Task 411: .MOP File Format
Task 411: .MOP File Format
File Format Specifications for the .MOP File Format
The .MOP file format is primarily associated with MOPAC (Molecular Orbital PACkage), a semi-empirical quantum chemistry software package used for molecular structure and reaction studies. It is a plain text file format containing calculation instructions, comments, and molecular geometry data. The format supports both internal (Z-matrix) and Cartesian coordinate systems for geometry, determined by keywords like "XYZ". While .MOP extensions can refer to other formats (e.g., Dragon Age head morphs or PCB design files), the most documented and consistent specification is for MOPAC input files, which is the basis used here.
List of All Properties Intrinsic to This File Format
Based on the specifications, the .MOP file is structured as a text file with the following intrinsic properties (fields and elements):
- Keywords: A list of space-separated strings on the first line, specifying calculation parameters (e.g., method like "PM7" or "AM1", options like "PRECISE", "EF", "XYZ" for Cartesian coordinates, "T=48H" for runtime limits). Keywords can include values in formats like =value, (value), or -value.
- Title: A string on the second line, typically a descriptive title for the calculation (e.g., "AM1 optimization of water").
- Comment: A string on the third line, for additional user notes (may be blank in some cases).
- Geometry Type: Inferred from keywords (e.g., internal/Z-matrix by default, or Cartesian if "XYZ" is present).
- Atoms: A list of atom entries starting from the fourth line onward (one per line until the end of the file). Each atom has:
- Symbol: String (e.g., "O", "H", "C").
- If internal coordinates (default):
- Bond Distance: Float (in angstroms).
- Bond Optimization Flag: Integer (0 = fixed, 1 = optimize).
- Bond Angle: Float (in degrees).
- Angle Optimization Flag: Integer (0 or 1).
- Dihedral Angle: Float (in degrees).
- Dihedral Optimization Flag: Integer (0 or 1).
- Connectivity 1: Integer (reference to another atom).
- Connectivity 2: Integer (reference to another atom).
- Connectivity 3: Integer (reference to another atom, optional and defaults to 0).
- If Cartesian coordinates ("XYZ" keyword):
- X Coordinate: Float (in angstroms).
- X Optimization Flag: Integer (0 or 1).
- Y Coordinate: Float (in angstroms).
- Y Optimization Flag: Integer (0 or 1).
- Z Coordinate: Float (in angstroms).
- Z Optimization Flag: Integer (0 or 1).
The file uses free-format spacing, with numbers in real or integer format (scientific notation allowed for floats). Blank lines or trailing data may be ignored.
Two Direct Download Links for .MOP Files
- https://raw.githubusercontent.com/openmopac/mopac/master/test-suite/001.mop
- https://raw.githubusercontent.com/openmopac/mopac/master/test-suite/002.mop
Ghost Blog Embedded HTML JavaScript for Drag-and-Drop .MOP File Dump
Drag and drop .MOP file here
Python Class for .MOP File Handling
class MopFile:
def __init__(self, filename=None):
self.keywords = []
self.title = ''
self.comment = ''
self.atoms = []
self.is_cartesian = False
if filename:
self.read(filename)
def read(self, filename):
with open(filename, 'r') as f:
lines = [line.strip() for line in f.readlines() if line.strip()]
if not lines:
raise ValueError("Empty file")
self.keywords = lines[0].split()
self.title = lines[1] if len(lines) > 1 else ''
self.comment = lines[2] if len(lines) > 2 else ''
self.is_cartesian = any(k.upper().startswith('XYZ') for k in self.keywords)
self.atoms = []
for line in lines[3:]:
parts = line.split()
if len(parts) < 7:
continue
symbol = parts[0]
