File: build-xyz-files.patch

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From: Debian Science Maintainers
 <debian-science-maintainers@lists.alioth.debian.org>
Date: Mon, 29 Sep 2025 16:11:15 +0200
Subject: build-xyz-files

lines added to build .xyz files from the original data
---
 src/acid_anhydrides/CMakeLists.txt      |  7 ++++
 src/alcohols/CMakeLists.txt             |  7 ++++
 src/aldehydes/CMakeLists.txt            |  7 ++++
 src/alkanes/CMakeLists.txt              |  7 ++++
 src/alkenes/CMakeLists.txt              |  7 ++++
 src/alkynes/CMakeLists.txt              |  7 ++++
 src/amides/CMakeLists.txt               |  7 ++++
 src/amines/CMakeLists.txt               |  7 ++++
 src/amino_acids/CMakeLists.txt          |  7 ++++
 src/aromatics/CMakeLists.txt            |  7 ++++
 src/carbamides/CMakeLists.txt           |  7 ++++
 src/carbohydrates/CMakeLists.txt        |  7 ++++
 src/carboxylic_acids/CMakeLists.txt     |  7 ++++
 src/drugs/CMakeLists.txt                |  7 ++++
 src/esters/CMakeLists.txt               |  7 ++++
 src/ethers/CMakeLists.txt               |  7 ++++
 src/fatty_acids/CMakeLists.txt          |  7 ++++
 src/haloalkanes/CMakeLists.txt          |  7 ++++
 src/heteroaromatics/CMakeLists.txt      |  7 ++++
 src/ketones/CMakeLists.txt              |  7 ++++
 src/macrocycles/CMakeLists.txt          |  7 ++++
 src/natural_products/CMakeLists.txt     |  7 ++++
 src/nitriles/CMakeLists.txt             |  7 ++++
 src/nitroalkanes/CMakeLists.txt         |  7 ++++
 src/nucleobases/CMakeLists.txt          |  7 ++++
 src/peptides/CMakeLists.txt             |  7 ++++
 src/polycyclic_alkanes/CMakeLists.txt   |  7 ++++
 src/polycyclic_aromatics/CMakeLists.txt |  7 ++++
 src/sulfones/CMakeLists.txt             |  7 ++++
 src/sulfoxides/CMakeLists.txt           |  7 ++++
 src/thioethers/CMakeLists.txt           |  7 ++++
 src/thiols/CMakeLists.txt               |  7 ++++
 src/water/CMakeLists.txt                |  7 ++++
 tools/cmlwriter.py                      | 73 +++++++++++++++++----------------
 34 files changed, 269 insertions(+), 35 deletions(-)

diff --git a/src/acid_anhydrides/CMakeLists.txt b/src/acid_anhydrides/CMakeLists.txt
index 7956e7b..229eaea 100644
--- a/src/acid_anhydrides/CMakeLists.txt
+++ b/src/acid_anhydrides/CMakeLists.txt
@@ -43,6 +43,13 @@ foreach(cml_SRC_FILE ${cml_SRCS})
                        WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
     )
     set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}")
+    # Generate xyz files
+    set(xyz_FILE "${cml_WE}.xyz")
+    add_custom_command(TARGET ${CHEM_GROUP}
+                       COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -oxyz ${xyz_FILE}
+                       WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+    )
+    set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${xyz_FILE}")
     # Generate smi files
     set(smi_FILE "${cml_WE}.smi")
     add_custom_command(TARGET ${CHEM_GROUP}
diff --git a/src/alcohols/CMakeLists.txt b/src/alcohols/CMakeLists.txt
index 834d31e..0cea058 100644
--- a/src/alcohols/CMakeLists.txt
+++ b/src/alcohols/CMakeLists.txt
@@ -43,6 +43,13 @@ foreach(cml_SRC_FILE ${cml_SRCS})
                        WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
     )
     set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}")
+    # Generate xyz files
+    set(xyz_FILE "${cml_WE}.xyz")
+    add_custom_command(TARGET ${CHEM_GROUP}
+                       COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -oxyz ${xyz_FILE}
+                       WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+    )
+    set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${xyz_FILE}")
     # Generate smi files
     set(smi_FILE "${cml_WE}.smi")
     add_custom_command(TARGET ${CHEM_GROUP}
diff --git a/src/aldehydes/CMakeLists.txt b/src/aldehydes/CMakeLists.txt
index e486d21..946358e 100644
--- a/src/aldehydes/CMakeLists.txt
+++ b/src/aldehydes/CMakeLists.txt
@@ -43,6 +43,13 @@ foreach(cml_SRC_FILE ${cml_SRCS})
                        WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
     )
     set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}")
+    # Generate xyz files
+    set(xyz_FILE "${cml_WE}.xyz")
+    add_custom_command(TARGET ${CHEM_GROUP}
+                       COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -oxyz ${xyz_FILE}
+                       WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+    )
+    set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${xyz_FILE}")
     # Generate smi files
     set(smi_FILE "${cml_WE}.smi")
     add_custom_command(TARGET ${CHEM_GROUP}
