Bugs item #964842, was opened at 2004-06-02 04:37 Message generated for change (Settings changed) made by migueljmol You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=964842&group_id=23629
Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: File Input/Output Group: None Status: Open Resolution: None Priority: 5 Submitted By: Miguel (migueljmol) >Assigned to: Bob Hanson (hansonr) Summary: support internal coordinates Initial Comment: Need to support internal coordinates for MOPAC (& other?) files. While I am somewhat reluctant to say this, I suspect that this may be better off done in the ModelReader code instead of in the core. It is not like fractional coordinates, where we need to have support in the core. And this issue of 'artificial atoms' to get started is a problem. It seems to me that we should build a small amount of support into the ModelReader and/or Model classes. Then MOPAC can use it. The other thing that concerns me is that the ModelAdapter classes currently do not make any references to javax.vecmath ... it is supposed to be a simple implementation. So, who knows ... maybe it should be in the core. ---------------------------- Original Message ---------------------------- Subject: Re: [Jmol-developers] internal coordinates? From: "Bob Hanson" <[EMAIL PROTECTED]> Date: Tue, June 1, 2004 21:08 To: [email protected] -------------------------------------------------------------------------- Miguel, all you do is read these data in and immediately convert to cartesian coordinates. It's set up so that you stream the data in. The first three points are unique, because: a) The first point (#1) is automatically just at position 0,0,0. b) The second point (#2) is a given distance from that point, #NA=1 along X c) The third point (#3) is a given distance from atom #NA=2 with a given angle in the xy plane for NA-NB-#3. d) All additional points (#X) are referenced to previous points by indicating a distance from a previous point (NA-#X), an angle back to two points (NA-NB-#X), and a torsional angle back to three previous points (NA-NB-NC-#X) see http://www.cmbi.kun.nl/tutorials/cheminf/mopac/intc.html for a nice description of a "z-matrix" Bob Miguel wrote: >>internal coordinates SHOULD be very easy to use, particularly if they are handed >>to you and you don't have to generate them yourself. They are amazingly concise. > > > We are already handling fractional coordinates, so adding another coordinate system will not be difficult ... IF ... > > >>The only complication I can imagine is that they sometimes involve "phantom" or >>"temporary" atoms for starting points. >> >>For example, in this example we have a first atom at 0,0,0, then two phantom >>atoms on roughly perpendicular axes. They define the starting point for the next >>dihedral, and you are off and running. Mostly QM programs start with these so as >>to define positions when symmetry is an issue. >> >> ATOM CHEMICAL BOND LENGTH BOND ANGLE TWIST ANGLE >> NUMBER SYMBOL (ANGSTROMS) (DEGREES) (DEGREES) >> (I) NA:I NB:NA:I NC:NB:NA:I NA >> NB >> NC >> 1 C( 1) 0.000000 0.000000 0.000000 >> >> 2 XX( ) 4.117293 0.000000 0.000000 1 >> >> 3 XX( ) 2.303156 90.000000 0.000000 2 >> 1 >> >> 4 C( 2) 1.351924 * 133.488008 * 180.000000 * 1 >> 2 > > > ... IF ... there are three floats per atom. > > Q: Is it the case that there are only 3 numbers per atom? bondLength, BondAngle, and TorsonAngle? > > Q: What are NA, NB, and NC? > > > > Miguel > ---------------------------- Original Message ---------------------------- Subject: Re: [Jmol-developers] internal coordinates? From: "Egon Willighagen" <[EMAIL PROTECTED]> Date: Tue, June 1, 2004 21:00 To: [email protected] Cc: "Miguel" <[EMAIL PROTECTED]> -------------------------------------------------------------------------- On Tuesday 01 June 2004 20:48, Miguel wrote: > > internal coordinates SHOULD be very easy to use, particularly if they are handed > > to you and you don't have to generate them yourself. They are amazingly concise. > > We are already handling fractional coordinates, so adding another coordinate system will not be difficult ... IF ... > > ... IF ... there are three floats per atom. > > Q: Is it the case that there are only 3 numbers per atom? bondLength, BondAngle, and TorsonAngle? The system works differently... The first atom normally has nothing The second has a distance (to the first) The third has a distance (to the second) and an angle (first -> second -> third) The fourth has a distance (to the third) an angle (second -> third -> fourth) and an torsion (first -> sec -> third -> fourth) This is called the Z-matrix... > Q: What are NA, NB, and NC? That's file format specific... dunno... not Z-Matrix stuff ... Egon ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=964842&group_id=23629 ------------------------------------------------------- This SF.Net email is sponsored by xPML, a groundbreaking scripting language that extends applications into web and mobile media. 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