Update Documentation

docs/Writerside/s.tree

@@ -10,6 +10,12 @@
 		<toc-element topic="Automated-Xray-Glycan-Building.topic"/>
 		<toc-element topic="Automated-EM-Glycan-Building.topic"/>
 	</toc-element>
+	<toc-element toc-title="WURCS Functions">
+		<toc-element topic="Morph-Glycan.topic"/>
+		<toc-element topic="Find-WURCS.topic"/>
+		<toc-element topic="Model-Glycan-from-WURCS.topic"/>
+
+	</toc-element>
 	<toc-element toc-title="Utility Functions">
 		<toc-element topic="Compare-Structures.topic"/>
 		<toc-element topic="Find-Glycosylation-Sites.topic"/>

docs/Writerside/topics/Compare-Structures.topic

@@ -12,7 +12,7 @@
         of Sails.
     </p>
 
-    <chapter title="Compare Structures" id="compare">
+    <chapter title="Command" id="compare">
         <p>Syntax:</p>
 
         <code-block lang="shell">

docs/Writerside/topics/Find-Glycosylation-Sites.topic

@@ -12,7 +12,7 @@
         will output a JSON file with the residues that follow the respective motifs.
     </p>
 
-    <chapter title="Find Sites" id="find">
+    <chapter title="Command" id="find">
         <p>Syntax:</p>
 
         <code-block lang="shell">
@@ -21,7 +21,7 @@
 
         <p>Example:</p>
         <code-block lang="shell">
-            sails-find -model built.cif -logout potential_sites.json
+            sails-find -modelin built.cif -logout potential_sites.json
         </code-block>
     </chapter>
 

docs/Writerside/topics/Find-WURCS.topic

@@ -0,0 +1,64 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE topic
+        SYSTEM "https://resources.jetbrains.com/writerside/1.0/xhtml-entities.dtd">
+<topic xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+       xsi:noNamespaceSchemaLocation="https://resources.jetbrains.com/writerside/1.0/topic.v2.xsd"
+       title="Find WURCS Codes" id="Find-WURCS">
+
+    <p>
+        Sails provides a utility tool to find the WURCS code of a glycan in a macromolecule. A single WURCS code can
+        be generated for a known glycosite or all can be generated. These codes can be used to search glycomics databases.
+    </p>
+
+    <chapter title="Command" id="find">
+        <p>Syntax:</p>
+
+        <code-block lang="shell">
+            sails-wurcs find [OPTIONS]
+        </code-block>
+
+        <p>Example:</p>
+        <code-block lang="shell">
+            sails-wurcs find -modelin structure.cif -chain A -seqid 123
+        </code-block>
+
+        <code-block lang="shell">
+            sails-wurcs find -modelin structure.cif -all -logout all_wurcs.json
+        </code-block>
+    </chapter>
+
+    <chapter title="Options" id="options">
+        <p>Describe what each option is used for:</p>
+
+        <deflist type="medium">
+            <def title="-modelin">
+                Path to a model.
+                <p>Formats accepted: CIF or PDB</p>
+                <b>Required</b>
+            </def>
+            <def title="-logout">
+                Path to output JSON file
+                <p>Default: wurcs.json </p>
+            </def>
+            <def title="--all">
+                Ignore chain and seqid, and generate WURCS codes for all glycans that can be found for the input model
+            </def>
+            <def title="-chain">
+                Chain name containing the root protein residue
+                <p>Example: A</p>
+            </def>
+            <def title="-seqid">
+                Sequence Id of the root protein residue of a glycan (e.g. asparagine for an N-glycan)
+                <p>Example: 123</p>
+            </def>
+
+            <def title="-h, --help">
+                Displays help.
+            </def>
+        </deflist>
+    </chapter>
+
+    <seealso>
+        <!--Provide links to related how-to guides, overviews, and tutorials.-->
+    </seealso>
+</topic>

docs/Writerside/topics/Generate-SNFG-Diagrams.topic

@@ -52,11 +52,11 @@
                 Ignore chain and seqid, and generate all SNFGs that can be found for the input model
             </def>
             <def title="-chain">
-                Chain name
+                Chain name containing the root protein residue
                 <p>Example: A</p>
             </def>
             <def title="-seqid">
-                Sequence Id of desired SNFG root
+                Sequence Id of desired protein root residue
                 <p>Example: 123</p>
             </def>
 

