让gview显示氢键的脚本

wal

感觉这贴提出的需求好像挺有用的，利用个人库做了一个脚本，对一个体系的氢键设置键级为0.5的虚键，并利用gview显示。

用法：hb xx.gjf

1. $ hb h2o4_bane.gjf
   
2. H...X cutoff: 2.5 A
   
3. Donors: F,N,O,S
   
4. Acceptors: F,N,O,S
   
5. Job 1: perceived topology (8 covalent bonds); H-bonds added=4, already present=0
   
6.   O1-H3...O4  H...A=1.717 A  angle=170.3 deg  [added 0.5]
   
7.   O4-H6...O10  H...A=1.716 A  angle=170.3 deg  [added 0.5]
   
8.   O7-H8...O1  H...A=1.717 A  angle=170.2 deg  [added 0.5]
   
9.   O10-H12...O7  H...A=1.717 A  angle=170.1 deg  [added 0.5]
   
10. Wrote: h2o4_bane_hb.gjf
    
11. Hydrogen bonds: added 4, already present 0
    
12. $

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还可以调整D/A的元素表，指定cutoff，指定键角等

1. Usage: hb [options] input.gjf
   
2. 
   
3. Add 0.5-order H...X hydrogen-bond edges to Gaussian connectivity.
   
4. If the input already has Connectivity, it is preserved and reused;
   
5. otherwise covalent connectivity is perceived from Cartesian geometry.
   
6. 
   
7. Options:
   
8.   -o, --output FILE          Output GJF (default: <input>_hb.gjf)
   
9.   -d, --distance ANGSTROM    Maximum H...acceptor distance (default: 2.5)
   
10.       --min-angle DEG        Minimum donor-H...acceptor angle; 0 disables
    
11.                              angle filtering (default: 0)
    
12.       --donors LIST          Donor X elements (default: N,O,F,S)
    
13.       --acceptors LIST       Acceptor X elements
    
14.                              (default: N,O,F,S)
    
15.                              LIST is comma-separated or 'all'
    
16.       --topology-scale X     Covalent-perception cutoff scale
    
17.                              (default: 1.0)
    
18.   -q, --quiet                Suppress per-job/candidate details
    
19.   -h, --help                 Show this help

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二进制（linux）： hb (3.96 MB, 下载次数 Times of downloads: 0)

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测试： h2o4_bane.gjf (808 Bytes, 下载次数 Times of downloads: 0)

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