diff --git a/src/alkanes/CMakeLists.txt b/src/alkanes/CMakeLists.txt
index 531dfe2..e95036b 100644
--- a/src/alkanes/CMakeLists.txt
+++ b/src/alkanes/CMakeLists.txt
@@ -43,6 +43,13 @@ foreach(cml_SRC_FILE ${cml_SRCS})
                        WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
     )
     set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}")
+    # Generate xyz files
+    set(xyz_FILE "${cml_WE}.xyz")
+    add_custom_command(TARGET ${CHEM_GROUP}
+                       COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -oxyz ${xyz_FILE}
+                       WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+    )
+    set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${xyz_FILE}")
     # Generate smi files
     set(smi_FILE "${cml_WE}.smi")
     add_custom_command(TARGET ${CHEM_GROUP}
diff --git a/src/alkenes/CMakeLists.txt b/src/alkenes/CMakeLists.txt
index 36721c3..93d7e60 100644
--- a/src/alkenes/CMakeLists.txt
+++ b/src/alkenes/CMakeLists.txt
@@ -43,6 +43,13 @@ foreach(cml_SRC_FILE ${cml_SRCS})
                        WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
     )
     set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}")
+    # Generate xyz files
+    set(xyz_FILE "${cml_WE}.xyz")
+    add_custom_command(TARGET ${CHEM_GROUP}
+                       COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -oxyz ${xyz_FILE}
+                       WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+    )
+    set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${xyz_FILE}")
     # Generate smi files
     set(smi_FILE "${cml_WE}.smi")
     add_custom_command(TARGET ${CHEM_GROUP}
diff --git a/src/alkynes/CMakeLists.txt b/src/alkynes/CMakeLists.txt
index db0c0ea..a97c7d6 100644
--- a/src/alkynes/CMakeLists.txt
+++ b/src/alkynes/CMakeLists.txt
@@ -43,6 +43,13 @@ foreach(cml_SRC_FILE ${cml_SRCS})
                        WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
     )
     set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}")
+    # Generate xyz files
+    set(xyz_FILE "${cml_WE}.xyz")
+    add_custom_command(TARGET ${CHEM_GROUP}
+                       COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -oxyz ${xyz_FILE}
+                       WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+    )
+    set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${xyz_FILE}")
     # Generate smi files
     set(smi_FILE "${cml_WE}.smi")
     add_custom_command(TARGET ${CHEM_GROUP}
diff --git a/src/amides/CMakeLists.txt b/src/amides/CMakeLists.txt
index 609c2c8..0626309 100644
--- a/src/amides/CMakeLists.txt
+++ b/src/amides/CMakeLists.txt
@@ -43,6 +43,13 @@ foreach(cml_SRC_FILE ${cml_SRCS})
                        WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
     )
     set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}")
+    # Generate xyz files
+    set(xyz_FILE "${cml_WE}.xyz")
+    add_custom_command(TARGET ${CHEM_GROUP}
+                       COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -oxyz ${xyz_FILE}
+                       WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+    )
+    set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${xyz_FILE}")
     # Generate smi files
     set(smi_FILE "${cml_WE}.smi")
     add_custom_command(TARGET ${CHEM_GROUP}
diff --git a/src/amines/CMakeLists.txt b/src/amines/CMakeLists.txt
index cc88c5c..992138c 100644
--- a/src/amines/CMakeLists.txt
+++ b/src/amines/CMakeLists.txt
@@ -43,6 +43,13 @@ foreach(cml_SRC_FILE ${cml_SRCS})
                        WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
     )
     set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}")
+    # Generate xyz files
+    set(xyz_FILE "${cml_WE}.xyz")
+    add_custom_command(TARGET ${CHEM_GROUP}
+                       COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -oxyz ${xyz_FILE}
+                       WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+    )
+    set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${xyz_FILE}")
     # Generate smi files
     set(smi_FILE "${cml_WE}.smi")
     add_custom_command(TARGET ${CHEM_GROUP}
diff --git a/src/amino_acids/CMakeLists.txt b/src/amino_acids/CMakeLists.txt
index 2ed845a..3ae358d 100644
--- a/src/amino_acids/CMakeLists.txt
+++ b/src/amino_acids/CMakeLists.txt
@@ -43,6 +43,13 @@ foreach(cml_SRC_FILE ${cml_SRCS})
                        WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
     )
     set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}")
+    # Generate xyz files
+    set(xyz_FILE "${cml_WE}.xyz")
+    add_custom_command(TARGET ${CHEM_GROUP}
