Show how to populate struct_ref, closes #1

salilab · Aug 15, 2024 · 137e708 · 137e708
1 parent cd224c0
commit 137e708
Show file tree

Hide file tree

Showing 4 changed files with 140 additions and 6 deletions.
diff --git a/rnapolii/modeling/.template.deposition.ipynb b/rnapolii/modeling/.template.deposition.ipynb
@@ -165,6 +165,7 @@
     "import IMP.pmi.mmcif\n",
     "import ihm\n",
     "import ihm.location\n",
+    "import ihm.reference\n",
     "import ihm.model"
    ]
   },
@@ -737,6 +738,47 @@
     "last_step.num_models_end = 200000"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Add UniProt sequence information {#uniprot}\n",
+    "\n",
+    "Usually the sequences for each subunit we modeled are available in a reference database such as\n",
+    "[UniProt](https://www.uniprot.org/). IMP doesn't need to know the database accession codes in order\n",
+    "to perform the modeling, but it is useful to link them for the deposition. We can do this using the\n",
+    "python-ihm API to add ``ihm.reference.UniProtSequence`` objects. These are added per *entity*, not\n",
+    "per subunit (an entity has a unique sequence; if multiple subunits or copies have the same sequence,\n",
+    "they all map to the same entity). ProtocolOutput provides an `entities` dict, which maps our subunit\n",
+    "names (without copy numbers) to ``ihm.Entity`` objects:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "for subunit, accession in [('Rpb1', 'P04050'),\n",
+    "                           ('Rpb2', 'P08518')]:\n",
+    "    ref = ihm.reference.UniProtSequence.from_accession(accession)\n",
+    "    po.entities[subunit].references.append(ref)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Here, ``~ihm.reference.UniProtSequence.from_accession`` queries the UniProt API to get full information\n",
+    "(so requires a network connection). Alternatively, we could create ``ihm.reference.UniProtSequence``\n",
+    "objects outselves. Here we just populate the first two sequences for illustration.\n",
+    "\n",
+    "If for some reason the sequence modeled by IMP is different from that in UniProt, both the alignment\n",
+    "between the two and any single-point mutations should be annotated with ``ihm.reference.Alignment``\n",
+    "and ``ihm.reference.SeqDif`` objects. See the [pol_ii_g scripts](https://github.com/integrativemodeling/pol_ii_g/blob/a416964fe024352352789d1be8fbd7cfd288832f/production_scripts/sample.py#L288-L305)\n",
+    "for an example."
+   ]
+  },
   {
    "cell_type": "markdown",
    "metadata": {},
@@ -1073,7 +1115,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -1087,7 +1129,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.5"
+   "version": "3.12.5"
   }
  },
  "nbformat": 4,

