@yeyuan98/opencode-bioresearcher-plugin 1.6.6 → 1.6.8-alpha.0

package/dist/index.js

@@ -4,7 +4,7 @@ import { createBioResearcherDRAgent } from "./agents/bioresearcherDR/index";
 import { createBioResearcherDRWorkerAgent } from "./agents/bioresearcherDR_worker/index";
 import { tableTools } from "./tools/table/index";
 import { dbTools } from "./tools/db/index";
-import { blockingTimer, calculator, jsonExtract, jsonValidate, jsonInfer } from "./tools/misc/index";
+import { blockingTimer, calculator, jsonExtract, jsonValidate, jsonInfer, markdownToHtml } from "./tools/misc/index";
 import { parse_pubmed_articleSet } from "./tools/parser/pubmed";
 import { parse_obo_file } from "./tools/parser/obo";
 export const BioResearcherPlugin = async (input) => {
@@ -23,7 +23,7 @@ export const BioResearcherPlugin = async (input) => {
                 "tableGroupBy", "tablePivotSummary", "tableAppendRows", "tableUpdateCell",
                 "tableCreateFile", "dbQuery", "dbListTables", "dbDescribeTable",
                 "calculator", "blockingTimer", "jsonExtract", "jsonValidate", "jsonInfer",
-                "parse_pubmed_articleSet", "parse_obo_file",
+                "parse_pubmed_articleSet", "parse_obo_file", "markdownToHtml",
             ];
             if (!pluginToolIds.includes(input.toolID))
                 return;
@@ -38,7 +38,8 @@ export const BioResearcherPlugin = async (input) => {
             jsonValidate,
             jsonInfer,
             parse_pubmed_articleSet,
-            parse_obo_file
+            parse_obo_file,
+            markdownToHtml
         }
     };
 };

