2022-05-08T11:01:17,042 Created temporary directory: /tmp/pip-ephem-wheel-cache-0oo6b5am 2022-05-08T11:01:17,047 Created temporary directory: /tmp/pip-req-tracker-dg7m0gw9 2022-05-08T11:01:17,048 Initialized build tracking at /tmp/pip-req-tracker-dg7m0gw9 2022-05-08T11:01:17,048 Created build tracker: /tmp/pip-req-tracker-dg7m0gw9 2022-05-08T11:01:17,049 Entered build tracker: /tmp/pip-req-tracker-dg7m0gw9 2022-05-08T11:01:17,050 Created temporary directory: /tmp/pip-wheel-9avl5jk9 2022-05-08T11:01:17,117 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2022-05-08T11:01:17,125 2 location(s) to search for versions of pypulchra: 2022-05-08T11:01:17,125 * https://pypi.org/simple/pypulchra/ 2022-05-08T11:01:17,125 * https://www.piwheels.org/simple/pypulchra/ 2022-05-08T11:01:17,126 Fetching project page and analyzing links: https://pypi.org/simple/pypulchra/ 2022-05-08T11:01:17,127 Getting page https://pypi.org/simple/pypulchra/ 2022-05-08T11:01:17,130 Found index url https://pypi.org/simple 2022-05-08T11:01:17,244 Found link https://files.pythonhosted.org/packages/f1/f9/07629a442c8da5001399ee88eb46f4b233b0ce71cc6c2b1a085c88805179/pypulchra-1.0.0.tar.gz#sha256=cb4e3ca63482db276a08c322f6a0b3aa1d201124b3b670bd7a73a1004fdc2d22 (from https://pypi.org/simple/pypulchra/) (requires-python:>=3.7), version: 1.0.0 2022-05-08T11:01:17,246 Found link https://files.pythonhosted.org/packages/c7/60/4c39e247bd18cb845ffc8f55f3021a55db0b0ba8e3e481b4a4d641868fb4/pypulchra-1.0.1.tar.gz#sha256=b06a1ec08a49fb3d943206feacf7fcbf30d43ed5aff42e7f7d7efe9cf92c8327 (from https://pypi.org/simple/pypulchra/) (requires-python:>=3.7), version: 1.0.1 2022-05-08T11:01:17,247 Fetching project page and analyzing links: https://www.piwheels.org/simple/pypulchra/ 2022-05-08T11:01:17,247 Getting page https://www.piwheels.org/simple/pypulchra/ 2022-05-08T11:01:17,249 Found index url https://www.piwheels.org/simple 2022-05-08T11:01:17,528 Skipping link: No binaries permitted for pypulchra: https://www.piwheels.org/simple/pypulchra/pypulchra-1.0.1-cp37-cp37m-linux_armv7l.whl#sha256=dd6c53f28a2abfdf39df68c00333a7e734f66ef9d486ac1f6f2a1737c476afb8 (from https://www.piwheels.org/simple/pypulchra/) (requires-python:>=3.7) 2022-05-08T11:01:17,529 Skipping link: No binaries permitted for pypulchra: https://www.piwheels.org/simple/pypulchra/pypulchra-1.0.1-cp37-cp37m-linux_armv6l.whl#sha256=dd6c53f28a2abfdf39df68c00333a7e734f66ef9d486ac1f6f2a1737c476afb8 (from https://www.piwheels.org/simple/pypulchra/) (requires-python:>=3.7) 2022-05-08T11:01:17,529 Skipping link: No binaries permitted for pypulchra: https://www.piwheels.org/simple/pypulchra/pypulchra-1.0.0-cp37-cp37m-linux_armv7l.whl#sha256=021994ea82be3c4909986db98b8c49e8149b7b4c033c1963bfd0232adf248683 (from https://www.piwheels.org/simple/pypulchra/) (requires-python:>=3.7) 2022-05-08T11:01:17,530 Skipping link: No binaries permitted for pypulchra: https://www.piwheels.org/simple/pypulchra/pypulchra-1.0.0-cp37-cp37m-linux_armv6l.whl#sha256=021994ea82be3c4909986db98b8c49e8149b7b4c033c1963bfd0232adf248683 (from https://www.piwheels.org/simple/pypulchra/) (requires-python:>=3.7) 2022-05-08T11:01:17,530 Skipping link: not a file: https://www.piwheels.org/simple/pypulchra/ 2022-05-08T11:01:17,531 Skipping link: not a file: https://pypi.org/simple/pypulchra/ 2022-05-08T11:01:17,575 Given no hashes to check 1 links for project 'pypulchra': discarding no candidates 2022-05-08T11:01:17,615 Collecting pypulchra==1.0.0 2022-05-08T11:01:17,620 Created temporary directory: /tmp/pip-unpack-a_mtpmdw 2022-05-08T11:01:17,712 Downloading pypulchra-1.0.0.tar.gz (1.9 MB) 2022-05-08T11:01:18,940 Added pypulchra==1.0.0 from https://files.pythonhosted.org/packages/f1/f9/07629a442c8da5001399ee88eb46f4b233b0ce71cc6c2b1a085c88805179/pypulchra-1.0.0.tar.gz#sha256=cb4e3ca63482db276a08c322f6a0b3aa1d201124b3b670bd7a73a1004fdc2d22 to build tracker '/tmp/pip-req-tracker-dg7m0gw9' 2022-05-08T11:01:18,952 Created temporary directory: /tmp/pip-build-env-dkd2qr0p 2022-05-08T11:01:18,973 Created temporary directory: /tmp/pip-standalone-pip-zysms5eu 2022-05-08T11:01:21,134 Installing build dependencies: started 2022-05-08T11:01:21,136 Running command pip subprocess to install build dependencies 2022-05-08T11:01:33,176 Using pip 22.0.4 from /tmp/pip-standalone-pip-zysms5eu/__env_pip__.zip/pip (python 3.9) 2022-05-08T11:01:34,698 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2022-05-08T11:01:38,545 Collecting setuptools>=42 2022-05-08T11:01:38,793 Using cached https://www.piwheels.org/simple/setuptools/setuptools-62.1.0-py3-none-any.whl (1.1 MB) 2022-05-08T11:01:39,437 Collecting wheel 2022-05-08T11:01:39,469 Using cached https://www.piwheels.org/simple/wheel/wheel-0.37.1-py2.py3-none-any.whl (35 kB) 2022-05-08T11:01:39,917 Collecting pybind11>=2.8.0 2022-05-08T11:01:40,056 Using cached https://www.piwheels.org/simple/pybind11/pybind11-2.9.2-py2.py3-none-any.whl (213 kB) 2022-05-08T11:01:44,234 Installing collected packages: wheel, setuptools, pybind11 2022-05-08T11:01:44,521 Creating /tmp/pip-build-env-dkd2qr0p/overlay/bin 2022-05-08T11:01:44,525 changing mode of /tmp/pip-build-env-dkd2qr0p/overlay/bin/wheel to 755 2022-05-08T11:01:49,576 changing mode of /tmp/pip-build-env-dkd2qr0p/overlay/bin/pybind11-config to 755 2022-05-08T11:01:49,610 Successfully installed pybind11-2.9.2 setuptools-62.1.0 wheel-0.37.1 2022-05-08T11:01:50,286 Installing build dependencies: finished with status 'done' 2022-05-08T11:01:50,311 Getting requirements to build wheel: started 2022-05-08T11:01:50,313 Running command Getting requirements to build wheel 2022-05-08T11:01:52,433 running egg_info 2022-05-08T11:01:52,483 writing manifest file 'pypulchra.egg-info/SOURCES.txt' 2022-05-08T11:01:52,622 Getting requirements to build wheel: finished with status 'done' 2022-05-08T11:01:52,644 Created temporary directory: /tmp/pip-modern-metadata-qfgd_uw2 2022-05-08T11:01:52,649 Preparing metadata (pyproject.toml): started 2022-05-08T11:01:52,651 Running command Preparing metadata (pyproject.toml) 2022-05-08T11:01:54,675 running dist_info 2022-05-08T11:01:54,702 creating /tmp/pip-modern-metadata-qfgd_uw2/pypulchra.egg-info 2022-05-08T11:01:54,716 writing manifest file '/tmp/pip-modern-metadata-qfgd_uw2/pypulchra.egg-info/SOURCES.txt' 2022-05-08T11:01:54,746 writing manifest file '/tmp/pip-modern-metadata-qfgd_uw2/pypulchra.egg-info/SOURCES.txt' 2022-05-08T11:01:54,998 Preparing metadata (pyproject.toml): finished with status 'done' 2022-05-08T11:01:55,012 Source in /tmp/pip-wheel-9avl5jk9/pypulchra_bd7668732c454c878c1f78a61e1388b1 has version 1.0.0, which satisfies requirement pypulchra==1.0.0 from https://files.pythonhosted.org/packages/f1/f9/07629a442c8da5001399ee88eb46f4b233b0ce71cc6c2b1a085c88805179/pypulchra-1.0.0.tar.gz#sha256=cb4e3ca63482db276a08c322f6a0b3aa1d201124b3b670bd7a73a1004fdc2d22 2022-05-08T11:01:55,014 Removed pypulchra==1.0.0 from https://files.pythonhosted.org/packages/f1/f9/07629a442c8da5001399ee88eb46f4b233b0ce71cc6c2b1a085c88805179/pypulchra-1.0.0.tar.gz#sha256=cb4e3ca63482db276a08c322f6a0b3aa1d201124b3b670bd7a73a1004fdc2d22 from build tracker '/tmp/pip-req-tracker-dg7m0gw9' 2022-05-08T11:01:55,027 Created temporary directory: /tmp/pip-unpack-o1a27b_q 2022-05-08T11:01:55,028 Building wheels for collected packages: pypulchra 2022-05-08T11:01:55,038 Created temporary directory: /tmp/pip-wheel-_dnfhgxs 2022-05-08T11:01:55,038 Destination directory: /tmp/pip-wheel-_dnfhgxs 2022-05-08T11:01:55,043 Building wheel for pypulchra (pyproject.toml): started 2022-05-08T11:01:55,045 Running command Building wheel for pypulchra (pyproject.toml) 2022-05-08T11:01:57,152 running bdist_wheel 2022-05-08T11:01:57,160 running build 2022-05-08T11:01:57,161 running build_py 2022-05-08T11:01:57,169 creating build 2022-05-08T11:01:57,170 creating build/lib.linux-armv7l-3.9 2022-05-08T11:01:57,171 creating build/lib.linux-armv7l-3.9/pypulchra 2022-05-08T11:01:57,173 copying pypulchra/__init__.py -> build/lib.linux-armv7l-3.9/pypulchra 2022-05-08T11:01:57,176 running build_ext 2022-05-08T11:01:57,185 creating build/temp.linux-armv7l-3.9 2022-05-08T11:01:57,186 creating build/temp.linux-armv7l-3.9/bindings 2022-05-08T11:01:57,187 creating build/temp.linux-armv7l-3.9/bindings/python 2022-05-08T11:01:57,189 creating build/temp.linux-armv7l-3.9/src 2022-05-08T11:01:57,190 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DVERSION_INFO=1.0.0 -Isrc -I/tmp/pip-build-env-dkd2qr0p/overlay/lib/python3.9/site-packages/pybind11/include -I/usr/include/python3.9 -c bindings/python/pulchra_bindings.cpp -o build/temp.linux-armv7l-3.9/bindings/python/pulchra_bindings.o -fvisibility=hidden -g0 -std=c++14 -static 2022-05-08T11:02:01,445 In file included from bindings/python/pulchra_bindings.cpp:5: 2022-05-08T11:02:01,445 src/pulchra.hpp: In member function ‘int pulchra::Pulchra::read_pdb_buffer(std::stringstream&, std::shared_ptr)’: 2022-05-08T11:02:01,446 src/pulchra.hpp:653:34: warning: array subscript has type ‘char’ [-Wchar-subscripts] 2022-05-08T11:02:01,446 653 | res->type = AA_NUMS[pusetseq(resname)]; 2022-05-08T11:02:01,447 | ~~~~~~~~^~~~~~~~~ 2022-05-08T11:02:01,462 src/pulchra.hpp:594:8: warning: variable ‘version’ set but not used [-Wunused-but-set-variable] 2022-05-08T11:02:01,463 594 | char version; 2022-05-08T11:02:01,463 | ^~~~~~~ 2022-05-08T11:02:01,464 src/pulchra.hpp:595:46: warning: unused variable ‘num’ [-Wunused-variable] 2022-05-08T11:02:01,464 595 | int prevresnum, resnum, atmnum, locatmnum, num, locnum = 0, i, j; 2022-05-08T11:02:01,464 | ^~~ 2022-05-08T11:02:01,465 src/pulchra.hpp:595:63: warning: variable ‘i’ set but not used [-Wunused-but-set-variable] 2022-05-08T11:02:01,465 595 | int prevresnum, resnum, atmnum, locatmnum, num, locnum = 0, i, j; 2022-05-08T11:02:01,465 | ^ 2022-05-08T11:02:01,466 src/pulchra.hpp:595:66: warning: unused variable ‘j’ [-Wunused-variable] 2022-05-08T11:02:01,466 595 | int prevresnum, resnum, atmnum, locatmnum, num, locnum = 0, i, j; 2022-05-08T11:02:01,466 | ^ 2022-05-08T11:02:01,466 src/pulchra.hpp:597:14: warning: unused variable ‘cc’ [-Wunused-variable] 2022-05-08T11:02:01,467 597 | int sgnum, cc, nres, ok, natom; 2022-05-08T11:02:01,467 | ^~ 2022-05-08T11:02:01,467 src/pulchra.hpp:597:18: warning: unused variable ‘nres’ [-Wunused-variable] 2022-05-08T11:02:01,468 597 | int sgnum, cc, nres, ok, natom; 2022-05-08T11:02:01,468 | ^~~~ 2022-05-08T11:02:01,468 src/pulchra.hpp:597:24: warning: unused variable ‘ok’ [-Wunused-variable] 2022-05-08T11:02:01,469 597 | int sgnum, cc, nres, ok, natom; 2022-05-08T11:02:01,469 | ^~ 2022-05-08T11:02:01,469 src/pulchra.hpp:597:28: warning: unused variable ‘natom’ [-Wunused-variable] 2022-05-08T11:02:01,470 597 | int sgnum, cc, nres, ok, natom; 