ethanol\npython3 scripts/smiles_to_3d.py \"CCO\" -o ethanol.png\n\n# Benzene (white background, Kekulé style)\npython3 scripts/smiles_to_3d.py \"c1ccccc1\" -o benzene.png --bg white --kekulize\n\n# Caffeine\npython3 scripts/smiles_to_3d.py \"CN1C=NC2=C1C(=O)N(C(=O)N2C)C\" -o caffeine.png\n\n# Aspirin (no hydrogens)\npython3 scripts/smiles_to_3d.py \"CC(=O)OC1=CC=CC=C1C(=O)O\" -o aspirin.png --no-hydrogen\n\nPDB Mode\npython3 scripts/pdb_to_3d.py --pdb <PDB_ID_or_file> -o output.png\n\n\nArguments:\n\n--pdb — PDB file path or 4-character PDB ID (auto-downloads from RCSB) (required)\n-o, --output — output PNG path (default: pdb_molecule.png)\n--chain — select specific chain (e.g., A)\n--residues — residue range (e.g., 1-50 or 10,20,30-40)\n--ligand-only — render only ligands (HETATM, excluding water)\n--no-hydrogen — hide hydrogen atoms\n--no-water / --keep-water — filter/keep water molecules (default: filter)\n--bg — background color: black / white / blue (default: blue)\n--view — viewing angle: auto / side / top / front or θ,φ in degrees (default: auto)\n--resolution — resolution multiplier, e.g., 0.5 for half, 2.0 for double (default: 1.0)\n--sphere-scale — override sphere scale factor (default: auto)\n--bond-radius — override bond radius (default: auto)\n\nExamples:\n\n# Download and render G-quadruplex from RCSB\npython3 scripts/pdb_to_3d.py --pdb 1KF1 --no-hydrogen -o g4.png\n\n# Side view\npython3 scripts/pdb_to_3d.py --pdb 1KF1 --no-hydrogen --view side -o g4_side.png\n\n# Ligands only\npython3 scripts/pdb_to_3d.py --pdb 1KF1 --ligand-only -o ligands.png\n\n# Specific chain and residues\npython3 scripts/pdb_to_3d.py --pdb 1KF1 --chain A --residues 1-12 -o partial.png\n\n# Local PDB file\npython3 scripts/pdb_to_3d.py --pdb structure.pdb -o out.png\n\n# Large protein at lower resolution\npython3 scripts/pdb_to_3d.py --pdb 2HYY --no-hydrogen --resolution 0.5 -o protein.png\n\nOutput\n1200×1200 PNG with POV-Ray ray tracing\nCPK color scheme (C=dark gray, O=red, N=blue, H=white, P=orange, S=yellow, K=purple, ...)\nAromatic bonds rendered as solid + dashed lines (SMILES mode)\nDouble bonds rendered as two parallel solid lines\n--kekulize option converts aromatic bonds to alternating single/double\nMetal ions displayed with ionic radius (large spheres), no coordination bonds drawn\nAuto-selects best viewing angle (PCA-based)\nAuto-scales sphere/bond sizes for large molecules\nWater molecules filtered by default (PDB mode)\nKnown Limitations\nVery large molecules (>2000 atoms) may be slow to render (use --resolution 0.5)\nPDB mode renders all bonds as single bonds (no double/aromatic distinction)\nMetal coordination bonds are not rendered\nPOV-Ray must be installed (which povray)\nbiopython required only for PDB mode (optional dependency)\nLicense\n\nMIT"
  },
  "trust": {
    "sourceLabel": "tencent",
    "provenanceUrl": "https://clawhub.ai/Zhao-Zehua/mol-render",
    "publisherUrl": "https://clawhub.ai/Zhao-Zehua/mol-render",
    "owner": "Zhao-Zehua",
    "version": "1.0.0",
    "license": null,
    "verificationStatus": "Indexed source record"
  },
  "links": {
    "detailUrl": "https://openagent3.xyz/skills/mol-render",
    "downloadUrl": "https://openagent3.xyz/downloads/mol-render",
    "agentUrl": "https://openagent3.xyz/skills/mol-render/agent",
    "manifestUrl": "https://openagent3.xyz/skills/mol-render/agent.json",
    "briefUrl": "https://openagent3.xyz/skills/mol-render/agent.md"
  }
}