diff --git a/rnapolii/modeling/deposition-colab.ipynb b/rnapolii/modeling/deposition-colab.ipynb
@@ -22,6 +22,7 @@
         " - [Polishing the deposition](#polishing)\n",
         "  - [Cross-linker type](#xltype)\n",
         "  - [Correct number of output models](#fixnummodel)\n",
+        "  - [Add UniProt sequence information](#uniprot)\n",
         "  - [Add model coordinates](#addcoords)\n",
         "  - [Replace local links with DOIs](#adddois)\n",
         " - [Output](#output)\n",
@@ -161,6 +162,7 @@
         "import IMP.pmi.mmcif\n",
         "import ihm\n",
         "import ihm.location\n",
+        "import ihm.reference\n",
         "import ihm.model"
       ]
     },
@@ -729,6 +731,47 @@
         "last_step.num_models_end = 200000"
       ]
     },
+    {
+      "cell_type": "markdown",
+      "metadata": {},
+      "source": [
+        "## Add UniProt sequence information<a id=\"uniprot\"></a>\n",
+        "\n",
+        "Usually the sequences for each subunit we modeled are available in a reference database such as\n",
+        "[UniProt](https://www.uniprot.org/). IMP doesn't need to know the database accession codes in order\n",
+        "to perform the modeling, but it is useful to link them for the deposition. We can do this using the\n",
+        "python-ihm API to add [ihm.reference.UniProtSequence](https://python-ihm.readthedocs.io/en/latest/reference.html#ihm.reference.UniProtSequence) objects. These are added per *entity*, not\n",
+        "per subunit (an entity has a unique sequence; if multiple subunits or copies have the same sequence,\n",
+        "they all map to the same entity). ProtocolOutput provides an `entities` dict, which maps our subunit\n",
+        "names (without copy numbers) to [ihm.Entity](https://python-ihm.readthedocs.io/en/latest/main.html#ihm.Entity) objects:"
+      ]
+    },
+    {
+      "cell_type": "code",
+      "execution_count": null,
+      "metadata": {},
+      "outputs": [],
+      "source": [
+        "for subunit, accession in [('Rpb1', 'P04050'),\n",
+        "                           ('Rpb2', 'P08518')]:\n",
+        "    ref = ihm.reference.UniProtSequence.from_accession(accession)\n",
+        "    po.entities[subunit].references.append(ref)"
+      ]
+    },
+    {
+      "cell_type": "markdown",
+      "metadata": {},
+      "source": [
+        "Here, [from_accession](https://python-ihm.readthedocs.io/en/latest/reference.html#ihm.reference.UniProtSequence.from_accession) queries the UniProt API to get full information\n",
+        "(so requires a network connection). Alternatively, we could create [ihm.reference.UniProtSequence](https://python-ihm.readthedocs.io/en/latest/reference.html#ihm.reference.UniProtSequence)\n",
+        "objects outselves. Here we just populate the first two sequences for illustration.\n",
+        "\n",
+        "If for some reason the sequence modeled by IMP is different from that in UniProt, both the alignment\n",
+        "between the two and any single-point mutations should be annotated with [ihm.reference.Alignment](https://python-ihm.readthedocs.io/en/latest/reference.html#ihm.reference.Alignment)\n",
+        "and [ihm.reference.SeqDif](https://python-ihm.readthedocs.io/en/latest/reference.html#ihm.reference.SeqDif) objects. See the [pol_ii_g scripts](https://github.com/integrativemodeling/pol_ii_g/blob/a416964fe024352352789d1be8fbd7cfd288832f/production_scripts/sample.py#L288-L305)\n",
+        "for an example."
+      ]
+    },
     {
       "cell_type": "markdown",
       "metadata": {},
@@ -1065,7 +1108,7 @@
   ],
   "metadata": {
     "kernelspec": {
-      "display_name": "Python 3",
+      "display_name": "Python 3 (ipykernel)",
       "language": "python",
       "name": "python3"
     },
@@ -1079,7 +1122,7 @@
       "name": "python",
       "nbconvert_exporter": "python",
       "pygments_lexer": "ipython3",
-      "version": "3.9.5"
+      "version": "3.12.5"
     }
   },
   "nbformat": 4,