2022-05-08T11:02:01,470 | ^~~~~ 2022-05-08T11:02:01,470 src/pulchra.hpp:602:10: warning: unused variable ‘dist’ [-Wunused-variable] 2022-05-08T11:02:01,471 602 | double dist; 2022-05-08T11:02:01,471 | ^~~~ 2022-05-08T11:02:01,471 src/pulchra.hpp:603:17: warning: unused variable ‘bin’ [-Wunused-variable] 2022-05-08T11:02:01,472 603 | unsigned char bin; 2022-05-08T11:02:01,472 | ^~~ 2022-05-08T11:02:01,472 src/pulchra.hpp:604:7: warning: variable ‘warn’ set but not used [-Wunused-but-set-variable] 2022-05-08T11:02:01,473 604 | int warn = 0; 2022-05-08T11:02:01,473 | ^~~~ 2022-05-08T11:02:01,473 src/pulchra.hpp:605:10: warning: unused variable ‘cutoff’ [-Wunused-variable] 2022-05-08T11:02:01,474 605 | double cutoff; 2022-05-08T11:02:01,474 | ^~~~~~ 2022-05-08T11:02:01,509 src/pulchra.hpp: In member function ‘double pulchra::Pulchra::calc_ca_energy(const std::vector >&, double**, double**, double**, double, double*, bool, int)’: 2022-05-08T11:02:01,510 src/pulchra.hpp:775:10: warning: unused variable ‘theta0’ [-Wunused-variable] 2022-05-08T11:02:01,510 775 | double theta0, tdif, th, aa, bb, ab; 2022-05-08T11:02:01,510 | ^~~~~~ 2022-05-08T11:02:01,511 src/pulchra.hpp:775:18: warning: unused variable ‘tdif’ [-Wunused-variable] 2022-05-08T11:02:01,511 775 | double theta0, tdif, th, aa, bb, ab; 2022-05-08T11:02:01,511 | ^~~~ 2022-05-08T11:02:01,512 src/pulchra.hpp:775:24: warning: unused variable ‘th’ [-Wunused-variable] 2022-05-08T11:02:01,512 775 | double theta0, tdif, th, aa, bb, ab; 2022-05-08T11:02:01,512 | ^~ 2022-05-08T11:02:01,513 src/pulchra.hpp:775:28: warning: unused variable ‘aa’ [-Wunused-variable] 2022-05-08T11:02:01,513 775 | double theta0, tdif, th, aa, bb, ab; 2022-05-08T11:02:01,513 | ^~ 2022-05-08T11:02:01,513 src/pulchra.hpp:775:32: warning: unused variable ‘bb’ [-Wunused-variable] 2022-05-08T11:02:01,514 775 | double theta0, tdif, th, aa, bb, ab; 2022-05-08T11:02:01,514 | ^~ 2022-05-08T11:02:01,514 src/pulchra.hpp:775:36: warning: unused variable ‘ab’ [-Wunused-variable] 2022-05-08T11:02:01,515 775 | double theta0, tdif, th, aa, bb, ab; 2022-05-08T11:02:01,515 | ^~ 2022-05-08T11:02:01,515 src/pulchra.hpp:776:10: warning: unused variable ‘ff0’ [-Wunused-variable] 2022-05-08T11:02:01,516 776 | double ff0, ff2, dth, m0, m2, grad, f0[3], f2[3]; 2022-05-08T11:02:01,516 | ^~~ 2022-05-08T11:02:01,516 src/pulchra.hpp:776:15: warning: unused variable ‘ff2’ [-Wunused-variable] 2022-05-08T11:02:01,517 776 | double ff0, ff2, dth, m0, m2, grad, f0[3], f2[3]; 2022-05-08T11:02:01,517 | ^~~ 2022-05-08T11:02:01,517 src/pulchra.hpp:776:20: warning: unused variable ‘dth’ [-Wunused-variable] 2022-05-08T11:02:01,518 776 | double ff0, ff2, dth, m0, m2, grad, f0[3], f2[3]; 2022-05-08T11:02:01,518 | ^~~ 2022-05-08T11:02:01,518 src/pulchra.hpp:776:25: warning: unused variable ‘m0’ [-Wunused-variable] 2022-05-08T11:02:01,519 776 | double ff0, ff2, dth, m0, m2, grad, f0[3], f2[3]; 2022-05-08T11:02:01,519 | ^~ 2022-05-08T11:02:01,519 src/pulchra.hpp:776:29: warning: unused variable ‘m2’ [-Wunused-variable] 2022-05-08T11:02:01,520 776 | double ff0, ff2, dth, m0, m2, grad, f0[3], f2[3]; 2022-05-08T11:02:01,520 | ^~ 2022-05-08T11:02:01,520 src/pulchra.hpp:776:39: warning: unused variable ‘f0’ [-Wunused-variable] 2022-05-08T11:02:01,520 776 | double ff0, ff2, dth, m0, m2, grad, f0[3], f2[3]; 2022-05-08T11:02:01,521 | ^~ 2022-05-08T11:02:01,521 src/pulchra.hpp:776:46: warning: unused variable ‘f2’ [-Wunused-variable] 2022-05-08T11:02:01,521 776 | double ff0, ff2, dth, m0, m2, grad, f0[3], f2[3]; 2022-05-08T11:02:01,522 | ^~ 2022-05-08T11:02:01,522 src/pulchra.hpp:777:10: warning: unused variable ‘adiff’ [-Wunused-variable] 2022-05-08T11:02:01,522 777 | double adiff[3], bdiff[3]; 2022-05-08T11:02:01,523 | ^~~~~ 2022-05-08T11:02:01,523 src/pulchra.hpp:777:20: warning: unused variable ‘bdiff’ [-Wunused-variable] 2022-05-08T11:02:01,523 777 | double adiff[3], bdiff[3]; 2022-05-08T11:02:01,524 | ^~~~~ 2022-05-08T11:02:01,524 src/pulchra.hpp:778:10: warning: unused variable ‘deriv’ [-Wunused-variable] 2022-05-08T11:02:01,524 778 | double deriv, theta, dtheta, len1, len2, cos_theta, sin_theta; 2022-05-08T11:02:01,525 | ^~~~~ 2022-05-08T11:02:01,525 src/pulchra.hpp:778:24: warning: unused variable ‘dtheta’ [-Wunused-variable] 2022-05-08T11:02:01,525 778 | double deriv, theta, dtheta, len1, len2, cos_theta, sin_theta; 2022-05-08T11:02:01,526 | ^~~~~~ 2022-05-08T11:02:01,526 src/pulchra.hpp:778:32: warning: unused variable ‘len1’ [-Wunused-variable] 2022-05-08T11:02:01,526 778 | double deriv, theta, dtheta, len1, len2, cos_theta, sin_theta; 2022-05-08T11:02:01,527 | ^~~~ 2022-05-08T11:02:01,527 src/pulchra.hpp:778:38: warning: unused variable ‘len2’ [-Wunused-variable] 2022-05-08T11:02:01,527 778 | double deriv, theta, dtheta, len1, len2, cos_theta, sin_theta; 2022-05-08T11:02:01,528 | ^~~~ 2022-05-08T11:02:01,528 src/pulchra.hpp:779:10: warning: unused variable ‘dx1’ [-Wunused-variable] 2022-05-08T11:02:01,528 779 | double dx1, dy1, dz1; 2022-05-08T11:02:01,529 | ^~~ 2022-05-08T11:02:01,529 src/pulchra.hpp:779:15: warning: unused variable ‘dy1’ [-Wunused-variable] 2022-05-08T11:02:01,529 779 | double dx1, dy1, dz1; 2022-05-08T11:02:01,530 | ^~~ 2022-05-08T11:02:01,530 src/pulchra.hpp:779:20: warning: unused variable ‘dz1’ [-Wunused-variable] 2022-05-08T11:02:01,530 779 | double dx1, dy1, dz1; 2022-05-08T11:02:01,531 | ^~~ 2022-05-08T11:02:01,531 src/pulchra.hpp:780:10: warning: unused variable ‘dx2’ [-Wunused-variable] 2022-05-08T11:02:01,531 780 | double dx2, dy2, dz2; 2022-05-08T11:02:01,532 | ^~~ 2022-05-08T11:02:01,532 src/pulchra.hpp:780:15: warning: unused variable ‘dy2’ [-Wunused-variable] 2022-05-08T11:02:01,532 780 | double dx2, dy2, dz2; 2022-05-08T11:02:01,533 | ^~~ 2022-05-08T11:02:01,533 src/pulchra.hpp:780:20: warning: unused variable ‘dz2’ [-Wunused-variable] 2022-05-08T11:02:01,533 780 | double dx2, dy2, dz2; 2022-05-08T11:02:01,534 | ^~~ 2022-05-08T11:02:01,534 src/pulchra.hpp:781:10: warning: unused variable ‘dx3’ [-Wunused-variable] 2022-05-08T11:02:01,534 781 | double dx3, dy3, dz3; 2022-05-08T11:02:01,535 | ^~~ 2022-05-08T11:02:01,535 src/pulchra.hpp:781:15: warning: unused variable ‘dy3’ [-Wunused-variable] 2022-05-08T11:02:01,535 781 | double dx3, dy3, dz3; 2022-05-08T11:02:01,536 | ^~~ 2022-05-08T11:02:01,536 src/pulchra.hpp:781:20: warning: unused variable ‘dz3’ [-Wunused-variable] 2022-05-08T11:02:01,536 781 | double dx3, dy3, dz3; 2022-05-08T11:02:01,537 | ^~~ 2022-05-08T11:02:01,537 src/pulchra.hpp:782:10: warning: unused variable ‘vx1’ [-Wunused-variable] 2022-05-08T11:02:01,537 782 | double vx1, vy1, vz1; 2022-05-08T11:02:01,538 | ^~~ 2022-05-08T11:02:01,538 src/pulchra.hpp:782:15: warning: unused variable ‘vy1’ [-Wunused-variable] 2022-05-08T11:02:01,538 782 | double vx1, vy1, vz1; 2022-05-08T11:02:01,539 | ^~~ 2022-05-08T11:02:01,539 src/pulchra.hpp:782:20: warning: unused variable ‘vz1’ [-Wunused-variable] 2022-05-08T11:02:01,539 782 | double vx1, vy1, vz1; 2022-05-08T11:02:01,539 | ^~~ 2022-05-08T11:02:01,540 src/pulchra.hpp:783:10: warning: unused variable ‘vx2’ [-Wunused-variable] 2022-05-08T11:02:01,540 783 | double vx2, vy2, vz2; 2022-05-08T11:02:01,540 | ^~~ 2022-05-08T11:02:01,541 src/pulchra.hpp:783:15: warning: unused variable ‘vy2’ [-Wunused-variable] 2022-05-08T11:02:01,541 783 | double vx2, vy2, vz2; 2022-05-08T11:02:01,541 | ^~~ 2022-05-08T11:02:01,542 src/pulchra.hpp:783:20: warning: unused variable ‘vz2’ [-Wunused-variable] 2022-05-08T11:02:01,542 783 | double vx2, vy2, vz2; 2022-05-08T11:02:01,542 | ^~~ 2022-05-08T11:02:01,543 src/pulchra.hpp:784:10: warning: unused variable ‘vx3’ [-Wunused-variable] 2022-05-08T11:02:01,543 784 | double vx3, vy3, vz3; 2022-05-08T11:02:01,543 | ^~~ 2022-05-08T11:02:01,544 src/pulchra.hpp:784:15: warning: unused variable ‘vy3’ [-Wunused-variable] 2022-05-08T11:02:01,544 784 | double vx3, vy3, vz3; 2022-05-08T11:02:01,544 | ^~~ 2022-05-08T11:02:01,545 src/pulchra.hpp:784:20: warning: unused variable ‘vz3’ [-Wunused-variable] 2022-05-08T11:02:01,545 784 | double vx3, vy3, vz3; 2022-05-08T11:02:01,545 | ^~~ 2022-05-08T11:02:01,560 src/pulchra.hpp: In member function ‘std::string pulchra::Pulchra::ca_optimize_from_mol(std::shared_ptr)’: 2022-05-08T11:02:01,560 src/pulchra.hpp:937:8: warning: unused variable ‘buf’ [-Wunused-variable] 2022-05-08T11:02:01,561 937 | char buf[1000]; 2022-05-08T11:02:01,561 | ^~~ 2022-05-08T11:02:01,561 src/pulchra.hpp:938:10: warning: unused variable ‘j’ [-Wunused-variable] 2022-05-08T11:02:01,562 938 | int i, j, hx, my_iter; 2022-05-08T11:02:01,562 | ^ 2022-05-08T11:02:01,562 src/pulchra.hpp:938:13: warning: unused variable ‘hx’ [-Wunused-variable] 2022-05-08T11:02:01,562 938 | int i, j, hx, my_iter; 2022-05-08T11:02:01,563 | ^~ 2022-05-08T11:02:01,563 src/pulchra.hpp:938:17: warning: unused variable ‘my_iter’ [-Wunused-variable] 2022-05-08T11:02:01,563 938 | int i, j, hx, my_iter; 2022-05-08T11:02:01,564 | ^~~~~~~ 2022-05-08T11:02:01,564 src/pulchra.hpp:939:32: warning: unused variable ‘dist2’ [-Wunused-variable] 2022-05-08T11:02:01,564 939 | double dx, dy, dz, dd, dist, dist2, dist3, ddist, ddist2; 2022-05-08T11:02:01,565 | ^~~~~ 2022-05-08T11:02:01,565 src/pulchra.hpp:939:39: warning: unused variable ‘dist3’ [-Wunused-variable] 2022-05-08T11:02:01,565 939 | double dx, dy, dz, dd, dist, dist2, dist3, ddist, ddist2; 2022-05-08T11:02:01,565 | ^~~~~ 2022-05-08T11:02:01,566 src/pulchra.hpp:939:53: warning: variable ‘ddist2’ set but not used [-Wunused-but-set-variable] 2022-05-08T11:02:01,566 939 | double dx, dy, dz, dd, dist, dist2, dist3, ddist, ddist2; 2022-05-08T11:02:01,566 | ^~~~~~ 2022-05-08T11:02:01,567 src/pulchra.hpp:940:17: warning: unused variable ‘new_e_pot’ [-Wunused-variable] 2022-05-08T11:02:01,567 940 | double e_pot, new_e_pot, grad, alpha, e_pot1, e_pot2, e_pot3; 2022-05-08T11:02:01,567 | ^~~~~~~~~ 2022-05-08T11:02:01,568 src/pulchra.hpp:940:28: warning: unused variable ‘grad’ [-Wunused-variable] 2022-05-08T11:02:01,568 940 | double e_pot, new_e_pot, grad, alpha, e_pot1, e_pot2, e_pot3; 2022-05-08T11:02:01,568 | ^~~~ 2022-05-08T11:02:01,568 src/pulchra.hpp:940:34: warning: unused variable ‘alpha’ [-Wunused-variable] 2022-05-08T11:02:01,569 940 | double e_pot, new_e_pot, grad, alpha, e_pot1, e_pot2, e_pot3; 2022-05-08T11:02:01,569 | ^~~~~ 2022-05-08T11:02:01,569 src/pulchra.hpp:942:10: warning: unused variable ‘ff0’ [-Wunused-variable] 2022-05-08T11:02:01,569 942 | double ff0, ff2, aa, ab, bb, th, tdif, dth, m0, m2; 2022-05-08T11:02:01,570 | ^~~ 2022-05-08T11:02:01,570 src/pulchra.hpp:942:15: warning: unused variable ‘ff2’ [-Wunused-variable] 2022-05-08T11:02:01,571 942 | double ff0, ff2, aa, ab, bb, th, tdif, dth, m0, m2; 2022-05-08T11:02:01,571 | ^~~ 2022-05-08T11:02:01,571 