Benzyl titanium
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2605 字
13 分钟
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SMILES to
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Usage
conda install -c conda-forge rdkitmain.py
import sys
import os
from rdkit import Chem
from rdkit.Chem import AllChem
from rdkit.Chem import Draw
def convert_smiles(smiles_string, output_file, output_format='pdb', generate_3d=True, image_size=200):
"""
Universal SMILES conversion function
Args:
smiles_string: SMILES string to convert
output_file: Output file path
output_format: 'pdb', 'mol', or 'png'
generate_3d: Whether to generate 3D coordinates (for pdb/mol)
image_size: Size for PNG images (default: 200px square)
"""
print(f"Converting SMILES to {output_format.upper()}: {smiles_string}")
try:
print(f"Parsing SMILES: {smiles_string}")
mol = Chem.MolFromSmiles(smiles_string)
if mol is None:
print("Invalid SMILES string")
return False
print(f"Successfully parsed SMILES")
print(f"Molecular formula: {Chem.MolToSmiles(mol)}")
print(f"Number of atoms: {mol.GetNumAtoms()}")
if output_format == 'png':
# For image generation, use 2D coordinates
print(f"Generating 2D molecular image...")
AllChem.Compute2DCoords(mol)
print(f"Saving as PNG image: {output_file} ({image_size}x{image_size}px)")
img = Draw.MolToImage(mol, size=(image_size, image_size))
img.save(output_file)
else:
# For PDB/MOL files, add hydrogens and handle 3D
mol_with_h = Chem.AddHs(mol)
print(f"Number of atoms after adding hydrogens: {mol_with_h.GetNumAtoms()}")
if generate_3d:
print("Generating 3D coordinates...")
try:
embed_result = AllChem.EmbedMolecule(mol_with_h, AllChem.ETKDG())
if embed_result == -1:
print("First embedding failed, trying alternative method...")
AllChem.EmbedMolecule(mol_with_h)
minimize_result = AllChem.MMFFOptimizeMolecule(mol_with_h)
if minimize_result != 0:
print("Energy minimization may not have fully converged")
print("3D coordinates generated successfully")
except Exception as e:
print(f"3D coordinate generation warning: {e}")
print("Using 2D coordinates...")
AllChem.Compute2DCoords(mol_with_h)
else:
AllChem.Compute2DCoords(mol_with_h)
# Save file based on format
if output_format == 'pdb':
print(f"Saving as PDB file: {output_file}")
Chem.MolToPDBFile(mol_with_h, output_file)
elif output_format == 'mol':
print(f"Saving as MOL file: {output_file}")
Chem.MolToMolFile(mol_with_h, output_file)
if os.path.exists(output_file) and os.path.getsize(output_file) > 0:
print(f"Conversion successful: {output_file}")
return True
else:
print("Output file creation failed")
return False
except Exception as e:
print(f"Conversion failed: {e}")
return False
def interactive_conversion():
"""Interactive molecular conversion tool"""
print("=" * 60)
print("🔬 Interactive Molecular Format Conversion Tool")
print("=" * 60)
print("This tool converts SMILES strings to PDB, MOL, or PNG files")
print("=" * 60)
while True:
print("\n" + "-" * 60)
print("Options:")
print("1. Convert SMILES to PDB (3D)")
print("2. Convert SMILES to PDB (2D)")
print("3. Convert SMILES to MOL (3D)")
print("4. Convert SMILES to MOL (2D)")
print("5. Convert SMILES to PNG (2D)")
print("6. Exit")
print("-" * 60)
try:
choice = input("Please select an option (1-6): ").strip()
if choice == '6':
print("\n👋 Goodbye!")
break
elif choice not in ['1', '2', '3', '4', '5']:
print("❌ Invalid choice. Please select 1-6.")
continue
# Get SMILES input
print("\n" + "=" * 40)
smiles = input("Enter SMILES string: ").strip()
if not smiles:
print("❌ Please enter a valid SMILES string")
continue
# Determine format and settings based on choice
if choice == '5':
output_format = 'png'
default_ext = '.png'
generate_3d = False # Images are always 2D
# Get image size for PNG
print("\n" + "-" * 40)
print("Enter image size in pixels (e.g., 400 for 400x400px)")
print("-" * 40)
size_input = input("Image size (px) [default: 200px]: ").strip()
if not size_input:
image_size = 200
else:
try:
image_size = int(size_input)
if image_size <= 0:
print("❌ Invalid size, using default 200px")
image_size = 200
except ValueError:
print("❌ Invalid size, using default 200px")
image_size = 200
elif choice in ['1', '2']:
output_format = 'pdb'
default_ext = '.pdb'
generate_3d = (choice == '1')
image_size = 200 # Not used for PDB/MOL
else: # choice in ['3', '4']
output_format = 'mol'
default_ext = '.mol'
generate_3d = (choice == '3')
image_size = 200 # Not used for PDB/MOL
# Get output filename
output_name = input(f"Enter output filename (default: output{default_ext}): ").strip()
if not output_name:
output_name = f"output{default_ext}"
elif not output_name.endswith(default_ext):
output_name += default_ext
print(f"\n🔄 Converting SMILES to {output_format.upper()}...")
