From c4bd7d6c3888ea835c98ec20de2ffd7ba74dd988 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ant=C3=B4nio=20Camargo?=
 <apcamargo@users.noreply.github.com>
Date: Mon, 23 Dec 2024 12:13:42 -0800
Subject: [PATCH 1/8] Add `pdb2fasta`

---
 recipes/pdb2fasta/build.sh  |  4 ++++
 recipes/pdb2fasta/meta.yaml | 36 ++++++++++++++++++++++++++++++++++++
 2 files changed, 40 insertions(+)
 create mode 100644 recipes/pdb2fasta/build.sh
 create mode 100644 recipes/pdb2fasta/meta.yaml

diff --git a/recipes/pdb2fasta/build.sh b/recipes/pdb2fasta/build.sh
new file mode 100644
index 0000000000000..43a72037a8c87
--- /dev/null
+++ b/recipes/pdb2fasta/build.sh
@@ -0,0 +1,4 @@
+#!/bin/bash -euo
+
+g++ -O3 pdb2fasta.cpp -o pdb2fasta -static
+mv pdb2fasta ${PREFIX}/bin
diff --git a/recipes/pdb2fasta/meta.yaml b/recipes/pdb2fasta/meta.yaml
new file mode 100644
index 0000000000000..1f966cda7ecd4
--- /dev/null
+++ b/recipes/pdb2fasta/meta.yaml
@@ -0,0 +1,36 @@
+{% 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
+
+build:
+  number: 0
+  run_exports:
+    - {{ pin_subpackage('pdb2fasta', max_pin="x") }}
+
+requirements:
+  build:
+    - {{ compiler('cxx') }}
+
+test:
+  commands:
+    - pdb2fasta
+
+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

From 8f1cca6b3ceef10d874054a3238236ee132b4f6b Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ant=C3=B4nio=20Camargo?=
 <apcamargo@users.noreply.github.com>
Date: Mon, 23 Dec 2024 15:02:25 -0800
Subject: [PATCH 2/8] Use ${CXX}

---
 recipes/pdb2fasta/build.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/recipes/pdb2fasta/build.sh b/recipes/pdb2fasta/build.sh
index 43a72037a8c87..0f8270df52e27 100644
--- a/recipes/pdb2fasta/build.sh
+++ b/recipes/pdb2fasta/build.sh
@@ -1,4 +1,4 @@
 #!/bin/bash -euo
 
-g++ -O3 pdb2fasta.cpp -o pdb2fasta -static
+${CXX} -O3 pdb2fasta.cpp -o pdb2fasta -static
 mv pdb2fasta ${PREFIX}/bin

From 368580be4a442271723d4271d07acb4167c8ac2c Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ant=C3=B4nio=20Camargo?=
 <apcamargo@users.noreply.github.com>
Date: Mon, 23 Dec 2024 17:45:39 -0800
Subject: [PATCH 3/8] Use `CXXFLAGS`

---
 recipes/pdb2fasta/build.sh | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/recipes/pdb2fasta/build.sh b/recipes/pdb2fasta/build.sh
index 0f8270df52e27..323dd53499196 100644
--- a/recipes/pdb2fasta/build.sh
+++ b/recipes/pdb2fasta/build.sh
@@ -1,4 +1,5 @@
 #!/bin/bash -euo
 
-${CXX} -O3 pdb2fasta.cpp -o pdb2fasta -static
+mkdir -p ${PREFIX}/bin
+${CXX} ${CXXFLAGS} -static pdb2fasta.cpp -o pdb2fasta
 mv pdb2fasta ${PREFIX}/bin

From 6cb9d6d85328c345a6404a9426b10aa4781285e7 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ant=C3=B4nio=20Camargo?=
 <apcamargo@users.noreply.github.com>
Date: Mon, 23 Dec 2024 18:03:27 -0800
Subject: [PATCH 4/8] Patch stdlib