+                       COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -oxyz ${xyz_FILE}
+                       WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+    )
+    set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${xyz_FILE}")
     # Generate smi files
     set(smi_FILE "${cml_WE}.smi")
     add_custom_command(TARGET ${CHEM_GROUP}
diff --git a/src/aromatics/CMakeLists.txt b/src/aromatics/CMakeLists.txt
index 3e894ad..037a532 100644
--- a/src/aromatics/CMakeLists.txt
+++ b/src/aromatics/CMakeLists.txt
@@ -43,6 +43,13 @@ foreach(cml_SRC_FILE ${cml_SRCS})
                        WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
     )
     set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}")
+    # Generate xyz files
+    set(xyz_FILE "${cml_WE}.xyz")
+    add_custom_command(TARGET ${CHEM_GROUP}
+                       COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -oxyz ${xyz_FILE}
+                       WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+    )
+    set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${xyz_FILE}")
     # Generate smi files
     set(smi_FILE "${cml_WE}.smi")
     add_custom_command(TARGET ${CHEM_GROUP}
diff --git a/src/carbamides/CMakeLists.txt b/src/carbamides/CMakeLists.txt
index 9b0830a..c23ffd4 100644
--- a/src/carbamides/CMakeLists.txt
+++ b/src/carbamides/CMakeLists.txt
@@ -43,6 +43,13 @@ foreach(cml_SRC_FILE ${cml_SRCS})
                        WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
     )
     set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}")
+    # Generate xyz files
+    set(xyz_FILE "${cml_WE}.xyz")
+    add_custom_command(TARGET ${CHEM_GROUP}
+                       COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -oxyz ${xyz_FILE}
+                       WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+    )
+    set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${xyz_FILE}")
     # Generate smi files
     set(smi_FILE "${cml_WE}.smi")
     add_custom_command(TARGET ${CHEM_GROUP}
diff --git a/src/carbohydrates/CMakeLists.txt b/src/carbohydrates/CMakeLists.txt
index ad5518f..63c001d 100644
--- a/src/carbohydrates/CMakeLists.txt
+++ b/src/carbohydrates/CMakeLists.txt
@@ -43,6 +43,13 @@ foreach(cml_SRC_FILE ${cml_SRCS})
                        WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
     )
     set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}")
+    # Generate xyz files
+    set(xyz_FILE "${cml_WE}.xyz")
+    add_custom_command(TARGET ${CHEM_GROUP}
+                       COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -oxyz ${xyz_FILE}
+                       WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+    )
+    set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${xyz_FILE}")
     # Generate smi files
     set(smi_FILE "${cml_WE}.smi")
     add_custom_command(TARGET ${CHEM_GROUP}
diff --git a/src/carboxylic_acids/CMakeLists.txt b/src/carboxylic_acids/CMakeLists.txt
index f0bcc29..79d71d7 100644
--- a/src/carboxylic_acids/CMakeLists.txt
+++ b/src/carboxylic_acids/CMakeLists.txt
@@ -43,6 +43,13 @@ foreach(cml_SRC_FILE ${cml_SRCS})
                        WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
     )
     set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}")
+    # Generate xyz files
+    set(xyz_FILE "${cml_WE}.xyz")
+    add_custom_command(TARGET ${CHEM_GROUP}
+                       COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -oxyz ${xyz_FILE}
+                       WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+    )
+    set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${xyz_FILE}")
     # Generate smi files
     set(smi_FILE "${cml_WE}.smi")
     add_custom_command(TARGET ${CHEM_GROUP}
diff --git a/src/drugs/CMakeLists.txt b/src/drugs/CMakeLists.txt
index b83a77d..ff93418 100644
--- a/src/drugs/CMakeLists.txt
+++ b/src/drugs/CMakeLists.txt
@@ -43,6 +43,13 @@ foreach(cml_SRC_FILE ${cml_SRCS})
                        WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
     )
     set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}")
+    # Generate xyz files
+    set(xyz_FILE "${cml_WE}.xyz")
+    add_custom_command(TARGET ${CHEM_GROUP}
+                       COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -oxyz ${xyz_FILE}
+                       WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+    )
+    set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${xyz_FILE}")
     # Generate smi files
     set(smi_FILE "${cml_WE}.smi")
     add_custom_command(TARGET ${CHEM_GROUP}
