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fixed and renamed ""coords2dihedrals_inner.py"->"coords2projected_dih…
…edrals.py"
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,29 @@ | ||
| #!/bin/sh | ||
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| BRANCH_OF_LOG="180.0" | ||
| if [ "$#" -eq 2 ]; then | ||
| BRANCH_OF_LOG="$1" | ||
| shift 1 | ||
| fi | ||
| ATOM_SELECTION="$@" | ||
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| if [ -z "${EXTRACTCOORDS}" ] | ||
| then | ||
| EXTRACTCOORDS="pdb2coords.py ${ATOM_SELECTION} -blank" | ||
| fi | ||
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| while read pdb_file_name; do | ||
| #echo "pdb_file = \"${pdb_file_name}\"" | ||
| echo "${0##*/} processing $pdb_file_name" >&2 | ||
| pdb2helix.py < "$pdb_file_name" > helix_intervals_projected_dihedrals.tmp | ||
| while read interval; do | ||
| command="select_interval.py $interval < \"$pdb_file_name\" | ${EXTRACTCOORDS} | coords2projected_dihedrals.py $BRANCH_OF_LOG | tr \"\n\" \" \"" | ||
| #echo "${command}" | ||
| eval "$command" | ||
| echo "" | ||
| done < helix_intervals_projected_dihedrals.tmp | ||
| done | ||
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| rm -f helix_intervals_projected_dihedrals.tmp | ||
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|
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,29 @@ | ||
| #!/bin/sh | ||
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| BRANCH_OF_LOG="360.0" | ||
| if [ "$#" -eq 2 ]; then | ||
| BRANCH_OF_LOG="$1" | ||
| shift 1 | ||
| fi | ||
| ATOM_SELECTION="$@" | ||
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| if [ -z "${EXTRACTCOORDS}" ] | ||
| then | ||
| EXTRACTCOORDS="pdb2coords.py ${ATOM_SELECTION} -blank" | ||
| fi | ||
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| while read pdb_file_name; do | ||
| #echo "pdb_file = \"${pdb_file_name}\"" | ||
| echo "${0##*/} processing $pdb_file_name" >&2 | ||
| pdb2sheet.py < "$pdb_file_name" > sheet_intervals_projected_dihedrals.tmp | ||
| while read interval; do | ||
| command="select_interval.py $interval < \"$pdb_file_name\" | ${EXTRACTCOORDS} | coords2projected_dihedrals.py $BRANCH_OF_LOG | tr \"\n\" \" \"" | ||
| #echo "${command}" | ||
| eval "$command" | ||
| echo "" | ||
| done < sheet_intervals_projected_dihedrals.tmp | ||
| done | ||
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| rm -f sheet_intervals_projected_dihedrals.tmp | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,29 @@ | ||
| #!/bin/sh | ||
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| BRANCH_OF_LOG="" | ||
| if [ "$#" -eq 2 ]; then | ||
| BRANCH_OF_LOG="$1" | ||
| shift 1 | ||
| fi | ||
| ATOM_SELECTION="$@" | ||
|
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| if [ -z "${EXTRACTCOORDS}" ] | ||
| then | ||
| EXTRACTCOORDS="pdb2coords.py ${ATOM_SELECTION} -blank" | ||
| fi | ||
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| while read pdb_file_name; do | ||
| #echo "pdb_file = \"${pdb_file_name}\"" | ||
| echo "${0##*/} processing $pdb_file_name" >&2 | ||
| pdb2turn.py < "$pdb_file_name" > turn_intervals_projected_dihedrals.tmp | ||
| while read interval; do | ||
| command="select_interval.py $interval < \"$pdb_file_name\" | ${EXTRACTCOORDS} | coords2projected_dihedrals.py $BRANCH_OF_LOG | tr \"\n\" \" \"" | ||
| #echo "${command}" | ||
| eval "$command" | ||
| echo "" | ||
| done < turn_intervals_projected_dihedrals.tmp | ||
| done | ||
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| rm -f turn_intervals_projected_dihedrals.tmp | ||
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54 changes: 54 additions & 0 deletions
54
doc/extract_geometry/README_coords2projected_dihedrals.txt
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,54 @@ | ||
| Typical Usage: | ||
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| coords2dihedrals.py 180 < 12column_text_file.dat | ||
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| This script reads a 12-column numeric text file representing the positions | ||
| of 4 atoms. Then it calculates the "projected dihedral", which I define | ||
| as the difference in direction between two infinitely long lines: | ||
| -The first line passes through the first two atoms, | ||
| -The other line (the "last line") passes through the last two atoms. | ||
| The "projected dihedral" angle can be thought of as the largest possible | ||
| apparent angle between these two lines when viewed from all possible | ||
| viewing directions. A pair of points (one on each line) is determined | ||
| that are closest to each other. The "projected dihedral" angle is the angle | ||
| one sees when viewing these two lines from direction of the axis connecting | ||
| these two closest points. Note: If these two lines are parallel to each other | ||
| or if these 4 points are coplanar, the "projected" dihedral angle is undefined. | ||
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| Example input file: | ||
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| 30.13 11.46 15.12 35.28 -2.32 12.61 30.68 -4.45 16.30 28.68 8.46 10.24 | ||
| 28.68 8.42 10.24 30.68 -4.45 16.30 25.22 -4.75 19.42 27.57 3.37 8.06 | ||
| 27.57 3.37 8.06 25.22 -4.75 19.42 20.45 -1.27 20.09 25.80 -2.26 6.61 | ||
| 25.80 -2.23 6.61 20.45 -1.27 20.09 15.47 1.36 18.12 21.67 -5.88 7.17 | ||
| : | ||
| The 12 numbers on each line represent the x,y,z coordinates of 4 atoms. | ||
| (This is the format of the files generated by the "pdb2coords.py" script.) | ||
| For each line containing 12 numbers, this script returns a tuple | ||
| containing 4 numbers: | ||
| -The "projected dihedral" angle for these 4 atoms (in degrees) | ||
| -The distance from the first atom to the first closest point | ||
| (IE The point on the first line that is closest to the last line) | ||
| -The distance between the pair of points on each line that are closest | ||
| to each other, | ||
| -The distance from the last atom to the last closest point | ||
| (IE The point on the last line that is closest to the first line) | ||
| (When a line contains the wrong number of numbers, | ||
| the script prints out a list of 4 impossibe negative values: | ||
| "-720 -1 -1 -1" to let the caller know that | ||
| this particular angle could not be computed.) | ||
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| Note: | ||
| The "IUPAC/IUB" dihedral-angle convention is used: | ||
| 4 atoms in the "trans" conformation have a dihedral angle of 180 degrees. | ||
| By default, dihedral angles are calculated in the range from 0 to 360.0 degrees. | ||
| (This means there is discontinuity in the angle at 0 degrees.) | ||
| However this may be a bad choice for polymers which can alternate between | ||
| helical conformations which are left and right handed. | ||
| In some cases, you may want to have the discontinuity appear at 180 degrees. | ||
| (or some other angle which is sparsely populated). | ||
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| So you can supply an optional argument (the "branch_of_log") which indicates | ||
| where the discontinuity in the dihedral angle will appear. | ||
| Dihedral angles returned by this program will lie in the range: | ||
| [branch_of_log-360, branch_of_log) |
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