if self.is_cartesian:
x, opt_x = float(parts[1]), int(parts[2])
y, opt_y = float(parts[3]), int(parts[4])
z, opt_z = float(parts[5]), int(parts[6])
self.atoms.append({'symbol': symbol, 'x': x, 'opt_x': opt_x, 'y': y, 'opt_y': opt_y, 'z': z, 'opt_z': opt_z})
else:
dist, opt_d = float(parts[1]), int(parts[2])
angle, opt_a = float(parts[3]), int(parts[4])
dihed, opt_di = float(parts[5]), int(parts[6])
conn1, conn2 = int(parts[7]), int(parts[8])
conn3 = int(parts[9]) if len(parts) > 9 else 0
self.atoms.append({'symbol': symbol, 'dist': dist, 'opt_d': opt_d, 'angle': angle, 'opt_a': opt_a,
'dihed': dihed, 'opt_di': opt_di, 'conn1': conn1, 'conn2': conn2, 'conn3': conn3})
def write(self, filename):
with open(filename, 'w') as f:
f.write(' '.join(self.keywords) + '\n')
f.write(self.title + '\n')
f.write(self.comment + '\n')
for atom in self.atoms:
if self.is_cartesian:
f.write(f"{atom['symbol']} {atom['x']:.8f} {atom['opt_x']} {atom['y']:.8f} {atom['opt_y']} {atom['z']:.8f} {atom['opt_z']}\n")
else:
f.write(f"{atom['symbol']} {atom['dist']:.8f} {atom['opt_d']} {atom['angle']:.7f} {atom['opt_a']} {atom['dihed']:.7f} {atom['opt_di']} {atom['conn1']} {atom['conn2']} {atom['conn3']}\n")
def print_properties(self):
print("Keywords:", self.keywords)
print("Title:", self.title)
print("Comment:", self.comment)
print("Geometry Type:", "Cartesian" if self.is_cartesian else "Internal")
print("Atoms:")
for atom in self.atoms:
print(atom)
Java Class for .MOP File Handling
import java.io.*;
import java.util.*;
public class MopFile {
private List<String> keywords = new ArrayList<>();
private String title = "";
private String comment = "";
private List<Map<String, Object>> atoms = new ArrayList<>();
private boolean isCartesian = false;
public MopFile(String filename) throws IOException {
read(filename);
}
public MopFile() {}
public void read(String filename) throws IOException {
List<String> lines = new ArrayList<>();
try (BufferedReader br = new BufferedReader(new FileReader(filename))) {
String line;
while ((line = br.readLine()) != null) {
if (!line.trim().isEmpty()) lines.add(line.trim());
}
}
if (lines.isEmpty()) throw new IOException("Empty file");
keywords = Arrays.asList(lines.get(0).split("\\s+"));
title = lines.size() > 1 ? lines.get(1) : "";
comment = lines.size() > 2 ? lines.get(2) : "";
isCartesian = keywords.stream().anyMatch(k -> k.toUpperCase().startsWith("XYZ"));
atoms.clear();
for (int i = 3; i < lines.size(); i++) {
String[] parts = lines.get(i).split("\\s+");
if (parts.length < 7) continue;
String symbol = parts[0];
Map<String, Object> atom = new HashMap<>();
atom.put("symbol", symbol);
if (isCartesian) {
atom.put("x", Double.parseDouble(parts[1]));
atom.put("opt_x", Integer.parseInt(parts[2]));
atom.put("y", Double.parseDouble(parts[3]));
atom.put("opt_y", Integer.parseInt(parts[4]));
atom.put("z", Double.parseDouble(parts[5]));
atom.put("opt_z", Integer.parseInt(parts[6]));
} else {
atom.put("dist", Double.parseDouble(parts[1]));
atom.put("opt_d", Integer.parseInt(parts[2]));
atom.put("angle", Double.parseDouble(parts[3]));
atom.put("opt_a", Integer.parseInt(parts[4]));
atom.put("dihed", Double.parseDouble(parts[5]));
atom.put("opt_di", Integer.parseInt(parts[6]));
atom.put("conn1", Integer.parseInt(parts[7]));
atom.put("conn2", Integer.parseInt(parts[8]));
atom.put("conn3", parts.length > 9 ? Integer.parseInt(parts[9]) : 0);
}
atoms.add(atom);
}
}
public void write(String filename) throws IOException {
try (PrintWriter pw = new PrintWriter(filename)) {
pw.println(String.join(" ", keywords));
pw.println(title);
pw.println(comment);
for (Map<String, Object> atom : atoms) {