diff --git a/rnapolii/modeling/deposition.ipynb b/rnapolii/modeling/deposition.ipynb
@@ -22,6 +22,7 @@
         " - [Polishing the deposition](#polishing)\n",
         "  - [Cross-linker type](#xltype)\n",
         "  - [Correct number of output models](#fixnummodel)\n",
+        "  - [Add UniProt sequence information](#uniprot)\n",
         "  - [Add model coordinates](#addcoords)\n",
         "  - [Replace local links with DOIs](#adddois)\n",
         " - [Output](#output)\n",
@@ -133,6 +134,7 @@
         "import IMP.pmi.mmcif\n",
         "import ihm\n",
         "import ihm.location\n",
+        "import ihm.reference\n",
         "import ihm.model"
       ]
     },
@@ -701,6 +703,47 @@
         "last_step.num_models_end = 200000"
       ]
     },
+    {
+      "cell_type": "markdown",
+      "metadata": {},
+      "source": [
+        "## Add UniProt sequence information<a id=\"uniprot\"></a>\n",
+        "\n",
+        "Usually the sequences for each subunit we modeled are available in a reference database such as\n",
+        "[UniProt](https://www.uniprot.org/). IMP doesn't need to know the database accession codes in order\n",
+        "to perform the modeling, but it is useful to link them for the deposition. We can do this using the\n",
+        "python-ihm API to add [ihm.reference.UniProtSequence](https://python-ihm.readthedocs.io/en/latest/reference.html#ihm.reference.UniProtSequence) objects. These are added per *entity*, not\n",
+        "per subunit (an entity has a unique sequence; if multiple subunits or copies have the same sequence,\n",
+        "they all map to the same entity). ProtocolOutput provides an `entities` dict, which maps our subunit\n",
+        "names (without copy numbers) to [ihm.Entity](https://python-ihm.readthedocs.io/en/latest/main.html#ihm.Entity) objects:"
+      ]
+    },
+    {
+      "cell_type": "code",
+      "execution_count": null,
+      "metadata": {},
+      "outputs": [],
+      "source": [
+        "for subunit, accession in [('Rpb1', 'P04050'),\n",
+        "                           ('Rpb2', 'P08518')]:\n",
+        "    ref = ihm.reference.UniProtSequence.from_accession(accession)\n",
+        "    po.entities[subunit].references.append(ref)"
+      ]
+    },
+    {
+      "cell_type": "markdown",
+      "metadata": {},
+      "source": [
+        "Here, [from_accession](https://python-ihm.readthedocs.io/en/latest/reference.html#ihm.reference.UniProtSequence.from_accession) queries the UniProt API to get full information\n",
+        "(so requires a network connection). Alternatively, we could create [ihm.reference.UniProtSequence](https://python-ihm.readthedocs.io/en/latest/reference.html#ihm.reference.UniProtSequence)\n",
+        "objects outselves. Here we just populate the first two sequences for illustration.\n",
+        "\n",
+        "If for some reason the sequence modeled by IMP is different from that in UniProt, both the alignment\n",
+        "between the two and any single-point mutations should be annotated with [ihm.reference.Alignment](https://python-ihm.readthedocs.io/en/latest/reference.html#ihm.reference.Alignment)\n",
+        "and [ihm.reference.SeqDif](https://python-ihm.readthedocs.io/en/latest/reference.html#ihm.reference.SeqDif) objects. See the [pol_ii_g scripts](https://github.com/integrativemodeling/pol_ii_g/blob/a416964fe024352352789d1be8fbd7cfd288832f/production_scripts/sample.py#L288-L305)\n",
+        "for an example."
+      ]
+    },
     {
       "cell_type": "markdown",
       "metadata": {},
@@ -1037,7 +1080,7 @@
   ],
   "metadata": {
     "kernelspec": {
-      "display_name": "Python 3",
+      "display_name": "Python 3 (ipykernel)",
       "language": "python",
       "name": "python3"
     },
@@ -1051,7 +1094,7 @@
       "name": "python",
       "nbconvert_exporter": "python",
       "pygments_lexer": "ipython3",
-      "version": "3.9.5"
+      "version": "3.12.5"
     }
   },
   "nbformat": 4,

diff --git a/rnapolii/modeling/deposition.py b/rnapolii/modeling/deposition.py
@@ -6,6 +6,7 @@
 import IMP.pmi.mmcif
 import ihm
 import ihm.location
+import ihm.reference
 import ihm.model
 
 import IMP
@@ -267,6 +268,11 @@
 # Correct number of output models to account for multiple runs
 last_step.num_models_end = 200000
 
+for subunit, accession in [('Rpb1', 'P04050'),
+                           ('Rpb2', 'P08518')]:
+    ref = ihm.reference.UniProtSequence.from_accession(accession)
+    po.entities[subunit].references.append(ref)
+
 # Get last protocol in the file
 protocol = po.system.orphan_protocols[-1]
 # State that we filtered the 200000 frames down to one cluster of