# MICAN
Protein structure alignment program that can handle
- M: multiple-chain complexs
- I: inverse direction of SSEs
- C: Ca only models
- A: alternative alignments
- N: non-sequential alignments
## Author information
Author: S. Minami, K. Sawada, and G. Chikenji
Web Site: http://www.tbp.cse.nagoya-u.ac.jp/MICAN
## References
1. BMC Bioinformatics 2013, 14(24), S. Minami, K. Sawada, and G. Chikenji
2. Bioinformatics 2018, 34(19), S. Minami, K. Sawada, M Ota, and G. Chikenji
## License
[MIT](https://choosealicense.com/licenses/mit/)
# Easy instllation
```
pip install pymican
```
# Python module usage
1. install pymican
```
pip install pymican
```
2. usage
```python
# import module
from pymican import mican
# create object
m = mican()
# calculate alignment
aln = m.align(pdb1='pdbfile1', pdb2='pdbfile2', options='extra-mican-options')
# get TM-score, RMSD, etc.
print(aln.TMscore)
print(aln.rmsd)
```
Attributes of Alignment object
```
MICAN alignment class
Attributes
----------
outdict : dict
Alignment info
mode : str
Alignment mode
pdb1, pdb2 : str
PDB file path
size1, size2 : int
Size of protein structure
nalign : int
Number of aligned residues
rmsd : float
RMSD of aligned residues
TMscore : float
TM-score
sTMscore : float
SSE weighted TM-score
seq_identity : float
Sequence identity as percentage [0,100]
DALIscore : float
DALI z-score
SPscore : float
SP-score
TMscore1, TMscore2 : float
TM-score normalized by each protein length
coverage1, coverage2 : float
Aligned coverage for each protein length
translation_rot : numpy.array(3,3)
Rotation matrix for superposition protein1 on protein2
translation_vec : numpy.array(3)
Translation vector for superposition protein1 on protein2
alignment : pandas.DataFrame
Residue-Residue alignment info
alignlst : List[pandas.item]
Alignment info for iterator methods
Methods
-------
translate_xyz(xyz: np.array(N,3)) -> np.array(N,3)
Rotate & translate xyz coordinates
```
# Compilation and usage
1. To compile MICAN software: please type this command
```
% make
```
2. To run MICAN software:
```
% mican protein1 protein2 -a align.aln -o sup.pdb
```
-- e.g. --
```
% mican test/test1.1.pdb test/test1.2.pdb -a align.aln -o sup.pdb
```
For more details, please read the usage.
```
USAGE: % mican protein1 protein2 [OPTION]
Description:
-f fast mode (same as "-g 15")
-s sequential (SQ) alignment mode
-w rewiring (RW) alignment mode
-r rewiring & reverse (RR) alignment mode
-R reverse constrained alignment mode
-x silent mode (without any output on the console)
-p print alignment progress
-c1 ChainIDs chain ID specifier for protein1 (e.g. -c1 A, -c1 ABC)
-c2 ChainIDs chain ID specifier for protein2
-o Filename superposition file (rasmol-script)
-a Filename alignment file
-m Filename translation matrix file
-n Integer number of solutions output (default=5)
-i Integer output i-th solution on stdout & superposition file
-t Integer selection score ([0]:sTMscore, 1:TMscore, 2:SPscore)
-g Integer number of GH candidates used (default=50)
-l Integer minimum segment length (default=3)
-d Real fix TM-score scaling factor d0
-q Real maximum distance between Ca atoms to be aligned (default=10.0)
Simple usage (SQ):
% mican protein1 protein2
% mican protein1 protein2 -a align.aln -o sup.pdb
Rewiring mode alignment (RW):
% mican protein1 protein2 -w
Rewiring & reverse mode alignment (RR):
% mican protein1 protein2 -r
To visualize superposition:
% mican protein1 protein2 -o sup.pdb
% rasmol -script sup.pdb
```
Raw data
