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Geometry functions
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promod3.core. EvaluateGromacsPosRule (rule, number, anchors)
Constructs number positions with the given Gromacs rule and anchor positions
(see Gromacs manual for details).
Parameters: |
- rule (
int ) – Gromacs rule
- number (
int ) – Desired number of positions (max. 3)
- anchors (
list of Vec3 ) – Anchor positions (max. 4)
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Returns: | Constructed number positions.
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Return type: | list of Vec3
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promod3.core. ConstructCTerminalOxygens (c_pos, ca_pos, n_pos)
Constructs positions of O and OXT atoms for C terminal.
Parameters: |
- c_pos (
Vec3 ) – Position of C atom
- n_pos (
Vec3 ) – Position of nitrogen atom
- ca_pos (
Vec3 ) – Position of C-alpha atom
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Returns: | Positions of O and OXT atoms.
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Return type: | tuple of Vec3
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promod3.core. ConstructAtomPos (A, B, C, bond_length, angle, dihedral)
Constructs position of atom “D” based on bond length (C-D), angle (B-C-D) and
dihedral (A-B-C-D).
Parameters: |
- A (
Vec3 ) – Position of atom A
- B (
Vec3 ) – Position of atom B
- C (
Vec3 ) – Position of atom C
- bond_length (
float ) – Bond length (C-D)
- angle (
float ) – Angle (B-C-D)
- dihedral (
float ) – Dihedral (A-B-C-D)
|
Returns: | Position of atom D
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Return type: | Vec3
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promod3.core. ConstructCBetaPos (n_pos, ca_pos, c_pos)
Constructs position of C-beta atom given the positions of the backbone nitrogen,
C-alpha and C atoms.
Parameters: |
- n_pos (
Vec3 ) – Position of nitrogen atom
- ca_pos (
Vec3 ) – Position of C-alpha atom
- c_pos (
Vec3 ) – Position of C atom
|
Returns: | Position of C-beta atom
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Return type: | Vec3
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promod3.core. RotationAroundLine (axis, anchor, angle)
Creates a geometric transform leading to a rotation with specified angle
around a line defined by axis and anchor.
Parameters: |
- axis (
Vec3 ) – Axis of rotation
- anchor (
Vec3 ) – Anchor for rotation
- angle (
float ) – Angle (in radians in range [-pi,pi]) of rotation
|
Returns: | Transformation matrix
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Return type: | Mat4
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promod3.core. RotationAroundLine (axis, angle)
Creates a 3x3 matrix for a rotation by a specified angle around an axis
going through the origin.
Parameters: |
- axis (
Vec3 ) – Axis of rotation
- angle (
float ) – Angle (in radians in range [-pi,pi]) of rotation
|
Returns: | Rotation matrix
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Return type: | Mat3
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class
promod3.core. StemCoords
-
class
promod3.core. StemCoords (res)
Simple container class to store N, CA and C coordinates.
Parameters: | res (ost.mol.ResidueHandle ) – Residue handle from which to extract N, CA and C coordinates. |
Raises: | RuntimeError if res does not contain N, CA and C
atoms. |
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n_coord
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ca_coord
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c_coord
Position of nitrogen / alpha carbon / carbon atom.
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class
promod3.core. StemPairOrientation
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class
promod3.core. StemPairOrientation (n_stem, c_stem)
Relative orientation of a pair of stems. Can be used to define gaps with four
angles and one distance and is used in the fragment database for fast lookups.
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distance
Distance of C atom of stem A to N atom of stem B.
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angle_one
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angle_two
Angles defining relative orientation of stem B with respect to stem A.
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angle_three
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angle_four
Angles defining relative orientation of stem A with respect to stem B.
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