diff --git a/src/esters/CMakeLists.txt b/src/esters/CMakeLists.txt
index eed8b17..e210d2c 100644
--- a/src/esters/CMakeLists.txt
+++ b/src/esters/CMakeLists.txt
@@ -43,6 +43,13 @@ foreach(cml_SRC_FILE ${cml_SRCS})
                        WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
     )
     set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}")
+    # Generate xyz files
+    set(xyz_FILE "${cml_WE}.xyz")
+    add_custom_command(TARGET ${CHEM_GROUP}
+                       COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -oxyz ${xyz_FILE}
+                       WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+    )
+    set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${xyz_FILE}")
     # Generate smi files
     set(smi_FILE "${cml_WE}.smi")
     add_custom_command(TARGET ${CHEM_GROUP}
diff --git a/src/ethers/CMakeLists.txt b/src/ethers/CMakeLists.txt
index 24b1a21..96dd396 100644
--- a/src/ethers/CMakeLists.txt
+++ b/src/ethers/CMakeLists.txt
@@ -43,6 +43,13 @@ foreach(cml_SRC_FILE ${cml_SRCS})
                        WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
     )
     set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}")
+    # Generate xyz files
+    set(xyz_FILE "${cml_WE}.xyz")
+    add_custom_command(TARGET ${CHEM_GROUP}
+                       COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -oxyz ${xyz_FILE}
+                       WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+    )
+    set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${xyz_FILE}")
     # Generate smi files
     set(smi_FILE "${cml_WE}.smi")
     add_custom_command(TARGET ${CHEM_GROUP}
diff --git a/src/fatty_acids/CMakeLists.txt b/src/fatty_acids/CMakeLists.txt
index 4fcb342..81c85ec 100644
--- a/src/fatty_acids/CMakeLists.txt
+++ b/src/fatty_acids/CMakeLists.txt
@@ -43,6 +43,13 @@ foreach(cml_SRC_FILE ${cml_SRCS})
                        WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
     )
     set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}")
+    # Generate xyz files
+    set(xyz_FILE "${cml_WE}.xyz")
+    add_custom_command(TARGET ${CHEM_GROUP}
+                       COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -oxyz ${xyz_FILE}
+                       WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+    )
+    set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${xyz_FILE}")
     # Generate smi files
     set(smi_FILE "${cml_WE}.smi")
     add_custom_command(TARGET ${CHEM_GROUP}
diff --git a/src/haloalkanes/CMakeLists.txt b/src/haloalkanes/CMakeLists.txt
index 221945a..b208b4d 100644
--- a/src/haloalkanes/CMakeLists.txt
+++ b/src/haloalkanes/CMakeLists.txt
@@ -43,6 +43,13 @@ foreach(cml_SRC_FILE ${cml_SRCS})
                        WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
     )
     set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}")
+    # Generate xyz files
+    set(xyz_FILE "${cml_WE}.xyz")
+    add_custom_command(TARGET ${CHEM_GROUP}
+                       COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -oxyz ${xyz_FILE}
+                       WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+    )
+    set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${xyz_FILE}")
     # Generate smi files
     set(smi_FILE "${cml_WE}.smi")
     add_custom_command(TARGET ${CHEM_GROUP}
diff --git a/src/heteroaromatics/CMakeLists.txt b/src/heteroaromatics/CMakeLists.txt
index b6235b9..e2f5a48 100644
--- a/src/heteroaromatics/CMakeLists.txt
+++ b/src/heteroaromatics/CMakeLists.txt
@@ -43,6 +43,13 @@ foreach(cml_SRC_FILE ${cml_SRCS})
                        WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
     )
     set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}")
+    # Generate xyz files
+    set(xyz_FILE "${cml_WE}.xyz")
+    add_custom_command(TARGET ${CHEM_GROUP}
+                       COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -oxyz ${xyz_FILE}
+                       WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+    )
+    set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${xyz_FILE}")
     # Generate smi files
     set(smi_FILE "${cml_WE}.smi")
     add_custom_command(TARGET ${CHEM_GROUP}
diff --git a/src/ketones/CMakeLists.txt b/src/ketones/CMakeLists.txt
index 4fb8227..2b3d41c 100644
--- a/src/ketones/CMakeLists.txt
+++ b/src/ketones/CMakeLists.txt
@@ -43,6 +43,13 @@ foreach(cml_SRC_FILE ${cml_SRCS})
                        WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
     )
     set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}")
+    # Generate xyz files
+    set(xyz_FILE "${cml_WE}.xyz")
