From d86822af28443e66e41e5565351c1764895f81ac Mon Sep 17 00:00:00 2001
From: Valerij Talagayev <82884038+talagayev@users.noreply.github.com>
Date: Tue, 3 Dec 2024 01:50:36 +0100
Subject: [PATCH 1/2] Addition of CMS Topology Parser

---
 package/MDAnalysis/topology/CMSParser.py | 120 +++++++++++++++++++++++
 1 file changed, 120 insertions(+)
 create mode 100644 package/MDAnalysis/topology/CMSParser.py

diff --git a/package/MDAnalysis/topology/CMSParser.py b/package/MDAnalysis/topology/CMSParser.py
new file mode 100644
index 00000000000..a778cdcc3ad
--- /dev/null
+++ b/package/MDAnalysis/topology/CMSParser.py
@@ -0,0 +1,120 @@
+import numpy as np
+import re
+
+from ..lib.util import openany
+from ..core.topologyattrs import (
+    Atomnames,
+    Atomids,
+    Resids,
+    Resnames,
+    Resnums,
+    Segids,
+    Resindices,
+)
+from ..core.topology import Topology
+from .base import TopologyReaderBase, change_squash
+
+
+class CMSParser(TopologyReaderBase):
+    """Parser for CMS file format."""
+    format = 'CMS'
+    
+    def __init__(self, filename):
+        super().__init__(filename=filename)
+
+    def parse(self, **kwargs):
+        """Parse the CMS file and debug data extraction."""
+        
+        with open(self.filename, 'rt') as inf:
+            # Read all lines
+            lines = inf.readlines()
+
+        # Extract the number of atoms (n_atoms) from the m_atom[] line
+        n_atoms = 0
+        for line in lines:
+            line = line.strip()
+            if line.startswith("m_atom["):
+                # Extract the number of atoms from m_atom[] (e.g., m_atom[100])
+                parts = line.split('[')
+                n_atoms = int(parts[1].split(']')[0])
+                break
+
+        # If the number of atoms wasn't found, raise an error
+        if n_atoms == 0:
+            raise ValueError("Number of atoms (n_atoms) could not be found in the file.")
+        
+        # Create arrays
+        resids = np.zeros(n_atoms, dtype=np.int32)
+        resnames = np.zeros(n_atoms, dtype=object)
+        segids = np.zeros(n_atoms, dtype=object)
+        atomnames = np.zeros(n_atoms, dtype=object)
+        atom_ids = np.zeros(n_atoms, dtype=np.int32)
+
+        #Parse the atom data after the third occurrence of ":::"
+        colon_count = 0  # Counter for ":::" markers
+        atom_block = False
+
+        atom_idx = 0
+
+        # Regex pattern to split while keeping quoted strings together
+        split_pattern = r'".*?"|\S+'
+
+        for line in lines:
+            line = line.strip()
+
+            # Count occurrences of ":::" and start atom block after the third occurrence
+            if ":::" in line:
+                colon_count += 1
+                if colon_count < 3:
+                    continue
+                else:
+                    atom_block = True
+                    continue  # Skip the ":::" marker line
+
+            if atom_block:
+                # Stop processing when encountering a line starting with '}'
+                if line.startswith("}") or line.startswith('{'):
+                    break
+
+                details = re.findall(split_pattern, line)
+                details = [item.strip('"') for item in details]
+
+                if len(details) >= 7:
+                    try:
+                        # Extract atom data
+                        atom_id = int(details[0])  # Atom ID
+                        resid = int(details[5])  # Residue ID
+                        segid = details[7].strip()  # Segment ID
+
+                        resname = details[11].strip()  # Residue name
+                        atomname = details[12].strip()  # Atom name
+
+                        if atomname == '': 
+                            atomname = details[14].strip()
+
+                        # Fill the allocated arrays with parsed data
+                        resids[atom_idx] = resid
+                        resnames[atom_idx] = resname
+                        segids[atom_idx] = segid
+                        atomnames[atom_idx] = atomname
+                        atom_ids[atom_idx] = atom_id
+
+                        atom_idx += 1
+
+                    except (ValueError, IndexError):
+                        # Skip malformed lines
+                        print(f"Skipping invalid line: {line}")
+
+        print(segids)
+
+        attrs = [
+            Atomnames(atomnames),
+            Atomids(atom_ids),
+            Resids(resids),
+            Resnames(resnames),
+            Segids(segids),
+        ]
+
+        topology = Topology(n_atoms=n_atoms, n_res=len(resids), n_seg=len(segids), attrs=attrs)
+
+        return topology

From 3602eecfcdc4996f0ebf166c276981e73b0fd541 Mon Sep 17 00:00:00 2001
From: Valerij Talagayev <82884038+talagayev@users.noreply.github.com>
Date: Tue, 3 Dec 2024 01:52:47 +0100
Subject: [PATCH 2/2] Update __init__.py

Addition of CMSParser
---
 package/MDAnalysis/topology/__init__.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/package/MDAnalysis/topology/__init__.py b/package/MDAnalysis/topology/__init__.py
index 951567ec615..faa6a1ab2fb 100644
--- a/package/MDAnalysis/topology/__init__.py
+++ b/package/MDAnalysis/topology/__init__.py
@@ -307,7 +307,7 @@
 __all__ = ['core', 'PSFParser', 'PDBParser', 'PQRParser', 'GROParser',
            'CRDParser', 'TOPParser', 'PDBQTParser', 'TPRParser',
            'LAMMPSParser', 'XYZParser', 'GMSParser', 'DLPolyParser',
-           'HoomdXMLParser','GSDParser', 'ITPParser']
+           'HoomdXMLParser','GSDParser', 'ITPParser', 'CMSParser']
 
 from . import core
 from . import PSFParser
@@ -332,3 +332,4 @@
 from . import MinimalParser
 from . import ITPParser
 from . import FHIAIMSParser
+from . import CMSParser