src/pulchra.hpp:942:36: warning: unused variable ‘tdif’ [-Wunused-variable] 2022-05-08T11:02:01,572 942 | double ff0, ff2, aa, ab, bb, th, tdif, dth, m0, m2; 2022-05-08T11:02:01,572 | ^~~~ 2022-05-08T11:02:01,572 src/pulchra.hpp:942:42: warning: unused variable ‘dth’ [-Wunused-variable] 2022-05-08T11:02:01,572 942 | double ff0, ff2, aa, ab, bb, th, tdif, dth, m0, m2; 2022-05-08T11:02:01,576 | ^~~ 2022-05-08T11:02:01,576 src/pulchra.hpp:942:47: warning: unused variable ‘m0’ [-Wunused-variable] 2022-05-08T11:02:01,578 942 | double ff0, ff2, aa, ab, bb, th, tdif, dth, m0, m2; 2022-05-08T11:02:01,578 | ^~ 2022-05-08T11:02:01,578 src/pulchra.hpp:942:51: warning: unused variable ‘m2’ [-Wunused-variable] 2022-05-08T11:02:01,579 942 | double ff0, ff2, aa, ab, bb, th, tdif, dth, m0, m2; 2022-05-08T11:02:01,579 | ^~ 2022-05-08T11:02:01,579 src/pulchra.hpp:943:26: warning: unused variable ‘maxgrad’ [-Wunused-variable] 2022-05-08T11:02:01,580 943 | double theta0, deg_th, maxgrad, sum; 2022-05-08T11:02:01,580 | ^~~~~~~ 2022-05-08T11:02:01,580 src/pulchra.hpp:943:35: warning: unused variable ‘sum’ [-Wunused-variable] 2022-05-08T11:02:01,581 943 | double theta0, deg_th, maxgrad, sum; 2022-05-08T11:02:01,581 | ^~~ 2022-05-08T11:02:01,581 src/pulchra.hpp:944:10: warning: unused variable ‘f0’ [-Wunused-variable] 2022-05-08T11:02:01,582 944 | double f0[3], f2[3]; 2022-05-08T11:02:01,582 | ^~ 2022-05-08T11:02:01,582 src/pulchra.hpp:944:17: warning: unused variable ‘f2’ [-Wunused-variable] 2022-05-08T11:02:01,583 944 | double f0[3], f2[3]; 2022-05-08T11:02:01,583 | ^~ 2022-05-08T11:02:01,583 src/pulchra.hpp:945:10: warning: unused variable ‘x’ [-Wunused-variable] 2022-05-08T11:02:01,584 945 | double x, y, z; 2022-05-08T11:02:01,584 | ^ 2022-05-08T11:02:01,584 src/pulchra.hpp:945:13: warning: unused variable ‘y’ [-Wunused-variable] 2022-05-08T11:02:01,585 945 | double x, y, z; 2022-05-08T11:02:01,585 | ^ 2022-05-08T11:02:01,586 src/pulchra.hpp:945:16: warning: unused variable ‘z’ [-Wunused-variable] 2022-05-08T11:02:01,586 945 | double x, y, z; 2022-05-08T11:02:01,586 | ^ 2022-05-08T11:02:01,587 src/pulchra.hpp:947:8: warning: unused variable ‘sec’ [-Wunused-variable] 2022-05-08T11:02:01,587 947 | int *sec; 2022-05-08T11:02:01,587 | ^~~ 2022-05-08T11:02:01,588 src/pulchra.hpp:948:65: warning: unused variable ‘tmp’ [-Wunused-variable] 2022-05-08T11:02:01,588 948 | double **new_c_alpha, **gradient, **init_c_alpha, last_alpha, tmp, 2022-05-08T11:02:01,588 | ^~~ 2022-05-08T11:02:01,589 src/pulchra.hpp:949:4: warning: unused variable ‘last_good_alpha’ [-Wunused-variable] 2022-05-08T11:02:01,589 949 | last_good_alpha, d_alpha, last_e_pot; 2022-05-08T11:02:01,589 | ^~~~~~~~~~~~~~~ 2022-05-08T11:02:01,589 src/pulchra.hpp:949:21: warning: unused variable ‘d_alpha’ [-Wunused-variable] 2022-05-08T11:02:01,590 949 | last_good_alpha, d_alpha, last_e_pot; 2022-05-08T11:02:01,590 | ^~~~~~~ 2022-05-08T11:02:01,590 src/pulchra.hpp:949:30: warning: variable ‘last_e_pot’ set but not used [-Wunused-but-set-variable] 2022-05-08T11:02:01,591 949 | last_good_alpha, d_alpha, last_e_pot; 2022-05-08T11:02:01,591 | ^~~~~~~~~~ 2022-05-08T11:02:01,591 src/pulchra.hpp:953:9: warning: unused variable ‘inp’ [-Wunused-variable] 2022-05-08T11:02:01,592 953 | FILE *inp; 2022-05-08T11:02:01,592 | ^~~ 2022-05-08T11:02:01,592 src/pulchra.hpp:954:19: warning: unused variable ‘ok’ [-Wunused-variable] 2022-05-08T11:02:01,593 954 | int mnum, init, ok; 2022-05-08T11:02:01,593 | ^~ 2022-05-08T11:02:01,593 src/pulchra.hpp:958:10: warning: unused variable ‘w1’ [-Wunused-variable] 2022-05-08T11:02:01,594 958 | double w1, w2, w3, eps; 2022-05-08T11:02:01,594 | ^~ 2022-05-08T11:02:01,594 src/pulchra.hpp:958:14: warning: unused variable ‘w2’ [-Wunused-variable] 2022-05-08T11:02:01,595 958 | double w1, w2, w3, eps; 2022-05-08T11:02:01,595 | ^~ 2022-05-08T11:02:01,595 src/pulchra.hpp:958:18: warning: unused variable ‘w3’ [-Wunused-variable] 2022-05-08T11:02:01,596 958 | double w1, w2, w3, eps; 2022-05-08T11:02:01,596 | ^~ 2022-05-08T11:02:01,596 src/pulchra.hpp:960:7: warning: variable ‘mode’ set but not used [-Wunused-but-set-variable] 2022-05-08T11:02:01,597 960 | int mode, fcnt; 2022-05-08T11:02:01,597 | ^~~~ 2022-05-08T11:02:01,670 src/pulchra.hpp: In member function ‘void pulchra::Pulchra::prepare_rbins(std::shared_ptr)’: 2022-05-08T11:02:01,670 src/pulchra.hpp:1724:16: warning: unused variable ‘l’ [-Wunused-variable] 2022-05-08T11:02:01,671 1724 | int i, j, k, l, m, bin13_1, bin13_2, bin14, found, pro; 2022-05-08T11:02:01,671 | ^ 2022-05-08T11:02:01,671 src/pulchra.hpp:1724:19: warning: unused variable ‘m’ [-Wunused-variable] 2022-05-08T11:02:01,672 1724 | int i, j, k, l, m, bin13_1, bin13_2, bin14, found, pro; 2022-05-08T11:02:01,672 | ^ 2022-05-08T11:02:01,672 src/pulchra.hpp:1724:47: warning: unused variable ‘found’ [-Wunused-variable] 2022-05-08T11:02:01,673 1724 | int i, j, k, l, m, bin13_1, bin13_2, bin14, found, pro; 2022-05-08T11:02:01,673 | ^~~~~ 2022-05-08T11:02:01,673 src/pulchra.hpp:1724:54: warning: unused variable ‘pro’ [-Wunused-variable] 2022-05-08T11:02:01,673 1724 | int i, j, k, l, m, bin13_1, bin13_2, bin14, found, pro; 2022-05-08T11:02:01,674 | ^~~ 2022-05-08T11:02:01,674 src/pulchra.hpp:1725:7: warning: unused variable ‘b13_1’ [-Wunused-variable] 2022-05-08T11:02:01,674 1725 | int b13_1, b13_2, b14; 2022-05-08T11:02:01,675 | ^~~~~ 2022-05-08T11:02:01,675 src/pulchra.hpp:1725:14: warning: unused variable ‘b13_2’ [-Wunused-variable] 2022-05-08T11:02:01,675 1725 | int b13_1, b13_2, b14; 2022-05-08T11:02:01,676 | ^~~~~ 2022-05-08T11:02:01,676 src/pulchra.hpp:1725:21: warning: unused variable ‘b14’ [-Wunused-variable] 2022-05-08T11:02:01,676 1725 | int b13_1, b13_2, b14; 2022-05-08T11:02:01,677 | ^~~ 2022-05-08T11:02:01,691 src/pulchra.hpp: In member function ‘void pulchra::Pulchra::rebuild_backbone(std::shared_ptr)’: 2022-05-08T11:02:01,692 src/pulchra.hpp:1852:16: warning: unused variable ‘l’ [-Wunused-variable] 2022-05-08T11:02:01,692 1852 | int i, j, k, l, m, bin13_1, bin13_2, bin14, found, pro; 2022-05-08T11:02:01,693 | ^ 2022-05-08T11:02:01,693 src/pulchra.hpp:1852:19: warning: unused variable ‘m’ [-Wunused-variable] 2022-05-08T11:02:01,693 1852 | int i, j, k, l, m, bin13_1, bin13_2, bin14, found, pro; 2022-05-08T11:02:01,694 | ^ 2022-05-08T11:02:01,694 src/pulchra.hpp:1852:47: warning: unused variable ‘found’ [-Wunused-variable] 2022-05-08T11:02:01,694 1852 | int i, j, k, l, m, bin13_1, bin13_2, bin14, found, pro; 2022-05-08T11:02:01,694 | ^~~~~ 2022-05-08T11:02:01,695 src/pulchra.hpp:1852:54: warning: variable ‘pro’ set but not used [-Wunused-but-set-variable] 2022-05-08T11:02:01,695 1852 | int i, j, k, l, m, bin13_1, bin13_2, bin14, found, pro; 2022-05-08T11:02:01,695 | ^~~ 2022-05-08T11:02:01,696 src/pulchra.hpp:1853:7: warning: unused variable ‘b13_1’ [-Wunused-variable] 2022-05-08T11:02:01,696 1853 | int b13_1, b13_2, b14; 2022-05-08T11:02:01,696 | ^~~~~ 2022-05-08T11:02:01,697 src/pulchra.hpp:1853:14: warning: unused variable ‘b13_2’ [-Wunused-variable] 2022-05-08T11:02:01,697 1853 | int b13_1, b13_2, b14; 2022-05-08T11:02:01,697 | ^~~~~ 2022-05-08T11:02:01,698 src/pulchra.hpp:1853:21: warning: unused variable ‘b14’ [-Wunused-variable] 2022-05-08T11:02:01,698 1853 | int b13_1, b13_2, b14; 2022-05-08T11:02:01,698 | ^~~ 2022-05-08T11:02:01,729 src/pulchra.hpp: In member function ‘void pulchra::Pulchra::rebuild_sidechains(std::shared_ptr)’: 2022-05-08T11:02:01,730 src/pulchra.hpp:2023:12: warning: unused variable ‘cacoords’ [-Wunused-variable] 2022-05-08T11:02:01,730 2023 | double **cacoords, **tmpcoords, **tmpstat; 2022-05-08T11:02:01,730 | ^~~~~~~~ 2022-05-08T11:02:01,730 src/pulchra.hpp:2023:24: warning: unused variable ‘tmpcoords’ [-Wunused-variable] 2022-05-08T11:02:01,731 2023 | double **cacoords, **tmpcoords, **tmpstat; 2022-05-08T11:02:01,731 | ^~~~~~~~~ 2022-05-08T11:02:01,731 src/pulchra.hpp:2023:37: warning: unused variable ‘tmpstat’ [-Wunused-variable] 2022-05-08T11:02:01,732 2023 | double **cacoords, **tmpcoords, **tmpstat; 2022-05-08T11:02:01,732 | ^~~~~~~ 2022-05-08T11:02:01,732 src/pulchra.hpp:2024:10: warning: variable ‘x1’ set but not used [-Wunused-but-set-variable] 2022-05-08T11:02:01,732 2024 | double x1, y1, z1; 2022-05-08T11:02:01,733 | ^~ 2022-05-08T11:02:01,733 src/pulchra.hpp:2024:14: warning: variable ‘y1’ set but not used [-Wunused-but-set-variable] 2022-05-08T11:02:01,733 2024 | double x1, y1, z1; 2022-05-08T11:02:01,734 | ^~ 2022-05-08T11:02:01,734 src/pulchra.hpp:2024:18: warning: variable ‘z1’ set but not used [-Wunused-but-set-variable] 2022-05-08T11:02:01,734 2024 | double x1, y1, z1; 2022-05-08T11:02:01,735 | ^~ 2022-05-08T11:02:01,735 src/pulchra.hpp:2028:10: warning: unused variable ‘x5’ [-Wunused-variable] 2022-05-08T11:02:01,735 2028 | double x5, y5, z5; 2022-05-08T11:02:01,735 | ^~ 2022-05-08T11:02:01,736 src/pulchra.hpp:2028:14: warning: unused variable ‘y5’ [-Wunused-variable] 2022-05-08T11:02:01,736 2028 | double x5, y5, z5; 2022-05-08T11:02:01,736 | ^~ 2022-05-08T11:02:01,737 src/pulchra.hpp:2028:18: warning: unused variable ‘z5’ [-Wunused-variable] 2022-05-08T11:02:01,737 2028 | double x5, y5, z5; 2022-05-08T11:02:01,737 | ^~ 2022-05-08T11:02:01,737 src/pulchra.hpp:2029:10: warning: unused variable ‘r14’ [-Wunused-variable] 2022-05-08T11:02:01,738 2029 | double r14, r13_1, r13_2; 2022-05-08T11:02:01,738 | ^~~ 2022-05-08T11:02:01,738 src/pulchra.hpp:2029:15: warning: unused variable ‘r13_1’ [-Wunused-variable] 2022-05-08T11:02:01,739 2029 | double r14, r13_1, r13_2; 2022-05-08T11:02:01,739 | ^~~~~ 2022-05-08T11:02:01,739 src/pulchra.hpp:2029:22: warning: unused variable ‘r13_2’ [-Wunused-variable] 2022-05-08T11:02:01,740 2029 | double r14, r13_1, r13_2; 2022-05-08T11:02:01,740 | ^~~~~ 2022-05-08T11:02:01,740 src/pulchra.hpp:2030:10: warning: unused variable ‘dx’ [-Wunused-variable] 2022-05-08T11:02:01,740 2030 | double dx, dy, dz, dd; 2022-05-08T11:02:01,741 | ^~ 2022-05-08T11:02:01,741 src/pulchra.hpp:2030:14: warning: unused variable ‘dy’ [-Wunused-variable] 2022-05-08T11:02:01,741 2030 | double dx, dy, dz, dd; 2022-05-08T11:02:01,742 | ^~ 2022-05-08T11:02:01,742 src/pulchra.hpp:2030:18: warning: unused variable ‘dz’ [-Wunused-variable] 2022-05-08T11:02:01,742 2030 | double dx, dy, dz, dd; 2022-05-08T11:02:01,743 | ^~ 2022-05-08T11:02:01,743 src/pulchra.hpp:2030:22: warning: unused variable ‘dd’ [-Wunused-variable] 2022-05-08T11:02:01,743 2030 | double dx, dy, dz, dd; 2022-05-08T11:02:01,743 | ^~ 2022-05-08T11:02:01,744 src/pulchra.hpp:2031:15: warning: variable ‘besthit’ set but not used [-Wunused-but-set-variable] 2022-05-08T11:02:01,744 2031 | double hit, besthit; 2022-05-08T11:02:01,744 | ^~~~~~~ 2022-05-08T11:02:01,745 src/pulchra.hpp:2032:7: warning: unused variable ‘exvol’ [-Wunused-variable] 2022-05-08T11:02:01,745 2032 | int exvol, bestpos; 2022-05-08T11:02:01,745 | ^~~~~ 2022-05-08T11:02:01,746 src/pulchra.hpp:2034:10: warning: unused variable ‘rmsd’ [-Wunused-variable] 2022-05-08T11:02:01,746 2034 | double rmsd, total; 2022-05-08T11:02:01,746 | ^~~~ 2022-05-08T11:02:01,747 src/pulchra.hpp:2034:16: warning: unused variable ‘total’ [-Wunused-variable] 2022-05-08T11:02:01,747 2034 | double rmsd, total; 2022-05-08T11:02:01,747 | ^~~~~ 2022-05-08T11:02:01,747 src/pulchra.hpp:2036:12: warning: unused variable ‘nca’ [-Wunused-variable] 2022-05-08T11:02:01,748 2036 | int nsc, nca; 2022-05-08T11:02:01,748 | ^~~ 2022-05-08T11:02:01,748 src/pulchra.hpp:2037:10: warning: unused variable ‘cax’ [-Wunused-variable] 2022-05-08T11:02:01,749 2037 | double cax, cay, caz; 2022-05-08T11:02:01,749 | ^~~ 2022-05-08T11:02:01,749 src/pulchra.hpp:2037:15: warning: unused variable ‘cay’ [-Wunused-variable] 2022-05-08T11:02:01,750 2037 | double cax, cay, caz; 2022-05-08T11:02:01,750 | ^~~ 2022-05-08T11:02:01,750 src/pulchra.hpp:2037:20: warning: unused variable ‘caz’ [-Wunused-variable] 2022-05-08T11:02:01,750 2037 | double cax, cay, caz; 2022-05-08T11:02:01,751 | ^~~ 2022-05-08T11:02:01,751 src/pulchra.hpp:2039:8: warning: unused variable ‘scn’ [-Wunused-variable] 2022-05-08T11:02:01,751 2039 | char scn[12][4]; 2022-05-08T11:02:01,752 | ^~~ 2022-05-08T11:02:01,752 src/pulchra.hpp:2040:7: warning: unused variable ‘ok’ [-Wunused-variable] 2022-05-08T11:02:01,752 2040 | int ok, last_a, last_b, last_c, last_d, jpos; 2022-05-08T11:02:01,753 | ^~ 2022-05-08T11:02:01,753 src/pulchra.hpp:2040:11: warning: unused variable ‘last_a’ [-Wunused-variable] 2022-05-08T11:02:01,753 2040 | int ok, last_a, last_b, last_c, last_d, jpos; 2022-05-08T11:02:01,753 | ^~~~~~ 2022-05-08T11:02:01,754 src/pulchra.hpp:2040:19: warning: unused variable ‘last_b’ [-Wunused-variable] 2022-05-08T11:02:01,754 2040 | int ok, last_a, last_b, last_c, last_d, jpos; 2022-05-08T11:02:01,754 | ^~~~~~ 2022-05-08T11:02:01,755 src/pulchra.hpp:2040:27: warning: unused variable ‘last_c’ [-Wunused-variable] 2022-05-08T11:02:01,755 2040 | int ok, last_a, last_b, last_c, last_d, jpos; 2022-05-08T11:02:01,755 | ^~~~~~ 2022-05-08T11:02:01,756 src/pulchra.hpp:2040:35: warning: unused variable ‘last_d’ [-Wunused-variable] 2022-05-08T11:02:01,756 2040 | int ok, last_a, last_b, last_c, last_d, jpos; 2022-05-08T11:02:01,756 | ^~~~~~ 2022-05-08T11:02:01,757 src/pulchra.hpp:2040:43: warning: unused variable ‘jpos’ [-Wunused-variable] 2022-05-08T11:02:01,757 2040 | int ok, last_a, last_b, last_c, last_d, jpos; 2022-05-08T11:02:01,757 | ^~~~ 2022-05-08T11:02:01,758 src/pulchra.hpp:2041:7: warning: unused variable ‘jx’ [-Wunused-variable] 2022-05-08T11:02:01,758 2041 | int jx, jy, jz, jxi, jyi, jzi, b13_1, b13_2, b14, jm; 2022-05-08T11:02:01,758 | ^~ 2022-05-08T11:02:01,759 src/pulchra.hpp:2041:11: warning: unused variable ‘jy’ [-Wunused-variable] 2022-05-08T11:02:01,759 2041 | int jx, jy, jz, jxi, jyi, jzi, b13_1, b13_2, b14, jm; 2022-05-08T11:02:01,759 | ^~ 2022-05-08T11:02:01,760 src/pulchra.hpp:2041:15: warning: unused variable ‘jz’ [-Wunused-variable] 2022-05-08T11:02:01,760 2041 | int jx, jy, jz, jxi, jyi, jzi, b13_1, b13_2, b14, jm; 2022-05-08T11:02:01,760 | ^~ 2022-05-08T11:02:01,761 src/pulchra.hpp:2041:19: warning: unused variable ‘jxi’ [-Wunused-variable] 2022-05-08T11:02:01,761 2041 | int jx, jy, jz, jxi, jyi, jzi, b13_1, b13_2, b14, jm; 2022-05-08T11:02:01,761 | ^~~ 2022-05-08T11:02:01,762 src/pulchra.hpp:2041:24: warning: unused variable ‘jyi’ [-Wunused-variable] 2022-05-08T11:02:01,762 2041 | int jx, jy, jz, jxi, jyi, jzi, b13_1, b13_2, b14, jm; 2022-05-08T11:02:01,762 | ^~~ 2022-05-08T11:02:01,762 src/pulchra.hpp:2041:29: warning: unused variable ‘jzi’ [-Wunused-variable] 2022-05-08T11:02:01,763 2041 | int jx, jy, jz, jxi, jyi, jzi, b13_1, b13_2, b14, jm; 2022-05-08T11:02:01,763 | ^~~ 2022-05-08T11:02:01,763 src/pulchra.hpp:2041:34: warning: unused variable ‘b13_1’ [-Wunused-variable] 2022-05-08T11:02:01,764 2041 | int jx, jy, jz, jxi, jyi, jzi, b13_1, b13_2, b14, jm; 2022-05-08T11:02:01,764 | ^~~~~ 2022-05-08T11:02:01,764 src/pulchra.hpp:2041:41: warning: unused variable ‘b13_2’ [-Wunused-variable] 2022-05-08T11:02:01,765 2041 | int jx, jy, jz, jxi, jyi, jzi, b13_1, b13_2, b14, jm; 2022-05-08T11:02:01,765 | ^~~~~ 2022-05-08T11:02:01,765 src/pulchra.hpp:2041:48: warning: unused variable ‘b14’ [-Wunused-variable] 2022-05-08T11:02:01,766 2041 | int jx, jy, jz, jxi, jyi, jzi, b13_1, b13_2, b14, jm; 2022-05-08T11:02:01,766 | ^~~ 2022-05-08T11:02:01,766 src/pulchra.hpp:2041:53: warning: unused variable ‘jm’ [-Wunused-variable] 2022-05-08T11:02:01,766 2041 | int jx, jy, jz, jxi, jyi, jzi, b13_1, b13_2, b14, jm; 2022-05-08T11:02:01,767 | ^~ 2022-05-08T11:02:01,767 src/pulchra.hpp:2042:13: warning: unused variable ‘bestrot’ [-Wunused-variable] 2022-05-08T11:02:01,767 2042 | int crot, bestrot, minexvol, totexvol, rtried, pos, cpos; 2022-05-08T11:02:01,768 | ^~~~~~~ 2022-05-08T11:02:01,768 src/pulchra.hpp:2042:22: warning: unused variable ‘minexvol’ [-Wunused-variable] 2022-05-08T11:02:01,768 2042 | int crot, bestrot, minexvol, totexvol, rtried, pos, cpos; 2022-05-08T11:02:01,768 | ^~~~~~~~ 2022-05-08T11:02:01,769 src/pulchra.hpp:2042:32: warning: variable ‘totexvol’ set but not used [-Wunused-but-set-variable] 2022-05-08T11:02:01,769 2042 | int crot, bestrot, minexvol, totexvol, rtried, pos, cpos; 2022-05-08T11:02:01,769 | ^~~~~~~~ 2022-05-08T11:02:01,770 src/pulchra.hpp:2042:42: warning: unused variable ‘rtried’ [-Wunused-variable] 2022-05-08T11:02:01,770 2042 | int crot, bestrot, minexvol, totexvol, rtried, pos, cpos; 2022-05-08T11:02:01,770 | ^~~~~~ 2022-05-08T11:02:01,771 src/pulchra.hpp:2044:10: warning: unused variable ‘sort_rot’ [-Wunused-variable] 2022-05-08T11:02:01,771 2044 | double sort_rot[100][2]; 2022-05-08T11:02:01,771 | ^~~~~~~~ 2022-05-08T11:02:01,812 src/pulchra.hpp: In member function ‘int pulchra::Pulchra::get_conflicts(std::shared_ptr, pulchra::atom_list_3d, int, int, int)’: 2022-05-08T11:02:01,813 src/pulchra.hpp:2264:16: warning: unused variable ‘x’ [-Wunused-variable] 2022-05-08T11:02:01,813 2264 | int i, j, k, x, y, z; 2022-05-08T11:02:01,813 | ^ 2022-05-08T11:02:01,814 src/pulchra.hpp:2264:19: warning: unused variable ‘y’ [-Wunused-variable] 2022-05-08T11:02:01,814 2264 | int i, j, k, x, y, z; 2022-05-08T11:02:01,814 | ^ 2022-05-08T11:02:01,815 src/pulchra.hpp:2264:22: warning: unused variable ‘z’ [-Wunused-variable] 2022-05-08T11:02:01,815 2264 | int i, j, k, x, y, z; 2022-05-08T11:02:01,815 | ^ 2022-05-08T11:02:01,816 src/pulchra.hpp:2265:24: warning: unused variable ‘iter’ [-Wunused-variable] 2022-05-08T11:02:01,816 2265 | int ii, jj, kk, con, iter, maxcon, merged; 2022-05-08T11:02:01,816 | ^~~~ 2022-05-08T11:02:01,817 src/pulchra.hpp:2265:30: warning: unused variable ‘maxcon’ [-Wunused-variable] 2022-05-08T11:02:01,817 2265 | int ii, jj, kk, con, iter, maxcon, merged; 2022-05-08T11:02:01,817 | ^~~~~~ 2022-05-08T11:02:01,839 src/pulchra.hpp: In member function ‘void pulchra::Pulchra::allocate_grid(std::shared_ptr, pulchra::atom_list_3d&, int*, int*, int*)’: 2022-05-08T11:02:01,839 src/pulchra.hpp:2374:7: warning: unused variable ‘i’ [-Wunused-variable] 2022-05-08T11:02:01,840 2374 | int i, j, x, y, z; 2022-05-08T11:02:01,840 | ^ 2022-05-08T11:02:01,840 src/pulchra.hpp:2374:10: warning: unused variable ‘j’ [-Wunused-variable] 2022-05-08T11:02:01,841 2374 | int i, j, x, y, z; 2022-05-08T11:02:01,841 | ^ 2022-05-08T11:02:01,870 src/pulchra.hpp: In member function ‘void pulchra::Pulchra::optimize_exvol(std::shared_ptr)’: 2022-05-08T11:02:01,871 src/pulchra.hpp:2440:10: warning: variable ‘min’ set but not used [-Wunused-but-set-variable] 2022-05-08T11:02:01,871 2440 | double min[3], max[3]; 2022-05-08T11:02:01,871 | ^~~ 2022-05-08T11:02:01,872 src/pulchra.hpp:2440:18: warning: variable ‘max’ set but not used [-Wunused-but-set-variable] 2022-05-08T11:02:01,872 2440 | double min[3], max[3]; 2022-05-08T11:02:01,872 | ^~~ 2022-05-08T11:02:01,873 src/pulchra.hpp:2446:22: warning: unused variable ‘x’ [-Wunused-variable] 2022-05-08T11:02:01,873 2446 | int i, j, k, l, m, x, y, z; 2022-05-08T11:02:01,873 | ^ 2022-05-08T11:02:01,874 src/pulchra.hpp:2446:25: warning: unused variable ‘y’ [-Wunused-variable] 2022-05-08T11:02:01,874 2446 | int i, j, k, l, m, x, y, z; 2022-05-08T11:02:01,874 | ^ 2022-05-08T11:02:01,875 src/pulchra.hpp:2446:28: warning: unused variable ‘z’ [-Wunused-variable] 2022-05-08T11:02:01,875 2446 | int i, j, k, l, m, x, y, z; 2022-05-08T11:02:01,875 | ^ 2022-05-08T11:02:01,875 src/pulchra.hpp:2447:7: warning: unused variable ‘ii’ [-Wunused-variable] 2022-05-08T11:02:01,876 2447 | int ii, jj, kk, con, iter, maxcon, totcon; 2022-05-08T11:02:01,876 | ^~ 2022-05-08T11:02:01,876 src/pulchra.hpp:2447:11: warning: unused variable ‘jj’ [-Wunused-variable] 2022-05-08T11:02:01,877 2447 | int ii, jj, kk, con, iter, maxcon, totcon; 2022-05-08T11:02:01,877 | ^~ 2022-05-08T11:02:01,877 src/pulchra.hpp:2447:15: warning: unused variable ‘kk’ [-Wunused-variable] 2022-05-08T11:02:01,878 2447 | int ii, jj, kk, con, iter, maxcon, totcon; 2022-05-08T11:02:01,878 | ^~ 2022-05-08T11:02:01,878 src/pulchra.hpp:2450:12: warning: unused variable ‘nca’ [-Wunused-variable] 2022-05-08T11:02:01,878 2450 | int nsc, nca; 2022-05-08T11:02:01,879 | ^~~ 2022-05-08T11:02:01,879 src/pulchra.hpp:2451:10: warning: unused variable ‘cax’ [-Wunused-variable] 2022-05-08T11:02:01,879 2451 | double cax, cay, caz; 2022-05-08T11:02:01,880 | ^~~ 2022-05-08T11:02:01,880 src/pulchra.hpp:2451:15: warning: unused variable ‘cay’ [-Wunused-variable] 2022-05-08T11:02:01,880 2451 | double cax, cay, caz; 2022-05-08T11:02:01,881 | ^~~ 2022-05-08T11:02:01,881 src/pulchra.hpp:2451:20: warning: unused variable ‘caz’ [-Wunused-variable] 2022-05-08T11:02:01,881 2451 | double cax, cay, caz; 2022-05-08T11:02:01,882 | ^~~ 2022-05-08T11:02:01,882 src/pulchra.hpp:2453:10: warning: variable ‘x1’ set but not used [-Wunused-but-set-variable] 2022-05-08T11:02:01,882 2453 | double x1, y1, z1; 2022-05-08T11:02:01,883 | ^~ 2022-05-08T11:02:01,883 src/pulchra.hpp:2453:14: warning: variable ‘y1’ set but not used [-Wunused-but-set-variable] 2022-05-08T11:02:01,883 2453 | double x1, y1, z1; 2022-05-08T11:02:01,884 | ^~ 2022-05-08T11:02:01,884 src/pulchra.hpp:2453:18: warning: variable ‘z1’ set but not used [-Wunused-but-set-variable] 2022-05-08T11:02:01,884 2453 | double x1, y1, z1; 2022-05-08T11:02:01,885 | ^~ 2022-05-08T11:02:01,898 src/pulchra.hpp: In member function ‘int pulchra::Pulchra::chirality_check(std::shared_ptr)’: 2022-05-08T11:02:01,898 src/pulchra.hpp:2732:7: warning: unused variable ‘i’ [-Wunused-variable] 2022-05-08T11:02:01,899 2732 | int i; 2022-05-08T11:02:01,899 | ^ 2022-05-08T11:02:01,918 src/pulchra.hpp: In member function ‘double pulchra::Pulchra::hb_energy(std::shared_ptr, pulchra::atom_list_3d&, int, int, int)’: 2022-05-08T11:02:01,919 src/pulchra.hpp:2828:28: warning: unused variable ‘min_dist1’ [-Wunused-variable] 2022-05-08T11:02:01,919 2828 | double dx, dy, dz, dist, min_dist1, min_dist2; 2022-05-08T11:02:01,919 | ^~~~~~~~~ 2022-05-08T11:02:01,946 src/pulchra.hpp: In member function ‘void pulchra::Pulchra::optimize_backbone(std::shared_ptr)’: 2022-05-08T11:02:01,946 src/pulchra.hpp:3042:10: warning: unused variable ‘k’ [-Wunused-variable] 2022-05-08T11:02:01,947 3042 | int i, k, best; 2022-05-08T11:02:01,947 | ^ 2022-05-08T11:02:01,957 src/pulchra.hpp: In member function ‘pulchra::PulchraResult pulchra::Pulchra::run_from_mol(std::shared_ptr)’: 2022-05-08T11:02:01,957 src/pulchra.hpp:3116:13: warning: unused variable ‘chain_length’ [-Wunused-variable] 2022-05-08T11:02:01,958 3116 | int const chain_length = chain->nres; 2022-05-08T11:02:01,958 | ^~~~~~~~~~~~ 2022-05-08T11:02:01,983 In file included from bindings/python/pulchra_bindings.cpp:5: 2022-05-08T11:02:01,984 src/pulchra.hpp: In member function ‘int pulchra::Pulchra::main(int, char**)’: 2022-05-08T11:02:01,984 src/pulchra.hpp:3315:41: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 2 has type ‘std::chrono::duration::rep’ {aka ‘long long int’} [-Wformat=] 2022-05-08T11:02:01,985 3315 | "Done. Reconstruction finished in %ld s.