+    add_custom_command(TARGET ${CHEM_GROUP}
+                       COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -oxyz ${xyz_FILE}
+                       WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+    )
+    set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${xyz_FILE}")
     # Generate smi files
     set(smi_FILE "${cml_WE}.smi")
     add_custom_command(TARGET ${CHEM_GROUP}
diff --git a/src/macrocycles/CMakeLists.txt b/src/macrocycles/CMakeLists.txt
index be8af2e..e6c0b2b 100644
--- a/src/macrocycles/CMakeLists.txt
+++ b/src/macrocycles/CMakeLists.txt
@@ -43,6 +43,13 @@ foreach(cml_SRC_FILE ${cml_SRCS})
                        WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
     )
     set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}")
+    # Generate xyz files
+    set(xyz_FILE "${cml_WE}.xyz")
+    add_custom_command(TARGET ${CHEM_GROUP}
+                       COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -oxyz ${xyz_FILE}
+                       WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+    )
+    set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${xyz_FILE}")
     # Generate smi files
     set(smi_FILE "${cml_WE}.smi")
     add_custom_command(TARGET ${CHEM_GROUP}
diff --git a/src/natural_products/CMakeLists.txt b/src/natural_products/CMakeLists.txt
index cdd12d2..1fce7ef 100644
--- a/src/natural_products/CMakeLists.txt
+++ b/src/natural_products/CMakeLists.txt
@@ -43,6 +43,13 @@ foreach(cml_SRC_FILE ${cml_SRCS})
                        WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
     )
     set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}")
+    # Generate xyz files
+    set(xyz_FILE "${cml_WE}.xyz")
+    add_custom_command(TARGET ${CHEM_GROUP}
+                       COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -oxyz ${xyz_FILE}
+                       WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+    )
+    set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${xyz_FILE}")
     # Generate smi files
     set(smi_FILE "${cml_WE}.smi")
     add_custom_command(TARGET ${CHEM_GROUP}
diff --git a/src/nitriles/CMakeLists.txt b/src/nitriles/CMakeLists.txt
index 8d4894f..401e611 100644
--- a/src/nitriles/CMakeLists.txt
+++ b/src/nitriles/CMakeLists.txt
@@ -43,6 +43,13 @@ foreach(cml_SRC_FILE ${cml_SRCS})
                        WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
     )
     set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}")
+    # Generate xyz files
+    set(xyz_FILE "${cml_WE}.xyz")
+    add_custom_command(TARGET ${CHEM_GROUP}
+                       COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -oxyz ${xyz_FILE}
+                       WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+    )
+    set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${xyz_FILE}")
     # Generate smi files
     set(smi_FILE "${cml_WE}.smi")
     add_custom_command(TARGET ${CHEM_GROUP}
diff --git a/src/nitroalkanes/CMakeLists.txt b/src/nitroalkanes/CMakeLists.txt
index 2dc73eb..9cafe18 100644
--- a/src/nitroalkanes/CMakeLists.txt
+++ b/src/nitroalkanes/CMakeLists.txt
@@ -43,6 +43,13 @@ foreach(cml_SRC_FILE ${cml_SRCS})
                        WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
     )
     set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}")
+    # Generate xyz files
+    set(xyz_FILE "${cml_WE}.xyz")
+    add_custom_command(TARGET ${CHEM_GROUP}
+                       COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -oxyz ${xyz_FILE}
+                       WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+    )
+    set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${xyz_FILE}")
     # Generate smi files
     set(smi_FILE "${cml_WE}.smi")
     add_custom_command(TARGET ${CHEM_GROUP}
diff --git a/src/nucleobases/CMakeLists.txt b/src/nucleobases/CMakeLists.txt
index a311af3..329d7c8 100644
--- a/src/nucleobases/CMakeLists.txt
+++ b/src/nucleobases/CMakeLists.txt
@@ -43,6 +43,13 @@ foreach(cml_SRC_FILE ${cml_SRCS})
                        WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
     )
     set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}")
+    # Generate xyz files
+    set(xyz_FILE "${cml_WE}.xyz")
+    add_custom_command(TARGET ${CHEM_GROUP}
+                       COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -oxyz ${xyz_FILE}
+                       WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+    )
+    set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${xyz_FILE}")
     # Generate smi files
     set(smi_FILE "${cml_WE}.smi")