package/dist/skills/gromacs-guides/guides/create_index.md

@@ -1,96 +1,96 @@
-# Creating Index Files for Protein Chains
-
-## Basic Method
-
-```bash
-# Interactive mode
-gmx make_ndx -f <tpr_file> -o <index_file.ndx>
-
-# Non-interactive: split protein group by chain
-printf "splitch <protein_group>\nq\n" | gmx make_ndx -f <tpr_file> -o <index_file.ndx>
-```
-
-## Caveat: `splitch` Artefacts
-
-`splitch` uses topological connectivity and may incorrectly split a single chain into multiple groups when:
-- Hydrogen atoms were rebuilt by `pdb2gmx` (N-terminal residues get extra H1/H2/H3 atoms)
-- Residue numbering has gaps (e.g., residues 1-18, then 26-108)
-
-**Symptom**: After `splitch`, a single protein chain appears as multiple `Protein_chainN` groups where the atom counts don't match expected molecule boundaries.
-
-## Recommended Workflow: Fix Incorrectly Split Chains
-
-**Step 1: Identify the incorrect split**
-After `splitch`, press Enter (empty line) in `make_ndx` to list all groups. Compare atom counts against your expected molecule sizes.
-
-**Step 2: Merge the incorrectly split groups**
-```
-<group_N> | <group_M>
-```
-This creates a new merged group named `Protein_chainN_Protein_chainM` at the end of the list.
-
-**Step 3: Verify the merged group**
-Press Enter to list groups again. The merged group should have the correct total atom count.
-
-**Step 4: Delete the incorrect split groups**
-Delete in DESCENDING order to avoid index shifting confusion:
-```
-del <higher_index>
-del <lower_index>
-```
-After `k` deletions, the merged group index shifts down by `k`.
-
-**Step 5: Rename the merged group (optional)**
-```
-name <final_index> <custom_name>
-```
-
-## Generic Example (interactive `make_ndx` session)
-
-```
-> splitch 1
-Found N chains
- 1:  XXX atoms (a to b)
- 2:   YY atoms (c to d)     <-- suspiciously small, may be incorrect split
- 3:  ZZZ atoms (e to f)     <-- remainder of same chain
-
->                          <-- press Enter to list groups
-...
- N  Protein_chain1         XXX atoms
-N+1 Protein_chain2          YY atoms   <-- wrong split (too small)
-N+2 Protein_chain3         ZZZ atoms   <-- wrong split (remainder)
-...
-
-> N+1 | N+2                 <-- merge the incorrectly split groups
-Merged two groups with OR: YY ZZZ -> (YY+ZZZ)
-
->                          <-- press Enter to verify
-...
- M  Protein_chain2_Protein_chain3   (YY+ZZZ) atoms   <-- correct total!
-
-> del N+2                   <-- delete higher index first
-> del N+1                   <-- then lower index
-
->                          <-- press Enter
-...
- M-2  Protein_chain2_Protein_chain3   (YY+ZZZ) atoms   <-- shifted!
-
-> name M-2 <your_chain_name>
-> q
-```
-
-**Key insight**: After deleting `k` groups that were created AFTER the merged group, the merged group's index decreases by `k`.
-
-## Non-interactive Equivalent
-
-```bash
-printf "splitch 1\n<group_N> | <group_M>\ndel <higher>\ndel <lower>\nname <final> <name>\nq\n" | \
-  gmx make_ndx -f <tpr_file> -o <index_file.ndx>
-```
-
-## Creating C-alpha Groups
-
-In `make_ndx` interactive mode:
-```
-a CA & <chain_group>      # creates C-alpha selection for specified chain
-```
+# Creating Index Files for Protein Chains
+
+## Basic Method
+
+```bash
+# Interactive mode
+gmx make_ndx -f <tpr_file> -o <index_file.ndx>
+
+# Non-interactive: split protein group by chain
+printf "splitch <protein_group>\nq\n" | gmx make_ndx -f <tpr_file> -o <index_file.ndx>
+```
+
+## Caveat: `splitch` Artefacts
+
+`splitch` uses topological connectivity and may incorrectly split a single chain into multiple groups when:
+- Hydrogen atoms were rebuilt by `pdb2gmx` (N-terminal residues get extra H1/H2/H3 atoms)
+- Residue numbering has gaps (e.g., residues 1-18, then 26-108)
+
+**Symptom**: After `splitch`, a single protein chain appears as multiple `Protein_chainN` groups where the atom counts don't match expected molecule boundaries.
+
+## Recommended Workflow: Fix Incorrectly Split Chains
+
+**Step 1: Identify the incorrect split**
+After `splitch`, press Enter (empty line) in `make_ndx` to list all groups. Compare atom counts against your expected molecule sizes.
+
+**Step 2: Merge the incorrectly split groups**
+```
+<group_N> | <group_M>
+```
+This creates a new merged group named `Protein_chainN_Protein_chainM` at the end of the list.
+
+**Step 3: Verify the merged group**
+Press Enter to list groups again. The merged group should have the correct total atom count.
+
+**Step 4: Delete the incorrect split groups**
+Delete in DESCENDING order to avoid index shifting confusion:
+```
+del <higher_index>
+del <lower_index>
+```
+After `k` deletions, the merged group index shifts down by `k`.
+
+**Step 5: Rename the merged group (optional)**
+```
+name <final_index> <custom_name>
+```
+
+## Generic Example (interactive `make_ndx` session)
+
+```
+> splitch 1
+Found N chains
+ 1:  XXX atoms (a to b)
+ 2:   YY atoms (c to d)     <-- suspiciously small, may be incorrect split
+ 3:  ZZZ atoms (e to f)     <-- remainder of same chain
+
+>                          <-- press Enter to list groups
+...
+ N  Protein_chain1         XXX atoms
+N+1 Protein_chain2          YY atoms   <-- wrong split (too small)
+N+2 Protein_chain3         ZZZ atoms   <-- wrong split (remainder)
+...
+
+> N+1 | N+2                 <-- merge the incorrectly split groups
+Merged two groups with OR: YY ZZZ -> (YY+ZZZ)
+
+>                          <-- press Enter to verify
+...
+ M  Protein_chain2_Protein_chain3   (YY+ZZZ) atoms   <-- correct total!
+
+> del N+2                   <-- delete higher index first
+> del N+1                   <-- then lower index
+
+>                          <-- press Enter
+...
+ M-2  Protein_chain2_Protein_chain3   (YY+ZZZ) atoms   <-- shifted!
+
+> name M-2 <your_chain_name>
+> q
+```
+
+**Key insight**: After deleting `k` groups that were created AFTER the merged group, the merged group's index decreases by `k`.
+
+## Non-interactive Equivalent
+
+```bash
+printf "splitch 1\n<group_N> | <group_M>\ndel <higher>\ndel <lower>\nname <final> <name>\nq\n" | \
+  gmx make_ndx -f <tpr_file> -o <index_file.ndx>
+```
+
+## Creating C-alpha Groups
+
+In `make_ndx` interactive mode:
+```
+a CA & <chain_group>      # creates C-alpha selection for specified chain
+```