Add pdb2fasta (#52973)

Author: apcamargo

recipes/pdb2fasta/build.sh

@@ -0,0 +1,5 @@
+#!/bin/bash -euo
+
+mkdir -p ${PREFIX}/bin
+${CC} -O2 pdb2fasta.c -o pdb2fasta
+mv pdb2fasta ${PREFIX}/bin

recipes/pdb2fasta/meta.yaml

@@ -0,0 +1,38 @@
+{% set name = "pdb2fasta" %}
+{% set version = "1.0" %}
+
+package:
+  name: {{ name }}
+  version: {{ version }}
+
+source:
+  url: https://github.com/kad-ecoli/{{ name }}/archive/refs/tags/{{ version }}.tar.gz
+  sha256: 63c22998df75c0a1ee9c00051d4d401e45b13651a09b98bb2885a86bc342b7bf
+  patches:
+    - pdb2fasta.patch
+
+build:
+  number: 0
+  run_exports:
+    - {{ pin_subpackage('pdb2fasta', max_pin="x.x") }}
+
+requirements:
+  build:
+    - {{ compiler('c') }}
+
+test:
+  commands:
+    - pdb2fasta --help
+
+about:
+  home: "https://github.com/kad-ecoli/pdb2fasta"
+  license: "GPL-2-only"
+  license_family: GPL2
+  license_file: License.txt
+  summary: "Convert PDB structures to FASTA sequences."
+  dev_url: "https://github.com/kad-ecoli/pdb2fasta"
+
+extra:
+  additional-platforms:
+    - linux-aarch64
+    - osx-arm64

recipes/pdb2fasta/pdb2fasta.patch

@@ -0,0 +1,40 @@
+diff --git a/pdb2fasta.c b/pdb2fasta.c
+index 9642d03..9e8eef1 100644
+--- a/pdb2fasta.c
++++ b/pdb2fasta.c
+@@ -1,3 +1,4 @@
++#include<stdlib.h>
+ #include<stdio.h>
+ #include<string.h>
+ 
+@@ -99,14 +100,24 @@ char *pdb2fasta(char *pdb_file){
+ }
+ 
+ int main(int argc, char** argv){
+-    if (argc<2){
+-        printf("pdb2fasta pdb.pdb > seq.fasta\n");
+-        printf("    convert PDB file pdb.pdb to FASTA sequence file seq.fasta\n");
++    if (argc < 2){
++        printf("Usage: pdb2fasta pdb.pdb > seq.fasta\n");
++        printf("    Convert PDB file pdb.pdb to FASTA sequence file seq.fasta\n");
+         return argc;
+     }
+-    
+-    int i;
+-    for (i=1;i<argc;i++){
++
++    if (argc == 2 && strcmp(argv[1], "--help") == 0) {
++        printf("Usage: pdb2fasta [options] pdb.pdb\n");
++        printf("Options:\n");
++        printf("  --help    Display this help dialogue and exit\n");
++        printf("\nDescription:\n");
++        printf("  Convert a PDB file to a FASTA sequence format. Output is printed to stdout.\n");
++        printf("  Example:\n");
++        printf("    pdb2fasta pdb.pdb > seq.fasta\n");
++        return 0;
++    }
++
++    for (int i=1; i<argc; i++){
+         char *pdb_file=argv[i];
+         printf("%s",pdb2fasta(pdb_file));
+     }