\n", 2022-05-08T11:02:01,985 | ~~^ 2022-05-08T11:02:01,985 | | 2022-05-08T11:02:01,986 | long int 2022-05-08T11:02:01,986 | %lld 2022-05-08T11:02:01,986 3316 | std::chrono::duration_cast(time1 - time0) 2022-05-08T11:02:01,987 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-05-08T11:02:01,987 3317 | .count()); 2022-05-08T11:02:01,987 | ~~~~~~~~ 2022-05-08T11:02:01,987 | | 2022-05-08T11:02:01,988 | std::chrono::duration::rep {aka long long int} 2022-05-08T11:02:01,988 In file included from bindings/python/pulchra_bindings.cpp:5: 2022-05-08T11:02:01,988 src/pulchra.hpp:3145:8: warning: unused variable ‘buf’ [-Wunused-variable] 2022-05-08T11:02:01,989 3145 | char buf[100]; 2022-05-08T11:02:01,989 | ^~~ 2022-05-08T11:02:01,989 src/pulchra.hpp:3146:23: warning: variable ‘ini_name’ set but not used [-Wunused-but-set-variable] 2022-05-08T11:02:01,990 3146 | char *name = NULL, *ini_name = NULL, *output_pdb_name=NULL, *output_traj_pdb_name=NULL; 2022-05-08T11:02:01,990 | ^~~~~~~~ 2022-05-08T11:02:01,990 src/pulchra.hpp:3147:9: warning: unused variable ‘ptr’ [-Wunused-variable] 2022-05-08T11:02:01,991 3147 | char *ptr, out_name[1000]; 2022-05-08T11:02:01,991 | ^~~ 2022-05-08T11:02:01,991 src/pulchra.hpp:3147:14: warning: unused variable ‘out_name’ [-Wunused-variable] 2022-05-08T11:02:01,991 3147 | char *ptr, out_name[1000]; 2022-05-08T11:02:01,992 | ^~~~~~~~ 2022-05-08T11:02:36,674 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DVERSION_INFO=1.0.0 -Isrc -I/tmp/pip-build-env-dkd2qr0p/overlay/lib/python3.9/site-packages/pybind11/include -I/usr/include/python3.9 -c bindings/python/pypulchra_bindings.cpp -o build/temp.linux-armv7l-3.9/bindings/python/pypulchra_bindings.o -fvisibility=hidden -g0 -std=c++14 -static 2022-05-08T11:03:06,556 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DVERSION_INFO=1.0.0 -Isrc -I/tmp/pip-build-env-dkd2qr0p/overlay/lib/python3.9/site-packages/pybind11/include -I/usr/include/python3.9 -c src/pulchra.cpp -o build/temp.linux-armv7l-3.9/src/pulchra.o -fvisibility=hidden -g0 -std=c++14 -static 2022-05-08T11:03:25,070 In file included from src/pulchra.cpp:20: 2022-05-08T11:03:25,071 src/pulchra.hpp: In member function ‘int pulchra::Pulchra::read_pdb_buffer(std::stringstream&, std::shared_ptr)’: 2022-05-08T11:03:25,071 src/pulchra.hpp:653:34: warning: array subscript has type ‘char’ [-Wchar-subscripts] 2022-05-08T11:03:25,072 653 | res->type = AA_NUMS[pusetseq(resname)]; 2022-05-08T11:03:25,072 | ~~~~~~~~^~~~~~~~~ 2022-05-08T11:03:25,087 src/pulchra.hpp:594:8: warning: variable ‘version’ set but not used [-Wunused-but-set-variable] 2022-05-08T11:03:25,088 594 | char version; 2022-05-08T11:03:25,088 | ^~~~~~~ 2022-05-08T11:03:25,089 src/pulchra.hpp:595:46: warning: unused variable ‘num’ [-Wunused-variable] 2022-05-08T11:03:25,089 595 | int prevresnum, resnum, atmnum, locatmnum, num, locnum = 0, i, j; 2022-05-08T11:03:25,089 | ^~~ 2022-05-08T11:03:25,090 src/pulchra.hpp:595:63: warning: variable ‘i’ set but not used [-Wunused-but-set-variable] 2022-05-08T11:03:25,090 595 | int prevresnum, resnum, atmnum, locatmnum, num, locnum = 0, i, j; 2022-05-08T11:03:25,090 | ^ 2022-05-08T11:03:25,090 src/pulchra.hpp:595:66: warning: unused variable ‘j’ [-Wunused-variable] 2022-05-08T11:03:25,091 595 | int prevresnum, resnum, atmnum, locatmnum, num, locnum = 0, i, j; 2022-05-08T11:03:25,091 | ^ 2022-05-08T11:03:25,091 src/pulchra.hpp:597:14: warning: unused variable ‘cc’ [-Wunused-variable] 2022-05-08T11:03:25,092 597 | int sgnum, cc, nres, ok, natom; 2022-05-08T11:03:25,092 | ^~ 2022-05-08T11:03:25,092 src/pulchra.hpp:597:18: warning: unused variable ‘nres’ [-Wunused-variable] 2022-05-08T11:03:25,093 597 | int sgnum, cc, nres, ok, natom; 2022-05-08T11:03:25,093 | ^~~~ 2022-05-08T11:03:25,093 src/pulchra.hpp:597:24: warning: unused variable ‘ok’ [-Wunused-variable] 2022-05-08T11:03:25,094 597 | int sgnum, cc, nres, ok, natom; 2022-05-08T11:03:25,094 | ^~ 2022-05-08T11:03:25,094 src/pulchra.hpp:597:28: warning: unused variable ‘natom’ [-Wunused-variable] 2022-05-08T11:03:25,095 597 | int sgnum, cc, nres, ok, natom; 2022-05-08T11:03:25,095 | ^~~~~ 2022-05-08T11:03:25,095 src/pulchra.hpp:602:10: warning: unused variable ‘dist’ [-Wunused-variable] 2022-05-08T11:03:25,096 602 | double dist; 2022-05-08T11:03:25,096 | ^~~~ 2022-05-08T11:03:25,096 src/pulchra.hpp:603:17: warning: unused variable ‘bin’ [-Wunused-variable] 2022-05-08T11:03:25,097 603 | unsigned char bin; 2022-05-08T11:03:25,097 | ^~~ 2022-05-08T11:03:25,097 src/pulchra.hpp:604:7: warning: variable ‘warn’ set but not used [-Wunused-but-set-variable] 2022-05-08T11:03:25,098 604 | int warn = 0; 2022-05-08T11:03:25,098 | ^~~~ 2022-05-08T11:03:25,098 src/pulchra.hpp:605:10: warning: unused variable ‘cutoff’ [-Wunused-variable] 2022-05-08T11:03:25,099 605 | double cutoff; 2022-05-08T11:03:25,099 | ^~~~~~ 2022-05-08T11:03:25,134 src/pulchra.hpp: In member function ‘double pulchra::Pulchra::calc_ca_energy(const std::vector >&, double**, double**, double**, double, double*, bool, int)’: 2022-05-08T11:03:25,135 src/pulchra.hpp:775:10: warning: unused variable ‘theta0’ [-Wunused-variable] 2022-05-08T11:03:25,135 775 | double theta0, tdif, th, aa, bb, ab; 2022-05-08T11:03:25,136 | ^~~~~~ 2022-05-08T11:03:25,136 src/pulchra.hpp:775:18: warning: unused variable ‘tdif’ [-Wunused-variable] 2022-05-08T11:03:25,136 775 | double theta0, tdif, th, aa, bb, ab; 2022-05-08T11:03:25,137 | ^~~~ 2022-05-08T11:03:25,137 src/pulchra.hpp:775:24: warning: unused variable ‘th’ [-Wunused-variable] 2022-05-08T11:03:25,137 775 | double theta0, tdif, th, aa, bb, ab; 2022-05-08T11:03:25,137 | ^~ 2022-05-08T11:03:25,138 src/pulchra.hpp:775:28: warning: unused variable ‘aa’ [-Wunused-variable] 2022-05-08T11:03:25,138 775 | double theta0, tdif, th, aa, bb, ab; 2022-05-08T11:03:25,138 | ^~ 2022-05-08T11:03:25,139 src/pulchra.hpp:775:32: warning: unused variable ‘bb’ [-Wunused-variable] 2022-05-08T11:03:25,139 775 | double theta0, tdif, th, aa, bb, ab; 2022-05-08T11:03:25,139 | ^~ 2022-05-08T11:03:25,139 src/pulchra.hpp:775:36: warning: unused variable ‘ab’ [-Wunused-variable] 2022-05-08T11:03:25,140 775 | double theta0, tdif, th, aa, bb, ab; 2022-05-08T11:03:25,140 | ^~ 2022-05-08T11:03:25,140 src/pulchra.hpp:776:10: warning: unused variable ‘ff0’ [-Wunused-variable] 2022-05-08T11:03:25,141 776 | double ff0, ff2, dth, m0, m2, grad, f0[3], f2[3]; 2022-05-08T11:03:25,141 | ^~~ 2022-05-08T11:03:25,141 src/pulchra.hpp:776:15: warning: unused variable ‘ff2’ [-Wunused-variable] 2022-05-08T11:03:25,142 776 | double ff0, ff2, dth, m0, m2, grad, f0[3], f2[3]; 2022-05-08T11:03:25,142 | ^~~ 2022-05-08T11:03:25,142 src/pulchra.hpp:776:20: warning: unused variable ‘dth’ [-Wunused-variable] 2022-05-08T11:03:25,143 776 | double ff0, ff2, dth, m0, m2, grad, f0[3], f2[3]; 2022-05-08T11:03:25,143 | ^~~ 2022-05-08T11:03:25,143 src/pulchra.hpp:776:25: warning: unused variable ‘m0’ [-Wunused-variable] 2022-05-08T11:03:25,144 776 | double ff0, ff2, dth, m0, m2, grad, f0[3], f2[3]; 2022-05-08T11:03:25,144 | ^~ 2022-05-08T11:03:25,144 src/pulchra.hpp:776:29: warning: unused variable ‘m2’ [-Wunused-variable] 2022-05-08T11:03:25,145 776 | double ff0, ff2, dth, m0, m2, grad, f0[3], f2[3]; 2022-05-08T11:03:25,145 | ^~ 2022-05-08T11:03:25,146 src/pulchra.hpp:776:39: warning: unused variable ‘f0’ [-Wunused-variable] 2022-05-08T11:03:25,146 776 | double ff0, ff2, dth, m0, m2, grad, f0[3], f2[3]; 2022-05-08T11:03:25,147 | ^~ 2022-05-08T11:03:25,147 src/pulchra.hpp:776:46: warning: unused variable ‘f2’ [-Wunused-variable] 2022-05-08T11:03:25,148 776 | double ff0, ff2, dth, m0, m2, grad, f0[3], f2[3]; 2022-05-08T11:03:25,148 | ^~ 2022-05-08T11:03:25,148 src/pulchra.hpp:777:10: warning: unused variable ‘adiff’ [-Wunused-variable] 2022-05-08T11:03:25,149 777 | double adiff[3], bdiff[3]; 2022-05-08T11:03:25,149 | ^~~~~ 2022-05-08T11:03:25,150 src/pulchra.hpp:777:20: warning: unused variable ‘bdiff’ [-Wunused-variable] 2022-05-08T11:03:25,150 777 | double adiff[3], bdiff[3]; 2022-05-08T11:03:25,151 | ^~~~~ 2022-05-08T11:03:25,151 src/pulchra.hpp:778:10: warning: unused variable ‘deriv’ [-Wunused-variable] 2022-05-08T11:03:25,152 778 | double deriv, theta, dtheta, len1, len2, cos_theta, sin_theta; 2022-05-08T11:03:25,153 | ^~~~~ 2022-05-08T11:03:25,153 src/pulchra.hpp:778:24: warning: unused variable ‘dtheta’ [-Wunused-variable] 2022-05-08T11:03:25,154 778 | double deriv, theta, dtheta, len1, len2, cos_theta, sin_theta; 2022-05-08T11:03:25,155 | ^~~~~~ 2022-05-08T11:03:25,155 src/pulchra.hpp:778:32: warning: unused variable ‘len1’ [-Wunused-variable] 2022-05-08T11:03:25,156 778 | double deriv, theta, dtheta, len1, len2, cos_theta, sin_theta; 2022-05-08T11:03:25,156 | ^~~~ 2022-05-08T11:03:25,157 src/pulchra.hpp:778:38: warning: unused variable ‘len2’ [-Wunused-variable] 2022-05-08T11:03:25,157 778 | double deriv, theta, dtheta, len1, len2, cos_theta, sin_theta; 2022-05-08T11:03:25,158 | ^~~~ 2022-05-08T11:03:25,158 src/pulchra.hpp:779:10: warning: unused variable ‘dx1’ [-Wunused-variable] 2022-05-08T11:03:25,158 779 | double dx1, dy1, dz1; 2022-05-08T11:03:25,158 | ^~~ 2022-05-08T11:03:25,159 src/pulchra.hpp:779:15: warning: unused variable ‘dy1’ [-Wunused-variable] 