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"description": "# MICAN\nProtein structure alignment program that can handle\n- M: multiple-chain complexs\n- I: inverse direction of SSEs\n- C: Ca only models\n- A: alternative alignments\n- N: non-sequential alignments\n\n## Author information\nAuthor: S. Minami, K. Sawada, and G. Chikenji\n\nWeb Site: http://www.tbp.cse.nagoya-u.ac.jp/MICAN\n\n## References\n1. BMC Bioinformatics 2013, 14(24), S. Minami, K. Sawada, and G. Chikenji\n2. Bioinformatics 2018, 34(19), S. Minami, K. Sawada, M Ota, and G. Chikenji\n\n## License\n[MIT](https://choosealicense.com/licenses/mit/)\n# Easy instllation\n```\npip install pymican\n```\n\n# Python module usage\n1. install pymican\n```\npip install pymican\n```\n2. usage\n```python\n# import module\nfrom pymican import mican\n\n# create object\nm = mican()\n\n# calculate alignment\naln = m.align(pdb1='pdbfile1', pdb2='pdbfile2', options='extra-mican-options')\n\n# get TM-score, RMSD, etc.\nprint(aln.TMscore)\nprint(aln.rmsd)\n```\n\nAttributes of Alignment object\n```\n MICAN alignment class\n\n Attributes\n ----------\n outdict : dict\n Alignment info\n mode : str\n Alignment mode\n pdb1, pdb2 : str\n PDB file path\n size1, size2 : int\n Size of protein structure\n nalign : int\n Number of aligned residues\n rmsd : float\n RMSD of aligned residues\n TMscore : float\n TM-score\n sTMscore : float\n SSE weighted TM-score\n seq_identity : float\n Sequence identity as percentage [0,100]\n DALIscore : float\n DALI z-score\n SPscore : float\n SP-score\n TMscore1, TMscore2 : float\n TM-score normalized by each protein length\n coverage1, coverage2 : float\n Aligned coverage for each protein length\n translation_rot : numpy.array(3,3)\n Rotation matrix for superposition protein1 on protein2\n translation_vec : numpy.array(3)\n Translation vector for superposition protein1 on protein2\n alignment : pandas.DataFrame\n Residue-Residue alignment info\n alignlst : List[pandas.item]\n Alignment info for iterator methods\n\n Methods\n -------\n translate_xyz(xyz: np.array(N,3)) -> np.array(N,3)\n Rotate & translate xyz coordinates\n```\n\n# Compilation and usage\n1. To compile MICAN software: please type this command\n```\n% make\n```\n\n2. To run MICAN software:\n```\n% mican protein1 protein2 -a align.aln -o sup.pdb\n```\n\n-- e.g. --\n```\n% mican test/test1.1.pdb test/test1.2.pdb -a align.aln -o sup.pdb\n```\n\nFor more details, please read the usage.\n\n```\n USAGE: % mican protein1 protein2 [OPTION]\n\n Description:\n -f fast mode (same as \"-g 15\")\n -s sequential (SQ) alignment mode\n -w rewiring (RW) alignment mode\n -r rewiring & reverse (RR) alignment mode\n -R reverse constrained alignment mode\n -x silent mode (without any output on the console)\n -p print alignment progress\n -c1 ChainIDs chain ID specifier for protein1 (e.g. -c1 A, -c1 ABC)\n -c2 ChainIDs chain ID specifier for protein2\n -o Filename superposition file (rasmol-script)\n -a Filename alignment file\n -m Filename translation matrix file\n -n Integer number of solutions output (default=5)\n -i Integer output i-th solution on stdout & superposition file\n -t Integer selection score ([0]:sTMscore, 1:TMscore, 2:SPscore)\n -g Integer number of GH candidates used (default=50)\n -l Integer minimum segment length (default=3)\n -d Real fix TM-score scaling factor d0\n -q Real maximum distance between Ca atoms to be aligned (default=10.0)\n \n Simple usage (SQ):\n % mican protein1 protein2\n % mican protein1 protein2 -a align.aln -o sup.pdb\n\n Rewiring mode alignment (RW):\n % mican protein1 protein2 -w\n\n Rewiring & reverse mode alignment (RR):\n % mican protein1 protein2 -r\n\n To visualize superposition:\n % mican protein1 protein2 -o sup.pdb\n % rasmol -script sup.pdb\n```\n\n",
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