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IN NO EVENT SHALL +# THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES +# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS +# INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE +# OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +# +# DATE : 2008-09-26 +# REV : 1 + +''' +from __future__ import print_function +from pymol import cmd +from pymol import stored +from chempy import cpv + + +def centroid(selection='all', center=0, quiet=1): + + model = cmd.get_model(selection) + nAtom = len(model.atom) + + centroid = cpv.get_null() + + for a in model.atom: + centroid = cpv.add(centroid, a.coord) + centroid = cpv.scale(centroid, 1. / nAtom) + + if not int(quiet): + print(' centroid: [%8.3f,%8.3f,%8.3f]' % tuple(centroid)) + + if int(center): + cmd.alter_state(1, selection, "(x,y,z)=sub((x,y,z), centroid)", + space={'centroid': centroid, 'sub': cpv.sub}) + + return centroid + +cmd.extend("centroid", centroid) diff --git a/.pymol/startup/color_h.pyc b/.pymol/startup/color_h.pyc deleted file mode 100644 index 1a5076b..0000000 Binary files a/.pymol/startup/color_h.pyc and /dev/null differ diff --git a/.pymol/startup/dssp_stride.pyc b/.pymol/startup/dssp_stride.pyc deleted file mode 100644 index 3fcc8e3..0000000 Binary files a/.pymol/startup/dssp_stride.pyc and /dev/null differ diff --git a/.pymol/startup/propka.pyc b/.pymol/startup/propka.pyc deleted file mode 100644 index b85928e..0000000 Binary files a/.pymol/startup/propka.pyc and /dev/null differ diff --git a/.pymol/startup/show_contact_map.pyc b/.pymol/startup/show_contact_map.pyc deleted file mode 100644 index da840ad..0000000 Binary files a/.pymol/startup/show_contact_map.pyc and /dev/null differ diff --git a/.pymol/startup/spectrum_states.pyc b/.pymol/startup/spectrum_states.pyc deleted file mode 100644 index ad83b12..0000000 Binary files a/.pymol/startup/spectrum_states.pyc and /dev/null differ diff --git a/.pymol/startup/visualize_dca_scores.pyc b/.pymol/startup/visualize_dca_scores.pyc deleted file mode 100644 index ae36ff1..0000000 Binary files a/.pymol/startup/visualize_dca_scores.pyc and /dev/null differ diff --git a/.pymolrc b/.pymolrc index 4832bb2..6cf75c2 100644 --- a/.pymolrc +++ b/.pymolrc @@ -1,4 +1,21 @@ +set fetch_path, /tmp +set async_builds, on +set max_threads, 16 +set cache_mode + set opaque_background, 0 log_open /tmp/pymol_log.pml set cartoon_side_chain_helper, 1 set cartoon_highlight_color, grey50 + +set_key F1, as lines, solvent +set_key F2, hide everything, solvent +set_key F3, as spheres, inorganic and (n. NA or n. K or n. CL or n. CA or n. XE or n. RN) +set_key F4, hide everything, inorganic and (n. NA or n. K or n. CL or n. CA or n. XE or n. RN) +set_key F5, as sticks, organic +set_key F6, hide everything, organic + +set_key F9, set orthoscopic +set_key F10, set orthoscopic, off +set_key F11, ray +set_key F12, ray 1600,1600