docs/Writerside/topics/Model-Glycan-from-WURCS.topic

@@ -0,0 +1,58 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE topic
+        SYSTEM "https://resources.jetbrains.com/writerside/1.0/xhtml-entities.dtd">
+<topic xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+       xsi:noNamespaceSchemaLocation="https://resources.jetbrains.com/writerside/1.0/topic.v2.xsd"
+       title="Model Glycan from WURCS Code" id="Model-Glycan-from-WURCS">
+
+    <p>
+        Sails provides a utility tool to model a glycan into a structure from a known WURCS code and a root residue.
+        This may be useful to glycosylate predicted models or as a simple starting point for manual model building. The
+        glycan is placed with the mean torsion angles for a given linkage.
+    </p>
+
+    <chapter title="Command" id="find">
+        <p>Syntax:</p>
+
+        <code-block lang="shell">
+            sails-wurcs model [OPTIONS]
+        </code-block>
+
+        <p>Example:</p>
+        <code-block lang="shell">
+            sails-wurcs model -modelin structure.cif -wurcs "WURCS=2.0/..." -chain A -seqid 123
+        </code-block>
+    </chapter>
+
+    <chapter title="Options" id="options">
+        <p>Describe what each option is used for:</p>
+
+        <deflist type="medium">
+            <def title="-modelin">
+                Path to a model.
+                <p>Formats accepted: CIF or PDB</p>
+                <b>Required</b>
+            </def>
+            <def title="-modelout">
+                Path to the glycosylated output model.
+                <p>Formats accepted: CIF or PDB</p>
+                <p>Default: sails-model-out.cif </p>
+            </def>
+            <def title="-wurcs">
+                WURCS code of glycan to model.
+                <p>Must be in standard form without open chains and without circular glycans.</p>
+            </def>
+            <def title="-chain">
+                Chain name containing desired root residue
+                <p>Example: A</p>
+            </def>
+            <def title="-seqid">
+                Sequence Id of the root residue of the future glycan (e.g. asparagine for an N-glycan)
+                <p>Example: 123</p>
+            </def>
+            <def title="-h, --help">
+                Displays help.
+            </def>
+        </deflist>
+    </chapter>
+</topic>

docs/Writerside/topics/Morph-Glycan.topic

@@ -0,0 +1,57 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE topic
+        SYSTEM "https://resources.jetbrains.com/writerside/1.0/xhtml-entities.dtd">
+<topic xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+       xsi:noNamespaceSchemaLocation="https://resources.jetbrains.com/writerside/1.0/topic.v2.xsd"
+       title="Morph Glycan" id="Morph-Glycan">
+    <p>
+        Sails provides a utility tool to morph a modelled glycan into another form using a supplied WURCS code. The new
+        glycan will be superimposed onto the modelled glycan and may be useful to morph a high-mannose N-glycan into a
+        more processed kind, for example.
+    </p>
+
+    <chapter title="Command" id="find">
+        <p>Syntax:</p>
+
+        <code-block lang="shell">
+            sails-morph [OPTIONS]
+        </code-block>
+
+        <p>Example:</p>
+        <code-block lang="shell">
+            sails-morph -modelin structure.cif -chain A -seqid 123 -wurcs "WURCS=2.0/..."
+        </code-block>
+    </chapter>
+
+    <chapter title="Options" id="options">
+        <p>Describe what each option is used for:</p>
+
+        <deflist type="medium">
+            <def title="-modelin">
+                Path to a model.
+                <p>Formats accepted: CIF or PDB</p>
+                <b>Required</b>
+            </def>
+            <def title="-modelout">
+                Path to the morphed output model.
+                <p>Formats accepted: CIF or PDB</p>
+                <p>Default: sails-model-out.cif </p>
+            </def>
+            <def title="-wurcs">
+                WURCS code of glycan to model.
+                <p>Must be in standard form without open chains and without circular glycans.</p>
+            </def>
+            <def title="-chain">
+                Chain name containing the root protein residue
+                <p>Example: A</p>
+            </def>
+            <def title="-seqid">
+                Sequence Id of the root protein of the glycan (e.g. asparagine for an N-glycan)
+                <p>Example: 123</p>
+            </def>
+            <def title="-h, --help">
+                Displays help.
+            </def>
+        </deflist>
+    </chapter>
+</topic>