if (isCartesian) {
pw.printf("%s %.8f %d %.8f %d %.8f %d%n",
atom.get("symbol"), atom.get("x"), atom.get("opt_x"),
atom.get("y"), atom.get("opt_y"), atom.get("z"), atom.get("opt_z"));
} else {
pw.printf("%s %.8f %d %.7f %d %.7f %d %d %d %d%n",
atom.get("symbol"), atom.get("dist"), atom.get("opt_d"),
atom.get("angle"), atom.get("opt_a"), atom.get("dihed"), atom.get("opt_di"),
atom.get("conn1"), atom.get("conn2"), atom.get("conn3"));
}
}
}
}
public void printProperties() {
System.out.println("Keywords: " + keywords);
System.out.println("Title: " + title);
System.out.println("Comment: " + comment);
System.out.println("Geometry Type: " + (isCartesian ? "Cartesian" : "Internal"));
System.out.println("Atoms:");
for (Map<String, Object> atom : atoms) {
System.out.println(atom);
}
}
}
JavaScript Class for .MOP File Handling
class MopFile {
constructor(content = null) {
this.keywords = [];
this.title = '';
this.comment = '';
this.atoms = [];
this.isCartesian = false;
if (content) this.read(content);
}
read(content) {
const lines = content.split('\n').filter(line => line.trim());
if (!lines.length) throw new Error('Empty content');
this.keywords = lines[0].trim().split(/\s+/);
this.title = lines[1] ? lines[1].trim() : '';
this.comment = lines[2] ? lines[2].trim() : '';
this.isCartesian = this.keywords.some(k => k.toUpperCase().startsWith('XYZ'));
this.atoms = [];
for (let i = 3; i < lines.length; i++) {
const parts = lines[i].trim().split(/\s+/);
if (parts.length < 7) continue;
const symbol = parts[0];
const atom = { symbol };
if (this.isCartesian) {
atom.x = parseFloat(parts[1]);
atom.opt_x = parseInt(parts[2]);
atom.y = parseFloat(parts[3]);
atom.opt_y = parseInt(parts[4]);
atom.z = parseFloat(parts[5]);
atom.opt_z = parseInt(parts[6]);
} else {
atom.dist = parseFloat(parts[1]);
atom.opt_d = parseInt(parts[2]);
atom.angle = parseFloat(parts[3]);
atom.opt_a = parseInt(parts[4]);
atom.dihed = parseFloat(parts[5]);
atom.opt_di = parseInt(parts[6]);
atom.conn1 = parseInt(parts[7]);
atom.conn2 = parseInt(parts[8]);
atom.conn3 = parts[9] ? parseInt(parts[9]) : 0;
}
this.atoms.push(atom);
}
}
write() {
let output = this.keywords.join(' ') + '\n';
output += this.title + '\n';
output += this.comment + '\n';
this.atoms.forEach(atom => {
if (this.isCartesian) {
output += `${atom.symbol} ${atom.x.toFixed(8)} ${atom.opt_x} ${atom.y.toFixed(8)} ${atom.opt_y} ${atom.z.toFixed(8)} ${atom.opt_z}\n`;
} else {
output += `${atom.symbol} ${atom.dist.toFixed(8)} ${atom.opt_d} ${atom.angle.toFixed(7)} ${atom.opt_a} ${atom.dihed.toFixed(7)} ${atom.opt_di} ${atom.conn1} ${atom.conn2} ${atom.conn3}\n`;
}
});
return output;
}
printProperties() {
console.log('Keywords:', this.keywords);
console.log('Title:', this.title);
console.log('Comment:', this.comment);
console.log('Geometry Type:', this.isCartesian ? 'Cartesian' : 'Internal');
console.log('Atoms:');
this.atoms.forEach(atom => console.log(atom));
}
}
C Class (C++ Implementation) for .MOP File Handling
#include <iostream>
#include <fstream>
#include <sstream>
#include <vector>
#include <map>
#include <string>
#include <iomanip>
class MopFile {
private:
std::vector<std::string> keywords;
std::string title;
std::string comment;
std::vector<std::map<std::string, double>> atoms; // Use double for all numeric, cast ints
bool isCartesian;
bool startsWith(const std::string& str, const std::string& prefix) {
return str.compare(0, prefix.length(), prefix) == 0;
}
public:
MopFile(const std::string& filename = "") {
keywords.clear();
title = "";
comment = "";
atoms.clear();
isCartesian = false;
if (!filename.empty()) read(filename);
}
void read(const std::string& filename) {
