Finalizing chain visualization

.~lock.pdb_lab.docx#

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+,noah,NovaArchSys,27.10.2022 13:09,file:///home/noah/.config/libreoffice/4;

Schrick-Noah_CS-6643_Lab6.R

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-# Lab 6 for the University of Tulsa's CS-6643 Bioinformatics Course
-# GWAS
-# Professor: Dr. McKinney, Fall 2022
-# Noah L. Schrick - 1492657
-
-## Set Working Directory to file directory - RStudio approach
-setwd(dirname(rstudioapi::getActiveDocumentContext()$path))

Schrick-Noah_CS-6643_Lab7.R

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+# Lab 7 for the University of Tulsa's CS-6643 Bioinformatics Course
+# PDB
+# Professor: Dr. McKinney, Fall 2022
+# Noah L. Schrick - 1492657
+
+## Set Working Directory to file directory - RStudio approach
+setwd(dirname(rstudioapi::getActiveDocumentContext()$path))
+
+#### Part A: Obtaining PDB - no supporting R Code
+
+#### Part B: Visualize the 3D structure
+## Install Rpdb and load the pdb
+if (!require("Rpdb")) install.packages("Rpdb")
+library(Rpdb)
+x<-read.pdb("1TGH.pdb")
+natom(x)
+visualize(x,type="l")
+
+## Visualize the B and C chains
+B_chain_pdb <- subset(x$atoms, x$atoms$chainid=="B") 
+C_chain_pdb <- subset(x$atoms, x$atoms$chainid=="C") 
+# remove water:
+C_chain_pdb <- subset(C_chain_pdb,C_chain_pdb$resname!="HOH") 
+
+# visualize chains B and C
+BC_chains_pdb <- subset(x$atoms, x$atoms$chainid=="B" | 				                             x$atoms$chainid=="C")
+color.vec <- c(rep("red",natom(B_chain_pdb)),rep("green",natom(C_chain_pdb)))
+
+visualize(BC_chains_pdb,col=color.vec)
+addResLab(BC_chains_pdb)
+
+## Visualize B-C and A Chains
+A_chain_pdb <- subset(x$atoms, x$atoms$chainid=="A") 
+# remove water
+A_chain_pdb <- subset(A_chain_pdb, A_chain_pdb$resname!="HOH")  
+
+# visualize complex complex
+BCA_chains_pdb <- subset(x$atoms, x$atoms$chainid=="B" |  
+                           x$atoms$chainid=="C" | x$atoms$chainid=="A")
+BCA.color.vec <- c(rep("red",natom(B_chain_pdb)),rep("green",natom(C_chain_pdb)),rep("blue",natom(A_chain_pdb)))
+
+visualize(BCA_chains_pdb,col=BCA.color.vec)