package/scripts/bump_version.py

@@ -0,0 +1,67 @@
+import re
+import argparse
+
+
+def bump_version(version, args):
+    major, minor, patch = map(int, version.split("."))
+    if args.major:
+        major += 1
+
+    if args.minor:
+        minor += 1
+
+    if args.patch:
+        patch += 1
+
+    return f"{major}.{minor}.{patch}"
+
+
+def update_version_in_file(file_path, old_version, new_version):
+    with open(file_path, "r") as file:
+        content = file.read()
+
+    print(old_version, new_version)
+    updated_content = content.replace(old_version, new_version)
+
+    with open(file_path, "w") as file:
+        file.write(updated_content)
+
+
+def main():
+    parser = argparse.ArgumentParser(description="Bump project version.")
+    parser.add_argument("-major", action=argparse.BooleanOptionalAction)
+    parser.add_argument("-minor", action=argparse.BooleanOptionalAction)
+    parser.add_argument("-patch", action=argparse.BooleanOptionalAction)
+    args = parser.parse_args()
+
+    # Update __version__.py
+    version_file = "src/sails/__version__.py"
+    version_regex = r"(?:__version__\s*=\s*[\"'])(\d+\.\d+\.\d+)([\"'])"
+    with open(version_file, "r") as file:
+        match = re.search(version_regex, file.read())
+        if not match:
+            raise ValueError("Current version not found in __version__.py")
+        current_version = match.group(1)
+
+    # Update writerside.cfg
+    cfg_file = "../docs/Writerside/writerside.cfg"
+    cfg_version_regex = r'(<instance [^>]*version=")(\d+\.\d+\.\d+)(")'
+
+    with open(cfg_file, "r") as file:
+        match = re.search(cfg_version_regex, file.read())
+        if not match:
+            raise ValueError("Current version not found in writerside.cfg")
+        cfg_current_version = match.group(2)
+
+    if current_version != cfg_current_version:
+        raise RuntimeError("Docs and Python version mismatch")
+
+    new_version = bump_version(current_version, args)
+
+    print(f"Bumping version {current_version} -> {new_version}")
+    update_version_in_file(version_file, current_version, new_version)
+    update_version_in_file(cfg_file, current_version, new_version)
+
+
+if __name__ == "__main__":
+    main()

package/src/sails/morph.py

@@ -10,11 +10,15 @@ def parse_args():
     parser.add_argument("--version", action="version", version=__version__)
     parser.add_argument("-modelin", help="Path to input model", type=str, required=True)
     parser.add_argument(
-        "-modelout", help="Path to output model", type=str, required=False
+        "-modelout",
+        help="Path to output model",
+        type=str,
+        required=False,
+        default="sails-model-out.cif",
     )
     parser.add_argument("-chain", help="Name of target chain", type=str, required=True)
     parser.add_argument(
-        "-res", help="Name of target residue (protein)", type=int, required=True
+        "-seqid", help="Name of target residue (protein)", type=int, required=True
     )
     parser.add_argument(
         "-wurcs", help="WURCS identifier for new glycan", type=str, required=True

package/src/sails/wurcs.py

@@ -20,7 +20,7 @@ def parse_args():
         "find", parents=[parent], formatter_class=formatter
     )
     find_parser.add_argument(
-        "-all",
+        "--all",
         help="Find WURCS identifiers for all glycans",
         action=argparse.BooleanOptionalAction,
         required=False,
@@ -59,7 +59,10 @@ def parse_args():
         "-chain", help="Name of target chain", type=str, required=True
     )
     model_parser.add_argument(
-        "-res", help="Name of target residue (protein)", type=str, required=True
+        "-seqid",
+        help="Sequence ID of the root residue (protein)",
+        type=str,
+        required=True,
     )
 
     return parser.parse_args()