     add_custom_command(TARGET ${CHEM_GROUP}
diff --git a/src/peptides/CMakeLists.txt b/src/peptides/CMakeLists.txt
index a7737b8..1eaa1ba 100644
--- a/src/peptides/CMakeLists.txt
+++ b/src/peptides/CMakeLists.txt
@@ -43,6 +43,13 @@ foreach(cml_SRC_FILE ${cml_SRCS})
                        WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
     )
     set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}")
+    # Generate xyz files
+    set(xyz_FILE "${cml_WE}.xyz")
+    add_custom_command(TARGET ${CHEM_GROUP}
+                       COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -oxyz ${xyz_FILE}
+                       WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+    )
+    set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${xyz_FILE}")
     # Generate smi files
     set(smi_FILE "${cml_WE}.smi")
     add_custom_command(TARGET ${CHEM_GROUP}
diff --git a/src/polycyclic_alkanes/CMakeLists.txt b/src/polycyclic_alkanes/CMakeLists.txt
index a2cc739..4d4589f 100644
--- a/src/polycyclic_alkanes/CMakeLists.txt
+++ b/src/polycyclic_alkanes/CMakeLists.txt
@@ -43,6 +43,13 @@ foreach(cml_SRC_FILE ${cml_SRCS})
                        WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
     )
     set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}")
+    # Generate xyz files
+    set(xyz_FILE "${cml_WE}.xyz")
+    add_custom_command(TARGET ${CHEM_GROUP}
+                       COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -oxyz ${xyz_FILE}
+                       WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+    )
+    set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${xyz_FILE}")
     # Generate smi files
     set(smi_FILE "${cml_WE}.smi")
     add_custom_command(TARGET ${CHEM_GROUP}
diff --git a/src/polycyclic_aromatics/CMakeLists.txt b/src/polycyclic_aromatics/CMakeLists.txt
index b05d24e..8756f53 100644
--- a/src/polycyclic_aromatics/CMakeLists.txt
+++ b/src/polycyclic_aromatics/CMakeLists.txt
@@ -43,6 +43,13 @@ foreach(cml_SRC_FILE ${cml_SRCS})
                        WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
     )
     set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}")
+    # Generate xyz files
+    set(xyz_FILE "${cml_WE}.xyz")
+    add_custom_command(TARGET ${CHEM_GROUP}
+                       COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -oxyz ${xyz_FILE}
+                       WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+    )
+    set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${xyz_FILE}")
     # Generate smi files
     set(smi_FILE "${cml_WE}.smi")
     add_custom_command(TARGET ${CHEM_GROUP}
diff --git a/src/sulfones/CMakeLists.txt b/src/sulfones/CMakeLists.txt
index 97b2e6d..fb95770 100644
--- a/src/sulfones/CMakeLists.txt
+++ b/src/sulfones/CMakeLists.txt
@@ -43,6 +43,13 @@ foreach(cml_SRC_FILE ${cml_SRCS})
                        WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
     )
     set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}")
+    # Generate xyz files
+    set(xyz_FILE "${cml_WE}.xyz")
+    add_custom_command(TARGET ${CHEM_GROUP}
+                       COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -oxyz ${xyz_FILE}
+                       WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+    )
+    set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${xyz_FILE}")
     # Generate smi files
     set(smi_FILE "${cml_WE}.smi")
     add_custom_command(TARGET ${CHEM_GROUP}
diff --git a/src/sulfoxides/CMakeLists.txt b/src/sulfoxides/CMakeLists.txt
index 3191e0a..56a1791 100644
--- a/src/sulfoxides/CMakeLists.txt
+++ b/src/sulfoxides/CMakeLists.txt
@@ -43,6 +43,13 @@ foreach(cml_SRC_FILE ${cml_SRCS})
                        WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
     )
     set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}")
+    # Generate xyz files
+    set(xyz_FILE "${cml_WE}.xyz")
+    add_custom_command(TARGET ${CHEM_GROUP}
+                       COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -oxyz ${xyz_FILE}
+                       WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+    )
+    set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${xyz_FILE}")
     # Generate smi files
     set(smi_FILE "${cml_WE}.smi")
     add_custom_command(TARGET ${CHEM_GROUP}
diff --git a/src/thioethers/CMakeLists.txt b/src/thioethers/CMakeLists.txt
index 149c9cb..557f274 100644
--- a/src/thioethers/CMakeLists.txt
+++ b/src/thioethers/CMakeLists.txt
@@ -43,6 +43,13 @@ foreach(cml_SRC_FILE ${cml_SRCS})
                        WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
     )
