Revert "sci-biology/cmdock: remove unused patches"

This reverts commit 1298cd25348ad37dac19c0838415436a8c18d3f5.

Signed-off-by: Anna (cybertailor) Vyalkova <cyber+gentoo@sysrq.in>

4 files changed, 85 insertions, 0 deletions

diff --git a/sci-biology/cmdock/files/app_info_0.1.4.xml b/sci-biology/cmdock/files/app_info_0.1.4.xml
new file mode 100644
index 000000000..923a7b9ac
--- /dev/null
+++ b/sci-biology/cmdock/files/app_info_0.1.4.xml
@@ -0,0 +1,40 @@
+<app_info>
+<app>
+	<name>cmdock-boinc-zcp</name>
+	<user_friendly_name>CurieMarieDock on BOINC + zipped input, checkpoints and progress bar</user_friendly_name>
+</app>
+
+<file_info>
+	<name>cmdock-boinc-zcp_wrapper_@PV@</name>
+	<sticky/>
+	<executable/>
+</file_info>
+
+<file_info>
+	<name>cmdock-boinc-zcp_job_@PV@.xml</name>
+	<sticky/>
+</file_info>
+<file_info>
+	<name>docking_out.sd</name>
+	<sticky/>
+</file_info>
+
+<app_version>
+	<app_name>cmdock-boinc-zcp</app_name>
+	<version_num>200</version_num>
+	<file_ref>
+		<file_name>cmdock-boinc-zcp_wrapper_@PV@</file_name>
+		<main_program/>
+	</file_ref>
+	<file_ref>
+		<file_name>cmdock-boinc-zcp_job_@PV@.xml</file_name>
+		<open_name>job.xml</open_name>
+		<copy_file/>
+	</file_ref>
+	<file_ref>
+		<file_name>docking_out</file_name>
+		<open_name>docking_out</open_name>
+		<copy_file/>
+	</file_ref>
+</app_version>
+</app_info>
diff --git a/sci-biology/cmdock/files/cmdock-0.1.4-fix-detection.patch b/sci-biology/cmdock/files/cmdock-0.1.4-fix-detection.patch
new file mode 100644
index 000000000..fceae1e5c
--- /dev/null
+++ b/sci-biology/cmdock/files/cmdock-0.1.4-fix-detection.patch
@@ -0,0 +1,15 @@
+--- a/meson.build
++++ b/meson.build
+@@ -79,8 +79,10 @@
+ 
+ cpp_compiler = meson.get_compiler('cpp')
+ 
+-extended_encoders_available = (cpp_compiler.has_header('emmintrin.h') and
+-    host_machine.cpu_family() == 'x86' and host_machine.cpu_family() == 'x86_64')
++extended_encoders_available = (
++    cpp_compiler.has_header('emmintrin.h') and
++    (host_machine.cpu_family() == 'x86' or host_machine.cpu_family() == 'x86_64')
++)
+ 
+ if not extended_encoders_available
+   add_project_arguments('-DBUNDLE_NO_SSE', language: 'cpp')
diff --git a/sci-biology/cmdock/files/cmdock-boinc-zcp_job_0.1.4.xml b/sci-biology/cmdock/files/cmdock-boinc-zcp_job_0.1.4.xml
new file mode 100644
index 000000000..074bb29d4
--- /dev/null
+++ b/sci-biology/cmdock/files/cmdock-boinc-zcp_job_0.1.4.xml
@@ -0,0 +1,15 @@
+<job_desc>
+	<task>
+		<application>@PREFIX@/build/cmdock</application>
+		<stdout_filename>docking_log</stdout_filename>
+		<command_line>-c -j 1 -r target.prm -p @PREFIX@/data/scripts/dock.prm -f htvs.ptc -i ligands.sdf -o docking_out</command_line>
+		<checkpoint_filename>docking_out.chk</checkpoint_filename>
+		<fraction_done_filename>docking_out.progress</fraction_done_filename>
+		<setenv>CMDOCK_ROOT=@PREFIX@</setenv>
+		<setenv>LD_LIBRARY_PATH=@PREFIX@/build:$LD_LIBRARY_PATH</setenv>
+		<setenv>PERL5LIB=@PREFIX@/lib:$PERL5LIB</setenv>
+	</task>
+	<unzip_input>
+		<zipfilename>ligands.zip</zipfilename>
+	</unzip_input>
+</job_desc>
diff --git a/sci-biology/cmdock/files/cmdock-l_job_0.2.0.xml b/sci-biology/cmdock/files/cmdock-l_job_0.2.0.xml
new file mode 100644
index 000000000..a163eb29c
--- /dev/null
+++ b/sci-biology/cmdock/files/cmdock-l_job_0.2.0.xml
@@ -0,0 +1,15 @@
+<job_desc>
+	<task>
+		<application>cmdock</application>
+		<stdout_filename>docking_log</stdout_filename>
+		<command_line>-c -j 1 -b 1 -x -r target.prm -p "@PREFIX@/data/scripts/dock.prm" -f htvs.ptc -i ligands.sdf -o docking_out</command_line>
+		<checkpoint_filename>docking_out.chk</checkpoint_filename>
+		<fraction_done_filename>docking_out.progress</fraction_done_filename>
+		<setenv>CMDOCK_ROOT=@PREFIX@</setenv>
+		<setenv>LD_LIBRARY_PATH=@PREFIX@/lib:$LD_LIBRARY_PATH</setenv>
+		<setenv>PERL5LIB=@PREFIX@/lib:$PERL5LIB</setenv>
+	</task>
+	<unzip_input>
+		<zipfilename>ligands.zip</zipfilename>
+	</unzip_input>
+</job_desc>