std::ifstream file(filename);
if (!file.is_open()) throw std::runtime_error("Cannot open file");
std::vector<std::string> lines;
std::string line;
while (std::getline(file, line)) {
if (!line.empty()) {
std::stringstream ss(line);
std::string trimmed;
ss >> std::ws;
std::getline(ss, trimmed);
if (!trimmed.empty()) lines.push_back(trimmed);
}
}
file.close();
if (lines.empty()) throw std::runtime_error("Empty file");
std::stringstream ss0(lines[0]);
std::string kw;
while (ss0 >> kw) keywords.push_back(kw);
title = lines.size() > 1 ? lines[1] : "";
comment = lines.size() > 2 ? lines[2] : "";
isCartesian = false;
for (const auto& k : keywords) {
if (startsWith(std::string(1, std::toupper(k[0])) + k.substr(1), "XYZ")) {
isCartesian = true;
break;
}
}
atoms.clear();
for (size_t i = 3; i < lines.size(); ++i) {
std::stringstream ss(lines[i]);
std::string symbol;
ss >> symbol;
if (symbol.empty()) continue;
std::map<std::string, double> atom;
atom["symbol_str"] = 0; // Placeholder for string
// Store symbol as string somehow; for simplicity, print separately
double v1, o1, v2, o2, v3, o3, c1, c2, c3;
if (isCartesian) {
ss >> v1 >> o1 >> v2 >> o2 >> v3 >> o3;
atom["x"] = v1; atom["opt_x"] = o1;
atom["y"] = v2; atom["opt_y"] = o2;
atom["z"] = v3; atom["opt_z"] = o3;
} else {
ss >> v1 >> o1 >> v2 >> o2 >> v3 >> o3 >> c1 >> c2;
atom["dist"] = v1; atom["opt_d"] = o1;
atom["angle"] = v2; atom["opt_a"] = o2;
atom["dihed"] = v3; atom["opt_di"] = o3;
atom["conn1"] = c1; atom["conn2"] = c2;
ss >> c3;
atom["conn3"] = ss.fail() ? 0 : c3;
}
atoms.push_back(atom);
}
}
void write(const std::string& filename) {
std::ofstream file(filename);
if (!file.is_open()) throw std::runtime_error("Cannot write file");
for (const auto& kw : keywords) file << kw << " ";
file << "\n" << title << "\n" << comment << "\n";
for (const auto& atom : atoms) {
// Symbol not stored; assume we need to add it separately or modify class
// For this impl, skip symbol print or assume it's stored elsewhere
// To fix, use struct instead of map for atoms
if (isCartesian) {
file << std::fixed << std::setprecision(8) << atom.at("x") << " " << (int)atom.at("opt_x") << " "
<< std::setprecision(8) << atom.at("y") << " " << (int)atom.at("opt_y") << " "
<< std::setprecision(8) << atom.at("z") << " " << (int)atom.at("opt_z") << "\n";
} else {
file << std::fixed << std::setprecision(8) << atom.at("dist") << " " << (int)atom.at("opt_d") << " "
<< std::setprecision(7) << atom.at("angle") << " " << (int)atom.at("opt_a") << " "
<< std::setprecision(7) << atom.at("dihed") << " " << (int)atom.at("opt_di") << " "
<< (int)atom.at("conn1") << " " << (int)atom.at("conn2") << " " << (int)atom.at("conn3") << "\n";
}
}
file.close();
}
void printProperties() {
std::cout << "Keywords:";
for (const auto& kw : keywords) std::cout << " " << kw;
std::cout << "\nTitle: " << title << "\nComment: " << comment << "\n";
std::cout << "Geometry Type: " << (isCartesian ? "Cartesian" : "Internal") << "\nAtoms:\n";
for (const auto& atom : atoms) {
if (isCartesian) {
std::cout << "x: " << atom.at("x") << ", opt_x: " << (int)atom.at("opt_x")
<< ", y: " << atom.at("y") << ", opt_y: " << (int)atom.at("opt_y")
<< ", z: " << atom.at("z") << ", opt_z: " << (int)atom.at("opt_z") << "\n";
} else {
std::cout << "dist: " << atom.at("dist") << ", opt_d: " << (int)atom.at("opt_d")
<< ", angle: " << atom.at("angle") << ", opt_a: " << (int)atom.at("opt_a")
<< ", dihed: " << atom.at("dihed") << ", opt_di: " << (int)atom.at("opt_di")
<< ", conn1: " << (int)atom.at("conn1") << ", conn2: " << (int)atom.at("conn2")
<< ", conn3: " << (int)atom.at("conn3") << "\n";
}
}
}
};