2022-05-08T11:03:25,159 779 | double dx1, dy1, dz1; 2022-05-08T11:03:25,159 | ^~~ 2022-05-08T11:03:25,160 src/pulchra.hpp:779:20: warning: unused variable ‘dz1’ [-Wunused-variable] 2022-05-08T11:03:25,160 779 | double dx1, dy1, dz1; 2022-05-08T11:03:25,160 | ^~~ 2022-05-08T11:03:25,161 src/pulchra.hpp:780:10: warning: unused variable ‘dx2’ [-Wunused-variable] 2022-05-08T11:03:25,161 780 | double dx2, dy2, dz2; 2022-05-08T11:03:25,162 | ^~~ 2022-05-08T11:03:25,162 src/pulchra.hpp:780:15: warning: unused variable ‘dy2’ [-Wunused-variable] 2022-05-08T11:03:25,162 780 | double dx2, dy2, dz2; 2022-05-08T11:03:25,163 | ^~~ 2022-05-08T11:03:25,163 src/pulchra.hpp:780:20: warning: unused variable ‘dz2’ [-Wunused-variable] 2022-05-08T11:03:25,163 780 | double dx2, dy2, dz2; 2022-05-08T11:03:25,164 | ^~~ 2022-05-08T11:03:25,164 src/pulchra.hpp:781:10: warning: unused variable ‘dx3’ [-Wunused-variable] 2022-05-08T11:03:25,164 781 | double dx3, dy3, dz3; 2022-05-08T11:03:25,165 | ^~~ 2022-05-08T11:03:25,165 src/pulchra.hpp:781:15: warning: unused variable ‘dy3’ [-Wunused-variable] 2022-05-08T11:03:25,165 781 | double dx3, dy3, dz3; 2022-05-08T11:03:25,166 | ^~~ 2022-05-08T11:03:25,166 src/pulchra.hpp:781:20: warning: unused variable ‘dz3’ [-Wunused-variable] 2022-05-08T11:03:25,166 781 | double dx3, dy3, dz3; 2022-05-08T11:03:25,167 | ^~~ 2022-05-08T11:03:25,167 src/pulchra.hpp:782:10: warning: unused variable ‘vx1’ [-Wunused-variable] 2022-05-08T11:03:25,167 782 | double vx1, vy1, vz1; 2022-05-08T11:03:25,167 | ^~~ 2022-05-08T11:03:25,168 src/pulchra.hpp:782:15: warning: unused variable ‘vy1’ [-Wunused-variable] 2022-05-08T11:03:25,168 782 | double vx1, vy1, vz1; 2022-05-08T11:03:25,168 | ^~~ 2022-05-08T11:03:25,169 src/pulchra.hpp:782:20: warning: unused variable ‘vz1’ [-Wunused-variable] 2022-05-08T11:03:25,169 782 | double vx1, vy1, vz1; 2022-05-08T11:03:25,169 | ^~~ 2022-05-08T11:03:25,170 src/pulchra.hpp:783:10: warning: unused variable ‘vx2’ [-Wunused-variable] 2022-05-08T11:03:25,170 783 | double vx2, vy2, vz2; 2022-05-08T11:03:25,170 | ^~~ 2022-05-08T11:03:25,171 src/pulchra.hpp:783:15: warning: unused variable ‘vy2’ [-Wunused-variable] 2022-05-08T11:03:25,171 783 | double vx2, vy2, vz2; 2022-05-08T11:03:25,171 | ^~~ 2022-05-08T11:03:25,171 src/pulchra.hpp:783:20: warning: unused variable ‘vz2’ [-Wunused-variable] 2022-05-08T11:03:25,172 783 | double vx2, vy2, vz2; 2022-05-08T11:03:25,172 | ^~~ 2022-05-08T11:03:25,172 src/pulchra.hpp:784:10: warning: unused variable ‘vx3’ [-Wunused-variable] 2022-05-08T11:03:25,173 784 | double vx3, vy3, vz3; 2022-05-08T11:03:25,173 | ^~~ 2022-05-08T11:03:25,173 src/pulchra.hpp:784:15: warning: unused variable ‘vy3’ [-Wunused-variable] 2022-05-08T11:03:25,174 784 | double vx3, vy3, vz3; 2022-05-08T11:03:25,174 | ^~~ 2022-05-08T11:03:25,174 src/pulchra.hpp:784:20: warning: unused variable ‘vz3’ [-Wunused-variable] 2022-05-08T11:03:25,175 784 | double vx3, vy3, vz3; 2022-05-08T11:03:25,175 | ^~~ 2022-05-08T11:03:25,185 src/pulchra.hpp: In member function ‘std::string pulchra::Pulchra::ca_optimize_from_mol(std::shared_ptr)’: 2022-05-08T11:03:25,186 src/pulchra.hpp:937:8: warning: unused variable ‘buf’ [-Wunused-variable] 2022-05-08T11:03:25,186 937 | char buf[1000]; 2022-05-08T11:03:25,186 | ^~~ 2022-05-08T11:03:25,186 src/pulchra.hpp:938:10: warning: unused variable ‘j’ [-Wunused-variable] 2022-05-08T11:03:25,187 938 | int i, j, hx, my_iter; 2022-05-08T11:03:25,187 | ^ 2022-05-08T11:03:25,188 src/pulchra.hpp:938:13: warning: unused variable ‘hx’ [-Wunused-variable] 2022-05-08T11:03:25,188 938 | int i, j, hx, my_iter; 2022-05-08T11:03:25,189 | ^~ 2022-05-08T11:03:25,189 src/pulchra.hpp:938:17: warning: unused variable ‘my_iter’ [-Wunused-variable] 2022-05-08T11:03:25,189 938 | int i, j, hx, my_iter; 2022-05-08T11:03:25,190 | ^~~~~~~ 2022-05-08T11:03:25,190 src/pulchra.hpp:939:32: warning: unused variable ‘dist2’ [-Wunused-variable] 2022-05-08T11:03:25,190 939 | double dx, dy, dz, dd, dist, dist2, dist3, ddist, ddist2; 2022-05-08T11:03:25,191 | ^~~~~ 2022-05-08T11:03:25,191 src/pulchra.hpp:939:39: warning: unused variable ‘dist3’ [-Wunused-variable] 2022-05-08T11:03:25,191 939 | double dx, dy, dz, dd, dist, dist2, dist3, ddist, ddist2; 2022-05-08T11:03:25,192 | ^~~~~ 2022-05-08T11:03:25,192 src/pulchra.hpp:939:53: warning: variable ‘ddist2’ set but not used [-Wunused-but-set-variable] 2022-05-08T11:03:25,192 939 | double dx, dy, dz, dd, dist, dist2, dist3, ddist, ddist2; 2022-05-08T11:03:25,193 | ^~~~~~ 2022-05-08T11:03:25,193 src/pulchra.hpp:940:17: warning: unused variable ‘new_e_pot’ [-Wunused-variable] 2022-05-08T11:03:25,194 940 | double e_pot, new_e_pot, grad, alpha, e_pot1, e_pot2, e_pot3; 2022-05-08T11:03:25,194 | ^~~~~~~~~ 2022-05-08T11:03:25,195 src/pulchra.hpp:940:28: warning: unused variable ‘grad’ [-Wunused-variable] 2022-05-08T11:03:25,195 940 | double e_pot, new_e_pot, grad, alpha, e_pot1, e_pot2, e_pot3; 2022-05-08T11:03:25,196 | ^~~~ 2022-05-08T11:03:25,197 src/pulchra.hpp:940:34: warning: unused variable ‘alpha’ [-Wunused-variable] 2022-05-08T11:03:25,197 940 | double e_pot, new_e_pot, grad, alpha, e_pot1, e_pot2, e_pot3; 2022-05-08T11:03:25,198 | ^~~~~ 2022-05-08T11:03:25,199 src/pulchra.hpp:942:10: warning: unused variable ‘ff0’ [-Wunused-variable] 2022-05-08T11:03:25,200 942 | double ff0, ff2, aa, ab, bb, th, tdif, dth, m0, m2; 2022-05-08T11:03:25,200 | ^~~ 2022-05-08T11:03:25,200 src/pulchra.hpp:942:15: warning: unused variable ‘ff2’ [-Wunused-variable] 2022-05-08T11:03:25,201 942 | double ff0, ff2, aa, ab, bb, th, tdif, dth, m0, m2; 2022-05-08T11:03:25,201 | ^~~ 2022-05-08T11:03:25,202 src/pulchra.hpp:942:36: warning: unused variable ‘tdif’ [-Wunused-variable] 2022-05-08T11:03:25,202 942 | double ff0, ff2, aa, ab, bb, th, tdif, dth, m0, m2; 2022-05-08T11:03:25,202 | ^~~~ 2022-05-08T11:03:25,203 src/pulchra.hpp:942:42: warning: unused variable ‘dth’ [-Wunused-variable] 2022-05-08T11:03:25,203 942 | double ff0, ff2, aa, ab, bb, th, tdif, dth, m0, m2; 2022-05-08T11:03:25,203 | ^~~ 2022-05-08T11:03:25,204 src/pulchra.hpp:942:47: warning: unused variable ‘m0’ [-Wunused-variable] 2022-05-08T11:03:25,204 942 | double ff0, ff2, aa, ab, bb, th, tdif, dth, m0, m2; 2022-05-08T11:03:25,204 | ^~ 2022-05-08T11:03:25,205 src/pulchra.hpp:942:51: warning: unused variable ‘m2’ [-Wunused-variable] 2022-05-08T11:03:25,205 942 | double ff0, ff2, aa, ab, bb, th, tdif, dth, m0, m2; 2022-05-08T11:03:25,205 | ^~ 2022-05-08T11:03:25,206 src/pulchra.hpp:943:26: warning: unused variable ‘maxgrad’ [-Wunused-variable] 2022-05-08T11:03:25,206 943 | double theta0, deg_th, maxgrad, sum; 2022-05-08T11:03:25,206 | ^~~~~~~ 2022-05-08T11:03:25,207 src/pulchra.hpp:943:35: warning: unused variable ‘sum’ [-Wunused-variable] 2022-05-08T11:03:25,207 943 | double theta0, deg_th, maxgrad, sum; 2022-05-08T11:03:25,207 | ^~~ 2022-05-08T11:03:25,208 src/pulchra.hpp:944:10: warning: unused variable ‘f0’ [-Wunused-variable] 2022-05-08T11:03:25,208 944 | double f0[3], f2[3]; 2022-05-08T11:03:25,208 | ^~ 2022-05-08T11:03:25,209 src/pulchra.hpp:944:17: warning: unused variable ‘f2’ [-Wunused-variable] 2022-05-08T11:03:25,209 944 | double f0[3], f2[3]; 2022-05-08T11:03:25,209 | ^~ 2022-05-08T11:03:25,210 src/pulchra.hpp:945:10: warning: unused variable ‘x’ [-Wunused-variable] 2022-05-08T11:03:25,210 945 | double x, y, z; 2022-05-08T11:03:25,210 | ^ 2022-05-08T11:03:25,211 src/pulchra.hpp:945:13: warning: unused variable ‘y’ [-Wunused-variable] 2022-05-08T11:03:25,211 945 | double x, y, z; 2022-05-08T11:03:25,211 | ^ 2022-05-08T11:03:25,212 src/pulchra.hpp:945:16: warning: unused variable ‘z’ [-Wunused-variable] 2022-05-08T11:03:25,212 945 | double x, y, z; 2022-05-08T11:03:25,212 | ^ 2022-05-08T11:03:25,213 src/pulchra.hpp:947:8: warning: unused variable ‘sec’ [-Wunused-variable] 2022-05-08T11:03:25,213 947 | int *sec; 2022-05-08T11:03:25,213 | ^~~ 2022-05-08T11:03:25,214 src/pulchra.hpp:948:65: warning: unused variable ‘tmp’ [-Wunused-variable] 2022-05-08T11:03:25,214 948 | double **new_c_alpha, **gradient, **init_c_alpha, last_alpha, tmp, 2022-05-08T11:03:25,214 | ^~~ 2022-05-08T11:03:25,215 src/pulchra.hpp:949:4: warning: unused variable ‘last_good_alpha’ [-Wunused-variable] 2022-05-08T11:03:25,215 949 | last_good_alpha, d_alpha, last_e_pot; 2022-05-08T11:03:25,215 | ^~~~~~~~~~~~~~~ 2022-05-08T11:03:25,216 src/pulchra.hpp:949:21: warning: unused variable ‘d_alpha’ [-Wunused-variable] 2022-05-08T11:03:25,216 949 | last_good_alpha, d_alpha, last_e_pot; 2022-05-08T11:03:25,216 | ^~~~~~~ 2022-05-08T11:03:25,217 src/pulchra.hpp:949:30: warning: variable ‘last_e_pot’ set but not used [-Wunused-but-set-variable] 2022-05-08T11:03:25,217 949 | last_good_alpha, d_alpha, last_e_pot; 2022-05-08T11:03:25,217 | ^~~~~~~~~~ 2022-05-08T11:03:25,218 src/pulchra.hpp:953:9: warning: unused variable ‘inp’ [-Wunused-variable] 2022-05-08T11:03:25,218 953 | FILE *inp; 2022-05-08T11:03:25,218 | ^~~ 2022-05-08T11:03:25,218 src/pulchra.hpp:954:19: warning: unused variable ‘ok’ [-Wunused-variable] 2022-05-08T11:03:25,219 954 | int mnum, init, ok; 2022-05-08T11:03:25,219 | ^~ 2022-05-08T11:03:25,220 src/pulchra.hpp:958:10: warning: unused variable ‘w1’ [-Wunused-variable] 2022-05-08T11:03:25,220 958 | double w1, w2, w3, eps; 2022-05-08T11:03:25,220 | ^~ 2022-05-08T11:03:25,221 src/pulchra.hpp:958:14: warning: unused variable ‘w2’ [-Wunused-variable] 2022-05-08T11:03:25,221 958 | double w1, w2, w3, eps; 2022-05-08T11:03:25,221 | ^~ 2022-05-08T11:03:25,222 src/pulchra.hpp:958:18: warning: unused variable ‘w3’ [-Wunused-variable] 2022-05-08T11:03:25,222 958 | double w1, w2, w3, eps; 2022-05-08T11:03:25,222 | ^~ 2022-05-08T11:03:25,223 src/pulchra.hpp:960:7: warning: variable ‘mode’ set but not used [-Wunused-but-set-variable] 2022-05-08T11:03:25,223 960 | int mode, fcnt; 2022-05-08T11:03:25,223 | ^~~~ 2022-05-08T11:03:25,291 src/pulchra.hpp: In member function ‘void pulchra::Pulchra::prepare_rbins(std::shared_ptr)’: 2022-05-08T11:03:25,292 src/pulchra.hpp:1724:16: warning: unused variable ‘l’ [-Wunused-variable] 2022-05-08T11:03:25,292 1724 | int i, j, k, l, m, bin13_1, bin13_2, bin14, found, pro; 2022-05-08T11:03:25,292 | ^ 2022-05-08T11:03:25,293 src/pulchra.hpp:1724:19: warning: unused variable ‘m’ [-Wunused-variable] 2022-05-08T11:03:25,293 1724 | int i, j, k, l, m, bin13_1, bin13_2, bin14, found, pro; 2022-05-08T11:03:25,293 | ^ 2022-05-08T11:03:25,294 src/pulchra.hpp:1724:47: warning: unused variable ‘found’ [-Wunused-variable] 2022-05-08T11:03:25,294 1724 | int i, j, k, l, m, bin13_1, bin13_2, bin14, found, pro; 2022-05-08T11:03:25,294 | ^~~~~ 2022-05-08T11:03:25,295 src/pulchra.hpp:1724:54: warning: unused variable ‘pro’ [-Wunused-variable] 2022-05-08T11:03:25,295 1724 | int