print("=" * 40)
# Perform conversion using unified function
success = convert_smiles(smiles, output_name, output_format, generate_3d, image_size)
if success:
print("\n✅ Operation completed successfully!")
print(f"📁 Output file: {output_name}")
else:
print("\n❌ Operation failed!")
# Ask if user wants to continue
print("\n" + "-" * 40)
continue_choice = input("Perform another operation? (y/n): ").strip().lower()
if continue_choice not in ['y', 'yes']:
print("\n👋 Goodbye!")
break
except KeyboardInterrupt:
print("\n\n👋 Program interrupted. Goodbye!")
break
except Exception as e:
print(f"\n❌ An error occurred: {e}")
continue
def main():
"""Main function"""
try:
interactive_conversion()
except Exception as e:
print(f"❌ Unexpected error: {e}")
sys.exit(1)
if __name__ == "__main__":
main()python main.pyOptions:
- Convert SMILES to PDB (3D)
- Convert SMILES to PDB (2D)
- Convert SMILES to MOL (3D)
- Convert SMILES to MOL (2D)
- Convert SMILES to PNG (2D)
- Exit
Demo
PDB
HETATM 1 C1 UNL 1 1.331 -1.070 -1.935 1.00 0.00 C
HETATM 2 TI1 UNL 1 0.546 0.265 -0.454 1.00 0.00 TI
HETATM 3 C2 UNL 1 -0.769 -0.699 0.883 1.00 0.00 C
HETATM 4 C3 UNL 1 -1.746 -1.605 0.283 1.00 0.00 C
HETATM 5 C4 UNL 1 -1.453 -2.953 0.053 1.00 0.00 C
HETATM 6 C5 UNL 1 -2.372 -3.814 -0.510 1.00 0.00 C
HETATM 7 C6 UNL 1 -3.621 -3.347 -0.862 1.00 0.00 C
HETATM 8 C7 UNL 1 -3.952 -2.010 -0.650 1.00 0.00 C
HETATM 9 C8 UNL 1 -3.000 -1.190 -0.085 1.00 0.00 C
HETATM 10 C9 UNL 1 -0.350 1.978 -1.318 1.00 0.00 C
HETATM 11 C10 UNL 1 -1.818 2.040 -1.198 1.00 0.00 C
HETATM 12 C11 UNL 1 -2.366 2.644 -0.084 1.00 0.00 C
HETATM 13 C12 UNL 1 -3.747 2.701 0.001 1.00 0.00 C
HETATM 14 C13 UNL 1 -4.575 2.183 -0.977 1.00 0.00 C
HETATM 15 C14 UNL 1 -4.025 1.574 -2.100 1.00 0.00 C
HETATM 16 C15 UNL 1 -2.631 1.508 -2.200 1.00 0.00 C
HETATM 17 C16 UNL 1 2.246 0.924 0.721 1.00 0.00 C
HETATM 18 C17 UNL 1 1.697 1.383 2.028 1.00 0.00 C
HETATM 19 C18 UNL 1 1.298 2.690 2.248 1.00 0.00 C
HETATM 20 C19 UNL 1 0.788 3.109 3.467 1.00 0.00 C
HETATM 21 C20 UNL 1 0.677 2.179 4.498 1.00 0.00 C
HETATM 22 C21 UNL 1 1.064 0.867 4.316 1.00 0.00 C
HETATM 23 C22 UNL 1 1.574 0.488 3.069 1.00 0.00 C
HETATM 24 C23 UNL 1 2.757 -1.415 -1.690 1.00 0.00 C
HETATM 25 C24 UNL 1 3.722 -0.592 -2.265 1.00 0.00 C
HETATM 26 C25 UNL 1 5.044 -0.880 -2.056 1.00 0.00 C
HETATM 27 C26 UNL 1 5.468 -1.965 -1.290 1.00 0.00 C
HETATM 28 C27 UNL 1 4.502 -2.761 -0.735 1.00 0.00 C
HETATM 29 C28 UNL 1 3.145 -2.501 -0.924 1.00 0.00 C
HETATM 30 H1 UNL 1 1.265 -0.605 -2.934 1.00 0.00 H
HETATM 31 H2 UNL 1 0.759 -2.028 -1.886 1.00 0.00 H
HETATM 32 H3 UNL 1 -1.319 0.079 1.459 1.00 0.00 H
HETATM 33 H4 UNL 1 -0.198 -1.297 1.642 1.00 0.00 H
HETATM 34 H5 UNL 1 -0.469 -3.301 0.336 1.00 0.00 H
HETATM 35 H6 UNL 1 -2.128 -4.835 -0.675 1.00 0.00 H
HETATM 36 H7 UNL 1 -4.359 -4.009 -1.307 1.00 0.00 H
HETATM 37 H8 UNL 1 -4.940 -1.680 -0.939 1.00 0.00 H
HETATM 38 H9 UNL 1 -3.245 -0.154 0.087 1.00 0.00 H
HETATM 39 H10 UNL 1 0.083 2.901 -0.867 1.00 0.00 H
HETATM 40 H11 UNL 1 -0.084 2.071 -2.411 1.00 0.00 H
HETATM 41 H12 UNL 1 -1.726 3.055 0.691 1.00 0.00 H
HETATM 42 H13 UNL 1 -4.208 3.170 0.865 1.00 0.00 H
HETATM 43 H14 UNL 1 -5.656 2.226 -0.915 1.00 0.00 H
HETATM 44 H15 UNL 1 -4.661 1.165 -2.870 1.00 0.00 H
HETATM 45 H16 UNL 1 -2.198 1.041 -3.062 1.00 0.00 H
HETATM 46 H17 UNL 1 2.782 1.733 0.214 1.00 0.00 H
HETATM 47 H18 UNL 1 2.865 0.020 0.884 1.00 0.00 H
HETATM 48 H19 UNL 1 1.379 3.423 1.453 1.00 0.00 H
HETATM 49 H20 UNL 1 0.470 4.117 3.665 1.00 0.00 H
HETATM 50 H21 UNL 1 0.285 2.483 5.449 1.00 0.00 H
HETATM 51 H22 UNL 1 0.976 0.142 5.124 1.00 0.00 H
HETATM 52 H23 UNL 1 1.894 -0.546 2.881 1.00 0.00 H
HETATM 53 H24 UNL 1 3.452 0.264 -2.869 1.00 0.00 H
HETATM 54 H25 UNL 1 5.797 -0.257 -2.491 1.00 0.00 H
HETATM 55 H26 UNL 1 6.525 -2.150 -1.155 1.00 0.00 H
HETATM 56 H27 UNL 1 4.829 -3.616 -0.131 1.00 0.00 H
HETATM 57 H28 UNL 1 2.396 -3.145 -0.474 1.00 0.00 H
CONECT 1 2 24 30 31
CONECT 2 3 10 17
CONECT 3 4 32 33
CONECT 4 5 5 9
CONECT 5 6 34
CONECT 6 7 7 35
CONECT 7 8 36
CONECT 8 9 9 37
CONECT 9 38
CONECT 10 11 39 40
CONECT 11 12 12 16
CONECT 12 13 41
CONECT 13 14 14 42
CONECT 14 15 43
CONECT 15 16 16 44
CONECT 16 45
CONECT 17 18 46 47
CONECT 18 19 19 23
CONECT 19 20 48
CONECT 20 21 21 49
CONECT 21 22 50
CONECT 22 23 23 51
CONECT 23 52
CONECT 24 25 25 29
CONECT 25 26 53
CONECT 26 27 27 54
CONECT 27 28 55
CONECT 28 29 29 56
CONECT 29 57
ENDMOL
RDKit 3D
57 60 0 0 0 0 0 0 0 0999 V2000
-1.4830 2.2399 0.1876 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.1734 0.5496 0.1734 Ti 0 0 0 0 0 4 0 0 0 0 0 0
-0.7193 -0.9121 1.6006 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.8857 -0.3949 2.9775 C 0 0 0 0 0 0 0 0 0 0 0 0
0.1562 -0.3463 3.8815 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0202 0.1322 5.1686 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.1993 0.5919 5.6074 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.2670 0.5572 4.7245 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.1158 0.0778 3.4461 C 0 0 0 0 0 0 0 0 0 0 0 0
1.8430 1.2311 0.4360 C 0 0 0 0 0 0 0 0 0 0 0 0
2.8202 0.1909 0.0997 C 0 0 0 0 0 0 0 0 0 0 0 0
3.2937 0.0975 -1.2130 C 0 0 0 0 0 0 0 0 0 0 0 0
4.2238 -0.8810 -1.5657 C 0 0 0 0 0 0 0 0 0 0 0 0
4.7022 -1.7870 -0.6197 C 0 0 0 0 0 0 0 0 0 0 0 0
4.2315 -1.6936 0.6835 C 0 0 0 0 0 0 0 0 0 0 0 0