---
 recipes/pdb2fasta/build.sh        | 2 +-
 recipes/pdb2fasta/meta.yaml       | 2 ++
 recipes/pdb2fasta/pdb2fasta.patch | 8 ++++++++
 3 files changed, 11 insertions(+), 1 deletion(-)
 create mode 100644 recipes/pdb2fasta/pdb2fasta.patch

diff --git a/recipes/pdb2fasta/build.sh b/recipes/pdb2fasta/build.sh
index 323dd53499196..36f8ffb3ee0f0 100644
--- a/recipes/pdb2fasta/build.sh
+++ b/recipes/pdb2fasta/build.sh
@@ -1,5 +1,5 @@
 #!/bin/bash -euo
 
 mkdir -p ${PREFIX}/bin
-${CXX} ${CXXFLAGS} -static pdb2fasta.cpp -o pdb2fasta
+${CC} ${CFLAGS} pdb2fasta.cpp -o pdb2fasta
 mv pdb2fasta ${PREFIX}/bin
diff --git a/recipes/pdb2fasta/meta.yaml b/recipes/pdb2fasta/meta.yaml
index 1f966cda7ecd4..c6eb6eb29d547 100644
--- a/recipes/pdb2fasta/meta.yaml
+++ b/recipes/pdb2fasta/meta.yaml
@@ -8,6 +8,8 @@ package:
 source:
   url: https://github.com/kad-ecoli/{{ name }}/archive/refs/tags/{{ version }}.tar.gz
   sha256: 63c22998df75c0a1ee9c00051d4d401e45b13651a09b98bb2885a86bc342b7bf
+  patches:
+    - pdb2fasta.patch
 
 build:
   number: 0
diff --git a/recipes/pdb2fasta/pdb2fasta.patch b/recipes/pdb2fasta/pdb2fasta.patch
new file mode 100644
index 0000000000000..e97d2f625cabd
--- /dev/null
+++ b/recipes/pdb2fasta/pdb2fasta.patch
@@ -0,0 +1,8 @@
+diff --git a/pdb2fasta.c b/pdb2fasta.c
+index 9642d03..f197f1f 100644
+--- a/pdb2fasta.c
++++ b/pdb2fasta.c
+@@ -1,3 +1,4 @@
++#include<stdlib.h>
+ #include<stdio.h>
+ #include<string.h>

From 16703335e7f05f83130dc0923fdfa1daab63e262 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ant=C3=B4nio=20Camargo?=
 <apcamargo@users.noreply.github.com>
Date: Mon, 23 Dec 2024 18:09:25 -0800
Subject: [PATCH 5/8] Fix extension

---
 recipes/pdb2fasta/build.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/recipes/pdb2fasta/build.sh b/recipes/pdb2fasta/build.sh
index 36f8ffb3ee0f0..6c43b17ac63ef 100644
--- a/recipes/pdb2fasta/build.sh
+++ b/recipes/pdb2fasta/build.sh
@@ -1,5 +1,5 @@
 #!/bin/bash -euo
 
 mkdir -p ${PREFIX}/bin
-${CC} ${CFLAGS} pdb2fasta.cpp -o pdb2fasta
+${CC} ${CFLAGS} pdb2fasta.c -o pdb2fasta
 mv pdb2fasta ${PREFIX}/bin

From 79f3adddea77ad61699e57e4a3903858ca8d5fdc Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ant=C3=B4nio=20Camargo?=
 <apcamargo@users.noreply.github.com>
Date: Mon, 23 Dec 2024 18:29:44 -0800
Subject: [PATCH 6/8] Test with help dialogue

