Merge branch 'develop' into extpkg_0112

CueMol · Jan 12, 2025 · 1f08514 · 1f08514
2 parents e1fd23c + aef7016
commit 1f08514
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Showing 5 changed files with 78 additions and 13 deletions.
diff --git a/build_scripts/build_libcuemol2_posix/run.sh b/build_scripts/build_libcuemol2_posix/run.sh
@@ -4,11 +4,19 @@
 # usage: run.sh deplibs_dir [Debug]
 #
 
+usage()
+{
+    echo "usage: run.sh deplibs_dir [Debug]"
+    exit 1
+}
+
+if [ -z "${1:-}" ]; then
+   usage
+fi
+
 set -eux
 
 BASEDIR=$1
-# RUNNER_OS=$2
-# RUNNER_ARCH=$3
 
 REPOS_DIR=$(cd $(dirname $0)/../..; pwd)
 WORKSPACE=${GITHUB_WORKSPACE:-$REPOS_DIR}

diff --git a/build_scripts/build_libcuemol2_win.bat b/build_scripts/build_libcuemol2_win.bat
@@ -10,6 +10,16 @@ SET RUNNER_OS=Windows
 SET RUNNER_ARCH=X64
 SET TMPDIR=%BASEDIR%\tmp
 
+SET SCRIPT_DIR=%~dp0
+echo SCRIPT_DIR: %SCRIPT_DIR%
+if "%GITHUB_WORKSPACE%"=="" (
+   cd %SCRIPT_DIR%\..
+   for /f %%i in ('cd') do set TOP_DIR=%%i
+) ELSE (
+   SET TOP_DIR=%GITHUB_WORKSPACE%
+)
+echo TOP_DIR: %TOP_DIR%
+
 mkdir %TMPDIR%
 %~d1
 cd %TMPDIR%
@@ -25,7 +35,7 @@ REM Build libcuemol2
 SET INSTPATH=%DEPLIBS_DIR%\cuemol2
 rd /s /q build
 
-cmake -S %GITHUB_WORKSPACE% -B build ^
+cmake -S %TOP_DIR% -B build ^
  -DCMAKE_INSTALL_PREFIX=%INSTPATH% ^
  -DBoost_ROOT=%DEPLIBS_DIR%\boost_1_84_0 ^
  -DCGAL_ROOT=%DEPLIBS_DIR%\CGAL-4.14.3 ^

diff --git a/build_scripts/build_uxpgui_posix/run.sh b/build_scripts/build_uxpgui_posix/run.sh
@@ -5,6 +5,18 @@
 #  host_os ... macOS
 #  host_arch ... ARM64 X64
 
+usage()
+{
+    echo "usage: run.sh base_dir host_os host_arch"
+    echo "  host_os ... macOS"
+    echo "  host_arch ... ARM64 X64"
+    exit 1
+}
+
+if [ -z "${1:-}" ] || [ -z "${2:-}" ] || [ -z "${3:-}" ]; then
+   usage
+fi
+
 set -eux
 
 BASEDIR=$1

diff --git a/src/modules/importers/MmcifMolReader.cpp b/src/modules/importers/MmcifMolReader.cpp
@@ -430,10 +430,21 @@ void MmcifMolReader::readAtomLine()
     m_nBfac = findDataItem("B_iso_or_equiv");
 
     m_nAuthAtomID = findDataItem("auth_atom_id");
+    if (m_nAuthAtomID<0) {
+        LOG_DPRINTLN("mmCIF> Warning: auth_atom_id not found in _atom_site");
+    }
     m_nAuthCompID = findDataItem("auth_comp_id");
+    if (m_nAuthCompID<0) {
+        LOG_DPRINTLN("mmCIF> Warning: auth_comp_id not found in _atom_site");
+    }
     m_nAuthSeqID = findDataItem("auth_seq_id");
+    if (m_nAuthSeqID<0) {
+        LOG_DPRINTLN("mmCIF> Warning: auth_seq_id not found in _atom_site");
+    }
     m_nAuthAsymID = findDataItem("auth_asym_id");
-
+    if (m_nAuthAsymID<0) {
+        LOG_DPRINTLN("mmCIF> Warning: auth_asym_id not found in _atom_site");
+    }
     m_nModelID = findDataItem("pdbx_PDB_model_num");
 
     m_bLoopDefsOK = true;
@@ -458,25 +469,45 @@ void MmcifMolReader::readAtomLine()
 
   ElemID eleid = ElemSym::str2SymID(getToken(m_nTypeSymbol));
 
-  LString atomname1, atomname2;
+  LString atomname;
   if (m_nAuthAtomID>=0) {
-    atomname1 = getToken(m_nAuthAtomID);
-    if (atomname1.getAt(0)=='"')
-      atomname1 = atomname1.substr(1, atomname1.length()-2);
+    atomname = getToken(m_nAuthAtomID);
+  }
+  else if (m_nLabelAtomID>=0) {
+    atomname = getToken(m_nLabelAtomID);
+  }
+  else {
+    error("invalid mmCIF format, cannot get atom name (_atom_site.label_atom_id)");
+    return;
   }
-  if (m_nLabelAtomID>=0)
-    atomname2 = getToken(m_nLabelAtomID);
+  if (atomname.getAt(0)=='"')
+    atomname = atomname.substr(1, atomname.length()-2);
 
   LString resname1;
   if (m_nAuthCompID>=0) {
     resname1 = getToken(m_nAuthCompID);
   }
+  else if (m_nLabelCompID>=0) {
+    resname1 = getToken(m_nLabelCompID);
+  }
+  else {
+    error("invalid mmCIF format, cannot get residue name (_atom_site.label_comp_id)");
+    return;
+  }
 
   char confid = getConfID(m_nLabelAltID); //getToken(m_nLabelAltID);
 
   LString chain1;
-  if (m_nAuthAsymID>=0)
-    chain1 = getToken(m_nAuthAsymID);
+  if (m_nAuthAsymID>=0) {
+      chain1 = getToken(m_nAuthAsymID);
+  }
+  else if (m_nLabelAsymID>=0) {
+      chain1 = getToken(m_nLabelAsymID);
+  }
+  else {
+      error("invalid mmCIF format, cannot get chain name (_atom_site.label_asym_id)");
+      return;
+  }
 
   ResidIndex residx = getResidIndex(m_nAuthSeqID, m_nInsCode);
 
@@ -524,7 +555,7 @@ void MmcifMolReader::readAtomLine()
 
   MolAtomPtr pAtom = MolAtomPtr(MB_NEW MolAtom());
   pAtom->setParentUID(m_pMol->getUID());
-  pAtom->setName(atomname1);
+  pAtom->setName(atomname);
   pAtom->setElement(eleid);
   pAtom->setChainName(chain1);
   pAtom->setResIndex(residx);

diff --git a/uxp_gui/cuemol2/base/jar.mn b/uxp_gui/cuemol2/base/jar.mn
@@ -12,6 +12,10 @@ cuemol2.jar:
   content/cuemol2/cuemol2.css (content/cuemol2.css)
 #ifdef XP_MACOSX
   content/cuemol2/cuemol2-sysdep.css (content/macosx.css)
+#elif XP_WIN
+  content/cuemol2/cuemol2-sysdep.css (content/windows7.css)
+#elif MOZ_WIDGET_GTK
+  content/cuemol2/cuemol2-sysdep.css (content/gdk-x11.css)
 #endif
 #
 # Config Dialog