3.3134 -0.7236 1.0203 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.2820 -0.3615 -1.7725 C 0 0 0 0 0 0 0 0 0 0 0 0
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0.2475 -4.0828 -1.5349 C 0 0 0 0 0 0 0 0 0 0 0 0
0.4409 -2.7212 -1.6099 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.6145 2.8108 -1.1842 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.7617 3.8021 -1.6549 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.8793 4.3339 -2.9240 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.8836 3.8728 -3.7796 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.7366 2.8892 -3.3248 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.6109 2.3644 -2.0550 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.5107 2.0015 0.5168 H 0 0 0 0 0 0 0 0 0 0 0 0
-1.0276 3.0519 0.7984 H 0 0 0 0 0 0 0 0 0 0 0 0
-1.6107 -1.4643 1.2458 H 0 0 0 0 0 0 0 0 0 0 0 0
0.1093 -1.6594 1.6325 H 0 0 0 0 0 0 0 0 0 0 0 0
1.1427 -0.6926 3.6008 H 0 0 0 0 0 0 0 0 0 0 0 0
0.8531 0.1567 5.8497 H 0 0 0 0 0 0 0 0 0 0 0 0
-1.2815 0.9619 6.6193 H 0 0 0 0 0 0 0 0 0 0 0 0
-3.2119 0.9322 5.1191 H 0 0 0 0 0 0 0 0 0 0 0 0
-2.9813 0.0736 2.8000 H 0 0 0 0 0 0 0 0 0 0 0 0
1.9187 1.6216 1.4738 H 0 0 0 0 0 0 0 0 0 0 0 0
1.9648 2.1141 -0.2562 H 0 0 0 0 0 0 0 0 0 0 0 0
2.9497 0.7818 -1.9852 H 0 0 0 0 0 0 0 0 0 0 0 0
4.5954 -0.9553 -2.5931 H 0 0 0 0 0 0 0 0 0 0 0 0
5.4253 -2.5565 -0.8693 H 0 0 0 0 0 0 0 0 0 0 0 0
4.6203 -2.4090 1.3940 H 0 0 0 0 0 0 0 0 0 0 0 0
2.9697 -0.6811 2.0437 H 0 0 0 0 0 0 0 0 0 0 0 0
-1.0822 0.1015 -2.4067 H 0 0 0 0 0 0 0 0 0 0 0 0
0.6486 -0.2668 -2.3471 H 0 0 0 0 0 0 0 0 0 0 0 0
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-1.2314 -5.6289 -1.4885 H 0 0 0 0 0 0 0 0 0 0 0 0
1.0810 -4.7861 -1.4675 H 0 0 0 0 0 0 0 0 0 0 0 0
1.4527 -2.3407 -1.6014 H 0 0 0 0 0 0 0 0 0 0 0 0
0.0391 4.1857 -1.0045 H 0 0 0 0 0 0 0 0 0 0 0 0
-0.2319 5.1031 -3.3146 H 0 0 0 0 0 0 0 0 0 0 0 0
-1.9733 4.2921 -4.7750 H 0 0 0 0 0 0 0 0 0 0 0 0
-3.5152 2.5441 -4.0127 H 0 0 0 0 0 0 0 0 0 0 0 0
-3.3014 1.5950 -1.7403 H 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0
2 3 1 0
3 4 1 0
4 5 2 0
5 6 1 0
6 7 2 0
7 8 1 0
8 9 2 0
2 10 1 0
10 11 1 0
11 12 2 0
12 13 1 0
13 14 2 0
14 15 1 0
15 16 2 0
2 17 1 0
17 18 1 0
18 19 2 0
19 20 1 0
20 21 2 0
21 22 1 0
22 23 2 0
1 24 1 0
24 25 2 0
25 26 1 0
26 27 2 0
27 28 1 0
28 29 2 0
9 4 1 0
16 11 1 0
23 18 1 0
29 24 1 0
1 30 1 0
1 31 1 0
3 32 1 0
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5 34 1 0
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17 46 1 0
17 47 1 0
19 48 1 0
20 49 1 0
21 50 1 0
22 51 1 0
23 52 1 0
25 53 1 0
26 54 1 0
27 55 1 0
28 56 1 0
29 57 1 0
M ENDPNG