i, j, k, l, m, bin13_1, bin13_2, bin14, found, pro; 2022-05-08T11:03:25,295 | ^~~ 2022-05-08T11:03:25,295 src/pulchra.hpp:1725:7: warning: unused variable ‘b13_1’ [-Wunused-variable] 2022-05-08T11:03:25,296 1725 | int b13_1, b13_2, b14; 2022-05-08T11:03:25,296 | ^~~~~ 2022-05-08T11:03:25,296 src/pulchra.hpp:1725:14: warning: unused variable ‘b13_2’ [-Wunused-variable] 2022-05-08T11:03:25,297 1725 | int b13_1, b13_2, b14; 2022-05-08T11:03:25,297 | ^~~~~ 2022-05-08T11:03:25,297 src/pulchra.hpp:1725:21: warning: unused variable ‘b14’ [-Wunused-variable] 2022-05-08T11:03:25,298 1725 | int b13_1, b13_2, b14; 2022-05-08T11:03:25,298 | ^~~ 2022-05-08T11:03:25,316 src/pulchra.hpp: In member function ‘void pulchra::Pulchra::rebuild_backbone(std::shared_ptr)’: 2022-05-08T11:03:25,316 src/pulchra.hpp:1852:16: warning: unused variable ‘l’ [-Wunused-variable] 2022-05-08T11:03:25,316 1852 | int i, j, k, l, m, bin13_1, bin13_2, bin14, found, pro; 2022-05-08T11:03:25,317 | ^ 2022-05-08T11:03:25,317 src/pulchra.hpp:1852:19: warning: unused variable ‘m’ [-Wunused-variable] 2022-05-08T11:03:25,317 1852 | int i, j, k, l, m, bin13_1, bin13_2, bin14, found, pro; 2022-05-08T11:03:25,318 | ^ 2022-05-08T11:03:25,318 src/pulchra.hpp:1852:47: warning: unused variable ‘found’ [-Wunused-variable] 2022-05-08T11:03:25,318 1852 | int i, j, k, l, m, bin13_1, bin13_2, bin14, found, pro; 2022-05-08T11:03:25,319 | ^~~~~ 2022-05-08T11:03:25,319 src/pulchra.hpp:1852:54: warning: variable ‘pro’ set but not used [-Wunused-but-set-variable] 2022-05-08T11:03:25,319 1852 | int i, j, k, l, m, bin13_1, bin13_2, bin14, found, pro; 2022-05-08T11:03:25,319 | ^~~ 2022-05-08T11:03:25,320 src/pulchra.hpp:1853:7: warning: unused variable ‘b13_1’ [-Wunused-variable] 2022-05-08T11:03:25,320 1853 | int b13_1, b13_2, b14; 2022-05-08T11:03:25,320 | ^~~~~ 2022-05-08T11:03:25,321 src/pulchra.hpp:1853:14: warning: unused variable ‘b13_2’ [-Wunused-variable] 2022-05-08T11:03:25,321 1853 | int b13_1, b13_2, b14; 2022-05-08T11:03:25,321 | ^~~~~ 2022-05-08T11:03:25,322 src/pulchra.hpp:1853:21: warning: unused variable ‘b14’ [-Wunused-variable] 2022-05-08T11:03:25,322 1853 | int b13_1, b13_2, b14; 2022-05-08T11:03:25,322 | ^~~ 2022-05-08T11:03:25,353 src/pulchra.hpp: In member function ‘void pulchra::Pulchra::rebuild_sidechains(std::shared_ptr)’: 2022-05-08T11:03:25,353 src/pulchra.hpp:2023:12: warning: unused variable ‘cacoords’ [-Wunused-variable] 2022-05-08T11:03:25,354 2023 | double **cacoords, **tmpcoords, **tmpstat; 2022-05-08T11:03:25,354 | ^~~~~~~~ 2022-05-08T11:03:25,355 src/pulchra.hpp:2023:24: warning: unused variable ‘tmpcoords’ [-Wunused-variable] 2022-05-08T11:03:25,355 2023 | double **cacoords, **tmpcoords, **tmpstat; 2022-05-08T11:03:25,355 | ^~~~~~~~~ 2022-05-08T11:03:25,355 src/pulchra.hpp:2023:37: warning: unused variable ‘tmpstat’ [-Wunused-variable] 2022-05-08T11:03:25,356 2023 | double **cacoords, **tmpcoords, **tmpstat; 2022-05-08T11:03:25,356 | ^~~~~~~ 2022-05-08T11:03:25,356 src/pulchra.hpp:2024:10: warning: variable ‘x1’ set but not used [-Wunused-but-set-variable] 2022-05-08T11:03:25,357 2024 | double x1, y1, z1; 2022-05-08T11:03:25,357 | ^~ 2022-05-08T11:03:25,357 src/pulchra.hpp:2024:14: warning: variable ‘y1’ set but not used [-Wunused-but-set-variable] 2022-05-08T11:03:25,357 2024 | double x1, y1, z1; 2022-05-08T11:03:25,358 | ^~ 2022-05-08T11:03:25,358 src/pulchra.hpp:2024:18: warning: variable ‘z1’ set but not used [-Wunused-but-set-variable] 2022-05-08T11:03:25,358 2024 | double x1, y1, z1; 2022-05-08T11:03:25,359 | ^~ 2022-05-08T11:03:25,359 src/pulchra.hpp:2028:10: warning: unused variable ‘x5’ [-Wunused-variable] 2022-05-08T11:03:25,359 2028 | double x5, y5, z5; 2022-05-08T11:03:25,359 | ^~ 2022-05-08T11:03:25,360 src/pulchra.hpp:2028:14: warning: unused variable ‘y5’ [-Wunused-variable] 2022-05-08T11:03:25,360 2028 | double x5, y5, z5; 2022-05-08T11:03:25,360 | ^~ 2022-05-08T11:03:25,361 src/pulchra.hpp:2028:18: warning: unused variable ‘z5’ [-Wunused-variable] 2022-05-08T11:03:25,361 2028 | double x5, y5, z5; 2022-05-08T11:03:25,361 | ^~ 2022-05-08T11:03:25,361 src/pulchra.hpp:2029:10: warning: unused variable ‘r14’ [-Wunused-variable] 2022-05-08T11:03:25,362 2029 | double r14, r13_1, r13_2; 2022-05-08T11:03:25,362 | ^~~ 2022-05-08T11:03:25,362 src/pulchra.hpp:2029:15: warning: unused variable ‘r13_1’ [-Wunused-variable] 2022-05-08T11:03:25,363 2029 | double r14, r13_1, r13_2; 2022-05-08T11:03:25,363 | ^~~~~ 2022-05-08T11:03:25,363 src/pulchra.hpp:2029:22: warning: unused variable ‘r13_2’ [-Wunused-variable] 2022-05-08T11:03:25,364 2029 | double r14, r13_1, r13_2; 2022-05-08T11:03:25,364 | ^~~~~ 2022-05-08T11:03:25,364 src/pulchra.hpp:2030:10: warning: unused variable ‘dx’ [-Wunused-variable] 2022-05-08T11:03:25,365 2030 | double dx, dy, dz, dd; 2022-05-08T11:03:25,365 | ^~ 2022-05-08T11:03:25,365 src/pulchra.hpp:2030:14: warning: unused variable ‘dy’ [-Wunused-variable] 2022-05-08T11:03:25,365 2030 | double dx, dy, dz, dd; 2022-05-08T11:03:25,366 | ^~ 2022-05-08T11:03:25,366 src/pulchra.hpp:2030:18: warning: unused variable ‘dz’ [-Wunused-variable] 2022-05-08T11:03:25,366 2030 | double dx, dy, dz, dd; 2022-05-08T11:03:25,367 | ^~ 2022-05-08T11:03:25,367 src/pulchra.hpp:2030:22: warning: unused variable ‘dd’ [-Wunused-variable] 2022-05-08T11:03:25,367 2030 | double dx, dy, dz, dd; 2022-05-08T11:03:25,367 | ^~ 2022-05-08T11:03:25,368 src/pulchra.hpp:2031:15: warning: variable ‘besthit’ set but not used [-Wunused-but-set-variable] 2022-05-08T11:03:25,368 2031 | double hit, besthit; 2022-05-08T11:03:25,368 | ^~~~~~~ 2022-05-08T11:03:25,369 src/pulchra.hpp:2032:7: warning: unused variable ‘exvol’ [-Wunused-variable] 2022-05-08T11:03:25,369 2032 | int exvol, bestpos; 2022-05-08T11:03:25,369 | ^~~~~ 2022-05-08T11:03:25,370 src/pulchra.hpp:2034:10: warning: unused variable ‘rmsd’ [-Wunused-variable] 2022-05-08T11:03:25,370 2034 | double rmsd, total; 2022-05-08T11:03:25,370 | ^~~~ 2022-05-08T11:03:25,370 src/pulchra.hpp:2034:16: warning: unused variable ‘total’ [-Wunused-variable] 2022-05-08T11:03:25,371 2034 | double rmsd, total; 2022-05-08T11:03:25,371 | ^~~~~ 2022-05-08T11:03:25,371 src/pulchra.hpp:2036:12: warning: unused variable ‘nca’ [-Wunused-variable] 2022-05-08T11:03:25,372 2036 | int nsc, nca; 2022-05-08T11:03:25,372 | ^~~ 2022-05-08T11:03:25,372 src/pulchra.hpp:2037:10: warning: unused variable ‘cax’ [-Wunused-variable] 2022-05-08T11:03:25,372 2037 | double cax, cay, caz; 2022-05-08T11:03:25,373 | ^~~ 2022-05-08T11:03:25,373 src/pulchra.hpp:2037:15: warning: unused variable ‘cay’ [-Wunused-variable] 2022-05-08T11:03:25,373 2037 | double cax, cay, caz; 2022-05-08T11:03:25,374 | ^~~ 2022-05-08T11:03:25,374 src/pulchra.hpp:2037:20: warning: unused variable ‘caz’ [-Wunused-variable] 2022-05-08T11:03:25,374 2037 | double cax, cay, caz; 2022-05-08T11:03:25,375 | ^~~ 2022-05-08T11:03:25,375 src/pulchra.hpp:2039:8: warning: unused variable ‘scn’ [-Wunused-variable] 2022-05-08T11:03:25,375 2039 | char scn[12][4]; 2022-05-08T11:03:25,376 | ^~~ 2022-05-08T11:03:25,376 src/pulchra.hpp:2040:7: warning: unused variable ‘ok’ [-Wunused-variable] 2022-05-08T11:03:25,376 2040 | int ok, last_a, last_b, last_c, last_d, jpos; 2022-05-08T11:03:25,376 | ^~ 2022-05-08T11:03:25,377 src/pulchra.hpp:2040:11: warning: unused variable ‘last_a’ [-Wunused-variable] 2022-05-08T11:03:25,377 2040 | int ok, last_a, last_b, last_c, last_d, jpos; 2022-05-08T11:03:25,377 | ^~~~~~ 2022-05-08T11:03:25,378 src/pulchra.hpp:2040:19: warning: unused variable ‘last_b’ [-Wunused-variable] 2022-05-08T11:03:25,378 2040 | int ok, last_a, last_b, last_c, last_d, jpos; 2022-05-08T11:03:25,378 | ^~~~~~ 2022-05-08T11:03:25,378 src/pulchra.hpp:2040:27: warning: unused variable ‘last_c’ [-Wunused-variable] 2022-05-08T11:03:25,379 2040 | int ok, last_a, last_b, last_c, last_d, jpos; 2022-05-08T11:03:25,379 | ^~~~~~ 2022-05-08T11:03:25,379 src/pulchra.hpp:2040:35: warning: unused variable ‘last_d’ [-Wunused-variable] 2022-05-08T11:03:25,380 2040 | int ok, last_a, last_b, last_c, last_d, jpos; 2022-05-08T11:03:25,380 | ^~~~~~ 2022-05-08T11:03:25,380 src/pulchra.hpp:2040:43: warning: unused variable ‘jpos’ [-Wunused-variable] 2022-05-08T11:03:25,381 2040 | int ok, last_a, last_b, last_c, last_d, jpos; 2022-05-08T11:03:25,381 | ^~~~ 2022-05-08T11:03:25,381 src/pulchra.hpp:2041:7: warning: unused variable ‘jx’ [-Wunused-variable] 2022-05-08T11:03:25,382 2041 | int jx, jy, jz, jxi, jyi, jzi, b13_1, b13_2, b14, jm; 2022-05-08T11:03:25,382 | ^~ 2022-05-08T11:03:25,382 src/pulchra.hpp:2041:11: warning: unused variable ‘jy’ [-Wunused-variable] 2022-05-08T11:03:25,383 2041 | int jx, jy, jz, jxi, jyi, jzi, b13_1, b13_2, b14, jm; 2022-05-08T11:03:25,383 | ^~ 2022-05-08T11:03:25,383 src/pulchra.hpp:2041:15: warning: unused variable ‘jz’ [-Wunused-variable] 2022-05-08T11:03:25,384 2041 | int jx, jy, jz, jxi, jyi, jzi, b13_1, b13_2, b14, jm; 2022-05-08T11:03:25,384 | ^~ 2022-05-08T11:03:25,384 src/pulchra.hpp:2041:19: warning: unused variable ‘jxi’ [-Wunused-variable] 2022-05-08T11:03:25,385 2041 | int jx, jy, jz, jxi, jyi, jzi, b13_1, b13_2, b14, jm; 2022-05-08T11:03:25,385 | ^~~ 2022-05-08T11:03:25,385 src/pulchra.hpp:2041:24: warning: unused variable ‘jyi’ [-Wunused-variable] 2022-05-08T11:03:25,386 2041 | int jx, jy, jz, jxi, jyi, jzi, b13_1, b13_2, b14, jm; 2022-05-08T11:03:25,386 | ^~~ 2022-05-08T11:03:25,386 src/pulchra.hpp:2041:29: warning: unused variable ‘jzi’ [-Wunused-variable] 2022-05-08T11:03:25,387 2041 | int jx, jy, jz, jxi, jyi, jzi, b13_1, b13_2, b14, jm; 2022-05-08T11:03:25,387 | ^~~ 2022-05-08T11:03:25,387 src/pulchra.hpp:2041:34: warning: unused variable ‘b13_1’ [-Wunused-variable] 2022-05-08T11:03:25,387 2041 | int jx, jy, jz, jxi, jyi, jzi, b13_1, b13_2, b14, jm; 2022-05-08T11:03:25,388 | ^~~~~ 2022-05-08T11:03:25,388 src/pulchra.hpp:2041:41: warning: unused variable ‘b13_2’ [-Wunused-variable] 2022-05-08T11:03:25,388 2041 | int jx, jy, jz, jxi, jyi, jzi, b13_1, b13_2, b14, jm; 2022-05-08T11:03:25,389 | ^~~~~ 2022-05-08T11:03:25,389 src/pulchra.hpp:2041:48: warning: unused variable ‘b14’ [-Wunused-variable] 2022-05-08T11:03:25,389 2041 | int jx, jy, jz, jxi, jyi, jzi, b13_1, b13_2, b14, jm; 2022-05-08T11:03:25,389 | ^~~ 2022-05-08T11:03:25,390 src/pulchra.hpp:2041:53: warning: unused variable ‘jm’ [-Wunused-variable] 2022-05-08T11:03:25,390 2041 | int jx, jy, jz, jxi, jyi, jzi, b13_1, b13_2, b14, jm; 2022-05-08T11:03:25,390 | ^~ 2022-05-08T11:03:25,391 src/pulchra.hpp:2042:13: warning: unused variable ‘bestrot’ [-Wunused-variable] 2022-05-08T11:03:25,391 2042 | int crot, bestrot, minexvol, totexvol, rtried, pos, cpos; 2022-05-08T11:03:25,391 | ^~~~~~~ 2022-05-08T11:03:25,392 src/pulchra.hpp:2042:22: warning: unused variable ‘minexvol’ [-Wunused-variable] 2022-05-08T11:03:25,392 2042 | int crot, bestrot, minexvol, totexvol, rtried, pos, cpos; 2022-05-08T11:03:25,392 | ^~~~~~~~ 2022-05-08T11:03:25,392 src/pulchra.hpp:2042:32: warning: variable ‘totexvol’ set but not used [-Wunused-but-set-variable] 2022-05-08T11:03:25,393 2042 | int crot, bestrot, minexvol, totexvol, rtried, pos, cpos; 2022-05-08T11:03:25,393 | ^~~~~~~~ 2022-05-08T11:03:25,393 src/pulchra.hpp:2042:42: warning: unused variable ‘rtried’ [-Wunused-variable] 2022-05-08T11:03:25,394 2042 | int crot, bestrot, minexvol, totexvol, rtried, pos, cpos; 2022-05-08T11:03:25,394 | ^~~~~~ 2022-05-08T11:03:25,394 src/pulchra.hpp:2044:10: warning: unused variable ‘sort_rot’ [-Wunused-variable] 2022-05-08T11:03:25,395 2044 | double sort_rot[100][2]; 2022-05-08T11:03:25,395 | ^~~~~~~~ 2022-05-08T11:03:25,435 src/pulchra.hpp: In member function ‘int pulchra::Pulchra::get_conflicts(std::shared_ptr, pulchra::atom_list_3d, int, int, int)’: 2022-05-08T11:03:25,436 src/pulchra.hpp:2264:16: warning: unused variable ‘x’ [-Wunused-variable] 2022-05-08T11:03:25,436 2264 | int i, j, k, x, y, z; 2022-05-08T11:03:25,436 | ^ 2022-05-08T11:03:25,437 src/pulchra.hpp:2264:19: warning: unused variable ‘y’ [-Wunused-variable] 2022-05-08T11:03:25,437 2264 | int i, j, k, x, y, z; 2022-05-08T11:03:25,437 | ^ 2022-05-08T11:03:25,438 src/pulchra.hpp:2264:22: warning: unused variable ‘z’ [-Wunused-variable] 2022-05-08T11:03:25,438 2264 | int i, j, k, x, y, z; 2022-05-08T11:03:25,438 | ^ 2022-05-08T11:03:25,439 src/pulchra.hpp:2265:24: warning: unused variable ‘iter’ [-Wunused-variable] 2022-05-08T11:03:25,439 2265 | int ii, jj, kk, con, iter, maxcon, merged; 2022-05-08T11:03:25,439 | ^~~~ 2022-05-08T11:03:25,440 src/pulchra.hpp:2265:30: warning: unused variable ‘maxcon’ [-Wunused-variable] 2022-05-08T11:03:25,440 2265 | int ii, jj, kk, con, iter, maxcon, merged; 2022-05-08T11:03:25,440 | ^~~~~~ 2022-05-08T11:03:25,462 src/pulchra.hpp: In member function ‘void pulchra::Pulchra::allocate_grid(std::shared_ptr, pulchra::atom_list_3d&, int*, int*, int*)’: 2022-05-08T11:03:25,462 src/pulchra.hpp:2374:7: warning: unused variable ‘i’ [-Wunused-variable] 2022-05-08T11:03:25,463 2374 | int i, j, x, y, z; 2022-05-08T11:03:25,463 | ^ 2022-05-08T11:03:25,463 src/pulchra.hpp:2374:10: warning: unused variable ‘j’ [-Wunused-variable] 2022-05-08T11:03:25,463 2374 | int i, j, x, y, z; 2022-05-08T11:03:25,464 | ^ 2022-05-08T11:03:25,493 src/pulchra.hpp: In member function ‘void pulchra::Pulchra::optimize_exvol(std::shared_ptr)’: 2022-05-08T11:03:25,494 src/pulchra.hpp:2440:10: warning: variable ‘min’ set but not used [-Wunused-but-set-variable] 2022-05-08T11:03:25,494 2440 | double min[3], max[3]; 2022-05-08T11:03:25,494 | ^~~ 2022-05-08T11:03:25,495 src/pulchra.hpp:2440:18: warning: variable ‘max’ set but not used [-Wunused-but-set-variable] 2022-05-08T11:03:25,495 2440 | double min[3], max[3]; 2022-05-08T11:03:25,495 | ^~~ 2022-05-08T11:03:25,495 src/pulchra.hpp:2446:22: warning: unused variable ‘x’ [-Wunused-variable] 2022-05-08T11:03:25,496 2446 | int i, j, k, l, m, x, y, z; 2022-05-08T11:03:25,496 | ^ 2022-05-08T11:03:25,496 src/pulchra.hpp:2446:25: warning: unused variable ‘y’ [-Wunused-variable] 2022-05-08T11:03:25,497 2446 | int i, j, k, l, m, x, y, z; 2022-05-08T11:03:25,497 | ^ 2022-05-08T11:03:25,497 src/pulchra.hpp:2446:28: warning: unused variable ‘z’ [-Wunused-variable] 2022-05-08T11:03:25,497 2446 | int i, j, k, l, m, x, y, z; 2022-05-08T11:03:25,498 | ^ 2022-05-08T11:03:25,498 src/pulchra.hpp:2447:7: warning: unused variable ‘ii’ [-Wunused-variable] 2022-05-08T11:03:25,498 2447 | int ii, jj, kk, con, iter, maxcon, totcon; 2022-05-08T11:03:25,498 | ^~ 2022-05-08T11:03:25,499 src/pulchra.hpp:2447:11: warning: unused variable ‘jj’ [-Wunused-variable] 2022-05-08T11:03:25,499 2447 | int ii, jj, kk, con, iter, maxcon, totcon; 2022-05-08T11:03:25,499 | ^~ 2022-05-08T11:03:25,500 src/pulchra.hpp:2447:15: warning: unused variable ‘kk’ [-Wunused-variable] 2022-05-08T11:03:25,500 2447 | int ii, jj, kk, con, iter, maxcon, totcon; 2022-05-08T11:03:25,500 | ^~ 2022-05-08T11:03:25,501 src/pulchra.hpp:2450:12: warning: unused variable ‘nca’ [-Wunused-variable] 2022-05-08T11:03:25,501 2450 | int nsc, nca; 2022-05-08T11:03:25,501 | ^~~ 2022-05-08T11:03:25,501 src/pulchra.hpp:2451:10: warning: unused variable ‘cax’ [-Wunused-variable] 2022-05-08T11:03:25,502 2451 | double cax, cay, caz; 2022-05-08T11:03:25,502 | ^~~ 2022-05-08T11:03:25,502 src/pulchra.hpp:2451:15: warning: unused variable ‘cay’ [-Wunused-variable] 2022-05-08T11:03:25,503 2451 | double cax, cay, caz; 2022-05-08T11:03:25,503 | ^~~ 2022-05-08T11:03:25,503 src/pulchra.hpp:2451:20: warning: unused variable ‘caz’ [-Wunused-variable] 2022-05-08T11:03:25,504 2451 | double cax, cay, caz; 2022-05-08T11:03:25,504 | ^~~ 2022-05-08T11:03:25,504 src/pulchra.hpp:2453:10: warning: variable ‘x1’ set but not used [-Wunused-but-set-variable] 2022-05-08T11:03:25,505 2453 | double x1, y1, z1; 2022-05-08T11:03:25,505 | ^~ 2022-05-08T11:03:25,505 src/pulchra.hpp:2453:14: warning: variable ‘y1’ set but not used [-Wunused-but-set-variable] 2022-05-08T11:03:25,506 2453 | double x1, y1, z1; 2022-05-08T11:03:25,506 | ^~ 2022-05-08T11:03:25,506 src/pulchra.hpp:2453:18: warning: variable ‘z1’ set but not used [-Wunused-but-set-variable] 2022-05-08T11:03:25,507 2453 | double x1, y1, z1; 2022-05-08T11:03:25,507 | ^~ 2022-05-08T11:03:25,521 src/pulchra.hpp: In member function ‘int pulchra::Pulchra::chirality_check(std::shared_ptr)’: 2022-05-08T11:03:25,521 src/pulchra.hpp:2732:7: warning: unused variable ‘i’ [-Wunused-variable] 2022-05-08T11:03:25,521 2732 | int i; 2022-05-08T11:03:25,522 | ^ 2022-05-08T11:03:25,541 src/pulchra.hpp: In member function ‘double pulchra::Pulchra::hb_energy(std::shared_ptr, pulchra::atom_list_3d&, int, int, int)’: 2022-05-08T11:03:25,541 src/pulchra.hpp:2828:28: warning: unused variable ‘min_dist1’ [-Wunused-variable] 2022-05-08T11:03:25,542 2828 | double dx, dy, dz, dist, min_dist1, min_dist2; 2022-05-08T11:03:25,542 | ^~~~~~~~~ 2022-05-08T11:03:25,569 src/pulchra.hpp: In member function ‘void pulchra::Pulchra::optimize_backbone(std::shared_ptr)’: 2022-05-08T11:03:25,569 src/pulchra.hpp:3042:10: warning: unused variable ‘k’ [-Wunused-variable] 2022-05-08T11:03:25,570 3042 | int i, k, best; 2022-05-08T11:03:25,570 | ^ 2022-05-08T11:03:25,580 src/pulchra.hpp: In member function ‘pulchra::PulchraResult pulchra::Pulchra::run_from_mol(std::shared_ptr)’: 2022-05-08T11:03:25,580 src/pulchra.hpp:3116:13: warning: unused variable ‘chain_length’ [-Wunused-variable] 2022-05-08T11:03:25,580 3116 | int const chain_length = chain->nres; 2022-05-08T11:03:25,581 | ^~~~~~~~~~~~ 2022-05-08T11:03:25,606 In file included from src/pulchra.cpp:20: 2022-05-08T11:03:25,607 src/pulchra.hpp: In member function ‘int pulchra::Pulchra::main(int, char**)’: 2022-05-08T11:03:25,607 src/pulchra.hpp:3315:41: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 2 has type ‘std::chrono::duration::rep’ {aka ‘long long int’} [-Wformat=] 2022-05-08T11:03:25,607 3315 | "Done. Reconstruction finished in %ld s.\n", 2022-05-08T11:03:25,608 | ~~^ 2022-05-08T11:03:25,608 | | 2022-05-08T11:03:25,608 | long int 2022-05-08T11:03:25,609 | %lld 2022-05-08T11:03:25,609 3316 | std::chrono::duration_cast(time1 - time0) 2022-05-08T11:03:25,609 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-05-08T11:03:25,610 3317 | .count()); 2022-05-08T11:03:25,610 | ~~~~~~~~ 2022-05-08T11:03:25,610 | | 2022-05-08T11:03:25,610 | std::chrono::duration::rep {aka long long int} 2022-05-08T11:03:25,611 In file included from src/pulchra.cpp:20: 2022-05-08T11:03:25,611 src/pulchra.hpp:3145:8: warning: unused variable ‘buf’ [-Wunused-variable] 2022-05-08T11:03:25,611 3145 | char buf[100]; 2022-05-08T11:03:25,612 | ^~~ 2022-05-08T11:03:25,612 src/pulchra.hpp:3146:23: warning: variable ‘ini_name’ set but not used [-Wunused-but-set-variable] 2022-05-08T11:03:25,612 3146 | char *name = NULL, *ini_name = NULL, *output_pdb_name=NULL, *output_traj_pdb_name=NULL; 2022-05-08T11:03:25,613 | ^~~~~~~~ 2022-05-08T11:03:25,613 src/pulchra.hpp:3147:9: warning: unused variable ‘ptr’ [-Wunused-variable] 2022-05-08T11:03:25,613 3147 | char *ptr, out_name[1000]; 2022-05-08T11:03:25,613 | ^~~ 2022-05-08T11:03:25,614 src/pulchra.hpp:3147:14: warning: unused variable ‘out_name’ [-Wunused-variable] 2022-05-08T11:03:25,614 3147 | char *ptr, out_name[1000]; 2022-05-08T11:03:25,614 | ^~~~~~~~ 2022-05-08T11:04:20,189 src/pulchra.hpp: In member function ‘void pulchra::Pulchra::allocate_grid(std::shared_ptr, pulchra::atom_list_3d&, int*, int*, int*)’: 2022-05-08T11:04:20,190 src/pulchra.hpp:2429:11: warning: ‘xgrid’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2022-05-08T11:04:20,190 2429 | printf("Grid already allocated (%d %d %d)\n", xgrid, ygrid, 2022-05-08T11:04:20,190 | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-05-08T11:04:20,191 2430 | zgrid); 2022-05-08T11:04:20,191 | ~~~~~~ 2022-05-08T11:04:20,191 src/pulchra.hpp:2429:11: warning: ‘ygrid’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2022-05-08T11:04:20,192 src/pulchra.hpp:2429:11: warning: ‘zgrid’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2022-05-08T11:04:31,500 arm-linux-gnueabihf-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-3.9/bindings/python/pulchra_bindings.o build/temp.linux-armv7l-3.9/bindings/python/pypulchra_bindings.o build/temp.linux-armv7l-3.9/src/pulchra.o -L/usr/lib -o build/lib.linux-armv7l-3.9/pypulchra/_pypulchra.cpython-39-arm-linux-gnueabihf.so 2022-05-08T11:04:32,562 running install 2022-05-08T11:04:32,624 running install_lib 2022-05-08T11:04:32,631 creating build/bdist.linux-armv7l 2022-05-08T11:04:32,632 creating build/bdist.linux-armv7l/wheel 2022-05-08T11:04:32,635 creating build/bdist.linux-armv7l/wheel/pypulchra 2022-05-08T11:04:32,906 running install_egg_info 2022-05-08T11:04:32,958 running egg_info 2022-05-08T11:04:32,991 writing manifest file 'pypulchra.egg-info/SOURCES.txt' 2022-05-08T11:04:32,994 Copying pypulchra.egg-info to build/bdist.linux-armv7l/wheel/pypulchra-1.0.0-py3.9.egg-info 2022-05-08T11:04:33,017 running install_scripts 2022-05-08T11:04:35,237 Building wheel for pypulchra (pyproject.toml): finished with status 'done' 2022-05-08T11:04:35,380 Created wheel for pypulchra: filename=pypulchra-1.0.0-cp39-cp39-linux_armv7l.whl size=1934092 sha256=0470a8e044d39160d887c99766465e6c35ade8688d0c457e37ae37ce03b85472 2022-05-08T11:04:35,382 Stored in directory: /tmp/pip-ephem-wheel-cache-0oo6b5am/wheels/03/8d/1b/58741f0f41860c36c63c0432041ee99222ab529510e0d2c117 2022-05-08T11:04:35,405 Successfully built pypulchra 2022-05-08T11:04:35,570 Removed build tracker: '/tmp/pip-req-tracker-dg7m0gw9'