openbabel

Name: openbabel
Author: jinzhezenggroup

113stars23forks

How to install openbabel?

jinzhezenggroup/computational-chemistry-agent-skills/openbabel

$npx -y skills add jinzhezenggroup/computational-chemistry-agent-skills --skill openbabel

Installs into the current project.

Summary

A versatile CLI tool for converting molecular file formats, generating 3D atomic coordinates from SMILES, rendering 2D chemical structure images, and preparing or extracting structures for computational workflows. USE WHEN you need to convert between chemical file formats (e.g.,

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SKILL.md

1	# Open Babel
2
3	This skill provides practical Open Babel command patterns for common chemistry data tasks.
4
5	## Quick Start
6
7	Check installation through uvx:
8
9	```bash
10	uvx --from openbabel obabel -V
11	```
12
13	Typical conversion syntax:
14
15	```bash
16	uvx --from openbabel obabel input.ext -i<input_format> -o<output_format> -O output.ext
17	```
18
19	## Core Tasks
20
21	### 1) File format conversion
22
23	Convert XYZ to PDB:
24
25	```bash
26	uvx --from openbabel obabel C.xyz -ixyz -opdb -O C.pdb
27	```
28
29	Open Babel supports a large set of chemistry formats (e.g., xyz, mol, mol2, pdb, smi, Gaussian gjf/log/fchk, etc.).
30
31	### 2) Build structures from SMILES
32
33	Generate methane (3D coordinates required):
34
35	```bash
36	uvx --from openbabel obabel -:C --gen3d -omol -O C.mol
37	```
38
39	Generate a single carbon atom:
40
41	```bash
42	uvx --from openbabel obabel -:[C] --gen3d -omol -O C.mol
43	```
44
45	Generate methyl radical:
46
47	```bash
48	uvx --from openbabel obabel -:[CH3] --gen3d -omol -O CH3.mol
49	```
50
51	> Important: quote SMILES when they contain brackets or special characters.
52
53	Equivalent explicit form:
54
55	```bash
56	uvx --from openbabel obabel -:"[C]([H])([H])[H]" --gen3d -omol -O CH3.mol
57	```
58
59	### 3) Export SMILES from one or more structure files
60
61	```bash
62	uvx --from openbabel obabel C.mol C.mol2 C.pdb C.xyz --osmi -O C.smi
63	```
64
65	### 4) Render 2D structure images
66
67	Generate PNG:
68
69	```bash
70	uvx --from openbabel obabel -:"C([C@@H](C(=O)O)N)S" -opng -O cys.png
71	```
72
73	Generate SVG:
74
75	```bash
76	uvx --from openbabel obabel -:"C([C@@H](C(=O)O)N)S" -osvg -O cys.svg
77	```
78
79	Convert Gaussian log directly to image:
80
81	```bash
82	uvx --from openbabel obabel phosphate.log -ilog -opng -O phosphate.png
83	```
84
85	### 5) Gaussian workflow helper
86
87	Generate Gaussian input from SMILES, then patch header with `sed`:
88
89	```bash
90	uvx --from openbabel obabel -:CC --gen3d -ogjf \| sed "1c %nproc=28\n#opt b3lyp/6-31g(d,p)" > CC.gjf
91	```
92
93	Generate next-step input from a previous Gaussian log:
94
95	```bash
96	uvx --from openbabel obabel CC.log -ilog -ogjf \| sed "1c %nproc=28\n#freq b3lyp/6-31g(d,p)" > CC2.gjf
97	```
98
99	## Agent Checklist
100
101	When using this skill for users:
102
103	1. Confirm source file(s) and desired target format.
104	1. Prefer explicit `-i` and `-o` format flags for reproducibility.
105	1. Add `--gen3d` when converting SMILES to coordinate-bearing structures.
106	1. Quote SMILES strings that contain brackets/parentheses.
107	1. For Gaussian workflows, verify route section and resource lines (`%nproc`, method/basis) after generation.
108	1. Use `uvx --from openbabel obabel ...` consistently to minimize local dependency setup.
109
110	## References
111
112	- Open Babel project: https://openbabel.org/
113	- Open Babel GitHub: https://github.com/openbabel/openbabel
114	- openbabel package: https://pypi.org/project/openbabel/

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Type

openbabel

113stars23forks

View on GitHub

How to install openbabel?

jinzhezenggroup/computational-chemistry-agent-skills/openbabel

$npx -y skills add jinzhezenggroup/computational-chemistry-agent-skills --skill openbabel

Installs into the current project.