---
 recipes/pdb2fasta/build.sh        |  2 +-
 recipes/pdb2fasta/meta.yaml       |  2 +-
 recipes/pdb2fasta/pdb2fasta.patch | 34 ++++++++++++++++++++++++++++++-
 3 files changed, 35 insertions(+), 3 deletions(-)

diff --git a/recipes/pdb2fasta/build.sh b/recipes/pdb2fasta/build.sh
index 6c43b17ac63ef..6dfee62b849e2 100644
--- a/recipes/pdb2fasta/build.sh
+++ b/recipes/pdb2fasta/build.sh
@@ -1,5 +1,5 @@
 #!/bin/bash -euo
 
 mkdir -p ${PREFIX}/bin
-${CC} ${CFLAGS} pdb2fasta.c -o pdb2fasta
+${CC} -O2 pdb2fasta.c -o pdb2fasta
 mv pdb2fasta ${PREFIX}/bin
diff --git a/recipes/pdb2fasta/meta.yaml b/recipes/pdb2fasta/meta.yaml
index c6eb6eb29d547..f1a27eb513069 100644
--- a/recipes/pdb2fasta/meta.yaml
+++ b/recipes/pdb2fasta/meta.yaml
@@ -22,7 +22,7 @@ requirements:
 
 test:
   commands:
-    - pdb2fasta
+    - pdb2fasta --help
 
 about:
   home: "https://github.com/kad-ecoli/pdb2fasta"
diff --git a/recipes/pdb2fasta/pdb2fasta.patch b/recipes/pdb2fasta/pdb2fasta.patch
index e97d2f625cabd..d0cf696829648 100644
--- a/recipes/pdb2fasta/pdb2fasta.patch
+++ b/recipes/pdb2fasta/pdb2fasta.patch
@@ -1,8 +1,40 @@
 diff --git a/pdb2fasta.c b/pdb2fasta.c
-index 9642d03..f197f1f 100644
+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));
+     }

From 3f8a4cf9d4ed259d61bf8ed64ba7645808b9e903 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ant=C3=B4nio=20Camargo?=
 <apcamargo@users.noreply.github.com>
Date: Mon, 23 Dec 2024 18:41:54 -0800
Subject: [PATCH 7/8] Fix patch

---
 recipes/pdb2fasta/meta.yaml       | 2 +-
 recipes/pdb2fasta/pdb2fasta.patch | 6 +++---
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/recipes/pdb2fasta/meta.yaml b/recipes/pdb2fasta/meta.yaml
index f1a27eb513069..ac2cbe54733d3 100644
--- a/recipes/pdb2fasta/meta.yaml
+++ b/recipes/pdb2fasta/meta.yaml
@@ -14,7 +14,7 @@ source:
 build:
   number: 0
   run_exports:
-    - {{ pin_subpackage('pdb2fasta', max_pin="x") }}
+    - {{ pin_subpackage('pdb2fasta', max_pin="x.x") }}
 
 requirements:
   build:
diff --git a/recipes/pdb2fasta/pdb2fasta.patch b/recipes/pdb2fasta/pdb2fasta.patch
index d0cf696829648..b9182ba172719 100644
--- a/recipes/pdb2fasta/pdb2fasta.patch
+++ b/recipes/pdb2fasta/pdb2fasta.patch
@@ -6,10 +6,10 @@ index 9642d03..9e8eef1 100644
 +#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");
@@ -19,7 +19,7 @@ index 9642d03..9e8eef1 100644
 +        printf("    Convert PDB file pdb.pdb to FASTA sequence file seq.fasta\n");
          return argc;
      }
--
+-    
 -    int i;
 -    for (i=1;i<argc;i++){
 +

From f81d123b39fcd03243c663a265f0d67a57161123 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ant=C3=B4nio=20Camargo?=
 <apcamargo@users.noreply.github.com>
Date: Tue, 24 Dec 2024 04:11:33 -0800
Subject: [PATCH 8/8] Update compiler

---
 recipes/pdb2fasta/meta.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/recipes/pdb2fasta/meta.yaml b/recipes/pdb2fasta/meta.yaml
index ac2cbe54733d3..593a3eadf9376 100644
--- a/recipes/pdb2fasta/meta.yaml
+++ b/recipes/pdb2fasta/meta.yaml
@@ -18,7 +18,7 @@ build:
 
 requirements:
   build:
-    - {{ compiler('cxx') }}
+    - {{ compiler('c') }}
 
 test:
   commands: