# **Ramplot**
Ramplot is a utility designed to help researchers and students visualize and analyze protein structures using Ramachandran plots. Ramachandran plots are a fundamental tool in structural biology, providing a way to visualize the torsion angles of protein backbones and assess the validity of protein structures. Ramplot offers several input options and can generate various types of plots to help understand protein conformations better.
## Introduction
Ramplot is a versatile tool for visualizing different types of steric plots, enabling the study of protein and peptide conformations in specific regions. This utility, available for both online and offline use, consists of various applications that generate a wide range of Ramachandran maps, including 2D and 3D plots for standard and specialized categories such as Glycine (Gly), Valine/Isoleucine (Val/Ile), pre-Proline (pre-Pro), trans-Proline (trans-Pro), cis-Proline (cis-Pro), and a General category representing the remaining 16 amino acids.
You can also access Ramplot as a web server at https://ramplot.in.
## Reference
## Standalone
The Standalone version of ramplot is written in python3 and following libraries are necessary for the successful run:
- numpy
- pandas
- biopython
- matplotlib
- mdanalysis
- pytest-shutil
- setuptools
## Installations
```
pip install ramplot
```
or Using Source Code
```
python setup.py install
```
## USAGE
To know about the available option for the stanadlone, type the following command:
```
ramplot -h
```
To run the example, type the following command:
positional arguments:
{pdb,trajectory,TorsionAngle,ThreeTorsionAngle}
Available commands
pdb Run Ramachandran Plot Using PDB Files
trajectory Analysis of residue trajectory
TorsionAngle Run Ramachandran Plot Using Custom Torsion Angle CSV File
ThreeTorsionAngle Run Ramachandran Plot Using Custom Three Torsion Angle CSV File like PHI,PSI,THETA
To know about the available option for the pdb, type the following command:
```
ramplot pdb -h
```
options:
-h, --help show this help message and exit
-i INPUT, --input INPUT
Input PDB Folder Path
-m MAPTYPE, --MapType MAPTYPE
Specify Map Types All :0 2d Only : 2 3D Only :3 (Default: 0)
-r RESOLUTION, --Resolution RESOLUTION
Specify Resolution of Plots (Dafult resolution : 600 )
-p PLOTFILETYPE, --PlotFileType PLOTFILETYPE
Specify Output Plot File formet like png jpeg tif (Default file type : png )
-o OUTPUT, --Output OUTPUT
Specify Output Directory Folder Name or Path
**Input Folder:** It allow users to provide input in the folder path which contains PDB files.
**Output Folder:** Program will save the results in the Output Directory.".
**Maptype:** User should provide Map Types All : 0 2d Only : 2 3D Only : 3 (Default: 0 ).
**Resolution:** User should provide plot resolution in intiger, by default its 600.
**Plot File Type:** User should provide plot file type, such as, png, tif and jpeg, by default its png.
Example
```
ramplot pdb -h "Test/PDB/" -m 0 -r 600 -p png -o OutPut
```
To know about the available option for the trajectory, type the following command:
```
ramplot trajectory -h
```
options:
-h, --help show this help message and exit
-t INPUTTPR, --InputTPR INPUTTPR
Input TPR File Path
-x INPUTXTC, --InputXTC INPUTXTC
Input XTC File Path
-c INPUTRESIDUES, --InputResidues INPUTRESIDUES
Specify Input Residie like ChainResidueNo A101
-f FRAMEINTERVAL, --FrameInterval FRAMEINTERVAL
Specify Frame Interval (Default frame interval : 20
-m MAPTYPE, --MapType MAPTYPE
Specify Map Types All :0 2d Only : 1 3D Only :3
-r RESOLUTION, --Resolution RESOLUTION
Specify Resolution of Plots (Default resolution : 600 )
-p PLOTFILETYPE, --PlotFileType PLOTFILETYPE
Specify Output Plot File formet like png jpeg tif (Dafult file type : png )
-o OUTPUT, --Output OUTPUT
Specify Output Directory Folder Name or Path
**Input TPR File:** Provide Molecular Simulation Topology file.
**Input XTC File:** Provide Molecular Simulation Trajectory file.
**Input Residues:** Provide the chain and residue number in the format ChainResidueNumber, such as A101, A105...
**Frame Interval:** You need to provide a valid frame interval as an integer, which the program will use to extract PDB files from the trajectory. For example, if you specify an interval of 10, it will extract PDB files for every 10th frame.
**Output Folder:** Program will save the results in the Output Directory.".
Example
```
ramplot trajectory -t Test/mdsim.tpr -x Test/mdsim.xtc -c A101,A105 -f 10 -m 0 -r 600 -p png -o OutPut
```
To know about the available option for the torsion angle, type the following command:
```
ramplot TorsionAngle -h
```
options:
-h, --help show this help message and exit
-i INPUT, --input INPUT
Input Custom Torsion Angle CSV File Path File contains 6 columns with names
ID,Chain,Residue,ResidueNo,PHI,PSI . For sample output file you can visit ramplot.in
-m MAPTYPE, --MapType MAPTYPE
Specify Map Types All :0 2d Only : 1 3D Only :3
-r RESOLUTION, --Resolution RESOLUTION
Specify Resolution of Plots (Default resolution : 600 )
-p PLOTFILETYPE, --PlotFileType PLOTFILETYPE
Specify Output Plot File formet like png jpeg tif (Default file type : png )
-o OUTPUT, --Output OUTPUT
Specify Output Directory Folder Name or Path
**Input Folder:** Input Custom Torsion Angle CSV File Path File contains 6 columns with names ID,Chain,Residue,ResidueNo,PHI,PSI
**Output Folder:** Program will save the results in the Output Directory.
Example
```
ramplot TorsionAngle -i Test/CustomTorsionAngles.csv -m 0 -r 600 -p png -o OutPut
```
To know about the available option for the three rotatable bond angle, type the following command:
```
ramplot ThreeTorsionAngle -h
```
options:
-h, --help show this help message and exit
-i INPUT, --input INPUT
Input Custom Torsion Angle CSV File Path File contains 6 columns with names
ID,Chain,Residue,ResidueNo,PHI,PSI . For sample output file you can visit ramplot.in
-r RESOLUTION, --Resolution RESOLUTION
Specify Resolution of Plots (Default resolution : 600 )
-p PLOTFILETYPE, --PlotFileType PLOTFILETYPE
Specify Output Plot File formet like png jpeg tif (Default file type : png )
-o OUTPUT, --Output OUTPUT
Specify Output Directory Folder Name or Path
**Input Folder:** Custom Torsion Angle CSV File Path
The file should contain 7 columns with the following headers: ID, Chain, Residue, ResidueNo, PHI, PSI, and THETA.
**Output Folder:** Program will save the results in the Output Directory.
Example
```
ramplot ThreeTorsionAngle -i Test/CustomTorsionAnglesTheta.csv -m 0 -r 600 -p png -o OutPut
```
Ramplot Package Files
=======================
It contantain following files, brief descript of these files given below
LICENSE : License information
README.md : This file provide information about this package
ramplot : Main python program folder
test : Sample data files for test
setup.py : Python installation file
** For any query or suggestion, you can reach out to us: Mayank Kumar (mayank2801@gmail.com) and Prof. R.S. Rathore (rsrathore@cusb.ac.in). **
** Department of Bioinformatics, School of Earth Biological and Environmental Sciences, Central University of South Bihar, Gaya 824236, India ** "# ramplot"
"# ramplot"
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"description": "# **Ramplot**\r\nRamplot is a utility designed to help researchers and students visualize and analyze protein structures using Ramachandran plots. Ramachandran plots are a fundamental tool in structural biology, providing a way to visualize the torsion angles of protein backbones and assess the validity of protein structures. Ramplot offers several input options and can generate various types of plots to help understand protein conformations better.\r\n## Introduction\r\nRamplot is a versatile tool for visualizing different types of steric plots, enabling the study of protein and peptide conformations in specific regions. This utility, available for both online and offline use, consists of various applications that generate a wide range of Ramachandran maps, including 2D and 3D plots for standard and specialized categories such as Glycine (Gly), Valine/Isoleucine (Val/Ile), pre-Proline (pre-Pro), trans-Proline (trans-Pro), cis-Proline (cis-Pro), and a General category representing the remaining 16 amino acids.\r\nYou can also access Ramplot as a web server at https://ramplot.in.\r\n\r\n## Reference\r\n \r\n## Standalone\r\nThe Standalone version of ramplot is written in python3 and following libraries are necessary for the successful run:\r\n- numpy\r\n- pandas\r\n- biopython\r\n- matplotlib\r\n- mdanalysis\r\n- pytest-shutil\r\n- setuptools\r\n\r\n## Installations\r\n```\r\npip install ramplot\r\n\r\n```\r\nor Using Source Code\r\n```\r\npython setup.py install \r\n```\r\n## USAGE\r\nTo know about the available option for the stanadlone, type the following command:\r\n```\r\nramplot -h\r\n```\r\nTo run the example, type the following command:\r\npositional arguments:\r\n {pdb,trajectory,TorsionAngle,ThreeTorsionAngle}\r\n Available commands\r\n pdb Run Ramachandran Plot Using PDB Files\r\n trajectory Analysis of residue trajectory\r\n TorsionAngle Run Ramachandran Plot Using Custom Torsion Angle CSV File\r\n ThreeTorsionAngle Run Ramachandran Plot Using Custom Three Torsion Angle CSV File like PHI,PSI,THETA\r\n\r\nTo know about the available option for the pdb, type the following command:\r\n```\r\nramplot pdb -h \r\n```\r\noptions:\r\n -h, --help show this help message and exit\r\n -i INPUT, --input INPUT\r\n Input PDB Folder Path\r\n -m MAPTYPE, --MapType MAPTYPE\r\n Specify Map Types All :0 2d Only : 2 3D Only :3 (Default: 0)\r\n -r RESOLUTION, --Resolution RESOLUTION\r\n Specify Resolution of Plots (Dafult resolution : 600 )\r\n -p PLOTFILETYPE, --PlotFileType PLOTFILETYPE\r\n Specify Output Plot File formet like png jpeg tif (Default file type : png )\r\n -o OUTPUT, --Output OUTPUT\r\n Specify Output Directory Folder Name or Path\r\n\r\n**Input Folder:** It allow users to provide input in the folder path which contains PDB files.\r\n\r\n**Output Folder:** Program will save the results in the Output Directory.\".\r\n\r\n**Maptype:** User should provide Map Types All : 0 2d Only : 2 3D Only : 3 (Default: 0 ).\r\n\r\n**Resolution:** User should provide plot resolution in intiger, by default its 600. \r\n\r\n**Plot File Type:** User should provide plot file type, such as, png, tif and jpeg, by default its png.\r\n\r\nExample\r\n```\r\n\tramplot pdb -h \"Test/PDB/\" -m 0 -r 600 -p png -o OutPut\t\r\n```\r\nTo know about the available option for the trajectory, type the following command:\r\n```\r\nramplot trajectory -h \r\n```\r\noptions:\r\n -h, --help show this help message and exit\r\n -t INPUTTPR, --InputTPR INPUTTPR\r\n Input TPR File Path\r\n -x INPUTXTC, --InputXTC INPUTXTC\r\n Input XTC File Path\r\n -c INPUTRESIDUES, --InputResidues INPUTRESIDUES\r\n Specify Input Residie like ChainResidueNo A101\r\n -f FRAMEINTERVAL, --FrameInterval FRAMEINTERVAL\r\n Specify Frame Interval (Default frame interval : 20\r\n -m MAPTYPE, --MapType MAPTYPE\r\n Specify Map Types All :0 2d Only : 1 3D Only :3\r\n -r RESOLUTION, --Resolution RESOLUTION\r\n Specify Resolution of Plots (Default resolution : 600 )\r\n -p PLOTFILETYPE, --PlotFileType PLOTFILETYPE\r\n Specify Output Plot File formet like png jpeg tif (Dafult file type : png )\r\n -o OUTPUT, --Output OUTPUT\r\n Specify Output Directory Folder Name or Path\r\n\t\t\t\t\t\t\r\n**Input TPR File:** Provide Molecular Simulation Topology file.\r\n\r\n**Input XTC File:** Provide Molecular Simulation Trajectory file.\r\n\r\n**Input Residues:** Provide the chain and residue number in the format ChainResidueNumber, such as A101, A105...\r\n\r\n**Frame Interval:** You need to provide a valid frame interval as an integer, which the program will use to extract PDB files from the trajectory. For example, if you specify an interval of 10, it will extract PDB files for every 10th frame.\r\n\r\n**Output Folder:** Program will save the results in the Output Directory.\".\r\nExample\r\n```\r\n\tramplot trajectory -t Test/mdsim.tpr -x Test/mdsim.xtc -c A101,A105 -f 10 -m 0 -r 600 -p png -o OutPut\t\r\n```\r\nTo know about the available option for the torsion angle, type the following command:\r\n```\r\nramplot TorsionAngle -h \r\n```\r\noptions:\r\n -h, --help show this help message and exit\r\n -i INPUT, --input INPUT\r\n Input Custom Torsion Angle CSV File Path File contains 6 columns with names\r\n ID,Chain,Residue,ResidueNo,PHI,PSI . For sample output file you can visit ramplot.in\r\n -m MAPTYPE, --MapType MAPTYPE\r\n Specify Map Types All :0 2d Only : 1 3D Only :3\r\n -r RESOLUTION, --Resolution RESOLUTION\r\n Specify Resolution of Plots (Default resolution : 600 )\r\n -p PLOTFILETYPE, --PlotFileType PLOTFILETYPE\r\n Specify Output Plot File formet like png jpeg tif (Default file type : png )\r\n -o OUTPUT, --Output OUTPUT\r\n Specify Output Directory Folder Name or Path\r\n**Input Folder:** Input Custom Torsion Angle CSV File Path File contains 6 columns with names ID,Chain,Residue,ResidueNo,PHI,PSI\r\n\r\n**Output Folder:** Program will save the results in the Output Directory.\r\nExample\r\n```\r\n\tramplot TorsionAngle -i Test/CustomTorsionAngles.csv -m 0 -r 600 -p png -o OutPut\t\r\n```\r\nTo know about the available option for the three rotatable bond angle, type the following command:\r\n```\r\nramplot ThreeTorsionAngle -h \r\n```\r\noptions:\r\n -h, --help show this help message and exit\r\n -i INPUT, --input INPUT\r\n Input Custom Torsion Angle CSV File Path File contains 6 columns with names\r\n ID,Chain,Residue,ResidueNo,PHI,PSI . For sample output file you can visit ramplot.in\r\n -r RESOLUTION, --Resolution RESOLUTION\r\n Specify Resolution of Plots (Default resolution : 600 )\r\n -p PLOTFILETYPE, --PlotFileType PLOTFILETYPE\r\n Specify Output Plot File formet like png jpeg tif (Default file type : png )\r\n -o OUTPUT, --Output OUTPUT\r\n Specify Output Directory Folder Name or Path\r\n\t\t\t\t\t\t\r\n**Input Folder:** Custom Torsion Angle CSV File Path\r\nThe file should contain 7 columns with the following headers: ID, Chain, Residue, ResidueNo, PHI, PSI, and THETA.\r\n\r\n**Output Folder:** Program will save the results in the Output Directory.\r\nExample\r\n```\r\n\tramplot ThreeTorsionAngle -i Test/CustomTorsionAnglesTheta.csv -m 0 -r 600 -p png -o OutPut\t\r\n```\r\n\r\nRamplot Package Files\r\n=======================\r\nIt contantain following files, brief descript of these files given below\r\n\r\n\r\nLICENSE : License information\r\n\r\nREADME.md : This file provide information about this package\r\n\r\nramplot\t\t : Main python program folder\r\n\r\ntest\t\t : Sample data files for test\r\n\r\nsetup.py\t\t\t\t\t\t: Python installation file\r\n\r\n\r\n** For any query or suggestion, you can reach out to us: Mayank Kumar (mayank2801@gmail.com) and Prof. R.S. Rathore (rsrathore@cusb.ac.in). **\r\n** Department of Bioinformatics, School of Earth Biological and Environmental Sciences, Central University of South Bihar, Gaya 824236, India ** \"# ramplot\" \r\n\"# ramplot\" \r\n\r\n\r\n",
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