Summary

Files · 1

View on GitHub

SKILL.md

1	# Open Babel
2
3	This skill provides practical Open Babel command patterns for common chemistry data tasks.
4
5	## Quick Start
6
7	Check installation through uvx:
8
9	```bash
10	uvx --from openbabel obabel -V
11	```
12
13	Typical conversion syntax:
14
15	```bash
16	uvx --from openbabel obabel input.ext -i<input_format> -o<output_format> -O output.ext
17	```
18
19	## Core Tasks
20
21	### 1) File format conversion
22
23	Convert XYZ to PDB:
24
25	```bash
26	uvx --from openbabel obabel C.xyz -ixyz -opdb -O C.pdb
27	```
28
29	Open Babel supports a large set of chemistry formats (e.g., xyz, mol, mol2, pdb, smi, Gaussian gjf/log/fchk, etc.).
30
31	### 2) Build structures from SMILES
32
33	Generate methane (3D coordinates required):
34
35	```bash
36	uvx --from openbabel obabel -:C --gen3d -omol -O C.mol
37	```
38
39	Generate a single carbon atom:
40
41	```bash
42	uvx --from openbabel obabel -:[C] --gen3d -omol -O C.mol
43	```
44
45	Generate methyl radical:
46
47	```bash
48	uvx --from openbabel obabel -:[CH3] --gen3d -omol -O CH3.mol
49	```
50
51	> Important: quote SMILES when they contain brackets or special characters.
52
53	Equivalent explicit form:
54
55	```bash
56	uvx --from openbabel obabel -:"[C]([H])([H])[H]" --gen3d -omol -O CH3.mol
57	```
58
59	### 3) Export SMILES from one or more structure files
60
61	```bash
62	uvx --from openbabel obabel C.mol C.mol2 C.pdb C.xyz --osmi -O C.smi
63	```
64
65	### 4) Render 2D structure images
66
67	Generate PNG:
68
69	```bash
70	uvx --from openbabel obabel -:"C([C@@H](C(=O)O)N)S" -opng -O cys.png
71	```
72
73	Generate SVG:
74
75	```bash
76	uvx --from openbabel obabel -:"C([C@@H](C(=O)O)N)S" -osvg -O cys.svg
77	```
78
79	Convert Gaussian log directly to image:
80
81	```bash
82	uvx --from openbabel obabel phosphate.log -ilog -opng -O phosphate.png
83	```
84
85	### 5) Gaussian workflow helper
86
87	Generate Gaussian input from SMILES, then patch header with `sed`:
88
89	```bash
90	uvx --from openbabel obabel -:CC --gen3d -ogjf \| sed "1c %nproc=28\n#opt b3lyp/6-31g(d,p)" > CC.gjf
91	```
92
93	Generate next-step input from a previous Gaussian log:
94
95	```bash
96	uvx --from openbabel obabel CC.log -ilog -ogjf \| sed "1c %nproc=28\n#freq b3lyp/6-31g(d,p)" > CC2.gjf
97	```
98
99	## Agent Checklist
100
101	When using this skill for users:
102
103	1. Confirm source file(s) and desired target format.
104	1. Prefer explicit `-i` and `-o` format flags for reproducibility.
105	1. Add `--gen3d` when converting SMILES to coordinate-bearing structures.
106	1. Quote SMILES strings that contain brackets/parentheses.
107	1. For Gaussian workflows, verify route section and resource lines (`%nproc`, method/basis) after generation.
108	1. Use `uvx --from openbabel obabel ...` consistently to minimize local dependency setup.
109
110	## References
111
112	- Open Babel project: https://openbabel.org/
113	- Open Babel GitHub: https://github.com/openbabel/openbabel
114	- openbabel package: https://pypi.org/project/openbabel/

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Type