     set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}")
+    # Generate xyz files
+    set(xyz_FILE "${cml_WE}.xyz")
+    add_custom_command(TARGET ${CHEM_GROUP}
+                       COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -oxyz ${xyz_FILE}
+                       WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+    )
+    set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${xyz_FILE}")
     # Generate smi files
     set(smi_FILE "${cml_WE}.smi")
     add_custom_command(TARGET ${CHEM_GROUP}
diff --git a/src/thiols/CMakeLists.txt b/src/thiols/CMakeLists.txt
index bc41e5f..d8e5415 100644
--- a/src/thiols/CMakeLists.txt
+++ b/src/thiols/CMakeLists.txt
@@ -43,6 +43,13 @@ foreach(cml_SRC_FILE ${cml_SRCS})
                        WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
     )
     set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}")
+    # Generate xyz files
+    set(xyz_FILE "${cml_WE}.xyz")
+    add_custom_command(TARGET ${CHEM_GROUP}
+                       COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -oxyz ${xyz_FILE}
+                       WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+    )
+    set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${xyz_FILE}")
     # Generate smi files
     set(smi_FILE "${cml_WE}.smi")
     add_custom_command(TARGET ${CHEM_GROUP}
diff --git a/src/water/CMakeLists.txt b/src/water/CMakeLists.txt
index 4e6b19b..2bfb510 100644
--- a/src/water/CMakeLists.txt
+++ b/src/water/CMakeLists.txt
@@ -43,6 +43,13 @@ foreach(cml_SRC_FILE ${cml_SRCS})
                        WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
     )
     set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}")
+    # Generate xyz files
+    set(xyz_FILE "${cml_WE}.xyz")
+    add_custom_command(TARGET ${CHEM_GROUP}
+                       COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -oxyz ${xyz_FILE}
+                       WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+    )
+    set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${xyz_FILE}")
     # Generate smi files
     set(smi_FILE "${cml_WE}.smi")
     add_custom_command(TARGET ${CHEM_GROUP}
diff --git a/tools/cmlwriter.py b/tools/cmlwriter.py
index 2bb52be..6a04f09 100644
--- a/tools/cmlwriter.py
+++ b/tools/cmlwriter.py
@@ -13,7 +13,7 @@ class CMLWriter:
     """
     def __init__(self, fout, cml_handler, l10n_handler):
         """Creates an instance of the CMLWriter class.
-	"""
+        """
         self.fout = fout
         self.cml = cml_handler
         self.l10n = l10n_handler
@@ -100,7 +100,7 @@ class CMLWriter:
 
     def parseFormula(self, raw_formula):
         """Parse formula and return the HTML formula
-	"""
+        """
         formula = raw_formula.strip()
         formula_ar = formula.split(" ")
         formula = ""
@@ -111,7 +111,7 @@ class CMLWriter:
                 idx += 1
             elif idx % 2: # we are in the multiple section"
                 formula += "<sub>" + i + "</sub>"
-		idx += 1
+                idx += 1
             else: # we are in the element section
                 formula += i
                 idx += 1
@@ -125,6 +125,7 @@ class CMLWriter:
 
         cml_file = entry_details.path + '.cml'
         mol_file = entry_details.path + '.mol'
+        xyz_file = entry_details.path + '.xyz'
         smi_file = entry_details.path + '.smi'
         smiles =  ""
         if os.path.isfile(smi_file):
@@ -175,41 +176,41 @@ class CMLWriter:
             else:
                 bpK = str(int(self.cml.bp) + 273)
             xhtmlout.addBody('            <li>' + self.l10n.translate('Boiling point: ', lang) + self.cml.bp  + ' &deg;C (' + bpK + ' K)</li>')
-	#########################################################
-	# Writing synonyms
-	#
-	# Write only if synonyms (localized or english) are
-	# available
-	#########################################################
-	if entry_details.synDict.has_key(lang):
-	    if len(entry_details.synDict[lang]) == 1:
+        #########################################################
+        # Writing synonyms
+        #
+        # Write only if synonyms (localized or english) are
+        # available
+        #########################################################
+        if entry_details.synDict.has_key(lang):
+            if len(entry_details.synDict[lang]) == 1:
                 xhtmlout.addBody('            <li>' + self.l10n.translate('Synonym:', lang) )
-	    else:
+            else:
                 xhtmlout.addBody('            <li>' + self.l10n.translate('Synonyms:', lang) )
             xhtmlout.addBody('              <ul>')
