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View Code? Open in Web Editor NEWA standalone component to provide mappings between protein sequence positions and PDB 3D protein structure models
License: GNU Affero General Public License v3.0
A standalone component to provide mappings between protein sequence positions and PDB 3D protein structure models
License: GNU Affero General Public License v3.0
Tutorial of Running this project (Beta 1) Prerequest: OS: Linux 64bit java: openjdk_1.8.0 maven: 3.3.9 mysql: Ver 15.1 Distrib 10.0.21-MariaDB blast: 2.4.0+ *Please make sure java, mvn, mysql, blastp are all in your paths. How to run this project: Step 1. Init the Database 1. Create an empty database schema named as "pdb", username as "cbio", password as "cbio" in mysql: In mysql prompt,type: CREATE USER 'cbio'@'localhost' IDENTIFIED BY 'cbio'; GRANT ALL PRIVILEGES ON * . * TO 'cbio'@'localhost'; FLUSH PRIVILEGES; create database pdb; 2. In your code workspace, git clone https://github.com/cBioPortal/pdb-annotation.git 3. Change settings in src/main/resources/application.properties (i) Change workspace to the input sequences located ${workdir}. (ii)Change resource_dir to "~/pdb-annotation/pdb/src/main/resources/" (iii)Change ensembl_input_interval for memory performance consideration (iv) * If you want to use other test ensembl sequences, please change both ensembl_download_file and ensembl_fasta_file in your workspace 4. mvn package 5. in pdb-annotation/pdb-alignment-pipeline/target/: java -jar -Xmx7000m pdb-0.1.0.jar init Step 2. Check the API 1. in pdb-annotation/pdb-alignment-api/: mvn spring-boot:run 2. Swagger-UI: http://localhost:8080/swagger-ui.html 3. Directly using API: http://localhost:8080/pdb_annotation/StructureMappingQuery?ensemblId=ENSP00000483207.2 http://localhost:8080/pdb_annotation/ProteinIdentifierRecognitionQuery?ensemblId=ENSP00000483207.2 Step 3. Weekly update 1. in pdb-annotation/pdb-alignment-pipeline/target/: java -jar -Xmx7000m pdb-0.1.0.jar update Notes: Typical Running time for pipeline Init : 80219.905 Seconds (around 22 hours) Typical Running time for pipeline Update: 1062.796 Seconds (around 20 minutes) Test on Intel(R) Core(TM) i7-3770 CPU @ 3.40GHz, 8 cores, 8G Memory Linux version 3.18.7-200.fc21.x86_64 (gcc version 4.9.2 20141101 (Red Hat 4.9.2-1) (GCC) ) #1 SMP OpenJDK version "1.8.0_65" 64-Bit Server VM (build 25.65-b01, mixed mode) mysql Ver 15.1 Distrib 10.0.21-MariaDB, for Linux (x86_64) using EditLine wrapper Please let me know if you have questions.
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