             for synonym in entry_details.synDict[lang]:
                 xhtmlout.addBody('                <li>' + synonym + '</li>')
             xhtmlout.addBody('              </ul>')
             xhtmlout.addBody('            </li>')
-	elif entry_details.synDict.has_key('en'):
-	    if len(entry_details.synDict['en']) == 1:
+        elif entry_details.synDict.has_key('en'):
+            if len(entry_details.synDict['en']) == 1:
                 xhtmlout.addBody('            <li>' + self.l10n.translate('Synonym:', lang) )
-	    else:
+            else:
                 xhtmlout.addBody('            <li>' + self.l10n.translate('Synonyms:', lang) )
             xhtmlout.addBody('              <ul>')
             for synonym in entry_details.synDict['en']:
                 xhtmlout.addBody('                <li>' + synonym + ' (<i>en</i>)</li>')
             xhtmlout.addBody('              </ul>')
             xhtmlout.addBody('            </li>')
-	#########################################################
-	# Writing abbreviations 
-	#
-	# Write only if abbreviations are available
-	#########################################################
-	if len(entry_details.abbreviation):
-	    if len(entry_details.abbreviation) == 1:
+        #########################################################
+        # Writing abbreviations
+        #
+        # Write only if abbreviations are available
+        #########################################################
+        if len(entry_details.abbreviation):
+            if len(entry_details.abbreviation) == 1:
                 xhtmlout.addBody('            <li>' + self.l10n.translate('Abbreviation:', lang) )
-	    else:
+            else:
                 xhtmlout.addBody('            <li>' + self.l10n.translate('Abbreviations:', lang) )
             xhtmlout.addBody('              <ul>')
             for abbreviation in entry_details.abbreviation:
@@ -232,32 +233,34 @@ class CMLWriter:
         xhtmlout.addBody('            <li>' + self.l10n.translate('In CML format', lang) + '&nbsp;<a href="' + cml_file + '" title="CML"><img src="' + '../'*level + 'images/download.png" alt="Download cml file" /></a></li>')
         if os.path.isfile(mol_file):
             xhtmlout.addBody('            <li>' + self.l10n.translate('In MOL format', lang) + '&nbsp;<a href="' + mol_file + '" title="MOL"><img src="' + '../'*level + 'images/download.png" alt="Download mol file" /></a></li>')
+        if os.path.isfile(xyz_file):
+            xhtmlout.addBody('            <li>' + self.l10n.translate('In XYZ format', lang) + '&nbsp;<a href="' + xyz_file + '" title="XYZ"><img src="' + '../'*level + 'images/download.png" alt="Download xyz file" /></a></li>')
         xhtmlout.addBody('            <li>' + self.l10n.translate('Other formats', lang) + '&nbsp;'+self.selection+'</li>')
         xhtmlout.addBody('          </ul>')
         xhtmlout.addBody('        </div>')
         xhtmlout.addBody('        <div id="inchi">')
         xhtmlout.addBody('          <h3>' + self.l10n.translate('InChI', lang) + '</h3>')
-	if len(self.cml.inchi) > 80:
-	    htmlinchi = ""
-	    size = int(len(self.cml.inchi)/80)
-	    for i in range(0,size):
-	        htmlinchi += self.cml.inchi[i*80:(i+1)*80] + "<br />\n"
+        if len(self.cml.inchi) > 80:
+            htmlinchi = ""
+            size = int(len(self.cml.inchi)/80)
+            for i in range(0,size):
+                htmlinchi += self.cml.inchi[i*80:(i+1)*80] + "<br />\n"
             htmlinchi += self.cml.inchi[size*80:len(self.cml.inchi)]
-	else:
-	    htmlinchi = self.cml.inchi
+        else:
+            htmlinchi = self.cml.inchi
         xhtmlout.addBody('          <span class="inchi">' + htmlinchi + '</span>')
         xhtmlout.addBody('        </div>')
         if smiles:
             xhtmlout.addBody('        <div id="smiles">')
             xhtmlout.addBody('          <h3>' +  self.l10n.translate('SMILES', lang) + '</h3>')
             if len(smiles) > 80:
-	        htmlsmiles = ""
-  	        size = int(len(smiles)/80)
- 	        for i in range(0,size):
-	            htmlsmiles += smiles[i*80:(i+1)*80] + "<br />\n"
+                htmlsmiles = ""
+                size = int(len(smiles)/80)
+                for i in range(0,size):
+                    htmlsmiles += smiles[i*80:(i+1)*80] + "<br />\n"
                 htmlsmiles += smiles[size*80:len(smiles)]
             else:
-	        htmlsmiles = smiles
+                htmlsmiles = smiles
             xhtmlout.addBody('          <span class="smiles">' + htmlsmiles + '</span>')
             xhtmlout.addBody('        </div>')
         xhtmlout.addBody('      </div>')